@misc{13055, abstract = {Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect' Compared to previous versions: - raw image files added - correction of URLs within README.txt file }, author = {Stroeymeyt, Nathalie and Grasse, Anna V and Crespi, Alessandro and Mersch, Danielle and Cremer, Sylvia and Keller, Laurent}, publisher = {Zenodo}, title = {{Social network plasticity decreases disease transmission in a eusocial insect}}, doi = {10.5281/ZENODO.1322669}, year = {2018}, } @misc{13059, abstract = {This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled "Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method". It also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript. The repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`. For details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).}, author = {Garriga, Edgar and di Tommaso, Paolo and Magis, Cedrik and Erb, Ionas and Mansouri, Leila and Baltzis, Athanasios and Laayouni, Hafid and Kondrashov, Fyodor and Floden, Evan and Notredame, Cedric}, publisher = {Zenodo}, title = {{Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method}}, doi = {10.5281/ZENODO.2025846}, year = {2018}, } @article{132, abstract = {Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.}, author = {Sznurkowska, Magdalena and Hannezo, Edouard B and Azzarelli, Roberta and Rulands, Steffen and Nestorowa, Sonia and Hindley, Christopher and Nichols, Jennifer and Göttgens, Berthold and Huch, Meritxell and Philpott, Anna and Simons, Benjamin}, journal = {Developmental Cell}, number = {3}, pages = {360 -- 375}, publisher = {Cell Press}, title = {{Defining lineage potential and fate behavior of precursors during pancreas development}}, doi = {10.1016/j.devcel.2018.06.028}, volume = {46}, year = {2018}, } @article{13255, abstract = {Focused ion beams perfectly suit for patterning two-dimensional (2D) materials, but the optimization of irradiation parameters requires full microscopic understanding of defect production mechanisms. In contrast to freestanding 2D systems, the details of damage creation in supported 2D materials are not fully understood, whereas the majority of experiments have been carried out for 2D targets deposited on substrates. Here, we suggest a universal and computationally efficient scheme to model the irradiation of supported 2D materials, which combines analytical potential molecular dynamics with Monte Carlo simulations and makes it possible to independently assess the contributions to the damage from backscattered ions and atoms sputtered from the substrate. Using the scheme, we study the defect production in graphene and MoS2 sheets, which are the two most important and wide-spread 2D materials, deposited on a SiO2 substrate. For helium and neon ions with a wide range of initial ion energies including those used in a commercial helium ion microscope (HIM), we demonstrate that depending on the ion energy and mass, the defect production in 2D systems can be dominated by backscattered ions and sputtered substrate atoms rather than by the direct ion impacts and that the amount of damage in 2D materials heavily depends on whether a substrate is present or not. We also study the factors which limit the spatial resolution of the patterning process. Our results, which agree well with the available experimental data, provide not only insights into defect production but also quantitative information, which can be used for the minimization of damage during imaging in HIM or optimization of the patterning process.}, author = {Kretschmer, Silvan and Maslov, Mikhail and Ghaderzadeh, Sadegh and Ghorbani-Asl, Mahdi and Hlawacek, Gregor and Krasheninnikov, Arkady V.}, issn = {1944-8244}, journal = {ACS Applied Materials & Interfaces}, keywords = {General Materials Science}, number = {36}, pages = {30827--30836}, publisher = {American Chemical Society}, title = {{Supported two-dimensional materials under ion irradiation: The substrate governs defect production}}, doi = {10.1021/acsami.8b08471}, volume = {10}, year = {2018}, } @inproceedings{133, abstract = {Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs.}, author = {Kragl, Bernhard and Qadeer, Shaz and Henzinger, Thomas A}, issn = {1868-8969}, location = {Beijing, China}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Synchronizing the asynchronous}}, doi = {10.4230/LIPIcs.CONCUR.2018.21}, volume = {118}, year = {2018}, } @article{21094, abstract = {The X-ray crystal structures of a decamer sequence d(CGCGTACGCG)2 and a tetradecamer sequence d(CGCGCGTACGCGCG)2 are presented here. Both sequences are alternating pyrimidine-purine repeat sequences and they form disordered, pseudo-continuous left handed Z-type helices. They demonstrate interesting variants of the ‘bundles of columns of helices’ mode of packing.}, author = {Karthik, S. and Mandal, Pradeep K and Thirugnanasambandam, A. and Gautham, N.}, issn = {1532-2335}, journal = {Nucleosides, Nucleotides & Nucleic Acids}, number = {4}, pages = {279--293}, publisher = {Informa UK Limited}, title = {{Crystal structures of disordered Z-type helices}}, doi = {10.1080/15257770.2018.1517883}, volume = {38}, year = {2018}, } @article{21096, abstract = {By using a combination of readily accessible experimental and computational experiments in water, we explored the factors governing the association between polyanionic dyn[4]arene and a series of α,ω-alkyldiammonium ions of increasing chain length. We found that the lock-and-key concept based on the best match between the apolar and polar regions of the molecular partners failed to explain the observed selectivities. Instead, the dissection of the energetic and structural contributions demonstrated that the binding events were actually guided by two crucial solvent-related phenomena as the chain length of the guest increases: the expected decrease of the enthalpic cost of guest desolvation and the unexpected increase of the favourable enthalpy of complex solvation. By bringing to light the decisive enthalpic impact of complex solvation during the binding of polyelectrolytes by inclusion, this study may provide a missing piece to a puzzle that one day could display the global picture of molecular recognition in water.}, author = {Jeamet, Emeric and Septavaux, Jean and Héloin, Alexandre and Donnier-Maréchal, Marion and Dumartin, Melissa and Ourri, Benjamin and Mandal, Pradeep K and Huc, Ivan and Bignon, Emmanuelle and Dumont, Elise and Morell, Christophe and Francoia, Jean-Patrick and Perret, Florent and Vial, Laurent and Leclaire, Julien}, issn = {2041-6539}, journal = {Chemical Science}, number = {1}, pages = {277--283}, publisher = {Royal Society of Chemistry}, title = {{Wetting the lock and key enthalpically favours polyelectrolyte binding}}, doi = {10.1039/c8sc02966k}, volume = {10}, year = {2018}, } @article{21097, abstract = {Translation, the mRNA-templated synthesis of peptides by the ribosome, can be manipulated to incorporate variants of the 20 cognate amino acids. Such approaches for expanding the range of chemical entities that can be produced by the ribosome may accelerate the discovery of molecules that can perform functions for which poorly folded, short peptidic sequences are ill suited. Here, we show that the ribosome tolerates some artificial helical aromatic oligomers, so-called foldamers. Using a flexible tRNA-acylation ribozyme—flexizyme—foldamers were attached to tRNA, and the resulting acylated tRNAs were delivered to the ribosome to initiate the synthesis of non-cyclic and cyclic foldamer–peptide hybrid molecules. Passing through the ribosome exit tunnel requires the foldamers to unfold. Yet foldamers encode sufficient folding information to influence the peptide structure once translation is completed. We also show that in cyclic hybrids, the foldamer portion can fold into a helix and force the peptide segment to adopt a constrained and stretched conformation.}, author = {Rogers, Joseph M. and Kwon, Sunbum and Dawson, Simon J. and Mandal, Pradeep K and Suga, Hiroaki and Huc, Ivan}, issn = {1755-4349}, journal = {Nature Chemistry}, number = {4}, pages = {405--412}, publisher = {Springer Nature}, title = {{Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids}}, doi = {10.1038/s41557-018-0007-x}, volume = {10}, year = {2018}, } @article{21152, abstract = {Phospholipase A2 (PLA2) is one of the rate limiting enzymes involved in the production of arachidonic acid, a potent inflammatory mediator. PLA2 is widely distributed all over the animal kingdom. It is also seen in inflammatory exudation and venoms of different organisms. The studies demonstrated that PLA2 inhibitors have broad spectrum activities that they can either be used against inflammation or envenomation. In this study, the inhibitory activity of 1-napthaleneacetic acid (NAA) against porcine pancreatic PLA2 has been explained through isothermal titration calorimetry and enzyme kinetics studies. The atomic level of interactions of NAA with PLA2 was also studied using X-ray crystallography. Apart from these findings, the theoretical binding affinities and mode of interactions of two naphthalene-based NSAIDs such as naproxen (NAP) and nabumetone (NAB) were studied through molecular modeling. The studies proved that the selected ligands are binding at the doorway of the active site cleft and hindering the substrate entry to the active site. The study brings out a potential scaffold for the designing of broad spectrum PLA2 inhibitors which can be used for inflammation or envenomation. }, author = {Dileep, Kalarickal V. and Remya, Chandran and Tintu, Ignatius and Mandal, Pradeep K and Karthe, Ponnuraj and Haridas, Madathilkovilakathu and Sadasivan, Chittalakkottu}, issn = {1521-6551}, journal = {IUBMB Life}, number = {10}, pages = {995--1001}, publisher = {Wiley}, title = {{Crystal structure of phospholipase A2 in complex with 1‐naphthaleneacetic acid}}, doi = {10.1002/iub.1924}, volume = {70}, year = {2018}, } @article{21523, abstract = {In this paper, we report dispersion-engineered metasurfaces with distinct functionalities controlled by wavelength. Unlike previous approaches based on spatial multiplexing or vertical stacking of metasurfaces, we utilize a single phase profile with wavelength dependence encoded in the phase shifters’ dispersion. We designed and fabricated a multiwavelength achromatic metalens (MAM) with achromatic focusing for blue (B), green (G), yellow (Y), and red (R) light and two wavelength-controlled beam generators (WCBG): one focuses light with orbital angular momentum (OAM) states (l = 0,1,2) corresponding to three primary colors; the other produces ordinary focal spots (l = 0) for red and green light, while generating a vortex beam (l = 1) in the blue. A full color (RGB) hologram is also demonstrated in simulation. Our approach opens a path to applications ranging from near-eye displays and holography to compact multiwavelength beam generation.}, author = {Shi, Zhujun and Khorasaninejad, Mohammadreza and Huang, Yao-Wei and Roques-Carmes, Charles and Zhu, Alexander Y. and Chen, Wei Ting and Sanjeev, Vyshakh and Ding, Zhao-Wei and Tamagnone, Michele and Chaudhary, Kundan and Devlin, Robert C. and Qiu, Cheng-Wei and Capasso, Federico}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Metasurface, dispersion engineering, visible spectrum, titanium dioxide, orbital angular momentum states, achromatic metalens}, number = {4}, pages = {2420--2427}, publisher = {American Chemical Society }, title = {{Single-layer metasurface with controllable multiwavelength functions}}, doi = {10.1021/acs.nanolett.7b05458}, volume = {18}, year = {2018}, } @article{21533, abstract = {Recent advances in the fabrication of nanostructures and nanoscale features in metasurfaces offer new prospects for generating visible light emission from low-energy electrons. Here we present the experimental observation of visible light emission from low-energy free electrons interacting with nanoscale periodic surfaces through the Smith–Purcell (SP) effect. We demonstrate SP light emission from nanoscale gratings with periodicity as small as 50 nm, enabling the observation of tunable visible radiation from low-energy electrons (1.5 to 6 keV), an order of magnitude lower in energy than previously reported. We study the emission wavelength and intensity dependence on the grating pitch and electron energy, showing agreement between experiment and theory. Our results open the way to the production of SP-based nanophotonics integrated devices. Built inside electron microscopes, SP sources could enable the development of novel electron–optical correlated spectroscopic techniques and facilitate the observation of new quantum effects in light sources.}, author = {Massuda, Aviram and Roques-Carmes, Charles and Yang, Yujia and Kooi, Steven E. and Yang, Yi and Murdia, Chitraang and Berggren, Karl K. and Kaminer, Ido and Soljačić, Marin}, issn = {2330-4022}, journal = {ACS Photonics}, keywords = {light−matter interactions, periodic structures, nanophotonics, free-electron light sources}, number = {9}, pages = {3513--3518}, publisher = {American Chemical Society }, title = {{Smith–Purcell radiation from low-energy electrons}}, doi = {10.1021/acsphotonics.8b00743}, volume = {5}, year = {2018}, } @article{21545, abstract = {Free-electron radiation such as Cerenkov1, Smith–Purcell2 and transition radiation3,4 can be greatly affected by structured optical environments, as has been demonstrated in a variety of polaritonic5,6, photonic-crystal7 and metamaterial8,9,10 systems. However, the amount of radiation that can ultimately be extracted from free electrons near an arbitrary material structure has remained elusive. Here we derive a fundamental upper limit to the spontaneous photon emission and energy loss of free electrons, regardless of geometry, which illuminates the effects of material properties and electron velocities. We obtain experimental evidence for our theory with quantitative measurements of Smith–Purcell radiation. Our framework allows us to make two predictions. One is a new regime of radiation operation—at subwavelength separations, slower (non-relativistic) electrons can achieve stronger radiation than fast (relativistic) electrons. The other is a divergence of the emission probability in the limit of lossless materials. We further reveal that such divergences can be approached by coupling free electrons to photonic bound states in the continuum11,12,13. Our findings suggest that compact and efficient free-electron radiation sources from microwaves to the soft X-ray regime may be achievable without requiring ultrahigh accelerating voltages.}, author = {Yang, Yi and Massuda, Aviram and Roques-Carmes, Charles and Kooi, Steven E. and Christensen, Thomas and Johnson, Steven G. and Joannopoulos, John D. and Miller, Owen D. and Kaminer, Ido and Soljačić, Marin}, issn = {1745-2481}, journal = {Nature Physics}, pages = {894--899}, publisher = {Springer Nature}, title = {{Maximal spontaneous photon emission and energy loss from free electrons}}, doi = {10.1038/s41567-018-0180-2}, volume = {14}, year = {2018}, } @article{21563, abstract = {Quantum electrodynamics (QED) is one of the most precisely tested theories in the history of science, giving accurate predictions to a wide range of experimental observations. Recent experimental advances allow for the ability to probe physics on extremely short attosecond timescales, enabling ultrafast imaging of quantum dynamics. It is of great interest to extend our understanding of short-time quantum dynamics to QED, where the focus is typically on long-time observables such as 𝑆 matrices, decay rates, and cross sections. That said, solving the short-time dynamics of the QED Hamiltonian can lead to divergences, making it unclear how to arrive at physical predictions. We present an approach to regularize QED at short times and apply it to the problem of free-electron radiation into a medium, known as Cherenkov radiation. Our regularization method, which can be extended to other QED processes, is performed by subtracting the self-energy in free space from the self-energy calculated in the medium. Surprisingly, we find a number of previously unknown phenomena yielding corrections to the conventional Cherenkov effect that could be observed in current experiments. Specifically, the Cherenkov velocity threshold increases relative to the famous conventional theory. This modification to the conventional theory, which can be non-negligible in realistic scenarios, should result in the suppression of spontaneous emission in readily available experiments. Finally, we reveal a bifurcation process creating radiation into new Cherenkov angles, occurring in the strong-coupling regime, which would be realizable by considering the radiation dynamics of highly charged ions. Our results shed light on QED phenomena at short times and reveal surprising new physics in the Cherenkov effect.}, author = {Roques-Carmes, Charles and Rivera, Nicholas and Joannopoulos, John D. and Soljačić, Marin and Kaminer, Ido}, issn = {2160-3308}, journal = {Physical Review X}, number = {4}, publisher = {American Physical Society}, title = {{Nonperturbative quantum electrodynamics in the Cherenkov effect}}, doi = {10.1103/physrevx.8.041013}, volume = {8}, year = {2018}, } @article{21587, abstract = {Meta-lenses based on flat optics enabled a fundamental shift in lens production—providing an easier manufacturing process with an increase in lens profile precision and a reduction in size and weight. Here we present an analytical approach to correct spherical aberrations caused by light propagation through the substrate by adding a substrate-corrected phase profile, which differs from the original hyperbolic one. A meta-lens encoding the new phase profile would yield diffraction-limited focusing and an increase of up to 0.3 of its numerical aperture without changing the radius or focal length. In tightly focused laser spot applications such as direct laser lithography and laser printing, a substrate-corrected meta-lens can reduce the spatial footprint of the meta-lens.}, author = {Groever, Benedikt and Roques-Carmes, Charles and Byrnes, Steven J. and Capasso, Federico}, issn = {2155-3165}, journal = {Applied Optics}, number = {12}, pages = {2973--2980}, publisher = {Optica Publishing Group}, title = {{Substrate aberration and correction for meta-lens imaging: An analytical approach}}, doi = {10.1364/ao.57.002973}, volume = {57}, year = {2018}, } @inproceedings{21589, abstract = {We demonstrate single-layer metasurfaces with controllable multi-wavelength functions. A multiwavelength achromatic metalens for red, yellow, green and blue light, and metasurfaces generating focused beams with different orbital angular momentum states are designed and fabricated.}, author = {Shi, Z. and Khorasaninejad, M. and Huang, Y. W. and Roques-Carmes, Charles and Zhu, A. Y. and Chen, W. T. and Sanjeev, V. and Ding, Z.W. and Tamagnone, M. and Chaudhary, K. and Devlin, R. C. and Qiu, C. W. and Capasso, F.}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Metasurfaces with wavelength-controlled functions}}, doi = {10.1364/cleo_at.2018.jw2a.101}, year = {2018}, } @inproceedings{21616, abstract = {We present the time-dependent quantum electrodynamic theory of Cˇerenkov radiation, which reveals orders of magnitude corrections to the decay rate from the conventional theory, as well as significant modifications to the well-established Cˇerenkov dispersion relation.}, author = {Roques-Carmes, Charles and Rivera, Nicholas and Joannopoulos, John D. and Soljačic, Marin and Kaminer, Ido}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Quantum Čerenkov radiation in weakly and strongly-coupled regimes}}, doi = {10.1364/cleo_qels.2018.fm3h.5}, year = {2018}, } @inproceedings{21617, abstract = {We derive and experimentally validate limits of electron radiation and energy loss. We show slow electrons generate stronger radiation than relativistic ones at subwavelength separations and bound states in the continuum enable order-of-magnitude radiation enhancement.}, author = {Yang, Yi and Massuda, Aviram and Roques-Carmes, Charles and Kooi, Steven E. and Christensen, Thomas and Johnson, Steven G. and Joannopoulos, John D. and Miller, Owen D. and Kaminer, Ido and Soljačić, Marin}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Fundamental limits on spontaneous emission and energy loss of free electrons}}, doi = {10.1364/cleo_qels.2018.fw4g.2}, year = {2018}, } @inproceedings{21618, abstract = {Swift electrons moving closely to a periodic structure can generate far-field radiation. The radiated light is usually polarized in the direction of electron propagation. We have demonstrated manipulation of this polarization with properly designed metasurfaces.}, author = {Yang, Yujia and Roques-Carmes, Charles and Kaminer, Ido and Zaidi, Aun and Massuda, Aviram and Yang, Yi and Kooi, Steven E. and Berggren, K. K. and Soljačić, Marin}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Manipulating Smith-Purcell radiation polarization with metasurfaces}}, doi = {10.1364/cleo_qels.2018.fw4h.1}, year = {2018}, } @inproceedings{21619, abstract = {The Smith-Purcell effect is observed when an electron beam passes in the vicinity of a periodic structure. We propose a method to shape the spatial and spectral far-field radiation using complex periodic and aperiodic gratings.}, author = {Remez, Roei and Shapira, Niv and Roques-Carmes, Charles and Tirole, Romain and Yang, Yi and Lereah, Yossi and Soljačić, Marin and Kaminer, Ido and Arie, Ady}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Spectral and spatial shaping of Smith-Purcell radiation}}, doi = {10.1364/cleo_qels.2018.fw4h.3}, year = {2018}, } @inproceedings{21626, abstract = {We experimentally demonstrate the generation of tunable radiation from silicon-only periodic structures in the near-infrared (up to 1550nm). Spontaneous emission from low-energy electrons (down to 2 keV) is recorded in a modified scanning electron microscope, matching our theoretical predictions.}, author = {Roques-Carmes, Charles and Kooi, Steven E. and Massuda, Aviram and Zaidi, Aun and Yang, Yi and Yang, Yujia and Berggren, Karl K. and Kaminer, Ido and Soljačić, Marin}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Electron beam-induced tunable radiation from silicon-only structures in the near-infrared}}, doi = {10.1364/cleo_si.2018.sm4i.2}, year = {2018}, }