[{"page":"167 - 181","language":[{"iso":"eng"}],"publisher":"ACM","month":"05","day":"31","ec_funded":1,"publication_status":"published","status":"public","doi":"10.1145/2593882.2593900","abstract":[{"lang":"eng","text":"Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \\Probabilistic Programming" has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research."}],"publist_id":"5816","date_created":"2018-12-11T11:51:45Z","publication":"Proceedings of the on Future of Software Engineering","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1145/2593882.2593900","open_access":"1"}],"year":"2014","conference":{"start_date":"2014-05-31","location":"Hyderabad, India","end_date":"2014-06-07","name":"FOSE: Future of Software Engineering"},"quality_controlled":"1","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"title":"Probabilistic programming","date_published":"2014-05-31T00:00:00Z","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181.","ama":"Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: Proceedings of the on Future of Software Engineering. ACM; 2014:167-181. doi:10.1145/2593882.2593900","chicago":"Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In Proceedings of the on Future of Software Engineering, 167–81. ACM, 2014. https://doi.org/10.1145/2593882.2593900.","ieee":"A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in Proceedings of the on Future of Software Engineering, Hyderabad, India, 2014, pp. 167–181.","ista":"Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.","mla":"Gordon, Andrew, et al. “Probabilistic Programming.” Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–81, doi:10.1145/2593882.2593900.","apa":"Gordon, A., Henzinger, T. A., Nori, A., & Rajamani, S. (2014). Probabilistic programming. In Proceedings of the on Future of Software Engineering (pp. 167–181). Hyderabad, India: ACM. https://doi.org/10.1145/2593882.2593900"},"oa":1,"author":[{"last_name":"Gordon","full_name":"Gordon, Andrew","first_name":"Andrew"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Aditya","full_name":"Nori, Aditya","last_name":"Nori"},{"full_name":"Rajamani, Sriram","first_name":"Sriram","last_name":"Rajamani"}],"oa_version":"Published Version","date_updated":"2021-01-12T06:50:22Z","department":[{"_id":"ToHe"}],"_id":"1393","scopus_import":1},{"article_processing_charge":"No","volume":113,"publication":"Physical Review Letters","year":"2014","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3923"}],"date_created":"2023-08-10T06:38:38Z","quality_controlled":"1","title":"Two-pulse field-free orientation reveals anisotropy of molecular shape resonance","date_published":"2014-07-11T00:00:00Z","keyword":["General Physics and Astronomy"],"oa":1,"author":[{"last_name":"Kraus","full_name":"Kraus, P. M.","first_name":"P. M."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"full_name":"Wörner, H. J.","first_name":"H. J.","last_name":"Wörner"}],"citation":{"ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 113(2), 023001.","mla":"Kraus, P. M., et al. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters, vol. 113, no. 2, 023001, American Physical Society, 2014, doi:10.1103/physrevlett.113.023001.","apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.113.023001","short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Physical Review Letters 113 (2014).","ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse field-free orientation reveals anisotropy of molecular shape resonance. Physical Review Letters. 2014;113(2). doi:10.1103/physrevlett.113.023001","chicago":"Kraus, P. M., Denitsa Rangelova Baykusheva, and H. J. Wörner. “Two-Pulse Field-Free Orientation Reveals Anisotropy of Molecular Shape Resonance.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.113.023001.","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse field-free orientation reveals anisotropy of molecular shape resonance,” Physical Review Letters, vol. 113, no. 2. American Physical Society, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2023-08-22T09:02:56Z","type":"journal_article","scopus_import":"1","external_id":{"arxiv":["1311.3923"],"pmid":["25062172"]},"_id":"14020","arxiv":1,"language":[{"iso":"eng"}],"article_type":"original","intvolume":" 113","article_number":"023001","publisher":"American Physical Society","extern":"1","day":"11","publication_status":"published","month":"07","doi":"10.1103/physrevlett.113.023001","abstract":[{"text":"We report the observation of macroscopic field-free orientation, i.e., more than 73% of CO molecules pointing in the same direction. This is achieved through an all-optical scheme operating at high particle densities (>10(17) cm(-3)) that combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses. We show that the achieved orientation solely relies on the hyperpolarizability interaction as opposed to an ionization-depletion mechanism, thus, opening a wide range of applications. The achieved strong orientation enables us to reveal the molecular-frame anisotropies of the photorecombination amplitudes and phases caused by a shape resonance. The resonance appears as a local maximum in the even-harmonic emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in this spectral region through the combined effects of an asymmetric photorecombination phase and a subcycle Stark effect, generic for polar molecules, that we experimentally identify.","lang":"eng"}],"issue":"2","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"pmid":1,"status":"public"},{"article_type":"original","article_number":"124030","intvolume":" 47","language":[{"iso":"eng"}],"arxiv":1,"publisher":"IOP Publishing","month":"06","day":"10","extern":"1","publication_status":"published","publication_identifier":{"issn":["0953-4075"],"eissn":["1361-6455"]},"status":"public","doi":"10.1088/0953-4075/47/12/124030","abstract":[{"text":"We present the detailed analysis of a new two-pulse orientation scheme that achieves macroscopic field-free orientation at the high particle densities required for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923). Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour non-resonant femtosecond laser pulses. High-harmonic generation is used to probe the oriented wave-packet dynamics and reveals that a very high degree of orientation (Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting carbonyl sulphide molecules. We show that the present two-pulse scheme selectively enhances orientation created by the hyperpolarizability interaction whereas the ionization-depletion mechanism plays no role. We further control and optimize orientation through the delay between the one- and two-colour pump pulses. Finally, we demonstrate a complementary encoding of electronic-structure features, such as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress makes two-pulse field-free orientation an attractive tool for a broad class of time-resolved measurements.","lang":"eng"}],"issue":"12","date_created":"2023-08-10T06:38:48Z","publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","volume":47,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3923"}],"year":"2014","quality_controlled":"1","title":"Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules","keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"date_published":"2014-06-10T00:00:00Z","type":"journal_article","citation":{"mla":"Kraus, P. M., et al. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12, 124030, IOP Publishing, 2014, doi:10.1088/0953-4075/47/12/124030.","apa":"Kraus, P. M., Baykusheva, D. R., & Wörner, H. J. (2014). Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/0953-4075/47/12/124030","ista":"Kraus PM, Baykusheva DR, Wörner HJ. 2014. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 47(12), 124030.","chicago":"Kraus, P M, Denitsa Rangelova Baykusheva, and H J Wörner. “Two-Pulse Orientation Dynamics and High-Harmonic Spectroscopy of Strongly-Oriented Molecules.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2014. https://doi.org/10.1088/0953-4075/47/12/124030.","short":"P.M. Kraus, D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 47 (2014).","ama":"Kraus PM, Baykusheva DR, Wörner HJ. Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules. Journal of Physics B: Atomic, Molecular and Optical Physics. 2014;47(12). doi:10.1088/0953-4075/47/12/124030","ieee":"P. M. Kraus, D. R. Baykusheva, and H. J. Wörner, “Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 47, no. 12. IOP Publishing, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"first_name":"P M","full_name":"Kraus, P M","last_name":"Kraus"},{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"full_name":"Wörner, H J","first_name":"H J","last_name":"Wörner"}],"date_updated":"2023-08-22T09:04:30Z","oa_version":"Preprint","_id":"14021","scopus_import":"1","external_id":{"arxiv":["1311.3923"]}},{"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"status":"public","pmid":1,"abstract":[{"lang":"eng","text":"DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects."}],"doi":"10.1002/ange.201405991","issue":"47","month":"11","day":"17","extern":"1","publication_status":"published","publisher":"Wiley","page":"12949-12954","article_type":"original","intvolume":" 126","language":[{"iso":"eng"}],"_id":"14301","scopus_import":"1","external_id":{"pmid":["25346175"]},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Stahl E, Martin T, Praetorius FM, Dietz H. 2014. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 126(47), 12949–12954.","mla":"Stahl, Evi, et al. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition, vol. 126, no. 47, Wiley, 2014, pp. 12949–54, doi:10.1002/ange.201405991.","apa":"Stahl, E., Martin, T., Praetorius, F. M., & Dietz, H. (2014). Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/ange.201405991","ieee":"E. Stahl, T. Martin, F. M. Praetorius, and H. Dietz, “Facile and scalable preparation of pure and dense DNA origami solutions,” Angewandte Chemie International Edition, vol. 126, no. 47. Wiley, pp. 12949–12954, 2014.","ama":"Stahl E, Martin T, Praetorius FM, Dietz H. Facile and scalable preparation of pure and dense DNA origami solutions. Angewandte Chemie International Edition. 2014;126(47):12949-12954. doi:10.1002/ange.201405991","short":"E. Stahl, T. Martin, F.M. Praetorius, H. Dietz, Angewandte Chemie International Edition 126 (2014) 12949–12954.","chicago":"Stahl, Evi, Thomas Martin, Florian M Praetorius, and Hendrik Dietz. “Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions.” Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/ange.201405991."},"oa":1,"author":[{"last_name":"Stahl","first_name":"Evi","full_name":"Stahl, Evi"},{"last_name":"Martin","full_name":"Martin, Thomas","first_name":"Thomas"},{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"}],"date_updated":"2023-11-07T12:14:30Z","oa_version":"Published Version","quality_controlled":"1","title":"Facile and scalable preparation of pure and dense DNA origami solutions","date_published":"2014-11-17T00:00:00Z","date_created":"2023-09-06T12:51:14Z","publication":"Angewandte Chemie International Edition","article_processing_charge":"No","volume":126,"main_file_link":[{"url":"https://doi.org/10.1002/ange.201405991","open_access":"1"}],"year":"2014"},{"date_created":"2021-02-01T13:43:31Z","publication":"Soft Matter","volume":10,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.5662"}],"year":"2014","quality_controlled":"1","title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","date_published":"2014-03-21T00:00:00Z","keyword":["General Chemistry","Condensed Matter Physics"],"type":"journal_article","citation":{"mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:10.1039/c3sm52815d.","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d","ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.","ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter, vol. 10, no. 11. Royal Society of Chemistry , 2014.","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d"},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa":1,"author":[{"full_name":"Takagi, Daisuke","first_name":"Daisuke","last_name":"Takagi"},{"last_name":"Palacci","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","full_name":"Palacci, Jérémie A"},{"last_name":"Braunschweig","full_name":"Braunschweig, Adam B.","first_name":"Adam B."},{"full_name":"Shelley, Michael J.","first_name":"Michael J.","last_name":"Shelley"},{"last_name":"Zhang","first_name":"Jun","full_name":"Zhang, Jun"}],"date_updated":"2023-02-23T13:47:35Z","oa_version":"Preprint","_id":"9050","scopus_import":"1","external_id":{"pmid":["24800268"],"arxiv":["1309.5662"]},"article_type":"original","article_number":"1784","intvolume":" 10","language":[{"iso":"eng"}],"arxiv":1,"publisher":"Royal Society of Chemistry ","month":"03","day":"21","extern":"1","publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"status":"public","pmid":1,"abstract":[{"lang":"eng","text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter."}],"doi":"10.1039/c3sm52815d","issue":"11"},{"title":"Light-activated self-propelled colloids","date_published":"2014-11-28T00:00:00Z","keyword":["General Engineering","General Physics and Astronomy","General Mathematics"],"quality_controlled":"1","date_created":"2021-02-18T14:31:11Z","main_file_link":[{"url":"https://doi.org/10.1098/rsta.2013.0372","open_access":"1"}],"year":"2014","volume":372,"article_processing_charge":"No","publication":"Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences","_id":"9166","external_id":{"arxiv":["1410.7278"],"pmid":["25332383"]},"scopus_import":"1","type":"journal_article","date_updated":"2021-02-22T10:44:16Z","oa_version":"Published Version","oa":1,"author":[{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci"},{"first_name":"S.","full_name":"Sacanna, S.","last_name":"Sacanna"},{"last_name":"Kim","full_name":"Kim, S.-H.","first_name":"S.-H."},{"last_name":"Yi","first_name":"G.-R.","full_name":"Yi, G.-R."},{"full_name":"Pine, D. J.","first_name":"D. J.","last_name":"Pine"},{"last_name":"Chaikin","full_name":"Chaikin, P. M.","first_name":"P. M."}],"citation":{"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.","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.","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","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","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.","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."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"The Royal Society","intvolume":" 372","article_number":"20130372","article_type":"original","arxiv":1,"language":[{"iso":"eng"}],"status":"public","pmid":1,"publication_identifier":{"issn":["1364-503X"],"eissn":["1471-2962"]},"issue":"2029","abstract":[{"lang":"eng","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."}],"doi":"10.1098/rsta.2013.0372","month":"11","publication_status":"published","extern":"1","day":"28"},{"publication_status":"published","day":"13","extern":"1","month":"03","issue":"6","doi":"10.1016/j.cell.2014.01.029","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"pmid":1,"status":"public","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"language":[{"iso":"eng"}],"intvolume":" 156","article_type":"original","page":"1286-1297","publisher":"Elsevier","oa_version":"Published Version","date_updated":"2021-12-14T08:22:36Z","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.01.029.","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297."},"author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"oa":1,"type":"journal_article","external_id":{"pmid":["24630728"]},"scopus_import":"1","_id":"9458","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2014.01.029","open_access":"1"}],"year":"2014","publication":"Cell","article_processing_charge":"No","volume":156,"date_created":"2021-06-04T12:00:16Z","date_published":"2014-03-13T00:00:00Z","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","quality_controlled":"1"},{"_id":"9479","scopus_import":"1","external_id":{"pmid":["25344531"]},"type":"journal_article","author":[{"last_name":"Mérai","full_name":"Mérai, Zsuzsanna","first_name":"Zsuzsanna"},{"last_name":"Chumak","full_name":"Chumak, Nina","first_name":"Nina"},{"first_name":"Marcelina","full_name":"García-Aguilar, Marcelina","last_name":"García-Aguilar"},{"last_name":"Hsieh","full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"first_name":"Vera K.","full_name":"Schoft, Vera K.","last_name":"Schoft"},{"full_name":"Bindics, János","first_name":"János","last_name":"Bindics"},{"last_name":"Ślusarz","full_name":"Ślusarz, Lucyna","first_name":"Lucyna"},{"first_name":"Stéphanie","full_name":"Arnoux, Stéphanie","last_name":"Arnoux"},{"first_name":"Susanne","full_name":"Opravil, Susanne","last_name":"Opravil"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Tamaru","full_name":"Tamaru, Hisashi","first_name":"Hisashi"}],"oa":1,"citation":{"mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1418564111","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ieee":"Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” Proceedings of the National Academy of Sciences, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 2014;111(45):16166-16171. doi:10.1073/pnas.1418564111","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"oa_version":"Published Version","date_updated":"2021-12-14T08:23:26Z","quality_controlled":"1","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","date_published":"2014-11-11T00:00:00Z","date_created":"2021-06-07T07:23:43Z","article_processing_charge":"No","volume":111,"publication":"Proceedings of the National Academy of Sciences","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"year":"2014","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"status":"public","pmid":1,"doi":"10.1073/pnas.1418564111","abstract":[{"text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","lang":"eng"}],"issue":"45","month":"11","extern":"1","day":"11","publication_status":"published","publisher":"National Academy of Sciences","article_type":"original","page":"16166-16171","intvolume":" 111","language":[{"iso":"eng"}]},{"arxiv":1,"language":[{"iso":"eng"}],"article_number":"P1.45","intvolume":" 21","article_type":"original","publisher":"The Electronic Journal of Combinatorics","publication_status":"published","day":"28","extern":"1","month":"02","issue":"1","abstract":[{"lang":"eng","text":"Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture."}],"doi":"10.37236/3752","status":"public","publication_identifier":{"eissn":["1077-8926"]},"year":"2014","main_file_link":[{"open_access":"1","url":"https://doi.org/10.37236/3752"}],"publication":"The Electronic Journal of Combinatorics","volume":21,"article_processing_charge":"No","date_created":"2021-06-23T06:29:35Z","title":"On the number of spanning trees in random regular graphs","date_published":"2014-02-28T00:00:00Z","quality_controlled":"1","date_updated":"2023-02-23T14:02:12Z","oa_version":"Published Version","citation":{"ista":"Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.","apa":"Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752","mla":"Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752.","ieee":"C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” The Electronic Journal of Combinatorics, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014.","ama":"Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752","short":"C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014).","chicago":"Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics. The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Greenhill, Catherine","first_name":"Catherine","last_name":"Greenhill"},{"last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567"},{"last_name":"Wind","first_name":"David","full_name":"Wind, David"}],"oa":1,"type":"journal_article","external_id":{"arxiv":["1309.6710"]},"scopus_import":"1","_id":"9594"},{"arxiv":1,"language":[{"iso":"eng"}],"intvolume":" 112","article_number":"026801","publisher":"American Physiological Society","extern":"1","day":"14","publication_status":"published","acknowledgement":"The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation.","month":"01","doi":"10.1103/PhysRevLett.112.026801","publist_id":"7958","abstract":[{"text":"Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (>1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range.","lang":"eng"}],"issue":"2","status":"public","volume":112,"publication":"APS Physics, Physical Review Letters","year":"2014","main_file_link":[{"url":"https://arxiv.org/abs/1306.2720","open_access":"1"}],"date_created":"2018-12-11T11:44:36Z","quality_controlled":"1","date_published":"2014-01-14T00:00:00Z","title":"Coherent operations and screening in multielectron spin qubits","author":[{"orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"},{"last_name":"Kuemmeth","full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand"},{"last_name":"Hanson","full_name":"Hanson, Micah","first_name":"Micah"},{"last_name":"Gossard","full_name":"Gossard, Arthur","first_name":"Arthur"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801.","mla":"Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” APS Physics, Physical Review Letters, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:10.1103/PhysRevLett.112.026801.","apa":"Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., & Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. American Physiological Society. https://doi.org/10.1103/PhysRevLett.112.026801","ieee":"A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” APS Physics, Physical Review Letters, vol. 112, no. 2. American Physiological Society, 2014.","ama":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 2014;112(2). doi:10.1103/PhysRevLett.112.026801","short":"A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” APS Physics, Physical Review Letters. American Physiological Society, 2014. https://doi.org/10.1103/PhysRevLett.112.026801."},"oa_version":"Preprint","date_updated":"2021-01-12T08:22:14Z","type":"journal_article","external_id":{"arxiv":["1306.2720"]},"_id":"96"},{"external_id":{"pmid":["24698954"]},"scopus_import":"1","file_date_updated":"2021-07-22T08:06:34Z","_id":"9655","file":[{"file_name":"2014_JournalOfStructuralBiology_Perkovic.pdf","file_size":3454628,"date_updated":"2021-07-22T08:06:34Z","content_type":"application/pdf","access_level":"open_access","success":1,"date_created":"2021-07-22T08:06:34Z","file_id":"9701","relation":"main_file","checksum":"a322991b43cdc5935c99db88d285aa3a","creator":"asandaue"}],"oa_version":"Published Version","date_updated":"2021-07-22T08:26:32Z","oa":1,"author":[{"last_name":"Perkovic","first_name":"Mario","full_name":"Perkovic, Mario"},{"first_name":"Michael","full_name":"Kunz, Michael","last_name":"Kunz"},{"last_name":"Endesfelder","full_name":"Endesfelder, Ulrike","first_name":"Ulrike"},{"last_name":"Bunse","full_name":"Bunse, Stefanie","first_name":"Stefanie"},{"last_name":"Wigge","first_name":"Christoph","full_name":"Wigge, Christoph"},{"last_name":"Yu","full_name":"Yu, Zhou","first_name":"Zhou"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Margot P.","full_name":"Scheffer, Margot P.","last_name":"Scheffer"},{"full_name":"Seybert, Anja","first_name":"Anja","last_name":"Seybert"},{"full_name":"Malkusch, Sebastian","first_name":"Sebastian","last_name":"Malkusch"},{"last_name":"Schuman","full_name":"Schuman, Erin M.","first_name":"Erin M."},{"full_name":"Heilemann, Mike","first_name":"Mike","last_name":"Heilemann"},{"last_name":"Frangakis","full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S."}],"citation":{"ista":"Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213.","apa":"Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2014.03.018","mla":"Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:10.1016/j.jsb.2014.03.018.","ama":"Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 2014;186(2):205-213. doi:10.1016/j.jsb.2014.03.018","short":"M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213.","chicago":"Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” Journal of Structural Biology. Elsevier, 2014. https://doi.org/10.1016/j.jsb.2014.03.018.","ieee":"M. Perkovic et al., “Correlative light- and electron microscopy with chemical tags,” Journal of Structural Biology, vol. 186, no. 2. Elsevier, pp. 205–213, 2014."},"has_accepted_license":"1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","date_published":"2014-05-01T00:00:00Z","title":"Correlative light- and electron microscopy with chemical tags","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (3.0)"},"year":"2014","article_processing_charge":"No","volume":186,"publication":"Journal of Structural Biology","date_created":"2021-07-14T09:05:42Z","ddc":["570"],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","issue":"2","abstract":[{"text":"Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.","lang":"eng"}],"doi":"10.1016/j.jsb.2014.03.018","pmid":1,"status":"public","publication_identifier":{"issn":["1047-8477"]},"publication_status":"published","extern":"1","day":"01","month":"05","publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":" 186","article_type":"original","page":"205-213"},{"language":[{"iso":"eng"}],"arxiv":1,"article_type":"original","article_number":"244112","intvolume":" 141","publisher":"AIP Publishing","day":"28","extern":"1","publication_status":"published","month":"12","doi":"10.1063/1.4904293","abstract":[{"text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.","lang":"eng"}],"issue":"24","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"status":"public","pmid":1,"publication":"The Journal of Chemical Physics","volume":141,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1308"}],"year":"2014","date_created":"2021-07-15T09:22:49Z","quality_controlled":"1","title":"Direct path integral estimators for isotope fractionation ratios","date_published":"2014-12-28T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:10.1063/1.4904293.","apa":"Cheng, B., & Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4904293","ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112.","ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” The Journal of Chemical Physics, vol. 141, no. 24. AIP Publishing, 2014.","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” The Journal of Chemical Physics. AIP Publishing, 2014. https://doi.org/10.1063/1.4904293.","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).","ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 2014;141(24). doi:10.1063/1.4904293"},"oa":1,"author":[{"last_name":"Cheng","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing"},{"last_name":"Ceriotti","full_name":"Ceriotti, Michele","first_name":"Michele"}],"date_updated":"2021-08-09T12:32:24Z","oa_version":"Preprint","type":"journal_article","scopus_import":"1","external_id":{"arxiv":["1412.1308"],"pmid":["25554138"]},"_id":"9662"},{"day":"01","extern":"1","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","publication_status":"published","month":"12","abstract":[{"text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.","lang":"eng"}],"doi":"10.1073/pnas.1410159111","issue":"50","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","pmid":1,"arxiv":1,"language":[{"iso":"eng"}],"page":"17869-17874","article_type":"original","intvolume":" 111","publisher":"National Academy of Sciences","citation":{"apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” Proceedings of the National Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 2014;111(50):17869-17874. doi:10.1073/pnas.1410159111","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"author":[{"last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela"},{"full_name":"Chebaro, Yassmine C.","first_name":"Yassmine C.","last_name":"Chebaro"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"}],"oa_version":"Published Version","date_updated":"2021-11-29T13:29:05Z","type":"journal_article","scopus_import":"1","external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"_id":"10382","publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","volume":111,"year":"2014","main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"date_created":"2021-11-29T13:09:53Z","quality_controlled":"1","title":"Crucial role of nonspecific interactions in amyloid nucleation","date_published":"2014-12-01T00:00:00Z","keyword":["multidisciplinary"]},{"publisher":"American Physical Society","language":[{"iso":"eng"}],"arxiv":1,"article_type":"original","intvolume":" 89","article_number":"052303","doi":"10.1103/physreve.89.052303","abstract":[{"lang":"eng","text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles."}],"issue":"5","publication_identifier":{"issn":["1539-3755"],"eissn":["1550-2376"]},"status":"public","pmid":1,"extern":"1","day":"06","publication_status":"published","month":"05","quality_controlled":"1","title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","date_published":"2014-05-06T00:00:00Z","volume":89,"article_processing_charge":"No","publication":"Physical Review E","year":"2014","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"date_created":"2021-11-29T13:10:33Z","scopus_import":"1","external_id":{"arxiv":["1310.0826"],"pmid":["25353796"]},"_id":"10383","author":[{"full_name":"Mallory, S. A.","first_name":"S. A.","last_name":"Mallory"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"},{"first_name":"C.","full_name":"Valeriani, C.","last_name":"Valeriani"},{"last_name":"Cacciuto","first_name":"A.","full_name":"Cacciuto, A."}],"oa":1,"citation":{"ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:10.1103/physreve.89.052303.","apa":"Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.052303","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” Physical Review E, vol. 89, no. 5. American Physical Society, 2014.","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303","short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","date_updated":"2021-11-29T13:29:01Z","type":"journal_article"},{"article_processing_charge":"No","publication":"55th Annual Symposium on Foundations of Computer Science","main_file_link":[{"url":"https://arxiv.org/abs/1402.0054","open_access":"1"}],"year":"2014","date_created":"2022-08-16T08:14:33Z","quality_controlled":"1","title":"Decremental single-source shortest paths on undirected graphs in near-linear total update time","date_published":"2014-10-01T00:00:00Z","conference":{"name":"FOCS: Annual Symposium on Foundations of Computer Science","start_date":"2014-10-18","location":"Philadelphia, PA, United States","end_date":"2014-10-21"},"author":[{"first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Decremental single-source shortest paths on undirected graphs in near-linear total update time. In 55th Annual Symposium on Foundations of Computer Science (pp. 146–155). Philadelphia, PA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2014.24","mla":"Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–55, doi:10.1109/focs.2014.24.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Decremental single-source shortest paths on undirected graphs in near-linear total update time. 55th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 146–155.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” in 55th Annual Symposium on Foundations of Computer Science, Philadelphia, PA, United States, 2014, pp. 146–155.","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” In 55th Annual Symposium on Foundations of Computer Science, 146–55. Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/focs.2014.24.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–155.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. In: 55th Annual Symposium on Foundations of Computer Science. Institute of Electrical and Electronics Engineers; 2014:146-155. doi:10.1109/focs.2014.24"},"date_updated":"2023-02-21T16:27:34Z","oa_version":"Preprint","type":"conference","scopus_import":"1","external_id":{"arxiv":["1402.0054"]},"_id":"11855","language":[{"iso":"eng"}],"arxiv":1,"page":"146-155","publisher":"Institute of Electrical and Electronics Engineers","extern":"1","day":"01","publication_status":"published","related_material":{"record":[{"status":"public","id":"11768","relation":"later_version"}]},"month":"10","doi":"10.1109/focs.2014.24","abstract":[{"text":"The decremental single-source shortest paths (SSSP) problem concerns maintaining the distances between a given source node s to every node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be easily solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach (JACM 1981) has been the fastest known algorithm for three decades. With the loss of a (1 + ε)-approximation factor, the running time was recently improved to O(n 2+o(1) ) by Bernstein and Roditty (SODA 2011), and more recently to O(n 1.8+o(1) + m 1+o(1) ) by Henzinger, Krinninger, and Nanongkai (SODA 2014). In this paper, we finally bring the running time of this case down to near-linear: We give a (1 + ε)-approximation algorithm with O(m 1+o(1) ) total update time, thus obtaining near-linear time. Moreover, we obtain O(m 1+o(1) log W) time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn log W) time is the O(mn 0.986 log W)-time algorithm by Henzinger, Krinninger, and Nanongkai (STOC 2014) which works for the general weighted directed case. In contrast to the previous results which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (d, ε)-hop set introduced by Cohen (JACM 2000) in the PRAM literature. A (d, ε)-hop set of a graph G = (V, E) is a set E' of weighted edges such that the distance between any pair of nodes in G can be (1 + ε)-approximated by their d-hop distance (given by a path containing at most d edges) on G'=(V, E∪E'). Our algorithm can maintain an (n o(1) , ε)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain the distances on this hop set, we develop a monotone bounded-hop Even-Shiloach tree. It results from extending and combining the monotone Even-Shiloach tree of Henzinger, Krinninger, and Nanongkai (FOCS 2013) with the bounded-hop SSSP technique of Bernstein (STOC 2013). These two new tools might be of independent interest.","lang":"eng"}],"publication_identifier":{"issn":["0272-5428"],"eisbn":["978-1-4799-6517-5"]},"status":"public"},{"publisher":"Association for Computing Machinery","article_number":"674 - 683","arxiv":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-145032710-7"],"issn":["0737-8017"]},"status":"public","abstract":[{"text":"We consider dynamic algorithms for maintaining Single-Source Reachability (SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed graphs under edge deletions (decremental algorithms). The previous fastest algorithm for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it has O(1) query time and O(mn) total update time (i.e., linear amortized update time if all edges are deleted). This algorithm serves as a building block for several other dynamic algorithms. The question whether its total update time can be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we answer this question affirmatively. We obtain a randomized algorithm which, in a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and (1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm to achieve roughly the same running time for Strongly Connected Components (SCC), improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating SSSP on weighted directed graphs, where the edge weights are integers from 1 to W. All our algorithms have constant query time in the worst case.","lang":"eng"}],"doi":"10.1145/2591796.2591869","month":"05","extern":"1","day":"01","publication_status":"published","conference":{"start_date":"2014-05-31","location":"New York, NY, United States","end_date":"2014-06-03","name":"STOC: Symposium on Theory of Computing"},"quality_controlled":"1","title":"Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs","date_published":"2014-05-01T00:00:00Z","date_created":"2022-08-16T09:41:57Z","article_processing_charge":"No","publication":"46th Annual ACM Symposium on Theory of Computing","main_file_link":[{"url":"https://arxiv.org/abs/1504.07959","open_access":"1"}],"year":"2014","_id":"11870","scopus_import":"1","external_id":{"arxiv":["1504.07959"]},"type":"conference","oa":1,"author":[{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"full_name":"Nanongkai, Danupon","first_name":"Danupon","last_name":"Nanongkai"}],"citation":{"short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2014.","ama":"Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In: 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2014. doi:10.1145/2591796.2591869","chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” In 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2014. https://doi.org/10.1145/2591796.2591869.","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs,” in 46th Annual ACM Symposium on Theory of Computing, New York, NY, United States, 2014.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. 46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 674–683.","mla":"Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” 46th Annual ACM Symposium on Theory of Computing, 674–683, Association for Computing Machinery, 2014, doi:10.1145/2591796.2591869.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In 46th Annual ACM Symposium on Theory of Computing. New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2591796.2591869"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-17T11:18:52Z","oa_version":"Preprint"},{"publication_identifier":{"isbn":["978-1-61197-374-7"],"eisbn":["978-1-61197-373-0"]},"status":"public","abstract":[{"text":"We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph in time per update. In particular, for minimum vertex cover we provide deterministic data structures for maintaining a (2 + ε) approximation in O(log n/ε2) amortized time per update. For maximum matching, we show how to maintain a (3 + e) approximation in O(m1/3/ε2) amortized time per update, and a (4 + ε) approximation in O(m1/3/ε2) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [13].","lang":"eng"}],"doi":"10.1137/1.9781611973730.54","month":"01","related_material":{"record":[{"id":"11890","relation":"later_version","status":"public"}]},"day":"01","extern":"1","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","page":"785-804","arxiv":1,"language":[{"iso":"eng"}],"_id":"11875","scopus_import":"1","external_id":{"arxiv":["1412.1318"]},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2014). Deterministic fully dynamic data structures for vertex cover and matching. In 26th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 785–804). San Diego, CA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973730.54","mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804, doi:10.1137/1.9781611973730.54.","ista":"Bhattacharya S, Henzinger MH, Italiano GF. 2014. Deterministic fully dynamic data structures for vertex cover and matching. 26th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 785–804.","chicago":"Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” In 26th Annual ACM-SIAM Symposium on Discrete Algorithms, 785–804. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973730.54.","short":"S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804.","ama":"Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. In: 26th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:785-804. doi:10.1137/1.9781611973730.54","ieee":"S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” in 26th Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2014, pp. 785–804."},"author":[{"last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan","first_name":"Sayan"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"full_name":"Italiano, Giuseppe F.","first_name":"Giuseppe F.","last_name":"Italiano"}],"oa":1,"oa_version":"Preprint","date_updated":"2023-02-21T16:32:06Z","conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2015-01-06","location":"San Diego, CA, United States","start_date":"2015-01-04"},"quality_controlled":"1","date_published":"2014-01-01T00:00:00Z","title":"Deterministic fully dynamic data structures for vertex cover and matching","date_created":"2022-08-16T12:36:42Z","publication":"26th Annual ACM-SIAM Symposium on Discrete Algorithms","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1318"}],"year":"2014"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"chicago":"Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” In 25th Annual ACM-SIAM Symposium on Discrete Algorithms, 1053–72. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973402.79.","short":"M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–1072.","ama":"Henzinger MH, Krinninger S, Nanongkai D. A subquadratic-time algorithm for decremental single-source shortest paths. In: 25th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:1053-1072. doi:10.1137/1.9781611973402.79","ieee":"M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A subquadratic-time algorithm for decremental single-source shortest paths,” in 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Portland, OR, United States, 2014, pp. 1053–1072.","apa":"Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). A subquadratic-time algorithm for decremental single-source shortest paths. In 25th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1053–1072). Portland, OR, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973402.79","mla":"Henzinger, Monika H., et al. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–72, doi:10.1137/1.9781611973402.79.","ista":"Henzinger MH, Krinninger S, Nanongkai D. 2014. A subquadratic-time algorithm for decremental single-source shortest paths. 25th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1053–1072."},"extern":"1","author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Krinninger","first_name":"Sebastian","full_name":"Krinninger, Sebastian"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"}],"oa":1,"date_updated":"2023-02-17T11:58:42Z","oa_version":"Published Version","publication_status":"published","type":"conference","month":"01","doi":"10.1137/1.9781611973402.79","abstract":[{"lang":"eng","text":"We study dynamic (1 + ∊)-approximation algorithms for the single-source shortest paths problem in an unweighted undirected n-node m-edge graph under edge deletions. The fastest algorithm for this problem is an algorithm with O(n2+o(1)) total update time and constant query time by Bernstein and Roditty (SODA 2011). In this paper, we improve the total update time to O(n1.8+o(1) + m1+o(1)) while keeping the query time constant. This running time is essentially tight when m = Ω(n1.8) since we need Ω(m) time even in the static setting. For smaller values of m, the running time of our algorithm is subquadratic, and is the first that breaks through the quadratic time barrier.\r\n\r\nIn obtaining this result, we develop a fast algorithm for what we call center cover data structure. We also make non-trivial extensions to our previous techniques called lazy-update and monotone Even-Shiloach trees (ICALP 2013 and FOCS 2013). As by-products of our new techniques, we obtain two new results for the decremental all-pairs shortest-paths problem. Our first result is the first approximation algorithm whose total update time is faster than Õ(mn) for all values of m. Our second result is a new trade-off between the total update time and the additive approximation guarantee."}],"scopus_import":"1","publication_identifier":{"isbn":["978-1-61197-338-9"],"eisbn":["978-1-61197-340-2"]},"status":"public","_id":"11876","publication":"25th Annual ACM-SIAM Symposium on Discrete Algorithms","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2014","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611973402.79","open_access":"1"}],"page":"1053-1072","date_created":"2022-08-16T12:58:31Z","quality_controlled":"1","date_published":"2014-01-01T00:00:00Z","title":"A subquadratic-time algorithm for decremental single-source shortest paths","publisher":"Society for Industrial and Applied Mathematics","conference":{"end_date":"2014-01-07","location":"Portland, OR, United States","start_date":"2014-01-05","name":"SODA: Symposium on Discrete Algorithms"}},{"status":"public","issue":"21","abstract":[{"lang":"eng","text":"Observations of flowing granular matter have suggested that same-material tribocharging depends on particle size, typically rendering large grains positive and small ones negative. Models assuming the transfer of trapped electrons can account for this trend, but have not been validated. Tracking individual grains in an electric field, we show quantitatively that charge is transferred based on size between materially identical grains. However, the surface density of trapped electrons, measured independently by thermoluminescence techniques, is orders of magnitude too small to account for the scale of charge transferred. This reveals that trapped electrons are not a necessary ingredient for same-material tribocharging."}],"publist_id":"7935","doi":"10.1103/PhysRevLett.112.218001","month":"05","publication_status":"published","acknowledgement":"This work was supported by the NSF through DMR-1309611. Access to the shared experimental facilities provided by the NSF-supported Chicago MRSEC (DMR-0820054) is gratefully acknowledged. S. L. F. and J. L. P. acknowledge funding from UIC NSF Grants No. 0850830 and No. 0602308. S. R. W. acknowledges support from a University of Chicago Millikan Fellowship and from Mrs. Joan Winstein through the Winstein Prize for Instrumentation.","day":"30","extern":"1","publisher":"American Physical Society","article_number":"218001","intvolume":" 112","language":[{"iso":"eng"}],"arxiv":1,"_id":"119","external_id":{"arxiv":["1309.2578"]},"type":"journal_article","oa_version":"Submitted Version","date_updated":"2021-01-12T06:48:58Z","citation":{"ista":"Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. 2014. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 112(21), 218001.","mla":"Waitukaitis, Scott R., et al. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters, vol. 112, no. 21, 218001, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.218001.","apa":"Waitukaitis, S. R., Lee, V., Pierson, J., Forman, S., & Jaeger, H. (2014). Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.218001","ieee":"S. R. Waitukaitis, V. Lee, J. Pierson, S. Forman, and H. Jaeger, “Size-dependent same-material tribocharging in insulating grains,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014.","ama":"Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.218001","short":"S.R. Waitukaitis, V. Lee, J. Pierson, S. Forman, H. Jaeger, APS Physics, Physical Review Letters 112 (2014).","chicago":"Waitukaitis, Scott R, Victor Lee, James Pierson, Steven Forman, and Heinrich Jaeger. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.218001."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R","first_name":"Scott R","last_name":"Waitukaitis"},{"full_name":"Lee, Victor","first_name":"Victor","last_name":"Lee"},{"first_name":"James","full_name":"Pierson, James","last_name":"Pierson"},{"first_name":"Steven","full_name":"Forman, Steven","last_name":"Forman"},{"first_name":"Heinrich","full_name":"Jaeger, Heinrich","last_name":"Jaeger"}],"oa":1,"date_published":"2014-05-30T00:00:00Z","title":"Size-dependent same-material tribocharging in insulating grains","quality_controlled":"1","date_created":"2018-12-11T11:44:44Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2578"}],"year":"2014","publication":"APS Physics, Physical Review Letters","volume":112},{"external_id":{"pmid":["24960695"]},"scopus_import":"1","_id":"11968","oa_version":"Published Version","date_updated":"2023-02-21T10:09:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"H.F. Hofbauer, F.H. Schopf, H. Schleifer, O.L. Knittelfelder, B. Pieber, G.N. Rechberger, H. Wolinski, M.L. Gaspar, C.O. Kappe, J. Stadlmann, K. Mechtler, A. Zenz, K. Lohner, O. Tehlivets, S.A. Henry, S.D. Kohlwein, Developmental Cell 29 (2014) P729-739.","ama":"Hofbauer HF, Schopf FH, Schleifer H, et al. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 2014;29(6):P729-739. doi:10.1016/j.devcel.2014.04.025","chicago":"Hofbauer, Harald F., Florian H. Schopf, Hannes Schleifer, Oskar L. Knittelfelder, Bartholomäus Pieber, Gerald N. Rechberger, Heimo Wolinski, et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell. Elsevier, 2014. https://doi.org/10.1016/j.devcel.2014.04.025.","ieee":"H. F. Hofbauer et al., “Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids,” Developmental Cell, vol. 29, no. 6. Elsevier, pp. P729-739, 2014.","ista":"Hofbauer HF, Schopf FH, Schleifer H, Knittelfelder OL, Pieber B, Rechberger GN, Wolinski H, Gaspar ML, Kappe CO, Stadlmann J, Mechtler K, Zenz A, Lohner K, Tehlivets O, Henry SA, Kohlwein SD. 2014. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 29(6), P729-739.","mla":"Hofbauer, Harald F., et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell, vol. 29, no. 6, Elsevier, 2014, pp. P729-739, doi:10.1016/j.devcel.2014.04.025.","apa":"Hofbauer, H. F., Schopf, F. H., Schleifer, H., Knittelfelder, O. L., Pieber, B., Rechberger, G. N., … Kohlwein, S. D. (2014). Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2014.04.025"},"author":[{"last_name":"Hofbauer","first_name":"Harald F.","full_name":"Hofbauer, Harald F."},{"full_name":"Schopf, Florian H.","first_name":"Florian H.","last_name":"Schopf"},{"last_name":"Schleifer","first_name":"Hannes","full_name":"Schleifer, Hannes"},{"last_name":"Knittelfelder","first_name":"Oskar L.","full_name":"Knittelfelder, Oskar L."},{"last_name":"Pieber","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"},{"last_name":"Rechberger","full_name":"Rechberger, Gerald N.","first_name":"Gerald N."},{"full_name":"Wolinski, Heimo","first_name":"Heimo","last_name":"Wolinski"},{"last_name":"Gaspar","first_name":"Maria L.","full_name":"Gaspar, Maria L."},{"first_name":"C. Oliver","full_name":"Kappe, C. Oliver","last_name":"Kappe"},{"last_name":"Stadlmann","full_name":"Stadlmann, Johannes","first_name":"Johannes"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"last_name":"Zenz","full_name":"Zenz, Alexandra","first_name":"Alexandra"},{"last_name":"Lohner","first_name":"Karl","full_name":"Lohner, Karl"},{"last_name":"Tehlivets","full_name":"Tehlivets, Oksana","first_name":"Oksana"},{"last_name":"Henry","full_name":"Henry, Susan A.","first_name":"Susan A."},{"last_name":"Kohlwein","first_name":"Sepp D.","full_name":"Kohlwein, Sepp D."}],"oa":1,"type":"journal_article","title":"Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids","date_published":"2014-06-23T00:00:00Z","quality_controlled":"1","year":"2014","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2014.04.025","open_access":"1"}],"publication":"Developmental Cell","article_processing_charge":"No","volume":29,"date_created":"2022-08-25T08:42:42Z","issue":"6","abstract":[{"lang":"eng","text":"Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon atoms. This particular chain length is evolutionarily highly conserved and presumably provides maximum stability and dynamic properties to biological membranes in response to nutritional or environmental cues. Here, we show that the relative proportion of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1), the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated by AMPK/Snf1-dependent phosphorylation, which is required to maintain an appropriate acyl-chain length distribution. Moreover, we find that the transcriptional repressor Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus, C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK/Snf1 control of PA acyl-chain length to determine the degree of derepression of Opi1 target genes. These findings reveal an unexpected regulatory link between the major energy-sensing kinase, membrane lipid composition, and transcription."}],"doi":"10.1016/j.devcel.2014.04.025","pmid":1,"status":"public","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"publication_status":"published","day":"23","extern":"1","month":"06","publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":" 29","page":"P729-739","article_type":"original"}]