@article{1334, abstract = {Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping.}, author = {Schönenberger, Philipp and O'Neill, Joseph and Csicsvari, Jozsef L}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Activity dependent plasticity of hippocampal place maps}}, doi = {10.1038/ncomms11824}, volume = {7}, year = {2016}, } @inproceedings{1335, abstract = {In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, location = {Edinburgh, United Kingdom}, pages = {23 -- 38}, publisher = {Springer}, title = {{Quantitative monitor automata}}, doi = {10.1007/978-3-662-53413-7_2}, volume = {9837}, year = {2016}, } @article{13385, abstract = {Novel light-responsive nanoparticles were synthesized by decorating the surfaces of gold and silver nanoparticles with a nitrospiropyran molecular photoswitch. Upon exposure to UV light in nonpolar solvents, these nanoparticles self-assembled to afford spherical aggregates, which disassembled rapidly when the UV stimulus was turned off. The sizes of these aggregates depended on the nanoparticle concentration, and their lifetimes could be controlled by adjusting the surface concentration of nitrospiropyran on the nanoparticles. The conformational flexibility of nitrospiropyran, which was altered by modifying the structure of the background ligand, had a profound impact on the self-assembly process. By coating the nanoparticles with a spiropyran lacking the nitro group, a conceptually different self-assembly system, relying on a reversible proton transfer, was realized. The resulting particles spontaneously (in the dark) assembled into aggregates that could be readily disassembled upon exposure to blue light.}, author = {Kundu, Pintu K. and Das, Sanjib and Ahrens, Johannes and Klajn, Rafal}, issn = {2040-3372}, journal = {Nanoscale}, keywords = {General Materials Science}, number = {46}, pages = {19280--19286}, publisher = {Royal Society of Chemistry}, title = {{Controlling the lifetimes of dynamic nanoparticle aggregates by spiropyran functionalization}}, doi = {10.1039/c6nr05959g}, volume = {8}, year = {2016}, } @article{13386, abstract = {Azobenzenealkanethiols in self-assembled monolayers (SAMs) on Au(111) exhibit reversible trans–cis photoisomerization when diluted with alkanethiol spacers. Using these mixed SAMs, we show switching of the linear optical and second-harmonic response. The effective switching of these surface optical properties relies on a reasonably large cross section and a high photoisomerization yield as well as a long lifetime of the metastable cis isomer. We quantified the switching process by X-ray absorption spectroscopy. The cross sections for the trans–cis and cis–trans photoisomerization with 365 and 455 nm light, respectively, are 1 order of magnitude smaller than in solution. In vacuum, the 365 nm photostationary state comprises 50–74% of the molecules in the cis form, limited by their rapid thermal isomerization back to the trans state. In contrast, the 455 nm photostationary state contains nearly 100% trans-azobenzene. We determined time constants for the thermal cis–trans isomerization of only a few minutes in vacuum and in a dry nitrogen atmosphere but of more than 1 day in ambient air. Our results suggest that adventitious water adsorbed on the surface of the SAM stabilizes the polar cis configuration of azobenzene under ambient conditions. The back reaction rate constants differing by 2 orders of magnitude underline the huge influence of the environment and, accordingly, its importance when comparing various experiments.}, author = {Moldt, Thomas and Przyrembel, Daniel and Schulze, Michael and Bronsch, Wibke and Boie, Larissa and Brete, Daniel and Gahl, Cornelius and Klajn, Rafal and Tegeder, Petra and Weinelt, Martin}, issn = {1520-5827}, journal = {Langmuir}, keywords = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science}, number = {42}, pages = {10795--10801}, publisher = {American Chemical Society}, title = {{Differing isomerization kinetics of azobenzene-functionalized self-assembled monolayers in ambient air and in vacuum}}, doi = {10.1021/acs.langmuir.6b01690}, volume = {32}, year = {2016}, } @article{13387, abstract = {Come on in, the water's fine! Non-photoresponsive nanoparticles can be reversibly assembled using light by placing them in an aqueous solution of a photo­acid. Upon exposure to visible light, the photoacid reduces the pH of the solution, which induces attractive interactions between the nanoparticles. In the dark, the resulting nanoparticle aggregates spontaneously disassemble. The process can be repeated many times.}, author = {Samanta, Dipak and Klajn, Rafal}, issn = {2195-1071}, journal = {Advanced Optical Materials}, keywords = {Atomic and Molecular Physics, and Optics, Electronic, Optical and Magnetic Materials}, number = {9}, pages = {1373--1377}, publisher = {Wiley}, title = {{Aqueous light-controlled self-assembly of nanoparticles}}, doi = {10.1002/adom.201600364}, volume = {4}, year = {2016}, } @misc{13388, abstract = {The Inside Cover picture illustrates the fluorescent properties of a gold nanocluster functionalized with several copies of a red-emitting merocyanine (image by Ella Marushchenko). The red fluorescence can be turned on and off reversibly by using an external stimulus.}, author = {Udayabhaskararao, T. and Kundu, Pintu K. and Ahrens, Johannes and Klajn, Rafal}, booktitle = {ChemPhysChem}, issn = {1439-7641}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {12}, pages = {1711--1711}, publisher = {Wiley}, title = {{Inside cover: Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters (ChemPhysChem 12/2016)}}, doi = {10.1002/cphc.201600480}, volume = {17}, year = {2016}, } @article{13389, abstract = {Au25 nanoclusters functionalized with a spiropyran molecular switch are synthesized via a ligand-exchange reaction at low temperature. The resulting nanoclusters are characterized by optical and NMR spectroscopies as well as by mass spectrometry. Spiropyran bound to nanoclusters isomerizes in a reversible fashion when exposed to UV and visible light, and its properties are similar to those of free spiropyran molecules in solution. The reversible photoisomerization entails the modulation of fluorescence as well as the light-controlled self-assembly of nanoclusters.}, author = {Udayabhaskararao, T. and Kundu, Pintu K. and Ahrens, Johannes and Klajn, Rafal}, issn = {1439-7641}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {12}, pages = {1805--1809}, publisher = {Wiley}, title = {{Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters}}, doi = {10.1002/cphc.201500897}, volume = {17}, year = {2016}, } @article{1339, abstract = {We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive actuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By measuring the resonance frequencies of the system, we show that the comb-drive actuator and the silicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate (1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%) placed close to the silicon beam. In contrast, the effective spring constant of the system is insensitive to either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator can be used to switch between different coupling rates with a frequency of at least 10 kHz. }, author = {Verbiest, Gerard and Xu, Duo and Goldsche, Matthias and Khodkov, Timofiy and Barzanjeh, Shabir and Von Den Driesch, Nils and Buca, Dan and Stampfer, Christoph}, journal = {Applied Physics Letter}, publisher = {American Institute of Physics}, title = {{Tunable mechanical coupling between driven microelectromechanical resonators}}, doi = {10.1063/1.4964122}, volume = {109}, year = {2016}, } @article{13390, author = {Klajn, Rafal}, issn = {1869-1870}, journal = {Science China Chemistry}, keywords = {General Chemistry}, number = {4}, pages = {420--421}, publisher = {Springer Nature}, title = {{Borrowing titania’s photoinduced electrons for molecular switching}}, doi = {10.1007/s11426-016-5573-4}, volume = {59}, year = {2016}, } @article{13391, abstract = {It is reported that spiropyran—a widely investigated molecular photoswitch—can be stabilized in aqueous environments in the presence of a variety of proteins, including human serum albumin, insulin fibrils, lysozyme, and glucose oxidase. The optical properties of the complexed photoswitch are protein dependent, with human serum albumin providing the spiropyran with emission features previously observed for a photoswitch confined in media of high viscosity. Despite being bound to the protein molecules, spiropyran can undergo a ring-opening reaction upon exposure to UV light. This photoisomerization process can affect the properties of the proteins: here, it is shown that the electrical conduction through human serum albumin to which the spiropyran is bound increases following the ring-opening reaction.}, author = {Amdursky, Nadav and Kundu, Pintu K. and Ahrens, Johannes and Huppert, Dan and Klajn, Rafal}, issn = {2192-6506}, journal = {ChemPlusChem}, keywords = {General Chemistry}, number = {1}, pages = {44--48}, publisher = {Wiley}, title = {{Noncovalent interactions with proteins modify the physicochemical properties of a molecular switch}}, doi = {10.1002/cplu.201500417}, volume = {81}, year = {2016}, } @inproceedings{1340, abstract = {We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11].}, author = {Hansen, Kristoffer and Ibsen-Jensen, Rasmus and Koucký, Michal}, location = {Liverpool, United Kingdom}, pages = {64 -- 76}, publisher = {Springer}, title = {{The big match in small space}}, doi = {10.1007/978-3-662-53354-3_6}, volume = {9928}, year = {2016}, } @inproceedings{1341, abstract = {In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.}, author = {Avni, Guy and Henzinger, Thomas A and Kupferman, Orna}, location = {Liverpool, United Kingdom}, pages = {153 -- 166}, publisher = {Springer}, title = {{Dynamic resource allocation games}}, doi = {10.1007/978-3-662-53354-3_13}, volume = {9928}, year = {2016}, } @article{1342, abstract = {A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics.}, author = {Baym, Michael and Lieberman, Tami and Kelsic, Eric and Chait, Remy P and Gross, Rotem and Yelin, Idan and Kishony, Roy}, journal = {Science}, number = {6304}, pages = {1147 -- 1151}, publisher = {American Association for the Advancement of Science}, title = {{Spatiotemporal microbial evolution on antibiotic landscapes}}, doi = {10.1126/science.aag0822}, volume = {353}, year = {2016}, } @article{1343, abstract = {The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a potential for explaining the mystery of high-temperature superconductivity. Recent progress in ultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using the tools of quantum simulation, which emerged as a promising alternative to the numerical calculations plagued by the infamous sign problem. However, the temperatures achieved using elaborate laser cooling protocols so far have been too high to show the appearance of antiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate that using the machinery of dissipative quantum state engineering, one can observe the emergence of the AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach is to add incoherent laser scattering in such a way that the AF state emerges as the dark state of the driven-dissipative dynamics. The proposed controlled dissipation channels described in this work are straightforward to add to already existing experimental setups.}, author = {Kaczmarczyk, Jan and Weimer, Hendrik and Lemeshko, Mikhail}, journal = {New Journal of Physics}, number = {9}, publisher = {IOP Publishing Ltd.}, title = {{Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model}}, doi = {10.1088/1367-2630/18/9/093042}, volume = {18}, year = {2016}, } @article{1344, abstract = {Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.}, author = {Fendrych, Matyas and Leung, Jeffrey and Friml, Jirí}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls}}, doi = {10.7554/eLife.19048}, volume = {5}, year = {2016}, } @article{1345, abstract = {The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components.}, author = {Molnar, Gergely and Fendrych, Matyas and Friml, Jirí}, journal = {Nature Plants}, publisher = {Nature Publishing Group}, title = {{Plasma membrane: Negative attraction}}, doi = {10.1038/nplants.2016.102}, volume = {2}, year = {2016}, } @article{1346, abstract = {ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.}, author = {Dejonghe, Wim and Kuenen, Sabine and Mylle, Evelien and Vasileva, Mina K and Keech, Olivier and Viotti, Corrado and Swerts, Jef and Fendrych, Matyas and Ortiz Morea, Fausto and Mishev, Kiril and Delang, Simon and Scholl, Stefan and Zarza, Xavier and Heilmann, Mareike and Kourelis, Jiorgos and Kasprowicz, Jaroslaw and Nguyen, Le and Drozdzecki, Andrzej and Van Houtte, Isabelle and Szatmári, Anna and Majda, Mateusz and Baisa, Gary and Bednarek, Sebastian and Robert, Stéphanie and Audenaert, Dominique and Testerink, Christa and Munnik, Teun and Van Damme, Daniël and Heilmann, Ingo and Schumacher, Karin and Winne, Johan and Friml, Jirí and Verstreken, Patrik and Russinova, Eugenia}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification}}, doi = {10.1038/ncomms11710}, volume = {7}, year = {2016}, } @article{1347, abstract = {During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem's constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.}, author = {Schmidt, Richard and Lemeshko, Mikhail}, journal = {Physical Review X}, number = {1}, publisher = {American Physical Society}, title = {{Deformation of a quantum many-particle system by a rotating impurity}}, doi = {10.1103/PhysRevX.6.011012}, volume = {6}, year = {2016}, } @article{13478, abstract = {HR 8799 is a star accompanied by four massive planets on wide orbits. The observed planetary configuration has been shown to be unstable on a timescale much shorter than the estimated age of the system (~30 Myr) unless the planets are locked into mean motion resonances. This condition is characterised by small-amplitude libration of one or more resonant angles that stabilise the system by preventing close encounters. We simulate planetary systems similar to the HR 8799 planetary system, exploring the parameter space in separation between the orbits, planetary masses and distance from the Sun to the star. We find systems that look like HR 8799 and remain stable for longer than the estimated age of HR 8799. None of our systems are forced into resonances. We find, with nominal masses (Mb = 5 MJup and Mc,d,e = 7 MJup) and in a narrow range of orbit separations, that 5 of 100 systems match the observations and lifetime. Considering a broad range of orbit separations, we find 12 of 900 similar systems. The systems survive significantly longer because of their slightly increased initial orbit separations compared to assuming circular orbits from the observed positions. A small increase in separation leads to a significant increase in survival time. The low eccentricity the orbits develop from gravitational interaction is enough for the planets to match the observations. With lower masses, but still comfortably within the estimated planet mass uncertainty, we find 18 of 100 matching and long-lived systems in a narrow orbital separation range. In the broad separation range, we find 82 of 900 matching systems. Our results imply that the planets in the HR 8799 system do not have to be in strong mean motion resonances. We also investigate the future of wide-orbit planetary systems using our HR 8799 analogues. We find that 80% of the systems have two planets left after strong planet-planet scattering and these are on eccentric orbits with semi-major axes of a1 ~ 10 AU and a2 ~ 30−1000 AU. We speculate that other wide-orbit planetary systems, such as AB Pic and HD 106906, are the remnants of HR 8799 analogues that underwent close encounters and dynamical instability.}, author = {Götberg, Ylva Louise Linsdotter and Davies, Melvyn B. and Mustill, Alexander J. and Johansen, Anders and Church, Ross P.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Long-term stability of the HR 8799 planetary system without resonant lock}}, doi = {10.1051/0004-6361/201526309}, volume = {592}, year = {2016}, } @inproceedings{1348, abstract = {A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest.}, author = {Fulek, Radoslav}, location = {Helsinki, Finland}, pages = {31 -- 42}, publisher = {Springer}, title = {{Bounded embeddings of graphs in the plane}}, doi = {10.1007/978-3-319-44543-4_3}, volume = {9843}, year = {2016}, }