[{"oa":1,"date_published":"2014-11-28T00:00:00Z","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","author":[{"first_name":"Jérémie A","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","orcid":"0000-0002-7253-9465"},{"full_name":"Sacanna, S.","first_name":"S.","last_name":"Sacanna"},{"first_name":"S.-H.","full_name":"Kim, S.-H.","last_name":"Kim"},{"last_name":"Yi","full_name":"Yi, G.-R.","first_name":"G.-R."},{"full_name":"Pine, D. J.","first_name":"D. J.","last_name":"Pine"},{"full_name":"Chaikin, P. M.","first_name":"P. M.","last_name":"Chaikin"}],"abstract":[{"text":"Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles.","lang":"eng"}],"quality_controlled":"1","citation":{"ista":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 372(2029), 20130372.","ieee":"J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin, “Light-activated self-propelled colloids,” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029. The Royal Society, 2014.","mla":"Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.","apa":"Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin, P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rsta.2013.0372","short":"J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 372 (2014).","ama":"Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372","chicago":"Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372."},"publication_status":"published","keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"oa_version":"Published Version","arxiv":1,"_id":"9166","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsta.2013.0372"}],"type":"journal_article","language":[{"iso":"eng"}],"pmid":1,"extern":"1","volume":372,"publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"article_number":"20130372","issue":"2029","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","month":"11","scopus_import":"1","title":"Light-activated self-propelled colloids","article_type":"original","article_processing_charge":"No","doi":"10.1098/rsta.2013.0372","external_id":{"pmid":["25332383"],"arxiv":["1410.7278"]},"year":"2014","status":"public","intvolume":" 372","date_updated":"2021-02-22T10:44:16Z","date_created":"2021-02-18T14:31:11Z","day":"28","publisher":"The Royal Society"},{"status":"public","intvolume":" 7","date_updated":"2021-01-12T08:21:57Z","date_created":"2018-12-11T11:49:14Z","day":"22","publisher":"Cell Press","_id":"925","language":[{"iso":"eng"}],"type":"journal_article","volume":7,"extern":"1","issue":"4","date_published":"2014-05-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Cell Reports","month":"05","author":[{"last_name":"Dong","full_name":"Dong, Bo","first_name":"Bo"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hayashi","full_name":"Hayashi, Shigeo","first_name":"Shigeo"}],"abstract":[{"text":"The morphological stability of biological tubes is crucial for the efficient circulation of fluids and gases. Failure of this stability causes irregularly shaped tubes found in multiple pathological conditions. Here, we report that Drosophila mutants of the ESCRT III component Shrub/Vps32 exhibit a strikingly elongated sinusoidal tube phenotype. This is caused by excessive apical membrane synthesis accompanied by the ectopic accumulation and overactivation of Crumbs in swollen endosomes. Furthermore, we demonstrate that the apical extracellular matrix (aECM) of the tracheal tube is a viscoelastic material coupled with the apical membrane. We present a simple mechanical model in which aECM elasticity, apical membrane growth, and their interaction are three vital parameters determining the stability of biological tubes. Our findings demonstrate a mechanical role for the extracellular matrix and suggest that the interaction of the apical membrane and an elastic aECM determines the final morphology of biological tubes independent of cell shape.","lang":"eng"}],"title":"Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape","acknowledgement":"We thank F. Gao, R.E. Ward, S. Luschnig, T. Okajima, M. Affolter, D. Bilder, E. Knust, T. Tanaka, A. Nakamura, C. Samakovlis, K. Saigo, M. Furuse, the Bloomington Stock Center, Drosophila Genetic Resource Center in Kyoto, Japan, and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; H. Wada for UAS-3×TagRFP fly and dye injection; Y.H. Zhang for plasmid and protocol for CBP preparation; and J. Prost and J.F. Joanny for their support for the project and discussion. We also thank T. Shibata, Y. Morishita, T. Kondo, and G. Sheng for critically reading the manuscript. This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from MEXT Japan to S.H. and the RIKEN Foreign Postdoctoral Researcher Program to B.D.","article_processing_charge":"No","citation":{"ama":"Dong B, Hannezo EB, Hayashi S. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 2014;7(4):941-950. doi:10.1016/j.celrep.2014.03.066","short":"B. Dong, E.B. Hannezo, S. Hayashi, Cell Reports 7 (2014) 941–950.","chicago":"Dong, Bo, Edouard B Hannezo, and Shigeo Hayashi. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports. Cell Press, 2014. https://doi.org/10.1016/j.celrep.2014.03.066.","apa":"Dong, B., Hannezo, E. B., & Hayashi, S. (2014). Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2014.03.066","ieee":"B. Dong, E. B. Hannezo, and S. Hayashi, “Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape,” Cell Reports, vol. 7, no. 4. Cell Press, pp. 941–950, 2014.","mla":"Dong, Bo, et al. “Balance between Apical Membrane Growth and Luminal Matrix Resistance Determines Epithelial Tubule Shape.” Cell Reports, vol. 7, no. 4, Cell Press, 2014, pp. 941–50, doi:10.1016/j.celrep.2014.03.066.","ista":"Dong B, Hannezo EB, Hayashi S. 2014. Balance between apical membrane growth and luminal matrix resistance determines epithelial tubule shape. Cell Reports. 7(4), 941–950."},"publist_id":"6515","publication_status":"published","doi":"10.1016/j.celrep.2014.03.066","oa_version":"None","year":"2014","page":"941 - 950"},{"intvolume":" 11","status":"public","day":"06","date_updated":"2021-01-12T08:21:57Z","date_created":"2018-12-11T11:49:14Z","_id":"926","publisher":"Royal Society of London","volume":11,"extern":"1","issue":"93","language":[{"iso":"eng"}],"type":"journal_article","publication":"Journal of the Royal Society Interface","month":"04","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Prost","full_name":"Prost, Jacques","first_name":"Jacques"},{"last_name":"Joanny","full_name":"Joanny, Jean","first_name":"Jean"}],"date_published":"2014-04-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea."}],"article_processing_charge":"No","citation":{"ista":"Hannezo EB, Prost J, Joanny J. 2014. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 11(93).","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Growth homeostatic regulation and stem cell dynamics in tissues,” Journal of the Royal Society Interface, vol. 11, no. 93. Royal Society of London, 2014.","mla":"Hannezo, Edouard B., et al. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface, vol. 11, no. 93, Royal Society of London, 2014, doi:10.1098/rsif.2013.0895.","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2014). Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2013.0895","ama":"Hannezo EB, Prost J, Joanny J. Growth homeostatic regulation and stem cell dynamics in tissues. Journal of the Royal Society Interface. 2014;11(93). doi:10.1098/rsif.2013.0895","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Growth Homeostatic Regulation and Stem Cell Dynamics in Tissues.” Journal of the Royal Society Interface. Royal Society of London, 2014. https://doi.org/10.1098/rsif.2013.0895.","short":"E.B. Hannezo, J. Prost, J. Joanny, Journal of the Royal Society Interface 11 (2014)."},"publist_id":"6516","publication_status":"published","title":"Growth homeostatic regulation and stem cell dynamics in tissues","acknowledgement":"We thank Jens Elgeti and Silvia Fre for fruitful discussions.","oa_version":"None","year":"2014","doi":"10.1098/rsif.2013.0895"},{"abstract":[{"lang":"eng","text":"Morphogenesis during embryo development requires the coordination of mechanical forces to generate the macroscopic shapes of organs. We propose a minimal theoretical model, based on cell adhesion and actomyosin contractility, which describes the various shapes of epithelial cells and the bending and buckling of epithelial sheets, as well as the relative stability of cellular tubes and spheres. We show that, to understand these processes, a full 3D description of the cells is needed, but that simple scaling laws can still be derived. The morphologies observed in vivo can be understood as stable points of mechanical equations and the transitions between them are either continuous or discontinuous. We then focus on epithelial sheet bending, a ubiquitous morphogenetic process. We calculate the curvature of an epithelium as a function of actin belt tension as well as of cell-cell and and cell-substrate tension. The model allows for a comparison of the relative stabilities of spherical or cylindrical cellular structures (acini or tubes). Finally, we propose a unique type of buckling instability of epithelia, driven by a flattening of individual cell shapes, and discuss experimental tests to verify our predictions."}],"author":[{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Jacques","full_name":"Prost, Jacques","last_name":"Prost"},{"full_name":"Joanny, Jean","first_name":"Jean","last_name":"Joanny"}],"month":"01","publication":"PNAS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-01-01T00:00:00Z","page":"27 - 32","year":"2014","oa_version":"None","doi":"10.1073/pnas.1312076111","publist_id":"6517","citation":{"ama":"Hannezo EB, Prost J, Joanny J. Theory of epithelial sheet morphology in three dimensions. PNAS. 2014;111(1):27-32. doi:10.1073/pnas.1312076111","short":"E.B. Hannezo, J. Prost, J. Joanny, PNAS 111 (2014) 27–32.","chicago":"Hannezo, Edouard B, Jacques Prost, and Jean Joanny. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1312076111.","apa":"Hannezo, E. B., Prost, J., & Joanny, J. (2014). Theory of epithelial sheet morphology in three dimensions. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1312076111","mla":"Hannezo, Edouard B., et al. “Theory of Epithelial Sheet Morphology in Three Dimensions.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. 27–32, doi:10.1073/pnas.1312076111.","ieee":"E. B. Hannezo, J. Prost, and J. Joanny, “Theory of epithelial sheet morphology in three dimensions,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. 27–32, 2014.","ista":"Hannezo EB, Prost J, Joanny J. 2014. Theory of epithelial sheet morphology in three dimensions. PNAS. 111(1), 27–32."},"publication_status":"published","article_processing_charge":"No","title":"Theory of epithelial sheet morphology in three dimensions","day":"01","date_created":"2018-12-11T11:49:14Z","date_updated":"2021-01-12T08:21:58Z","intvolume":" 111","status":"public","issue":"1","volume":111,"extern":"1","language":[{"iso":"eng"}],"type":"journal_article","_id":"927","publisher":"National Academy of Sciences"},{"publication_status":"published","citation":{"apa":"Aigner, D., Freunberger, S. A., Wilkening, M., Saf, R., Borisov, S. M., & Klimant, I. (2014). Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. Analytical Chemistry. ACS. https://doi.org/10.1021/ac502513g","ama":"Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. Analytical Chemistry. 2014;86(18):9293-9300. doi:10.1021/ac502513g","chicago":"Aigner, Daniel, Stefan Alexander Freunberger, Martin Wilkening, Robert Saf, Sergey M. Borisov, and Ingo Klimant. “Enhancing Photoinduced Electron Transfer Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry. ACS, 2014. https://doi.org/10.1021/ac502513g.","short":"D. Aigner, S.A. Freunberger, M. Wilkening, R. Saf, S.M. Borisov, I. Klimant, Analytical Chemistry 86 (2014) 9293–9300.","ista":"Aigner D, Freunberger SA, Wilkening M, Saf R, Borisov SM, Klimant I. 2014. Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols. Analytical Chemistry. 86(18), 9293–9300.","mla":"Aigner, Daniel, et al. “Enhancing Photoinduced Electron Transfer Efficiency of Fluorescent PH-Probes with Halogenated Phenols.” Analytical Chemistry, vol. 86, no. 18, ACS, 2014, pp. 9293–300, doi:10.1021/ac502513g.","ieee":"D. Aigner, S. A. Freunberger, M. Wilkening, R. Saf, S. M. Borisov, and I. Klimant, “Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols,” Analytical Chemistry, vol. 86, no. 18. ACS, pp. 9293–9300, 2014."},"article_processing_charge":"No","title":"Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols","quality_controlled":"1","article_type":"original","page":"9293-9300","oa_version":"None","year":"2014","doi":"10.1021/ac502513g","author":[{"last_name":"Aigner","first_name":"Daniel","full_name":"Aigner, Daniel"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"last_name":"Wilkening","first_name":"Martin","full_name":"Wilkening, Martin"},{"last_name":"Saf","full_name":"Saf, Robert","first_name":"Robert"},{"first_name":"Sergey M.","full_name":"Borisov, Sergey M.","last_name":"Borisov"},{"last_name":"Klimant","full_name":"Klimant, Ingo","first_name":"Ingo"}],"publication":"Analytical Chemistry","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-08-14T00:00:00Z","abstract":[{"lang":"eng","text":"Photoinduced electron transfer (PET), which causes pH-dependent quenching of fluorescent dyes, is more effectively introduced by phenolic groups than by amino groups which have been much more commonly used so far. That is demonstrated by fluorescence measurements involving several classes of fluorophores. Electrochemical measurements show that PET in several amino-modified dyes is thermodynamically favorable, even though it was not experimentally found, underlining the importance of kinetic aspects to the process. Consequently, the attachment of phenolic groups allows for fast and simple preparation of a wide selection of fluorescent pH-probes with tailor-made spectral properties, sensitive ranges, and individual advantages, so that a large number of applications can be realized. Fluorophores carrying phenolic groups may also be used for sensing analytes other than pH or molecular switching and signaling."}],"publisher":"ACS","_id":"7300","issue":"18","publication_identifier":{"issn":["0003-2700","1520-6882"]},"volume":86,"extern":"1","type":"journal_article","language":[{"iso":"eng"}],"intvolume":" 86","status":"public","day":"14","date_created":"2020-01-15T12:17:17Z","date_updated":"2021-01-12T08:12:53Z"},{"type":"journal_article","language":[{"iso":"eng"}],"issue":"7","publication_identifier":{"issn":["1932-7447","1932-7455"]},"extern":"1","volume":118,"publisher":"ACS","_id":"7301","date_created":"2020-01-15T12:17:28Z","date_updated":"2021-01-12T08:12:53Z","day":"29","status":"public","intvolume":" 118","doi":"10.1021/jp4093805","page":"3393-3401","oa_version":"None","year":"2014","title":"Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent","article_type":"original","quality_controlled":"1","publication_status":"published","citation":{"ista":"Li C, Fontaine O, Freunberger SA, Johnson L, Grugeon S, Laruelle S, Bruce PG, Armand M. 2014. Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry C. 118(7), 3393–3401.","ieee":"C. Li et al., “Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent,” The Journal of Physical Chemistry C, vol. 118, no. 7. ACS, pp. 3393–3401, 2014.","mla":"Li, Chunmei, et al. “Aprotic Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic Solvent.” The Journal of Physical Chemistry C, vol. 118, no. 7, ACS, 2014, pp. 3393–401, doi:10.1021/jp4093805.","apa":"Li, C., Fontaine, O., Freunberger, S. A., Johnson, L., Grugeon, S., Laruelle, S., … Armand, M. (2014). Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry C. ACS. https://doi.org/10.1021/jp4093805","short":"C. Li, O. Fontaine, S.A. Freunberger, L. Johnson, S. Grugeon, S. Laruelle, P.G. Bruce, M. Armand, The Journal of Physical Chemistry C 118 (2014) 3393–3401.","ama":"Li C, Fontaine O, Freunberger SA, et al. Aprotic Li–O2 battery: Influence of complexing agents on oxygen reduction in an aprotic solvent. The Journal of Physical Chemistry C. 2014;118(7):3393-3401. doi:10.1021/jp4093805","chicago":"Li, Chunmei, Olivier Fontaine, Stefan Alexander Freunberger, Lee Johnson, Sylvie Grugeon, Stéphane Laruelle, Peter G. Bruce, and Michel Armand. “Aprotic Li–O2 Battery: Influence of Complexing Agents on Oxygen Reduction in an Aprotic Solvent.” The Journal of Physical Chemistry C. ACS, 2014. https://doi.org/10.1021/jp4093805."},"article_processing_charge":"No","abstract":[{"text":"Several problems arise at the O2 (positive) electrode in the Li-air battery, including solvent/electrode decomposition and electrode passivation by insulating Li2O2. Progress partially depends on exploring the basic electrochemistry of O2 reduction. Here we describe the effect of complexing-cations on the electrochemical reduction of O2 in DMSO in the presence and absence of a Li salt. The solubility of alkaline peroxides in DMSO is enhanced by the complexing-cations, consistent with their strong interaction with reduced O2. The complexing-cations also increase the rate of the 1-electron O2 reduction to O2•– by up to six-fold (k° = 2.4 ×10–3 to 1.5 × 10–2 cm s–1) whether or not Li+ ions are present. In the absence of Li+, the complexing-cations also promote the reduction of O2•– to O22–. In the presence of Li+ and complexing-cations, and despite the interaction of the reduced O2 with the latter, SERS confirms that the product is still Li2O2.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-01-29T00:00:00Z","author":[{"last_name":"Li","full_name":"Li, Chunmei","first_name":"Chunmei"},{"last_name":"Fontaine","first_name":"Olivier","full_name":"Fontaine, Olivier"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"last_name":"Johnson","full_name":"Johnson, Lee","first_name":"Lee"},{"full_name":"Grugeon, Sylvie","first_name":"Sylvie","last_name":"Grugeon"},{"first_name":"Stéphane","full_name":"Laruelle, Stéphane","last_name":"Laruelle"},{"last_name":"Bruce","first_name":"Peter G.","full_name":"Bruce, Peter G."},{"last_name":"Armand","full_name":"Armand, Michel","first_name":"Michel"}],"month":"01","publication":"The Journal of Physical Chemistry C"},{"page":"2739-2752","year":"2014","oa_version":"Published Version","doi":"10.1039/c4ee00496e","citation":{"ieee":"A. Dunst, V. Epp, I. Hanzu, S. A. Freunberger, and M. Wilkening, “Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries,” Energy & Environmental Science, vol. 7, no. 8. RSC, pp. 2739–2752, 2014.","mla":"Dunst, A., et al. “Short-Range Li Diffusion vs. Long-Range Ionic Conduction in Nanocrystalline Lithium Peroxide Li2O2—the Discharge Product in Lithium-Air Batteries.” Energy & Environmental Science, vol. 7, no. 8, RSC, 2014, pp. 2739–52, doi:10.1039/c4ee00496e.","ista":"Dunst A, Epp V, Hanzu I, Freunberger SA, Wilkening M. 2014. Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries. Energy & Environmental Science. 7(8), 2739–2752.","ama":"Dunst A, Epp V, Hanzu I, Freunberger SA, Wilkening M. Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries. Energy & Environmental Science. 2014;7(8):2739-2752. doi:10.1039/c4ee00496e","chicago":"Dunst, A., V. Epp, I. Hanzu, Stefan Alexander Freunberger, and M. Wilkening. “Short-Range Li Diffusion vs. Long-Range Ionic Conduction in Nanocrystalline Lithium Peroxide Li2O2—the Discharge Product in Lithium-Air Batteries.” Energy & Environmental Science. RSC, 2014. https://doi.org/10.1039/c4ee00496e.","short":"A. Dunst, V. Epp, I. Hanzu, S.A. Freunberger, M. Wilkening, Energy & Environmental Science 7 (2014) 2739–2752.","apa":"Dunst, A., Epp, V., Hanzu, I., Freunberger, S. A., & Wilkening, M. (2014). Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries. Energy & Environmental Science. RSC. https://doi.org/10.1039/c4ee00496e"},"publication_status":"published","article_processing_charge":"No","quality_controlled":"1","article_type":"original","title":"Short-range Li diffusion vs. long-range ionic conduction in nanocrystalline lithium peroxide Li2O2—the discharge product in lithium-air batteries","abstract":[{"text":"Understanding charge carrier transport in Li2O2, the storage material in the non-aqueous Li-O2 battery, is key to the development of this high-energy battery. Here, we studied ionic transport properties and Li self-diffusion in nanocrystalline Li2O2 by conductivity and temperature variable 7Li NMR spectroscopy. Nanostructured Li2O2, characterized by a mean crystallite size of less than 50 nm as estimated from X-ray diffraction peak broadening, was prepared by high-energy ball milling of microcrystalline lithium peroxide with μm sized crystallites. At room temperature the overall conductivity σ of the microcrystalline reference sample turned out to be very low (3.4 × 10−13 S cm−1) which is in agreement with results from temperature-variable 7Li NMR line shape measurements. Ball-milling, however, leads to an increase of σ by approximately two orders of magnitude (1.1 × 10−10 S cm−1); correspondingly, the activation energy decreases from 0.89 eV to 0.82 eV. The electronic contribution σeon, however, is in the order of 9 × 10−12 S cm−1 which makes less than 10% of the total value. Interestingly, 7Li NMR lines of nano-Li2O2 undergo pronounced heterogeneous motional narrowing which manifests in a two-component line shape emerging with increasing temperatures. Most likely, the enhancement in σ can be traced back to the generation of a spin reservoir with highly mobile Li ions; these are expected to reside in the nearest neighbourhood of defects generated or near the structurally disordered and defect-rich interfacial regions formed during mechanical treatment.","lang":"eng"}],"author":[{"last_name":"Dunst","first_name":"A.","full_name":"Dunst, A."},{"full_name":"Epp, V.","first_name":"V.","last_name":"Epp"},{"last_name":"Hanzu","full_name":"Hanzu, I.","first_name":"I."},{"last_name":"Freunberger","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Wilkening","first_name":"M.","full_name":"Wilkening, M."}],"publication":"Energy & Environmental Science","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-08-01T00:00:00Z","publication_identifier":{"issn":["1754-5692","1754-5706"]},"issue":"8","volume":7,"extern":"1","language":[{"iso":"eng"}],"type":"journal_article","_id":"7302","publisher":"RSC","day":"01","date_created":"2020-01-15T12:17:43Z","date_updated":"2021-01-12T08:12:53Z","intvolume":" 7","status":"public"},{"date_published":"2014-03-05T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"The Lithium Air Battery: Fundamentals","month":"03","author":[{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"last_name":"Chen","first_name":"Yuhui","full_name":"Chen, Yuhui"},{"last_name":"Bardé","full_name":"Bardé, Fanny","first_name":"Fanny"},{"first_name":"Kensuke","full_name":"Takechi, Kensuke","last_name":"Takechi"},{"full_name":"Mizuno, Fuminori","first_name":"Fuminori","last_name":"Mizuno"},{"last_name":"Bruce","first_name":"Peter G.","full_name":"Bruce, Peter G."}],"abstract":[{"text":"The electrolyte in the non-aqueous (aprotic) lithium air battery has a profound influence on the reactions that occur at the anode and cathode, and hence its overall operation on discharge/charge. It must possess a wide range of attributes, exceeding the requirements of electrolytes for Lithium ion batteries by far. The most important additional issues are stability at both anode and cathode in the presence of O2. The known problems with cycling the Li metal/non-aqueous electrolyte interface are further complicated by O2. New and much less understood are the reactions at the O2 cathode/electrolyte interface where the highly reversible formation/decomposition of Li2O2 on discharge/charge is critical for the operation of the non-aqueous lithium air battery. Many aprotic electrolytes exhibit decomposition at the cathode during discharge and charge due to the presence of reactive reduced O2 species affecting potential, capacity and kinetics on discharge and charge, cyclability and calendar life. Identifying suitable electrolytes is one of the key challenges for the non-aqueous lithium air battery at the present time. Following the realisation that cyclability of such cells in the initially used organic carbonate electrolytes is due to back-to-back irreversible reactions the stability of the non-aqueous electrolytes became a major focus of research on rechargeable lithium air batteries. This realisation led to the establishment of a suite of experimental and computational methods capable of screening the stability of electrolytes. These allow for greater mechanistic understanding of the reactivity and guide the way towards designing more stable systems. A range of electrolytes based on ethers, amides, sulfones, ionic liquids and dimethyl sulfoxide have been investigated. All are more stable than the organic carbonates, but not all are equally stable. Even though it was soon realised, by a number of groups, that ethers exhibit side reactions on discharge and charge, they still remain the choice in many studies. To date dimethyl sulfoxide and dimethylacetamide were identified as the most stable electrolytes. In conjunction with the investigation of electrolyte stability the importance of electrode stability became more prominent. The stability of the electrolyte cannot be considered in isolation. Its stability depends on the synergy between electrolyte and electrode. Carbon based electrodes promote electrolyte decomposition and decompose on their own. Although great progress has been made in only a few years, future work on aprotic electrolytes for Li-O2 batteries will need to explore other electrolytes in the quest for yet lower cost, higher safety, stability and low volatility.","lang":"eng"}],"editor":[{"full_name":"Imanishi, Nobuyuki","first_name":"Nobuyuki","last_name":"Imanishi"},{"first_name":"Alan C.","full_name":"Luntz, Alan C.","last_name":"Luntz"},{"last_name":"Bruce","first_name":"Peter","full_name":"Bruce, Peter"}],"quality_controlled":"1","title":"Nonaqueous Electrolytes","article_processing_charge":"No","publication_status":"published","citation":{"short":"S.A. Freunberger, Y. Chen, F. Bardé, K. Takechi, F. Mizuno, P.G. Bruce, in:, N. Imanishi, A.C. Luntz, P. Bruce (Eds.), The Lithium Air Battery: Fundamentals, Springer Nature, New York, NY, 2014, pp. 23–58.","chicago":"Freunberger, Stefan Alexander, Yuhui Chen, Fanny Bardé, Kensuke Takechi, Fuminori Mizuno, and Peter G. Bruce. “Nonaqueous Electrolytes.” In The Lithium Air Battery: Fundamentals, edited by Nobuyuki Imanishi, Alan C. Luntz, and Peter Bruce, 23–58. New York, NY: Springer Nature, 2014. https://doi.org/10.1007/978-1-4899-8062-5_2.","ama":"Freunberger SA, Chen Y, Bardé F, Takechi K, Mizuno F, Bruce PG. Nonaqueous Electrolytes. In: Imanishi N, Luntz AC, Bruce P, eds. The Lithium Air Battery: Fundamentals. New York, NY: Springer Nature; 2014:23-58. doi:10.1007/978-1-4899-8062-5_2","apa":"Freunberger, S. A., Chen, Y., Bardé, F., Takechi, K., Mizuno, F., & Bruce, P. G. (2014). Nonaqueous Electrolytes. In N. Imanishi, A. C. Luntz, & P. Bruce (Eds.), The Lithium Air Battery: Fundamentals (pp. 23–58). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-4899-8062-5_2","mla":"Freunberger, Stefan Alexander, et al. “Nonaqueous Electrolytes.” The Lithium Air Battery: Fundamentals, edited by Nobuyuki Imanishi et al., Springer Nature, 2014, pp. 23–58, doi:10.1007/978-1-4899-8062-5_2.","ieee":"S. A. Freunberger, Y. Chen, F. Bardé, K. Takechi, F. Mizuno, and P. G. Bruce, “Nonaqueous Electrolytes,” in The Lithium Air Battery: Fundamentals, N. Imanishi, A. C. Luntz, and P. Bruce, Eds. New York, NY: Springer Nature, 2014, pp. 23–58.","ista":"Freunberger SA, Chen Y, Bardé F, Takechi K, Mizuno F, Bruce PG. 2014.Nonaqueous Electrolytes. In: The Lithium Air Battery: Fundamentals. , 23–58."},"doi":"10.1007/978-1-4899-8062-5_2","oa_version":"None","year":"2014","page":"23-58","status":"public","date_created":"2020-01-15T12:17:55Z","date_updated":"2021-01-12T08:12:54Z","day":"05","place":"New York, NY","publisher":"Springer Nature","_id":"7303","type":"book_chapter","language":[{"iso":"eng"}],"extern":"1","publication_identifier":{"isbn":["9781489980618"],"eisbn":["9781489980625"]}},{"type":"journal_article","language":[{"iso":"eng"}],"volume":39,"extern":"1","publication_identifier":{"issn":["0883-7694","1938-1425"]},"issue":"5","_id":"7304","publisher":"CUP","date_updated":"2021-01-12T08:12:54Z","date_created":"2020-01-15T12:18:05Z","day":"01","status":"public","intvolume":" 39","doi":"10.1557/mrs.2014.87","year":"2014","oa_version":"None","page":"443-452","quality_controlled":"1","article_type":"original","title":"Materials challenges in rechargeable lithium-air batteries","article_processing_charge":"No","citation":{"ieee":"D. G. Kwabi et al., “Materials challenges in rechargeable lithium-air batteries,” MRS Bulletin, vol. 39, no. 5. CUP, pp. 443–452, 2014.","mla":"Kwabi, D. G., et al. “Materials Challenges in Rechargeable Lithium-Air Batteries.” MRS Bulletin, vol. 39, no. 5, CUP, 2014, pp. 443–52, doi:10.1557/mrs.2014.87.","ista":"Kwabi DG, Ortiz-Vitoriano N, Freunberger SA, Chen Y, Imanishi N, Bruce PG, Shao-Horn Y. 2014. Materials challenges in rechargeable lithium-air batteries. MRS Bulletin. 39(5), 443–452.","ama":"Kwabi DG, Ortiz-Vitoriano N, Freunberger SA, et al. Materials challenges in rechargeable lithium-air batteries. MRS Bulletin. 2014;39(5):443-452. doi:10.1557/mrs.2014.87","short":"D.G. Kwabi, N. Ortiz-Vitoriano, S.A. Freunberger, Y. Chen, N. Imanishi, P.G. Bruce, Y. Shao-Horn, MRS Bulletin 39 (2014) 443–452.","chicago":"Kwabi, D.G., N. Ortiz-Vitoriano, Stefan Alexander Freunberger, Y. Chen, N. Imanishi, P.G. Bruce, and Y. Shao-Horn. “Materials Challenges in Rechargeable Lithium-Air Batteries.” MRS Bulletin. CUP, 2014. https://doi.org/10.1557/mrs.2014.87.","apa":"Kwabi, D. G., Ortiz-Vitoriano, N., Freunberger, S. A., Chen, Y., Imanishi, N., Bruce, P. G., & Shao-Horn, Y. (2014). Materials challenges in rechargeable lithium-air batteries. MRS Bulletin. CUP. https://doi.org/10.1557/mrs.2014.87"},"publication_status":"published","abstract":[{"text":"Lithium-air batteries have received extraordinary attention recently owing to their theoretical gravimetric energies being considerably higher than those of Li-ion batteries. There are, however, significant challenges to practical implementation, including low energy efficiency, cycle life, and power capability. These are due primarily to the lack of fundamental understanding of oxygen reduction and evolution reaction kinetics and parasitic reactions between oxygen redox intermediate species and nominally inactive battery components such as carbon in the oxygen electrode and electrolytes. In this article, we discuss recent advances in the mechanistic understanding of oxygen redox reactions in nonaqueous electrolytes and the search for electrolytes and electrode materials that are chemically stable in the oxygen electrode. In addition, methods to protect lithium metal against corrosion by water and dendrite formation in aqueous lithium-air batteries are discussed. Further materials innovations lie at the heart of research and development efforts that are needed to enable the development of lithium-oxygen batteries with enhanced round-trip efficiency and cycle life.","lang":"eng"}],"date_published":"2014-05-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"MRS Bulletin","month":"05","author":[{"last_name":"Kwabi","first_name":"D.G.","full_name":"Kwabi, D.G."},{"last_name":"Ortiz-Vitoriano","first_name":"N.","full_name":"Ortiz-Vitoriano, N."},{"first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"last_name":"Chen","full_name":"Chen, Y.","first_name":"Y."},{"last_name":"Imanishi","first_name":"N.","full_name":"Imanishi, N."},{"first_name":"P.G.","full_name":"Bruce, P.G.","last_name":"Bruce"},{"last_name":"Shao-Horn","full_name":"Shao-Horn, Y.","first_name":"Y."}]},{"abstract":[{"lang":"eng","text":"When lithium–oxygen batteries discharge, O2 is reduced at the cathode to form solid Li2O2. Understanding the fundamental mechanism of O2 reduction in aprotic solvents is therefore essential to realizing their technological potential. Two different models have been proposed for Li2O2 formation, involving either solution or electrode surface routes. Here, we describe a single unified mechanism, which, unlike previous models, can explain O2 reduction across the whole range of solvents and for which the two previous models are limiting cases. We observe that the solvent influences O2 reduction through its effect on the solubility of LiO2, or, more precisely, the free energy of the reaction LiO2* ⇌ Li(sol)+ + O2−(sol) + ion pairs + higher aggregates (clusters). The unified mechanism shows that low-donor-number solvents are likely to lead to premature cell death, and that the future direction of research for lithium–oxygen batteries should focus on the search for new, stable, high-donor-number electrolytes, because they can support higher capacities and can better sustain discharge."}],"author":[{"last_name":"Johnson","first_name":"Lee","full_name":"Johnson, Lee"},{"last_name":"Li","first_name":"Chunmei","full_name":"Li, Chunmei"},{"last_name":"Liu","first_name":"Zheng","full_name":"Liu, Zheng"},{"last_name":"Chen","full_name":"Chen, Yuhui","first_name":"Yuhui"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"},{"last_name":"Ashok","first_name":"Praveen C.","full_name":"Ashok, Praveen C."},{"last_name":"Praveen","full_name":"Praveen, Bavishna B.","first_name":"Bavishna B."},{"last_name":"Dholakia","first_name":"Kishan","full_name":"Dholakia, Kishan"},{"full_name":"Tarascon, Jean-Marie","first_name":"Jean-Marie","last_name":"Tarascon"},{"last_name":"Bruce","full_name":"Bruce, Peter G.","first_name":"Peter G."}],"month":"11","publication":"Nature Chemistry","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-11-10T00:00:00Z","page":"1091-1099","year":"2014","oa_version":"None","doi":"10.1038/nchem.2101","publication_status":"published","citation":{"mla":"Johnson, Lee, et al. “The Role of LiO2 Solubility in O2 Reduction in Aprotic Solvents and Its Consequences for Li–O2 Batteries.” Nature Chemistry, vol. 6, no. 12, Springer Nature, 2014, pp. 1091–99, doi:10.1038/nchem.2101.","ieee":"L. Johnson et al., “The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries,” Nature Chemistry, vol. 6, no. 12. Springer Nature, pp. 1091–1099, 2014.","ista":"Johnson L, Li C, Liu Z, Chen Y, Freunberger SA, Ashok PC, Praveen BB, Dholakia K, Tarascon J-M, Bruce PG. 2014. The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry. 6(12), 1091–1099.","chicago":"Johnson, Lee, Chunmei Li, Zheng Liu, Yuhui Chen, Stefan Alexander Freunberger, Praveen C. Ashok, Bavishna B. Praveen, Kishan Dholakia, Jean-Marie Tarascon, and Peter G. Bruce. “The Role of LiO2 Solubility in O2 Reduction in Aprotic Solvents and Its Consequences for Li–O2 Batteries.” Nature Chemistry. Springer Nature, 2014. https://doi.org/10.1038/nchem.2101.","ama":"Johnson L, Li C, Liu Z, et al. The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry. 2014;6(12):1091-1099. doi:10.1038/nchem.2101","short":"L. Johnson, C. Li, Z. Liu, Y. Chen, S.A. Freunberger, P.C. Ashok, B.B. Praveen, K. Dholakia, J.-M. Tarascon, P.G. Bruce, Nature Chemistry 6 (2014) 1091–1099.","apa":"Johnson, L., Li, C., Liu, Z., Chen, Y., Freunberger, S. A., Ashok, P. C., … Bruce, P. G. (2014). The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2101"},"article_processing_charge":"No","article_type":"original","quality_controlled":"1","title":"The role of LiO2 solubility in O2 reduction in aprotic solvents and its consequences for Li–O2 batteries","day":"10","date_updated":"2021-01-12T08:12:55Z","date_created":"2020-01-15T12:18:18Z","intvolume":" 6","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/nchem.2138"}]},"status":"public","issue":"12","publication_identifier":{"issn":["1755-4330","1755-4349"]},"volume":6,"extern":"1","language":[{"iso":"eng"}],"type":"journal_article","_id":"7305","publisher":"Springer Nature"},{"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","article_type":"original","title":"A bistable genetic switch based on designable DNA-binding domains","year":"2014","external_id":{"pmid":["25264186"]},"doi":"10.1038/ncomms6007","intvolume":" 5","status":"public","day":"29","date_created":"2020-01-25T15:57:17Z","date_updated":"2021-01-12T08:13:15Z","publisher":"Springer Nature","author":[{"first_name":"Tina","full_name":"Lebar, Tina","last_name":"Lebar"},{"id":"2A58201A-F248-11E8-B48F-1D18A9856A87","full_name":"Bezeljak, Urban","first_name":"Urban","orcid":"0000-0003-1365-5631","last_name":"Bezeljak"},{"first_name":"Anja","full_name":"Golob, Anja","last_name":"Golob"},{"last_name":"Jerala","full_name":"Jerala, Miha","first_name":"Miha"},{"last_name":"Kadunc","full_name":"Kadunc, Lucija","first_name":"Lucija"},{"first_name":"Boštjan","full_name":"Pirš, Boštjan","last_name":"Pirš"},{"full_name":"Stražar, Martin","first_name":"Martin","last_name":"Stražar"},{"last_name":"Vučko","first_name":"Dušan","full_name":"Vučko, Dušan"},{"last_name":"Zupančič","first_name":"Uroš","full_name":"Zupančič, Uroš"},{"last_name":"Benčina","first_name":"Mojca","full_name":"Benčina, Mojca"},{"last_name":"Forstnerič","first_name":"Vida","full_name":"Forstnerič, Vida"},{"last_name":"Gaber","full_name":"Gaber, Rok","first_name":"Rok"},{"last_name":"Lonzarić","full_name":"Lonzarić, Jan","first_name":"Jan"},{"last_name":"Majerle","full_name":"Majerle, Andreja","first_name":"Andreja"},{"last_name":"Oblak","first_name":"Alja","full_name":"Oblak, Alja"},{"last_name":"Smole","first_name":"Anže","full_name":"Smole, Anže"},{"last_name":"Jerala","first_name":"Roman","full_name":"Jerala, Roman"}],"publication":"Nature Communications","date_published":"2014-09-29T00:00:00Z","abstract":[{"text":"Bistable switches are fundamental regulatory elements of complex systems, ranging from electronics to living cells. Designed genetic toggle switches have been constructed from pairs of natural transcriptional repressors wired to inhibit one another. The complexity of the engineered regulatory circuits can be increased using orthogonal transcriptional regulators based on designed DNA-binding domains. However, a mutual repressor-based toggle switch comprising DNA-binding domains of transcription-activator-like effectors (TALEs) did not support bistability in mammalian cells. Here, the challenge of engineering a bistable switch based on monomeric DNA-binding domains is solved via the introduction of a positive feedback loop composed of activators based on the same TALE domains as their opposing repressors and competition for the same DNA operator site. This design introduces nonlinearity and results in epigenetic bistability. This principle could be used to employ other monomeric DNA-binding domains such as CRISPR for applications ranging from reprogramming cells to building digital biological memory.","lang":"eng"}],"citation":{"apa":"Lebar, T., Bezeljak, U., Golob, A., Jerala, M., Kadunc, L., Pirš, B., … Jerala, R. (2014). A bistable genetic switch based on designable DNA-binding domains. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms6007","short":"T. Lebar, U. Bezeljak, A. Golob, M. Jerala, L. Kadunc, B. Pirš, M. Stražar, D. Vučko, U. Zupančič, M. Benčina, V. Forstnerič, R. Gaber, J. Lonzarić, A. Majerle, A. Oblak, A. Smole, R. Jerala, Nature Communications 5 (2014).","chicago":"Lebar, Tina, Urban Bezeljak, Anja Golob, Miha Jerala, Lucija Kadunc, Boštjan Pirš, Martin Stražar, et al. “A Bistable Genetic Switch Based on Designable DNA-Binding Domains.” Nature Communications. Springer Nature, 2014. https://doi.org/10.1038/ncomms6007.","ama":"Lebar T, Bezeljak U, Golob A, et al. A bistable genetic switch based on designable DNA-binding domains. Nature Communications. 2014;5(1). doi:10.1038/ncomms6007","ista":"Lebar T, Bezeljak U, Golob A, Jerala M, Kadunc L, Pirš B, Stražar M, Vučko D, Zupančič U, Benčina M, Forstnerič V, Gaber R, Lonzarić J, Majerle A, Oblak A, Smole A, Jerala R. 2014. A bistable genetic switch based on designable DNA-binding domains. Nature Communications. 5(1), 5007.","ieee":"T. Lebar et al., “A bistable genetic switch based on designable DNA-binding domains,” Nature Communications, vol. 5, no. 1. Springer Nature, 2014.","mla":"Lebar, Tina, et al. “A Bistable Genetic Switch Based on Designable DNA-Binding Domains.” Nature Communications, vol. 5, no. 1, 5007, Springer Nature, 2014, doi:10.1038/ncomms6007."},"publication_status":"published","quality_controlled":"1","oa_version":"None","_id":"7361","article_number":"5007","publication_identifier":{"issn":["2041-1723"]},"issue":"1","volume":5,"extern":"1","pmid":1,"type":"journal_article","language":[{"iso":"eng"}]},{"intvolume":" 21","status":"public","day":"10","date_created":"2020-02-05T14:14:48Z","date_updated":"2023-02-23T13:08:22Z","publisher":"International Union of Crystallography","_id":"7455","extern":"1","volume":21,"issue":"2","publication_identifier":{"issn":["1600-5775"]},"type":"journal_article","language":[{"iso":"eng"}],"publication":"Journal of Synchrotron Radiation","month":"01","author":[{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso","first_name":"Tommaso","orcid":"0000-0001-9732-3815","last_name":"Costanzo"},{"first_name":"Federico","full_name":"Benzi, Federico","last_name":"Benzi"},{"last_name":"Ghigna","full_name":"Ghigna, Paolo","first_name":"Paolo"},{"last_name":"Pin","first_name":"Sonia","full_name":"Pin, Sonia"},{"first_name":"Giorgio","full_name":"Spinolo, Giorgio","last_name":"Spinolo"},{"last_name":"d'Acapito","first_name":"Francesco","full_name":"d'Acapito, Francesco"}],"date_published":"2014-01-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The reaction between NiO and (0001)- and ([1\\bar102])-oriented Al2O3 single crystals has been investigated on model experimental systems by using the ReflEXAFS technique. Depth-sensitive information is obtained by collecting data above and below the critical angle for total reflection. A systematic protocol for data analysis, based on the recently developed CARD code, was implemented, and a detailed description of the reactive systems was obtained. In particular, for ([1\\bar102])-oriented Al2O3, the reaction with NiO is almost complete after heating for 6 h at 1273 K, and an almost uniform layer of spinel is found below a mixed (NiO + spinel) layer at the very upmost part of the sample. In the case of the (0001)-oriented Al2O3, for the same temperature and heating time, the reaction shows a lower advancement degree and a residual fraction of at least 30% NiO is detected in the ReflEXAFS spectra. ","lang":"eng"}],"article_processing_charge":"No","publication_status":"published","citation":{"ista":"Costanzo T, Benzi F, Ghigna P, Pin S, Spinolo G, d’Acapito F. 2014. Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS). Journal of Synchrotron Radiation. 21(2), 395–400.","mla":"Costanzo, Tommaso, et al. “Studying the Surface Reaction between NiO and Al2O3viatotal Reflection EXAFS (ReflEXAFS).” Journal of Synchrotron Radiation, vol. 21, no. 2, International Union of Crystallography, 2014, pp. 395–400, doi:10.1107/s1600577513031299.","ieee":"T. Costanzo, F. Benzi, P. Ghigna, S. Pin, G. Spinolo, and F. d’Acapito, “Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS),” Journal of Synchrotron Radiation, vol. 21, no. 2. International Union of Crystallography, pp. 395–400, 2014.","apa":"Costanzo, T., Benzi, F., Ghigna, P., Pin, S., Spinolo, G., & d’Acapito, F. (2014). Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS). Journal of Synchrotron Radiation. International Union of Crystallography. https://doi.org/10.1107/s1600577513031299","ama":"Costanzo T, Benzi F, Ghigna P, Pin S, Spinolo G, d’Acapito F. Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS). Journal of Synchrotron Radiation. 2014;21(2):395-400. doi:10.1107/s1600577513031299","chicago":"Costanzo, Tommaso, Federico Benzi, Paolo Ghigna, Sonia Pin, Giorgio Spinolo, and Francesco d’Acapito. “Studying the Surface Reaction between NiO and Al2O3viatotal Reflection EXAFS (ReflEXAFS).” Journal of Synchrotron Radiation. International Union of Crystallography, 2014. https://doi.org/10.1107/s1600577513031299.","short":"T. Costanzo, F. Benzi, P. Ghigna, S. Pin, G. Spinolo, F. d’Acapito, Journal of Synchrotron Radiation 21 (2014) 395–400."},"title":"Studying the surface reaction between NiO and Al2O3viatotal reflection EXAFS (ReflEXAFS)","article_type":"original","quality_controlled":"1","oa_version":"None","year":"2014","page":"395-400","doi":"10.1107/s1600577513031299"},{"oa_version":"Published Version","quality_controlled":"1","citation":{"apa":"Tan, S., & Xue, H.-W. (2014). Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2014.10.047","chicago":"Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis by Phosphorylating and Promoting the Turnover of ACS5.” Cell Reports. Elsevier, 2014. https://doi.org/10.1016/j.celrep.2014.10.047.","short":"S. Tan, H.-W. Xue, Cell Reports 9 (2014) 1692–1702.","ama":"Tan S, Xue H-W. Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. Cell Reports. 2014;9(5):1692-1702. doi:10.1016/j.celrep.2014.10.047","ista":"Tan S, Xue H-W. 2014. Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. Cell Reports. 9(5), 1692–1702.","ieee":"S. Tan and H.-W. Xue, “Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5,” Cell Reports, vol. 9, no. 5. Elsevier, pp. 1692–1702, 2014.","mla":"Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis by Phosphorylating and Promoting the Turnover of ACS5.” Cell Reports, vol. 9, no. 5, Elsevier, 2014, pp. 1692–702, doi:10.1016/j.celrep.2014.10.047."},"publication_status":"published","date_published":"2014-12-11T00:00:00Z","oa":1,"author":[{"orcid":"0000-0002-0471-8285","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","first_name":"Shutang"},{"last_name":"Xue","first_name":"Hong-Wei","full_name":"Xue, Hong-Wei"}],"publication":"Cell Reports","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2211-1247"]},"issue":"5","volume":9,"extern":"1","_id":"7598","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1016/j.celrep.2014.10.047","page":"1692-1702","year":"2014","article_type":"original","title":"Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5","article_processing_charge":"No","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"dernst","checksum":"23c30de4ac98ce9879fc054121517626","file_size":2755808,"content_type":"application/pdf","date_created":"2020-03-23T12:23:40Z","date_updated":"2020-07-14T12:48:01Z","file_id":"7613","relation":"main_file","access_level":"open_access","file_name":"2014_CellPress_Tan.pdf"}],"file_date_updated":"2020-07-14T12:48:01Z","month":"12","ddc":["580"],"publisher":"Elsevier","date_updated":"2021-01-12T08:14:24Z","date_created":"2020-03-21T16:08:18Z","day":"11","status":"public","intvolume":" 9"},{"abstract":[{"lang":"eng","text":"Task allocation is a classic distributed problem in which a set of p potentially faulty processes must cooperate to perform a set of tasks. This paper considers a new dynamic version of the problem, in which tasks are injected adversarially during an asynchronous execution. We give the first asynchronous shared-memory algorithm for dynamic task allocation, and we prove that our solution is optimal within logarithmic factors. The main algorithmic idea is a randomized concurrent data structure called a dynamic to-do tree, which allows processes to pick new tasks to perform at random from the set of available tasks, and to insert tasks at random empty locations in the data structure. Our analysis shows that these properties avoid duplicating work unnecessarily. On the other hand, since the adversary controls the input as well the scheduling, it can induce executions where lots of processes contend for a few available tasks, which is inefficient. However, we prove that every algorithm has the same problem: given an arbitrary input, if OPT is the worst-case complexity of the optimal algorithm on that input, then the expected work complexity of our algorithm on the same input is O(OPT log3 m), where m is an upper bound on the number of tasks that are present in the system at any given time."}],"date_published":"2014-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"full_name":"Bender, Michael","first_name":"Michael","last_name":"Bender"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"first_name":"Seth","full_name":"Gilbert, Seth","last_name":"Gilbert"}],"doi":"10.1137/1.9781611973402.31","oa_version":"None","year":"2014","page":"416 - 435","acknowledgement":"Dan Alistarh - This author was supported by the SNF Postdoctoral Fellows Program, NSF grant CCF-1217921, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nJames Aspnes - Supported in part by NSF grant CCF-0916389.\r\nMichael A. Bender - This research was supported in part by NSF grants CCF 1114809, CCF 1217708, IIS 1247726, and IIS 1251137.\r\nRati Gelashvili - This work was supported in part by NSF grants CCF-1217921, CCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nSeth Gilbert - Supported by Singapore AcRF-2 MOE2011-T2-2-042.\r\n","title":"Dynamic task allocation in asynchronous shared memory","article_processing_charge":"No","citation":{"short":"D.-A. Alistarh, J. Aspnes, M. Bender, R. Gelashvili, S. Gilbert, in:, SIAM, 2014, pp. 416–435.","ama":"Alistarh D-A, Aspnes J, Bender M, Gelashvili R, Gilbert S. Dynamic task allocation in asynchronous shared memory. In: SIAM; 2014:416-435. doi:10.1137/1.9781611973402.31","chicago":"Alistarh, Dan-Adrian, James Aspnes, Michael Bender, Rati Gelashvili, and Seth Gilbert. “Dynamic Task Allocation in Asynchronous Shared Memory,” 416–35. SIAM, 2014. https://doi.org/10.1137/1.9781611973402.31.","apa":"Alistarh, D.-A., Aspnes, J., Bender, M., Gelashvili, R., & Gilbert, S. (2014). Dynamic task allocation in asynchronous shared memory (pp. 416–435). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1137/1.9781611973402.31","mla":"Alistarh, Dan-Adrian, et al. Dynamic Task Allocation in Asynchronous Shared Memory. SIAM, 2014, pp. 416–35, doi:10.1137/1.9781611973402.31.","ieee":"D.-A. Alistarh, J. Aspnes, M. Bender, R. Gelashvili, and S. Gilbert, “Dynamic task allocation in asynchronous shared memory,” presented at the SODA: Symposium on Discrete Algorithms, 2014, pp. 416–435.","ista":"Alistarh D-A, Aspnes J, Bender M, Gelashvili R, Gilbert S. 2014. Dynamic task allocation in asynchronous shared memory. SODA: Symposium on Discrete Algorithms, 416–435."},"publist_id":"6886","publication_status":"published","conference":{"name":"SODA: Symposium on Discrete Algorithms"},"date_created":"2018-12-11T11:48:24Z","date_updated":"2023-02-23T13:13:52Z","day":"01","status":"public","language":[{"iso":"eng"}],"type":"conference","extern":"1","publisher":"SIAM","_id":"768"},{"title":"Tight bounds for asynchronous renaming","acknowledgement":"The work of J. Aspnes was supported in part by NSF grant CCF-0916389. The work of S. Gilbert was\r\nsupported by Singapore AcRF-2 MOE 2011-T2-2-042.\r\nK. Censor-Hillel is a Shalon Fellow. Part of this work was performed while K. Censor-Hillel was a postdoc at\r\nMIT, supported by the Simons Postdoctoral Fellowship.","publist_id":"6887","publication_status":"published","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Tight Bounds for Asynchronous Renaming.” Journal of the ACM, vol. 61, no. 3, ACM, 2014, doi:10.1145/2597630.","ieee":"D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, and R. Guerraoui, “Tight bounds for asynchronous renaming,” Journal of the ACM, vol. 61, no. 3. ACM, 2014.","ista":"Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Guerraoui R. 2014. Tight bounds for asynchronous renaming. Journal of the ACM. 61(3).","short":"D.-A. Alistarh, J. Aspnes, K. Censor Hillel, S. Gilbert, R. Guerraoui, Journal of the ACM 61 (2014).","chicago":"Alistarh, Dan-Adrian, James Aspnes, Keren Censor Hillel, Seth Gilbert, and Rachid Guerraoui. “Tight Bounds for Asynchronous Renaming.” Journal of the ACM. ACM, 2014. https://doi.org/10.1145/2597630.","ama":"Alistarh D-A, Aspnes J, Censor Hillel K, Gilbert S, Guerraoui R. Tight bounds for asynchronous renaming. Journal of the ACM. 2014;61(3). doi:10.1145/2597630","apa":"Alistarh, D.-A., Aspnes, J., Censor Hillel, K., Gilbert, S., & Guerraoui, R. (2014). Tight bounds for asynchronous renaming. Journal of the ACM. ACM. https://doi.org/10.1145/2597630"},"article_processing_charge":"No","doi":"10.1145/2597630","oa_version":"None","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-05-01T00:00:00Z","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"last_name":"Censor Hillel","first_name":"Keren","full_name":"Censor Hillel, Keren"},{"last_name":"Gilbert","first_name":"Seth","full_name":"Gilbert, Seth"},{"last_name":"Guerraoui","first_name":"Rachid","full_name":"Guerraoui, Rachid"}],"month":"05","publication":"Journal of the ACM","abstract":[{"lang":"eng","text":"This article presents the first tight bounds on the time complexity of shared-memory renaming, a fundamental problem in distributed computing in which a set of processes need to pick distinct identifiers from a small namespace. We first prove an individual lower bound of ω(k) process steps for deterministic renaming into any namespace of size subexponential in k, where k is the number of participants. The bound is tight: it draws an exponential separation between deterministic and randomized solutions, and implies new tight bounds for deterministic concurrent fetch-and-increment counters, queues, and stacks. The proof is based on a new reduction from renaming to another fundamental problem in distributed computing: mutual exclusion. We complement this individual bound with a global lower bound of ω(klog(k/c)) on the total step complexity of renaming into a namespace of size ck, for any c = 1. This result applies to randomized algorithms against a strong adversary, and helps derive new global lower bounds for randomized approximate counter implementations, that are tight within logarithmic factors. On the algorithmic side, we give a protocol that transforms any sorting network into a randomized strong adaptive renaming algorithm, with expected cost equal to the depth of the sorting network. This gives a tight adaptive renaming algorithm with expected step complexity O(log k), where k is the contention in the current execution. This algorithm is the first to achieve sublinear time, and it is time-optimal as per our randomized lower bound. Finally, we use this renaming protocol to build monotone-consistent counters with logarithmic step complexity and linearizable fetch-and-increment registers with polylogarithmic cost."}],"_id":"769","publisher":"ACM","type":"journal_article","language":[{"iso":"eng"}],"issue":"3","volume":61,"extern":"1","status":"public","intvolume":" 61","date_created":"2018-12-11T11:48:24Z","date_updated":"2023-02-23T13:14:09Z","day":"01"},{"day":"01","date_created":"2020-04-30T10:35:39Z","date_updated":"2024-01-31T10:14:08Z","intvolume":" 28","status":"public","issue":"10","publication_identifier":{"issn":["0959-4388"]},"volume":28,"extern":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Elsevier","_id":"7699","author":[{"first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","last_name":"Sweeney","orcid":"0000-0001-9242-5601"},{"last_name":"Kelley","first_name":"Darcy B","full_name":"Kelley, Darcy B"}],"publication":"Current Opinion in Neurobiology","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-10-01T00:00:00Z","page":"34-41","year":"2014","oa_version":"None","doi":"10.1016/j.conb.2014.06.006","citation":{"ama":"Sweeney LB, Kelley DB. Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. 2014;28(10):34-41. doi:10.1016/j.conb.2014.06.006","short":"L.B. Sweeney, D.B. Kelley, Current Opinion in Neurobiology 28 (2014) 34–41.","chicago":"Sweeney, Lora B., and Darcy B Kelley. “Harnessing Vocal Patterns for Social Communication.” Current Opinion in Neurobiology. Elsevier, 2014. https://doi.org/10.1016/j.conb.2014.06.006.","apa":"Sweeney, L. B., & Kelley, D. B. (2014). Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2014.06.006","mla":"Sweeney, Lora B., and Darcy B. Kelley. “Harnessing Vocal Patterns for Social Communication.” Current Opinion in Neurobiology, vol. 28, no. 10, Elsevier, 2014, pp. 34–41, doi:10.1016/j.conb.2014.06.006.","ieee":"L. B. Sweeney and D. B. Kelley, “Harnessing vocal patterns for social communication,” Current Opinion in Neurobiology, vol. 28, no. 10. Elsevier, pp. 34–41, 2014.","ista":"Sweeney LB, Kelley DB. 2014. Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. 28(10), 34–41."},"publication_status":"published","article_processing_charge":"No","title":"Harnessing vocal patterns for social communication","article_type":"original","quality_controlled":"1"},{"abstract":[{"text":"Dynamic memory reclamation is arguably the biggest open problem in concurrent data structure design: All known solutions induce high overhead, or must be customized to the specific data structure by the programmer, or both. This paper presents StackTrack, the first concurrent memory reclamation scheme that can be applied automatically by a compiler, while maintaining efficiency. StackTrack eliminates most of the expensive bookkeeping required for memory reclamation by leveraging the power of hardware transactional memory (HTM) in a new way: it tracks thread variables dynamically, and in an atomic fashion. This effectively makes all memory references visible without having threads pay the overhead of writing out this information. Our empirical results show that this new approach matches or outperforms prior, non-automated, techniques.","lang":"eng"}],"date_published":"2014-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Patrick","full_name":"Eugster, Patrick","last_name":"Eugster"},{"first_name":"Maurice","full_name":"Herlihy, Maurice","last_name":"Herlihy"},{"last_name":"Matveev","full_name":"Matveev, Alexander","first_name":"Alexander"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"doi":"10.1145/2592798.2592808","year":"2014","oa_version":"None","acknowledgement":"Dan Alistarh - Part of this work was performed while the author was a Postdoctoral\r\nAssociate a MIT CSAIL, supported in part by NSF grant CCF-1217921,\r\nDoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle\r\nand Intel corporations.\r\nPatrick Eugester - Supported in part by DARPA grant N11AP20014 and NSF grant CNS-\r\n1117065.\r\nMaurice Herlihy - Supported by NSF grant 1301924.\r\nNir Shavit - Supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and\r\nIntel corporations.","title":"StackTrack: An automated transactional approach to concurrent memory reclamation","article_processing_charge":"No","publist_id":"6888","citation":{"ista":"Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. 2014. StackTrack: An automated transactional approach to concurrent memory reclamation. EuroSys: European Conference on Computer Systems.","mla":"Alistarh, Dan-Adrian, et al. StackTrack: An Automated Transactional Approach to Concurrent Memory Reclamation. ACM, 2014, doi:10.1145/2592798.2592808.","ieee":"D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, and N. Shavit, “StackTrack: An automated transactional approach to concurrent memory reclamation,” presented at the EuroSys: European Conference on Computer Systems, 2014.","apa":"Alistarh, D.-A., Eugster, P., Herlihy, M., Matveev, A., & Shavit, N. (2014). StackTrack: An automated transactional approach to concurrent memory reclamation. Presented at the EuroSys: European Conference on Computer Systems, ACM. https://doi.org/10.1145/2592798.2592808","chicago":"Alistarh, Dan-Adrian, Patrick Eugster, Maurice Herlihy, Alexander Matveev, and Nir Shavit. “StackTrack: An Automated Transactional Approach to Concurrent Memory Reclamation.” ACM, 2014. https://doi.org/10.1145/2592798.2592808.","ama":"Alistarh D-A, Eugster P, Herlihy M, Matveev A, Shavit N. StackTrack: An automated transactional approach to concurrent memory reclamation. In: ACM; 2014. doi:10.1145/2592798.2592808","short":"D.-A. Alistarh, P. Eugster, M. Herlihy, A. Matveev, N. Shavit, in:, ACM, 2014."},"publication_status":"published","conference":{"name":"EuroSys: European Conference on Computer Systems"},"date_created":"2018-12-11T11:48:24Z","date_updated":"2023-02-23T13:14:25Z","day":"01","status":"public","language":[{"iso":"eng"}],"type":"conference","extern":"1","_id":"770","publisher":"ACM"},{"abstract":[{"lang":"eng","text":"We consider the following natural problem: n failure-prone servers, communicating synchronously through message passing, must assign themselves one-to-one to n distinct items. Existing literature suggests two possible approaches to this problem. First, model it as an instance of tight renaming in synchronous message-passing systems; for deterministic solutions, a tight bound of ©(logn) communication rounds is known. Second, model the scenario as an instance of randomized load-balancing, for which elegant sub-logarithmic solutions exist. However, careful examination reveals that known load-balancing schemes do not apply to our scenario, because they either do not tolerate faults or do not ensure one-to-one allocation. It is thus natural to ask if sublogarithmic solutions exist for this apparently simple but intriguing problem. In this paper, we combine the two approaches to provide a new randomized solution for tight renaming, which terminates in O (log log n) communication rounds with high probability, against a strong adaptive adversary. Our solution, called Balls-into-Leaves, combines the deterministic approach with a new randomized scheme to obtain perfectly balanced allocations. The algorithm arranges the items as leaves of a tree, and participants repeatedly perform random choices among the leaves. The algorithm exchanges information in each round to split the participants into progressively smaller groups whose random choices do not conflict. We then extend the algorithm to terminate early in O(log log) rounds w.h.p., where is the actual number of failures. These results imply an exponential separation between deterministic and randomized algorithms for the tight renaming problem in message-passing systems."}],"month":"01","author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Denysyuk","first_name":"Oksana","full_name":"Denysyuk, Oksana"},{"first_name":"Luís","full_name":"Rodrígues, Luís","last_name":"Rodrígues"},{"full_name":"Shavit, Nir","first_name":"Nir","last_name":"Shavit"}],"date_published":"2014-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","oa_version":"None","page":"232 - 241","doi":"10.1145/2611462.2611499","article_processing_charge":"No","citation":{"apa":"Alistarh, D.-A., Denysyuk, O., Rodrígues, L., & Shavit, N. (2014). Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems (pp. 232–241). Presented at the PODC: Principles of Distributed Computing, ACM. https://doi.org/10.1145/2611462.2611499","chicago":"Alistarh, Dan-Adrian, Oksana Denysyuk, Luís Rodrígues, and Nir Shavit. “Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems,” 232–41. ACM, 2014. https://doi.org/10.1145/2611462.2611499.","ama":"Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems. In: ACM; 2014:232-241. doi:10.1145/2611462.2611499","short":"D.-A. Alistarh, O. Denysyuk, L. Rodrígues, N. Shavit, in:, ACM, 2014, pp. 232–241.","ista":"Alistarh D-A, Denysyuk O, Rodrígues L, Shavit N. 2014. Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems. PODC: Principles of Distributed Computing, 232–241.","mla":"Alistarh, Dan-Adrian, et al. Balls-into-Leaves: Sub-Logarithmic Renaming in Synchronous Message-Passing Systems. ACM, 2014, pp. 232–41, doi:10.1145/2611462.2611499.","ieee":"D.-A. Alistarh, O. Denysyuk, L. Rodrígues, and N. Shavit, “Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems,” presented at the PODC: Principles of Distributed Computing, 2014, pp. 232–241."},"publication_status":"published","publist_id":"6884","title":"Balls-into-Leaves: Sub-logarithmic renaming in synchronous message-passing systems","acknowledgement":"Dan Alistarh was partially supported by the SNF Post-\r\ndoctoral Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from\r\nthe Oracle and Intel corporations.\r\nOksana Denysyuk and Lu ́ıs Rodrigues were partially supported by Funda ̧c ̃ao para a Ciˆencia e Tecnologia (FCT) via\r\nthe project PEPITA (PTDC/EEI-SCR/2776/2012) and via\r\nthe INESC-ID multi-annual funding through the PIDDAC\r\nProgram fund grant, under project PEst-OE/EEI/LA0021/\r\n2013.\r\nNir Shavit was supported in part by NSF grants CCF-1217921 and CCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.","day":"01","conference":{"name":"PODC: Principles of Distributed Computing"},"date_updated":"2023-02-23T13:14:49Z","date_created":"2018-12-11T11:48:25Z","status":"public","extern":"1","language":[{"iso":"eng"}],"type":"conference","_id":"771","publisher":"ACM"},{"abstract":[{"lang":"eng","text":"Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. While obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most non-blocking commercial code is only lock-free. This paper suggests a simple solution to this problem. We show that, for a large class of lock-free algorithms, under scheduling conditions which approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can keep on designing simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes with the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1, but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst case adversary, in a stochastic model capturing their expected asymptotic behavior."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-01-01T00:00:00Z","oa":1,"author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"full_name":"Censor Hillel, Keren","first_name":"Keren","last_name":"Censor Hillel"},{"last_name":"Shavit","first_name":"Nir","full_name":"Shavit, Nir"}],"month":"01","doi":"10.1145/2591796.2591836","external_id":{"arxiv":["1311.3200"]},"page":"714 - 723","year":"2014","oa_version":"Preprint","acknowledgement":"Dan Alistarh - Part of this work was performed while the author was a Postdoctoral Associate at MIT CSAIL, where he was supported by SNF\r\nPostdoctoral Fellows Program, NSF grant CCF-1217921, DoE\r\nASCR grant ER26116/DE-SC0008923, and by grants from the Oracle and Intel corporations.\r\nKeron Censor-Hillel - Shalon Fellow\r\nNir Shavit - This work was supported in part by NSF grants CCF-1217921 and\r\nCCF-1301926, DoE ASCR grant ER26116/DE-SC0008923, and\r\nby grants from the Oracle and Intel corporations.","title":"Are lock-free concurrent algorithms practically wait-free?","publist_id":"6885","citation":{"mla":"Alistarh, Dan-Adrian, et al. Are Lock-Free Concurrent Algorithms Practically Wait-Free? ACM, 2014, pp. 714–23, doi:10.1145/2591796.2591836.","ieee":"D.-A. Alistarh, K. Censor Hillel, and N. Shavit, “Are lock-free concurrent algorithms practically wait-free?,” presented at the STOC: Symposium on Theory of Computing, 2014, pp. 714–723.","ista":"Alistarh D-A, Censor Hillel K, Shavit N. 2014. Are lock-free concurrent algorithms practically wait-free? STOC: Symposium on Theory of Computing, 714–723.","short":"D.-A. Alistarh, K. Censor Hillel, N. Shavit, in:, ACM, 2014, pp. 714–723.","ama":"Alistarh D-A, Censor Hillel K, Shavit N. Are lock-free concurrent algorithms practically wait-free? In: ACM; 2014:714-723. doi:10.1145/2591796.2591836","chicago":"Alistarh, Dan-Adrian, Keren Censor Hillel, and Nir Shavit. “Are Lock-Free Concurrent Algorithms Practically Wait-Free?,” 714–23. ACM, 2014. https://doi.org/10.1145/2591796.2591836.","apa":"Alistarh, D.-A., Censor Hillel, K., & Shavit, N. (2014). Are lock-free concurrent algorithms practically wait-free? (pp. 714–723). Presented at the STOC: Symposium on Theory of Computing, ACM. https://doi.org/10.1145/2591796.2591836"},"publication_status":"published","article_processing_charge":"No","date_updated":"2023-02-23T13:15:13Z","arxiv":1,"date_created":"2018-12-11T11:48:25Z","conference":{"name":"STOC: Symposium on Theory of Computing"},"day":"01","status":"public","type":"conference","language":[{"iso":"eng"}],"extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1311.3200","open_access":"1"}],"_id":"772","publisher":"ACM"},{"alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-01-01T00:00:00Z","author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"first_name":"Valerie","full_name":"King, Valerie","last_name":"King"},{"last_name":"Saia","first_name":"Jared","full_name":"Saia, Jared"}],"month":"01","editor":[{"last_name":"Kuhn","first_name":"Fabian","full_name":"Kuhn, Fabian"}],"abstract":[{"lang":"eng","text":"We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n/2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(n log3n) messages in expectation, which is again within logarithmic factors of optimal.We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt + t2log2t) total messages. Our protocol uses messages of size O(log n), and can therefore scale to large networks.\r\n\r\nWe consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary.\r\n\r\nOur approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model."}],"title":"Communication-efficient randomized consensus","publist_id":"6881","citation":{"ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. In: Kuhn F, ed. Vol 8784. Springer; 2014:61-75. doi:10.1007/978-3-662-45174-8_5","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, in:, F. Kuhn (Ed.), Springer, 2014, pp. 61–75.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” edited by Fabian Kuhn, 8784:61–75. Springer, 2014. https://doi.org/10.1007/978-3-662-45174-8_5.","apa":"Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2014). Communication-efficient randomized consensus. In F. Kuhn (Ed.) (Vol. 8784, pp. 61–75). Presented at the DISC: Distributed Computing, Austin, USA: Springer. https://doi.org/10.1007/978-3-662-45174-8_5","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” presented at the DISC: Distributed Computing, Austin, USA, 2014, vol. 8784, pp. 61–75.","mla":"Alistarh, Dan-Adrian, et al. Communication-Efficient Randomized Consensus. Edited by Fabian Kuhn, vol. 8784, Springer, 2014, pp. 61–75, doi:10.1007/978-3-662-45174-8_5.","ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2014. Communication-efficient randomized consensus. DISC: Distributed Computing, LNCS, vol. 8784, 61–75."},"publication_status":"published","article_processing_charge":"No","doi":"10.1007/978-3-662-45174-8_5","page":"61 - 75","oa_version":"None","year":"2014","status":"public","intvolume":" 8784","date_updated":"2023-02-23T13:15:36Z","date_created":"2018-12-11T11:48:25Z","conference":{"end_date":"2014-10-15","location":"Austin, USA","name":"DISC: Distributed Computing","start_date":"2014-10-12"},"day":"01","_id":"773","publisher":"Springer","type":"conference","language":[{"iso":"eng"}],"volume":8784,"extern":"1"}]