[{"day":"10","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Spin-orbit delays in photoemission","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"scopus_import":"1","publication":"Physical Review A","volume":95,"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Jordan, I.","first_name":"I.","last_name":"Jordan"},{"first_name":"M.","last_name":"Huppert","full_name":"Huppert, M."},{"first_name":"S.","last_name":"Pabst","full_name":"Pabst, S."},{"last_name":"Kheifets","first_name":"A. S.","full_name":"Kheifets, A. S."},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"full_name":"Wörner, H. J.","first_name":"H. J.","last_name":"Wörner"}],"intvolume":"        95","quality_controlled":"1","article_type":"original","year":"2017","article_processing_charge":"No","extern":"1","doi":"10.1103/physreva.95.013404","citation":{"ista":"Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. 2017. Spin-orbit delays in photoemission. Physical Review A. 95(1), 013404.","chicago":"Jordan, I., M. Huppert, S. Pabst, A. S. Kheifets, Denitsa Rangelova Baykusheva, and H. J. Wörner. “Spin-Orbit Delays in Photoemission.” <i>Physical Review A</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/physreva.95.013404\">https://doi.org/10.1103/physreva.95.013404</a>.","ieee":"I. Jordan, M. Huppert, S. Pabst, A. S. Kheifets, D. R. Baykusheva, and H. J. Wörner, “Spin-orbit delays in photoemission,” <i>Physical Review A</i>, vol. 95, no. 1. American Physical Society, 2017.","ama":"Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. Spin-orbit delays in photoemission. <i>Physical Review A</i>. 2017;95(1). doi:<a href=\"https://doi.org/10.1103/physreva.95.013404\">10.1103/physreva.95.013404</a>","short":"I. Jordan, M. Huppert, S. Pabst, A.S. Kheifets, D.R. Baykusheva, H.J. Wörner, Physical Review A 95 (2017).","mla":"Jordan, I., et al. “Spin-Orbit Delays in Photoemission.” <i>Physical Review A</i>, vol. 95, no. 1, 013404, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/physreva.95.013404\">10.1103/physreva.95.013404</a>.","apa":"Jordan, I., Huppert, M., Pabst, S., Kheifets, A. S., Baykusheva, D. R., &#38; Wörner, H. J. (2017). Spin-orbit delays in photoemission. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.95.013404\">https://doi.org/10.1103/physreva.95.013404</a>"},"date_published":"2017-01-10T00:00:00Z","abstract":[{"text":"Attosecond delays between photoelectron wave packets emitted from different electronic shells are now well established. Is there any delay between electrons originating from the same electronic shell but leaving the cation in different fine-structure states? This question is relevant for all attosecond photoemission studies involving heavy elements, be it atoms, molecules or solids. We answer this fundamental question by measuring energy-dependent delays between photoelectron wave packets associated with the 2P3/2 and 2P1/2 components of the electronic groundstates of Xe+ and Kr+. We observe delays reaching up to 33±6 as in the case of Xe. Our results are compared with two state-of-the-art theories. Whereas both theories quantitatively agree with the results obtained for Kr, neither of them fully reproduces the experimental results in Xe. Performing delay measurements very close to the ionization thresholds, we compare the agreement of several analytical formulas for the continuum-continuum delays with experimental data. Our results show an important influence of spin-orbit coupling on attosecond photoionization delays, highlight the requirement for additional theory development, and offer a precision benchmark for such work.","lang":"eng"}],"_id":"14009","date_updated":"2023-08-22T08:38:17Z","month":"01","language":[{"iso":"eng"}],"issue":"1","date_created":"2023-08-10T06:36:58Z","oa_version":"None","type":"journal_article","article_number":"013404"},{"doi":"10.1103/physrevlett.119.203201","month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.04474"}],"day":"17","pmid":1,"status":"public","arxiv":1,"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication":"Physical Review Letters","volume":119,"publisher":"American Physical Society","publication_status":"published","quality_controlled":"1","external_id":{"pmid":["29219334"],"arxiv":["1710.04474"]},"date_published":"2017-11-17T00:00:00Z","citation":{"ista":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20), 203201.","chicago":"Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/physrevlett.119.203201\">https://doi.org/10.1103/physrevlett.119.203201</a>.","ieee":"D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of electronic structure in bicircular high-harmonic spectroscopy,” <i>Physical Review Letters</i>, vol. 119, no. 20. American Physical Society, 2017.","ama":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure in bicircular high-harmonic spectroscopy. <i>Physical Review Letters</i>. 2017;119(20). doi:<a href=\"https://doi.org/10.1103/physrevlett.119.203201\">10.1103/physrevlett.119.203201</a>","mla":"Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” <i>Physical Review Letters</i>, vol. 119, no. 20, 203201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/physrevlett.119.203201\">10.1103/physrevlett.119.203201</a>.","short":"D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters 119 (2017).","apa":"Baykusheva, D. R., Brennecke, S., Lein, M., &#38; Wörner, H. J. (2017). Signatures of electronic structure in bicircular high-harmonic spectroscopy. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.119.203201\">https://doi.org/10.1103/physrevlett.119.203201</a>"},"date_updated":"2023-08-22T06:48:28Z","_id":"14031","abstract":[{"text":"High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy.","lang":"eng"}],"language":[{"iso":"eng"}],"issue":"20","oa":1,"date_created":"2023-08-10T06:48:12Z","oa_version":"Preprint","type":"journal_article","article_number":"203201","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Signatures of electronic structure in bicircular high-harmonic spectroscopy","scopus_import":"1","intvolume":"       119","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"full_name":"Brennecke, Simon","last_name":"Brennecke","first_name":"Simon"},{"full_name":"Lein, Manfred","first_name":"Manfred","last_name":"Lein"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"article_type":"original","year":"2017","keyword":["General Physics and Astronomy"],"article_processing_charge":"No","extern":"1"},{"related_material":{"record":[{"id":"1689","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Svoreňová, Mária","first_name":"Mária","last_name":"Svoreňová"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Ivana","last_name":"Cěrná","full_name":"Cěrná, Ivana"},{"last_name":"Belta","first_name":"Cǎlin","full_name":"Belta, Cǎlin"}],"intvolume":"        23","article_processing_charge":"No","year":"2017","scopus_import":"1","title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"oa":1,"issue":"2","type":"journal_article","date_created":"2018-12-11T11:51:50Z","oa_version":"Preprint","language":[{"iso":"eng"}],"_id":"1407","date_updated":"2025-06-11T06:33:00Z","abstract":[{"text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study.","lang":"eng"}],"page":"230 - 253","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_published":"2017-02-01T00:00:00Z","citation":{"apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &#38; Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>.","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. 2017;23(2):230-253. doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>"},"external_id":{"arxiv":["1410.5387"],"isi":["000390637000014"]},"quality_controlled":"1","arxiv":1,"status":"public","day":"01","publication_status":"published","publisher":"Elsevier","volume":23,"publication":"Nonlinear Analysis: Hybrid Systems","main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"ec_funded":1,"publist_id":"5800","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"doi":"10.1016/j.nahs.2016.04.006","month":"02"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1702.06457","open_access":"1"}],"month":"02","quality_controlled":"1","external_id":{"arxiv":["1702.06457"]},"publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","volume":54,"publisher":"ML Research Press","publication_status":"published","day":"21","status":"public","arxiv":1,"date_created":"2023-08-22T14:17:19Z","oa_version":"Preprint","type":"conference","oa":1,"citation":{"mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, vol. 54, ML Research Press, 2017, pp. 860–68.","short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","apa":"Locatello, F., Khanna, R., Tschannen, M., &#38; Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i> (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.","ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>. Vol 54. ML Research Press; 2017:860-868.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.","chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, 54:860–68. ML Research Press, 2017."},"department":[{"_id":"FrLo"}],"date_published":"2017-02-21T00:00:00Z","page":"860-868","_id":"14205","date_updated":"2023-09-13T09:49:10Z","abstract":[{"text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions.","lang":"eng"}],"language":[{"iso":"eng"}],"year":"2017","article_processing_charge":"No","extern":"1","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco"},{"last_name":"Khanna","first_name":"Rajiv","full_name":"Khanna, Rajiv"},{"full_name":"Tschannen, Michael","first_name":"Michael","last_name":"Tschannen"},{"full_name":"Jaggi, Martin","first_name":"Martin","last_name":"Jaggi"}],"intvolume":"        54","conference":{"end_date":"2017-04-22","name":"AISTATS: Conference on Artificial Intelligence and Statistics","location":"Fort Lauderdale, FL, United States","start_date":"2017-04-20"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe"},{"month":"05","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"citation":{"ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in <i>Advances in Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017.","ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: <i>Advances in Neural Information Processing Systems</i>. ; 2017.","ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In <i>Advances in Neural Information Processing Systems</i>, 2017.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” <i>Advances in Neural Information Processing Systems</i>, 2017.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017.","apa":"Locatello, F., Tschannen, M., Rätsch, G., &#38; Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In <i>Advances in Neural Information Processing Systems</i>. Long Beach, CA, United States."},"date_published":"2017-05-31T00:00:00Z","_id":"14206","date_updated":"2024-10-14T12:29:50Z","abstract":[{"lang":"eng","text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings."}],"type":"conference","date_created":"2023-08-22T14:17:38Z","oa_version":"Preprint","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.11041","open_access":"1"}],"publication_status":"published","publication":"Advances in Neural Information Processing Systems","arxiv":1,"publication_identifier":{"isbn":["9781510860964"]},"day":"31","conference":{"start_date":"2017-12-04","location":"Long Beach, CA, United States","end_date":"2017-12-09","name":"NeurIPS: Neural Information Processing Systems"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Greedy algorithms for cone constrained optimization with convergence guarantees","extern":"1","year":"2017","article_processing_charge":"No","external_id":{"arxiv":["1705.11041"]},"quality_controlled":"1","author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Jaggi","first_name":"Martin","full_name":"Jaggi, Martin"}]},{"doi":"10.1002/bit.26200","month":"04","pmid":1,"day":"01","status":"public","publication_identifier":{"issn":["0006-3592"]},"publication":"Biotechnology and Bioengineering","volume":114,"publisher":"Wiley","publication_status":"published","quality_controlled":"1","external_id":{"pmid":["27748519"]},"page":"777-784","citation":{"ama":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. <i>Biotechnology and Bioengineering</i>. 2017;114(4):777-784. doi:<a href=\"https://doi.org/10.1002/bit.26200\">10.1002/bit.26200</a>","ieee":"B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production,” <i>Biotechnology and Bioengineering</i>, vol. 114, no. 4. Wiley, pp. 777–784, 2017.","ista":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. 114(4), 777–784.","chicago":"Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz, and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” <i>Biotechnology and Bioengineering</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/bit.26200\">https://doi.org/10.1002/bit.26200</a>.","short":"B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology and Bioengineering 114 (2017) 777–784.","mla":"Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” <i>Biotechnology and Bioengineering</i>, vol. 114, no. 4, Wiley, 2017, pp. 777–84, doi:<a href=\"https://doi.org/10.1002/bit.26200\">10.1002/bit.26200</a>.","apa":"Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., &#38; Weuster-Botz, D. (2017). Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. <i>Biotechnology and Bioengineering</i>. Wiley. <a href=\"https://doi.org/10.1002/bit.26200\">https://doi.org/10.1002/bit.26200</a>"},"date_published":"2017-04-01T00:00:00Z","date_updated":"2023-11-07T12:36:20Z","_id":"14286","abstract":[{"lang":"eng","text":"The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection, and specific growth rate. The specific growth rate and the multiplicity of infection were identified as the crucial state variables that influence phage amplification rate on one hand and the concentration of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784."}],"language":[{"iso":"eng"}],"issue":"4","date_created":"2023-09-06T12:08:29Z","oa_version":"None","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production","scopus_import":"1","intvolume":"       114","author":[{"last_name":"Kick","first_name":"Benjamin","full_name":"Kick, Benjamin"},{"full_name":"Hensler, Samantha","last_name":"Hensler","first_name":"Samantha"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Dietz, Hendrik","last_name":"Dietz","first_name":"Hendrik"},{"full_name":"Weuster-Botz, Dirk","first_name":"Dirk","last_name":"Weuster-Botz"}],"article_type":"original","keyword":["Applied Microbiology and Biotechnology","Bioengineering","Biotechnology"],"year":"2017","article_processing_charge":"No","extern":"1"},{"quality_controlled":"1","external_id":{"pmid":["28336611"]},"status":"public","day":"24","pmid":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"volume":355,"publication":"Science","publication_status":"published","publisher":"American Association for the Advancement of Science","doi":"10.1126/science.aam5488","month":"03","intvolume":"       355","author":[{"last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"}],"article_type":"original","article_processing_charge":"No","year":"2017","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes","scopus_import":"1","issue":"6331","date_created":"2023-09-06T12:08:55Z","oa_version":"None","article_number":"eaam5488","type":"journal_article","_id":"14287","abstract":[{"lang":"eng","text":"We describe an approach to bottom-up fabrication that allows integration of the functional diversity of proteins into designed three-dimensional structural frameworks. A set of custom staple proteins based on transcription activator–like effector proteins folds a double-stranded DNA template into a user-defined shape. Each staple protein is designed to recognize and closely link two distinct double-helical DNA sequences at separate positions on the template. We present design rules for constructing megadalton-scale DNA-protein hybrid shapes; introduce various structural motifs, such as custom curvature, corners, and vertices; and describe principles for creating multilayer DNA-protein objects with enhanced rigidity. We demonstrate self-assembly of our hybrid nanostructures in one-pot mixtures that include the genetic information for the designed proteins, the template DNA, RNA polymerase, ribosomes, and cofactors for transcription and translation."}],"date_updated":"2023-11-07T12:33:05Z","date_published":"2017-03-24T00:00:00Z","citation":{"mla":"Praetorius, Florian M., and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” <i>Science</i>, vol. 355, no. 6331, eaam5488, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/science.aam5488\">10.1126/science.aam5488</a>.","short":"F.M. Praetorius, H. Dietz, Science 355 (2017).","apa":"Praetorius, F. M., &#38; Dietz, H. (2017). Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aam5488\">https://doi.org/10.1126/science.aam5488</a>","ieee":"F. M. Praetorius and H. Dietz, “Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes,” <i>Science</i>, vol. 355, no. 6331. American Association for the Advancement of Science, 2017.","ama":"Praetorius FM, Dietz H. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. <i>Science</i>. 2017;355(6331). doi:<a href=\"https://doi.org/10.1126/science.aam5488\">10.1126/science.aam5488</a>","ista":"Praetorius FM, Dietz H. 2017. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Science. 355(6331), eaam5488.","chicago":"Praetorius, Florian M, and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aam5488\">https://doi.org/10.1126/science.aam5488</a>."},"language":[{"iso":"eng"}]},{"doi":"10.1038/nature24650","month":"12","quality_controlled":"1","external_id":{"pmid":["29219963"]},"day":"07","pmid":1,"status":"public","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication":"Nature","volume":552,"publisher":"Springer Nature","publication_status":"published","issue":"7683","oa_version":"None","date_created":"2023-09-06T12:14:20Z","type":"journal_article","page":"84-87","citation":{"short":"F.M. Praetorius, B. Kick, K.L. Behler, M.N. Honemann, D. Weuster-Botz, H. Dietz, Nature 552 (2017) 84–87.","mla":"Praetorius, Florian M., et al. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>, vol. 552, no. 7683, Springer Nature, 2017, pp. 84–87, doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>.","apa":"Praetorius, F. M., Kick, B., Behler, K. L., Honemann, M. N., Weuster-Botz, D., &#38; Dietz, H. (2017). Biotechnological mass production of DNA origami. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>","ama":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. Biotechnological mass production of DNA origami. <i>Nature</i>. 2017;552(7683):84-87. doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>","ieee":"F. M. Praetorius, B. Kick, K. L. Behler, M. N. Honemann, D. Weuster-Botz, and H. Dietz, “Biotechnological mass production of DNA origami,” <i>Nature</i>, vol. 552, no. 7683. Springer Nature, pp. 84–87, 2017.","ista":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. 2017. Biotechnological mass production of DNA origami. Nature. 552(7683), 84–87.","chicago":"Praetorius, Florian M, Benjamin Kick, Karl L. Behler, Maximilian N. Honemann, Dirk Weuster-Botz, and Hendrik Dietz. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>."},"date_published":"2017-12-07T00:00:00Z","date_updated":"2023-11-07T12:24:49Z","_id":"14290","abstract":[{"lang":"eng","text":"DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12. These structures are customizable in that they can be site-specifically functionalized13 or constructed to exhibit machine-like14,15 or logic-gating behaviour16. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials3,16,17,18,19,20,21,22, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production23; the shorter staple strands are obtained through costly solid-phase synthesis24 or enzymatic processes25. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in many areas of science and technology."}],"language":[{"iso":"eng"}],"intvolume":"       552","author":[{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Kick, Benjamin","first_name":"Benjamin","last_name":"Kick"},{"full_name":"Behler, Karl L.","first_name":"Karl L.","last_name":"Behler"},{"full_name":"Honemann, Maximilian N.","first_name":"Maximilian N.","last_name":"Honemann"},{"last_name":"Weuster-Botz","first_name":"Dirk","full_name":"Weuster-Botz, Dirk"},{"last_name":"Dietz","first_name":"Hendrik","full_name":"Dietz, Hendrik"}],"article_type":"original","year":"2017","article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Biotechnological mass production of DNA origami","scopus_import":"1"},{"quality_controlled":"1","publication_identifier":{"issn":["0006-3495"]},"day":"03","status":"public","publisher":"Elsevier","publication_status":"published","publication":"Biophysical Journal","volume":112,"doi":"10.1016/j.bpj.2016.11.171","month":"02","article_type":"original","author":[{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Dietz, Hendrik","last_name":"Dietz","first_name":"Hendrik"}],"intvolume":"       112","extern":"1","year":"2017","keyword":["Biophysics"],"article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Genetically encoded DNA-protein hybrid origami","issue":"3","type":"journal_article","article_number":"25a","date_created":"2023-09-06T13:19:10Z","oa_version":"None","language":[{"iso":"eng"}],"date_published":"2017-02-03T00:00:00Z","citation":{"short":"F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).","mla":"Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>, vol. 112, no. 3, 25a, Elsevier, 2017, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>.","apa":"Praetorius, F. M., &#38; Dietz, H. (2017). Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>","ieee":"F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,” <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier, 2017.","ama":"Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. 2017;112(3). doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>","ista":"Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 112(3), 25a.","chicago":"Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>."},"abstract":[{"text":"Here we describe an approach to bottom-up fabrication with nanometer-precision that allows integrating the functional diversity of proteins in designed three-dimensional structural frameworks. We reimagined the successful DNA origami design principle using a set of custom staple proteins to fold a double-stranded DNA template into a user-defined shape. Each staple protein recognizes two distinct double-helical DNA sequences and can carry additional functionalities. The staple proteins we present here are based on the transcription activator-like (TAL) effector proteins. Due to their repetitive structure these proteins offer a unique programmability that enables us to construct numerous staple proteins targeting any desired DNA sequence. Our approach is general, meaning that many different objects may be created using the same set of rules, and it is modular, because components can be modified or exchanged individually. We present rules for constructing megadalton-scale DNA-protein hybrid nanostructures; introduce important structural motifs, such as curvature, corners, and vertices; describe principles for creating multi-layer DNA-protein objects with enhanced rigidity; and demonstrate the possibility to combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since all components can be encoded genetically, our structures should be amenable to biotechnological mass-production. Moreover, since the target objects can self-assemble at room temperature in near-physiological buffer, our hybrid origami may also provide an attractive method to realize positioning and scaffolding tasks in vivo. We expect our method to find application both in scaffolding protein functionalities and in manipulating the spatial arrangement of genomic DNA.","lang":"eng"}],"_id":"14308","date_updated":"2024-10-14T12:31:35Z"},{"external_id":{"arxiv":["1705.08944"],"pmid":["28530665"]},"quality_controlled":"1","publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"arxiv":1,"status":"public","pmid":1,"day":"22","publication_status":"published","publisher":"Springer Nature","volume":16,"publication":"Nature Materials","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1705.08944"}],"doi":"10.1038/nmat4909","month":"05","article_type":"original","intvolume":"        16","author":[{"first_name":"M","last_name":"Siavashpouri","full_name":"Siavashpouri, M"},{"last_name":"Wachauf","first_name":"CH","full_name":"Wachauf, CH"},{"full_name":"Zakhary, MJ","first_name":"MJ","last_name":"Zakhary"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Dietz, H","last_name":"Dietz","first_name":"H"},{"full_name":"Dogic, Z","first_name":"Z","last_name":"Dogic"}],"extern":"1","article_processing_charge":"No","year":"2017","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Molecular engineering of chiral colloidal liquid crystals using DNA origami","oa":1,"issue":"8","type":"journal_article","date_created":"2023-09-06T13:37:27Z","oa_version":"Preprint","language":[{"iso":"eng"}],"_id":"14309","date_updated":"2023-11-07T11:40:00Z","abstract":[{"lang":"eng","text":"Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials."}],"page":"849-856","citation":{"ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. 16(8), 849–856.","chicago":"Siavashpouri, M, CH Wachauf, MJ Zakhary, Florian M Praetorius, H Dietz, and Z Dogic. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” <i>Nature Materials</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nmat4909\">https://doi.org/10.1038/nmat4909</a>.","ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of chiral colloidal liquid crystals using DNA origami. <i>Nature Materials</i>. 2017;16(8):849-856. doi:<a href=\"https://doi.org/10.1038/nmat4909\">10.1038/nmat4909</a>","ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of chiral colloidal liquid crystals using DNA origami,” <i>Nature Materials</i>, vol. 16, no. 8. Springer Nature, pp. 849–856, 2017.","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, Nature Materials 16 (2017) 849–856.","mla":"Siavashpouri, M., et al. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” <i>Nature Materials</i>, vol. 16, no. 8, Springer Nature, 2017, pp. 849–56, doi:<a href=\"https://doi.org/10.1038/nmat4909\">10.1038/nmat4909</a>.","apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &#38; Dogic, Z. (2017). Molecular engineering of chiral colloidal liquid crystals using DNA origami. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nmat4909\">https://doi.org/10.1038/nmat4909</a>"},"date_published":"2017-05-22T00:00:00Z"},{"extern":"1","year":"2017","article_processing_charge":"No","quality_controlled":"1","author":[{"full_name":"Siavashpouri, Mahsa","last_name":"Siavashpouri","first_name":"Mahsa"},{"first_name":"Christian","last_name":"Wachauf","full_name":"Wachauf, Christian"},{"full_name":"Zakhary, Mark","first_name":"Mark","last_name":"Zakhary"},{"last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"},{"full_name":"Dogic, Zvonimir","first_name":"Zvonimir","last_name":"Dogic"}],"publisher":"APS","publication_status":"published","publication":"APS March Meeting 2017","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Molecular engineering of colloidal liquid crystals using DNA origami","type":"conference_abstract","oa_version":"None","date_created":"2023-09-06T13:40:20Z","month":"03","language":[{"iso":"eng"}],"citation":{"apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &#38; Dogic, Z. (2017). Molecular engineering of colloidal liquid crystals using DNA origami. In <i>APS March Meeting 2017</i>. APS.","mla":"Siavashpouri, Mahsa, et al. “Molecular Engineering of Colloidal Liquid Crystals Using DNA Origami.” <i>APS March Meeting 2017</i>, APS, 2017.","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, in:, APS March Meeting 2017, APS, 2017.","chicago":"Siavashpouri, Mahsa, Christian Wachauf, Mark Zakhary, Florian M Praetorius, Hendrik Dietz, and Zvonimir Dogic. “Molecular Engineering of Colloidal Liquid Crystals Using DNA Origami.” In <i>APS March Meeting 2017</i>. APS, 2017.","ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of colloidal liquid crystals using DNA origami. APS March Meeting 2017. .","ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of colloidal liquid crystals using DNA origami. In: <i>APS March Meeting 2017</i>. APS; 2017.","ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of colloidal liquid crystals using DNA origami,” in <i>APS March Meeting 2017</i>, 2017."},"date_published":"2017-03-01T00:00:00Z","date_updated":"2023-11-07T11:36:15Z","_id":"14310"},{"OA_type":"free access","project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.jsc.2016.03.008","month":"01","ec_funded":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.jsc.2016.03.008","open_access":"1"}],"corr_author":"1","publist_id":"5765","publication_identifier":{"issn":[" 0747-7171"]},"status":"public","day":"01","publication_status":"published","publisher":"Academic Press","volume":78,"publication":"Journal of Symbolic Computation","acknowledgement":"Michael Kerber acknowledges support by the Max Planck Center for Visual Computing and Communications (FKZ-01IMC01 and FKZ-01IM10001). Ulrich Bauer, Jan Reininghaus, and Hubert Wagner acknowledge support by the EU Project TOPOSYS (FP7-ICT-318493-STREP).","external_id":{"isi":["000384396000005"]},"quality_controlled":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology."}],"_id":"1433","date_updated":"2025-10-01T07:39:51Z","date_published":"2017-01-01T00:00:00Z","department":[{"_id":"HeEd"}],"page":"76 - 90","citation":{"chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” <i>Journal of Symbolic Computation</i>, vol. 78. Academic Press, pp. 76–90, 2017.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. 2017;78:76-90. doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>","apa":"Bauer, U., Kerber, M., Reininghaus, J., &#38; Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>","mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>, vol. 78, Academic Press, 2017, pp. 76–90, doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90."},"oa":1,"isi":1,"type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:51:59Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Phat - Persistent homology algorithms toolbox","article_type":"original","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10894"}]},"author":[{"full_name":"Bauer, Ulrich","first_name":"Ulrich","last_name":"Bauer"},{"last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"},{"first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"first_name":"Hubert","last_name":"Wagner","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"}],"intvolume":"        78","article_processing_charge":"No","year":"2017"},{"volume":56,"publication":"Angewandte Chemie International Edition","publication_status":"published","publisher":"Wiley","status":"public","day":"06","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"quality_controlled":"1","month":"11","doi":"10.1002/anie.201708524","OA_type":"closed access","title":"Silver makes better eElectrical contacts to thiol‐terminated silanes than Gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","year":"2017","extern":"1","intvolume":"        56","author":[{"last_name":"Li","first_name":"Haixing","full_name":"Li, Haixing"},{"full_name":"Su, Timothy A.","first_name":"Timothy A.","last_name":"Su"},{"first_name":"María","last_name":"Camarasa‐Gómez","full_name":"Camarasa‐Gómez, María"},{"full_name":"Hernangómez‐Pérez, Daniel","first_name":"Daniel","last_name":"Hernangómez‐Pérez"},{"full_name":"Henn, Simon E.","last_name":"Henn","first_name":"Simon E."},{"full_name":"Pokorný, Vladislav","first_name":"Vladislav","last_name":"Pokorný"},{"full_name":"Caniglia, Caravaggio D.","first_name":"Caravaggio D.","last_name":"Caniglia"},{"first_name":"Michael S.","last_name":"Inkpen","full_name":"Inkpen, Michael S."},{"first_name":"Richard","last_name":"Korytár","full_name":"Korytár, Richard"},{"full_name":"Steigerwald, Michael L.","first_name":"Michael L.","last_name":"Steigerwald"},{"full_name":"Nuckolls, Colin","last_name":"Nuckolls","first_name":"Colin"},{"full_name":"Evers, Ferdinand","first_name":"Ferdinand","last_name":"Evers"},{"full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089"}],"article_type":"letter_note","_id":"17936","abstract":[{"lang":"eng","text":"We report that the single‐molecule junction conductance of thiol‐terminated silanes with Ag electrodes are higher than the conductance of those formed with Au electrodes. These results are in contrast to the trends in the metal work function Φ(Ag)&lt;Φ(Au). As such, a better alignment of the Au Fermi level to the molecular orbital of silane that mediates charge transport would be expected. This conductance trend is reversed when we replace the thiols with amines, highlighting the impact of metal–S covalent and metal–NH<jats:sub>2</jats:sub> dative bonds in controlling the molecular conductance. Density functional theory calculations elucidate the crucial role of the chemical linkers in determining the level alignment when molecules are attached to different metal contacts. We also demonstrate that conductance of thiol‐terminated silanes with Pt electrodes is lower than the ones formed with Au and Ag electrodes, again in contrast to the trends in the metal work‐functions."}],"date_updated":"2024-12-17T10:06:36Z","page":"14145-14148","citation":{"chicago":"Li, Haixing, Timothy A. Su, María Camarasa‐Gómez, Daniel Hernangómez‐Pérez, Simon E. Henn, Vladislav Pokorný, Caravaggio D. Caniglia, et al. “Silver Makes Better EElectrical Contacts to Thiol‐terminated Silanes than Gold.” <i>Angewandte Chemie International Edition</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/anie.201708524\">https://doi.org/10.1002/anie.201708524</a>.","ista":"Li H, Su TA, Camarasa‐Gómez M, Hernangómez‐Pérez D, Henn SE, Pokorný V, Caniglia CD, Inkpen MS, Korytár R, Steigerwald ML, Nuckolls C, Evers F, Venkataraman L. 2017. Silver makes better eElectrical contacts to thiol‐terminated silanes than Gold. Angewandte Chemie International Edition. 56(45), 14145–14148.","ama":"Li H, Su TA, Camarasa‐Gómez M, et al. Silver makes better eElectrical contacts to thiol‐terminated silanes than Gold. <i>Angewandte Chemie International Edition</i>. 2017;56(45):14145-14148. doi:<a href=\"https://doi.org/10.1002/anie.201708524\">10.1002/anie.201708524</a>","ieee":"H. Li <i>et al.</i>, “Silver makes better eElectrical contacts to thiol‐terminated silanes than Gold,” <i>Angewandte Chemie International Edition</i>, vol. 56, no. 45. Wiley, pp. 14145–14148, 2017.","apa":"Li, H., Su, T. A., Camarasa‐Gómez, M., Hernangómez‐Pérez, D., Henn, S. E., Pokorný, V., … Venkataraman, L. (2017). Silver makes better eElectrical contacts to thiol‐terminated silanes than Gold. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201708524\">https://doi.org/10.1002/anie.201708524</a>","short":"H. Li, T.A. Su, M. Camarasa‐Gómez, D. Hernangómez‐Pérez, S.E. Henn, V. Pokorný, C.D. Caniglia, M.S. Inkpen, R. Korytár, M.L. Steigerwald, C. Nuckolls, F. Evers, L. Venkataraman, Angewandte Chemie International Edition 56 (2017) 14145–14148.","mla":"Li, Haixing, et al. “Silver Makes Better EElectrical Contacts to Thiol‐terminated Silanes than Gold.” <i>Angewandte Chemie International Edition</i>, vol. 56, no. 45, Wiley, 2017, pp. 14145–48, doi:<a href=\"https://doi.org/10.1002/anie.201708524\">10.1002/anie.201708524</a>."},"date_published":"2017-11-06T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"None","date_created":"2024-09-09T08:45:32Z","type":"journal_article","issue":"45"},{"publication":"Nature Nanotechnology","volume":12,"publisher":"Springer Nature","publication_status":"published","day":"01","pmid":1,"status":"public","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"quality_controlled":"1","external_id":{"pmid":["28805817"]},"month":"11","doi":"10.1038/nnano.2017.156","OA_type":"closed access","title":"Room-temperature current blockade in atomically defined single-cluster junctions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","year":"2017","article_processing_charge":"No","extern":"1","author":[{"full_name":"Lovat, Giacomo","last_name":"Lovat","first_name":"Giacomo"},{"first_name":"Bonnie","last_name":"Choi","full_name":"Choi, Bonnie"},{"first_name":"Daniel W.","last_name":"Paley","full_name":"Paley, Daniel W."},{"full_name":"Steigerwald, Michael L.","last_name":"Steigerwald","first_name":"Michael L."},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","first_name":"Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089"},{"full_name":"Roy, Xavier","last_name":"Roy","first_name":"Xavier"}],"intvolume":"        12","article_type":"original","page":"1050-1054","citation":{"mla":"Lovat, Giacomo, et al. “Room-Temperature Current Blockade in Atomically Defined Single-Cluster Junctions.” <i>Nature Nanotechnology</i>, vol. 12, Springer Nature, 2017, pp. 1050–54, doi:<a href=\"https://doi.org/10.1038/nnano.2017.156\">10.1038/nnano.2017.156</a>.","short":"G. Lovat, B. Choi, D.W. Paley, M.L. Steigerwald, L. Venkataraman, X. Roy, Nature Nanotechnology 12 (2017) 1050–1054.","apa":"Lovat, G., Choi, B., Paley, D. W., Steigerwald, M. L., Venkataraman, L., &#38; Roy, X. (2017). Room-temperature current blockade in atomically defined single-cluster junctions. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nnano.2017.156\">https://doi.org/10.1038/nnano.2017.156</a>","ieee":"G. Lovat, B. Choi, D. W. Paley, M. L. Steigerwald, L. Venkataraman, and X. Roy, “Room-temperature current blockade in atomically defined single-cluster junctions,” <i>Nature Nanotechnology</i>, vol. 12. Springer Nature, pp. 1050–1054, 2017.","ama":"Lovat G, Choi B, Paley DW, Steigerwald ML, Venkataraman L, Roy X. Room-temperature current blockade in atomically defined single-cluster junctions. <i>Nature Nanotechnology</i>. 2017;12:1050-1054. doi:<a href=\"https://doi.org/10.1038/nnano.2017.156\">10.1038/nnano.2017.156</a>","ista":"Lovat G, Choi B, Paley DW, Steigerwald ML, Venkataraman L, Roy X. 2017. Room-temperature current blockade in atomically defined single-cluster junctions. Nature Nanotechnology. 12, 1050–1054.","chicago":"Lovat, Giacomo, Bonnie Choi, Daniel W. Paley, Michael L. Steigerwald, Latha Venkataraman, and Xavier Roy. “Room-Temperature Current Blockade in Atomically Defined Single-Cluster Junctions.” <i>Nature Nanotechnology</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nnano.2017.156\">https://doi.org/10.1038/nnano.2017.156</a>."},"date_published":"2017-11-01T00:00:00Z","_id":"17937","abstract":[{"text":"Fabricating nanoscopic devices capable of manipulating and processing single units of charge is an essential step towards creating functional devices where quantum effects dominate transport characteristics. The archetypal single-electron transistor comprises a small conducting or semiconducting island separated from two metallic reservoirs by insulating barriers1,2,3,4,5. By enabling the transfer of a well-defined number of charge carriers between the island and the reservoirs, such a device may enable discrete single-electron operations6,7,8,9. Here, we describe a single-molecule junction comprising a redox-active, atomically precise cobalt chalcogenide cluster wired between two nanoscopic electrodes10,11. We observe current blockade at room temperature in thousands of single-cluster junctions. Below a threshold voltage, charge transfer across the junction is suppressed. The device is turned on when the temporary occupation of the core states by a transiting carrier is energetically enabled, resulting in a sequential tunnelling process and an increase in current by a factor of ∼600. We perform in situ and ex situ cyclic voltammetry as well as density functional theory calculations to unveil a two-step process mediated by an orbital localized on the core of the cluster in which charge carriers reside before tunnelling to the collector reservoir. As the bias window of the junction is opened wide enough to include one of the cluster frontier orbitals, the current blockade is lifted and charge carriers can tunnel sequentially across the junction.","lang":"eng"}],"date_updated":"2024-12-17T10:09:35Z","language":[{"iso":"eng"}],"oa_version":"None","date_created":"2024-09-09T08:46:15Z","type":"journal_article"},{"extern":"1","year":"2017","article_processing_charge":"No","article_type":"letter_note","author":[{"last_name":"Zang","first_name":"Yaping","full_name":"Zang, Yaping"},{"full_name":"Pinkard, Andrew","last_name":"Pinkard","first_name":"Andrew"},{"last_name":"Liu","first_name":"Zhen-Fei","full_name":"Liu, Zhen-Fei"},{"full_name":"Neaton, Jeffrey B.","first_name":"Jeffrey B.","last_name":"Neaton"},{"full_name":"Steigerwald, Michael L.","last_name":"Steigerwald","first_name":"Michael L."},{"full_name":"Roy, Xavier","first_name":"Xavier","last_name":"Roy"},{"first_name":"Latha","orcid":"0000-0002-6957-6089","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha"}],"intvolume":"       139","scopus_import":"1","title":"Electronically transparent Au–N bonds for molecular junctions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"None","date_created":"2024-09-09T08:47:04Z","issue":"42","language":[{"iso":"eng"}],"date_published":"2017-10-05T00:00:00Z","citation":{"chicago":"Zang, Yaping, Andrew Pinkard, Zhen-Fei Liu, Jeffrey B. Neaton, Michael L. Steigerwald, Xavier Roy, and Latha Venkataraman. “Electronically Transparent Au–N Bonds for Molecular Junctions.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/jacs.7b08370\">https://doi.org/10.1021/jacs.7b08370</a>.","ista":"Zang Y, Pinkard A, Liu Z-F, Neaton JB, Steigerwald ML, Roy X, Venkataraman L. 2017. Electronically transparent Au–N bonds for molecular junctions. Journal of the American Chemical Society. 139(42), 14845–14848.","ama":"Zang Y, Pinkard A, Liu Z-F, et al. Electronically transparent Au–N bonds for molecular junctions. <i>Journal of the American Chemical Society</i>. 2017;139(42):14845-14848. doi:<a href=\"https://doi.org/10.1021/jacs.7b08370\">10.1021/jacs.7b08370</a>","ieee":"Y. Zang <i>et al.</i>, “Electronically transparent Au–N bonds for molecular junctions,” <i>Journal of the American Chemical Society</i>, vol. 139, no. 42. American Chemical Society, pp. 14845–14848, 2017.","apa":"Zang, Y., Pinkard, A., Liu, Z.-F., Neaton, J. B., Steigerwald, M. L., Roy, X., &#38; Venkataraman, L. (2017). Electronically transparent Au–N bonds for molecular junctions. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.7b08370\">https://doi.org/10.1021/jacs.7b08370</a>","mla":"Zang, Yaping, et al. “Electronically Transparent Au–N Bonds for Molecular Junctions.” <i>Journal of the American Chemical Society</i>, vol. 139, no. 42, American Chemical Society, 2017, pp. 14845–48, doi:<a href=\"https://doi.org/10.1021/jacs.7b08370\">10.1021/jacs.7b08370</a>.","short":"Y. Zang, A. Pinkard, Z.-F. Liu, J.B. Neaton, M.L. Steigerwald, X. Roy, L. Venkataraman, Journal of the American Chemical Society 139 (2017) 14845–14848."},"page":"14845-14848","_id":"17939","date_updated":"2024-12-17T10:13:56Z","abstract":[{"text":"We report a series of single-molecule transport measurements carried out in an ionic environment with oligophenylenediamine wires. These molecules exhibit three discrete conducting states accessed by electrochemically modifying the contacts. Transport in these junctions is defined by the oligophenylene backbone, but the conductance is increased by factors of ∼20 and ∼400 when compared to traditional dative junctions. We propose that the higher-conducting states arise from in situ electrochemical conversion of the dative Au←N bond into a new type of Au–N contact. Density functional theory-based transport calculations establish that the new contacts dramatically increase the electronic coupling of the oligophenylene backbone to the Au electrodes, consistent with experimental transport data. The resulting contact resistance is the lowest reported to date; more generally, our work demonstrates a facile method for creating electronically transparent metal–organic interfaces.","lang":"eng"}],"external_id":{"pmid":["28981277"]},"quality_controlled":"1","publisher":"American Chemical Society","publication_status":"published","publication":"Journal of the American Chemical Society","volume":139,"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"pmid":1,"day":"05","status":"public","month":"10","OA_type":"closed access","doi":"10.1021/jacs.7b08370"},{"title":"Extreme conductance suppression in molecular siloxanes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":"       139","author":[{"full_name":"Li, Haixing","last_name":"Li","first_name":"Haixing"},{"last_name":"Garner","first_name":"Marc H.","full_name":"Garner, Marc H."},{"full_name":"Su, Timothy A.","first_name":"Timothy A.","last_name":"Su"},{"last_name":"Jensen","first_name":"Anders","full_name":"Jensen, Anders"},{"first_name":"Michael S.","last_name":"Inkpen","full_name":"Inkpen, Michael S."},{"first_name":"Michael L.","last_name":"Steigerwald","full_name":"Steigerwald, Michael L."},{"last_name":"Venkataraman","orcid":"0000-0002-6957-6089","first_name":"Latha","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"last_name":"Solomon","first_name":"Gemma C.","full_name":"Solomon, Gemma C."},{"full_name":"Nuckolls, Colin","last_name":"Nuckolls","first_name":"Colin"}],"article_type":"original","year":"2017","article_processing_charge":"No","extern":"1","citation":{"chicago":"Li, Haixing, Marc H. Garner, Timothy A. Su, Anders Jensen, Michael S. Inkpen, Michael L. Steigerwald, Latha Venkataraman, Gemma C. Solomon, and Colin Nuckolls. “Extreme Conductance Suppression in Molecular Siloxanes.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/jacs.7b05599\">https://doi.org/10.1021/jacs.7b05599</a>.","ista":"Li H, Garner MH, Su TA, Jensen A, Inkpen MS, Steigerwald ML, Venkataraman L, Solomon GC, Nuckolls C. 2017. Extreme conductance suppression in molecular siloxanes. Journal of the American Chemical Society. 139(30), 10212–10215.","ieee":"H. Li <i>et al.</i>, “Extreme conductance suppression in molecular siloxanes,” <i>Journal of the American Chemical Society</i>, vol. 139, no. 30. American Chemical Society, pp. 10212–10215, 2017.","ama":"Li H, Garner MH, Su TA, et al. Extreme conductance suppression in molecular siloxanes. <i>Journal of the American Chemical Society</i>. 2017;139(30):10212-10215. doi:<a href=\"https://doi.org/10.1021/jacs.7b05599\">10.1021/jacs.7b05599</a>","apa":"Li, H., Garner, M. H., Su, T. A., Jensen, A., Inkpen, M. S., Steigerwald, M. L., … Nuckolls, C. (2017). Extreme conductance suppression in molecular siloxanes. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.7b05599\">https://doi.org/10.1021/jacs.7b05599</a>","mla":"Li, Haixing, et al. “Extreme Conductance Suppression in Molecular Siloxanes.” <i>Journal of the American Chemical Society</i>, vol. 139, no. 30, American Chemical Society, 2017, pp. 10212–15, doi:<a href=\"https://doi.org/10.1021/jacs.7b05599\">10.1021/jacs.7b05599</a>.","short":"H. Li, M.H. Garner, T.A. Su, A. Jensen, M.S. Inkpen, M.L. Steigerwald, L. Venkataraman, G.C. Solomon, C. Nuckolls, Journal of the American Chemical Society 139 (2017) 10212–10215."},"page":"10212-10215","date_published":"2017-07-13T00:00:00Z","_id":"17940","abstract":[{"lang":"eng","text":"Single-molecule conductance studies have traditionally focused on creating highly conducting molecular wires. However, progress in nanoscale electronics demands insulators just as it needs conductors. Here we describe the single-molecule length-dependent conductance properties of the classic silicon dioxide insulator. We synthesize molecular wires consisting of Si–O repeat units and measure their conductance through the scanning tunneling microscope-based break-junction method. These molecules yield conductance lower than alkanes of the same length and the largest length-dependent conductance decay of any molecular systems measured to date. We calculate single-molecule junction transmission and the complex band structure of the infinite 1D material for siloxane, in comparison with silane and alkane, and show that the large conductance decay is intrinsic to the nature of the Si–O bond. This work highlights the potential for siloxanes to function as molecular insulators in electronics."}],"date_updated":"2024-12-18T07:27:18Z","language":[{"iso":"eng"}],"issue":"30","date_created":"2024-09-09T08:48:28Z","oa_version":"None","type":"journal_article","day":"13","pmid":1,"status":"public","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"publication":"Journal of the American Chemical Society","volume":139,"publisher":"American Chemical Society","publication_status":"published","quality_controlled":"1","external_id":{"pmid":["28702995"]},"doi":"10.1021/jacs.7b05599","OA_type":"closed access","month":"07"},{"quality_controlled":"1","publication_identifier":{"issn":["1932-7447"],"eissn":["1932-7455"]},"day":"09","status":"public","publisher":"American Chemical Society","publication_status":"published","publication":"The Journal of Physical Chemistry C","volume":121,"OA_type":"closed access","doi":"10.1021/acs.jpcc.7b03493","month":"06","article_type":"original","author":[{"full_name":"Tsuji, Yuta","last_name":"Tsuji","first_name":"Yuta"},{"full_name":"Stuyver, Thijs","first_name":"Thijs","last_name":"Stuyver"},{"last_name":"Gunasekaran","first_name":"Suman","full_name":"Gunasekaran, Suman"},{"first_name":"Latha","orcid":"0000-0002-6957-6089","last_name":"Venkataraman","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"intvolume":"       121","extern":"1","year":"2017","article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The influence of linkers on quantum interference: A linker theorem","issue":"27","type":"journal_article","oa_version":"None","date_created":"2024-09-09T08:49:27Z","language":[{"iso":"eng"}],"page":"14451-14462","date_published":"2017-06-09T00:00:00Z","citation":{"apa":"Tsuji, Y., Stuyver, T., Gunasekaran, S., &#38; Venkataraman, L. (2017). The influence of linkers on quantum interference: A linker theorem. <i>The Journal of Physical Chemistry C</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcc.7b03493\">https://doi.org/10.1021/acs.jpcc.7b03493</a>","mla":"Tsuji, Yuta, et al. “The Influence of Linkers on Quantum Interference: A Linker Theorem.” <i>The Journal of Physical Chemistry C</i>, vol. 121, no. 27, American Chemical Society, 2017, pp. 14451–62, doi:<a href=\"https://doi.org/10.1021/acs.jpcc.7b03493\">10.1021/acs.jpcc.7b03493</a>.","short":"Y. Tsuji, T. Stuyver, S. Gunasekaran, L. Venkataraman, The Journal of Physical Chemistry C 121 (2017) 14451–14462.","ieee":"Y. Tsuji, T. Stuyver, S. Gunasekaran, and L. Venkataraman, “The influence of linkers on quantum interference: A linker theorem,” <i>The Journal of Physical Chemistry C</i>, vol. 121, no. 27. American Chemical Society, pp. 14451–14462, 2017.","ama":"Tsuji Y, Stuyver T, Gunasekaran S, Venkataraman L. The influence of linkers on quantum interference: A linker theorem. <i>The Journal of Physical Chemistry C</i>. 2017;121(27):14451-14462. doi:<a href=\"https://doi.org/10.1021/acs.jpcc.7b03493\">10.1021/acs.jpcc.7b03493</a>","chicago":"Tsuji, Yuta, Thijs Stuyver, Suman Gunasekaran, and Latha Venkataraman. “The Influence of Linkers on Quantum Interference: A Linker Theorem.” <i>The Journal of Physical Chemistry C</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.jpcc.7b03493\">https://doi.org/10.1021/acs.jpcc.7b03493</a>.","ista":"Tsuji Y, Stuyver T, Gunasekaran S, Venkataraman L. 2017. The influence of linkers on quantum interference: A linker theorem. The Journal of Physical Chemistry C. 121(27), 14451–14462."},"_id":"17941","abstract":[{"lang":"eng","text":"How heteroatomic substitutions affect electron transport through π-conjugated hydrocarbons has been the subject of some debate. In this paper we investigate the effect of heteroatomic linkers in a molecular junction on the electron-transmission spectrum, focusing on the occurrence of quantum interference (QI) close to the Fermi level, where conductivity can be significantly suppressed. We find that the substitution or addition of heteroatoms to a carbon skeleton at the contact positions does not change the main feature of QI due to the underlying carbon skeleton. QI in the overall system thus remains a robust feature. This empirical observation leads us to derive, in two mathematical ways, that these findings can be generalized. We note that addition or substitution of a carbon atom by a heteroatom at the contact positions will increase or decrease the number of electrons in the π-system, which will lead to a change in the alignment of the molecular orbitals of the isolated system relative to the electrode Fermi level. Both Hückel and density functional theory calculations on model systems probe the effect of this Fermi level change and confirm qualitatively the implications of the underlying mathematical proofs."}],"date_updated":"2024-12-18T07:29:42Z"},{"type":"journal_article","oa_version":"None","date_created":"2024-09-09T08:50:14Z","issue":"7","language":[{"iso":"eng"}],"date_updated":"2024-12-18T07:32:14Z","_id":"17942","abstract":[{"lang":"eng","text":"Quantum interference effects, whether constructive or destructive, are key to predicting and understanding the electrical conductance of single molecules. Here, through theory and experiment, we investigate a family of benzene-like molecules that exhibit both constructive and destructive interference effects arising due to more than one contact between the molecule and each electrode. In particular, we demonstrate that the π-system of meta-coupled benzene can exhibit constructive interference and its para-coupled analog can exhibit destructive interference, and vice versa, depending on the specific through-space interactions. As a peculiarity, this allows a meta-coupled benzene molecule to exhibit higher conductance than a para-coupled benzene. Our results provide design principles for molecular electronic components with high sensitivity to through-space interactions and demonstrate that increasing the number of contacts between the molecule and electrodes can both increase and decrease the conductance."}],"date_published":"2017-06-26T00:00:00Z","citation":{"ieee":"A. Borges, J. Xia, S. H. Liu, L. Venkataraman, and G. C. Solomon, “The role of through-space interactions in modulating constructive and destructive interference effects in benzene,” <i>Nano Letters</i>, vol. 17, no. 7. American Chemical Society, pp. 4436–4442, 2017.","ama":"Borges A, Xia J, Liu SH, Venkataraman L, Solomon GC. The role of through-space interactions in modulating constructive and destructive interference effects in benzene. <i>Nano Letters</i>. 2017;17(7):4436-4442. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b01592\">10.1021/acs.nanolett.7b01592</a>","ista":"Borges A, Xia J, Liu SH, Venkataraman L, Solomon GC. 2017. The role of through-space interactions in modulating constructive and destructive interference effects in benzene. Nano Letters. 17(7), 4436–4442.","chicago":"Borges, Anders, Jianlong Xia, Sheng Hua Liu, Latha Venkataraman, and Gemma C. Solomon. “The Role of Through-Space Interactions in Modulating Constructive and Destructive Interference Effects in Benzene.” <i>Nano Letters</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.nanolett.7b01592\">https://doi.org/10.1021/acs.nanolett.7b01592</a>.","short":"A. Borges, J. Xia, S.H. Liu, L. Venkataraman, G.C. Solomon, Nano Letters 17 (2017) 4436–4442.","mla":"Borges, Anders, et al. “The Role of Through-Space Interactions in Modulating Constructive and Destructive Interference Effects in Benzene.” <i>Nano Letters</i>, vol. 17, no. 7, American Chemical Society, 2017, pp. 4436–42, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b01592\">10.1021/acs.nanolett.7b01592</a>.","apa":"Borges, A., Xia, J., Liu, S. H., Venkataraman, L., &#38; Solomon, G. C. (2017). The role of through-space interactions in modulating constructive and destructive interference effects in benzene. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.7b01592\">https://doi.org/10.1021/acs.nanolett.7b01592</a>"},"page":"4436-4442","extern":"1","article_processing_charge":"No","year":"2017","article_type":"letter_note","intvolume":"        17","author":[{"first_name":"Anders","last_name":"Borges","full_name":"Borges, Anders"},{"last_name":"Xia","first_name":"Jianlong","full_name":"Xia, Jianlong"},{"first_name":"Sheng Hua","last_name":"Liu","full_name":"Liu, Sheng Hua"},{"last_name":"Venkataraman","orcid":"0000-0002-6957-6089","first_name":"Latha","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"first_name":"Gemma C.","last_name":"Solomon","full_name":"Solomon, Gemma C."}],"scopus_import":"1","title":"The role of through-space interactions in modulating constructive and destructive interference effects in benzene","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","OA_type":"closed access","doi":"10.1021/acs.nanolett.7b01592","external_id":{"pmid":["28650176"]},"quality_controlled":"1","publication_status":"published","publisher":"American Chemical Society","volume":17,"publication":"Nano Letters","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"status":"public","day":"26","pmid":1},{"issue":"4","type":"journal_article","date_created":"2024-09-09T08:51:18Z","oa_version":"None","language":[{"iso":"eng"}],"citation":{"chicago":"Su, Timothy A., Haixing Li, Rebekka S. Klausen, Nathaniel T. Kim, Madhav Neupane, James L. Leighton, Michael L. Steigerwald, Latha Venkataraman, and Colin Nuckolls. “Silane and Germane Molecular Electronics.” <i>Accounts of Chemical Research</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.accounts.7b00059\">https://doi.org/10.1021/acs.accounts.7b00059</a>.","ista":"Su TA, Li H, Klausen RS, Kim NT, Neupane M, Leighton JL, Steigerwald ML, Venkataraman L, Nuckolls C. 2017. Silane and Germane molecular electronics. Accounts of Chemical Research. 50(4), 1088–1095.","ieee":"T. A. Su <i>et al.</i>, “Silane and Germane molecular electronics,” <i>Accounts of Chemical Research</i>, vol. 50, no. 4. American Chemical Society, pp. 1088–1095, 2017.","ama":"Su TA, Li H, Klausen RS, et al. Silane and Germane molecular electronics. <i>Accounts of Chemical Research</i>. 2017;50(4):1088-1095. doi:<a href=\"https://doi.org/10.1021/acs.accounts.7b00059\">10.1021/acs.accounts.7b00059</a>","apa":"Su, T. A., Li, H., Klausen, R. S., Kim, N. T., Neupane, M., Leighton, J. L., … Nuckolls, C. (2017). Silane and Germane molecular electronics. <i>Accounts of Chemical Research</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.accounts.7b00059\">https://doi.org/10.1021/acs.accounts.7b00059</a>","short":"T.A. Su, H. Li, R.S. Klausen, N.T. Kim, M. Neupane, J.L. Leighton, M.L. Steigerwald, L. Venkataraman, C. Nuckolls, Accounts of Chemical Research 50 (2017) 1088–1095.","mla":"Su, Timothy A., et al. “Silane and Germane Molecular Electronics.” <i>Accounts of Chemical Research</i>, vol. 50, no. 4, American Chemical Society, 2017, pp. 1088–95, doi:<a href=\"https://doi.org/10.1021/acs.accounts.7b00059\">10.1021/acs.accounts.7b00059</a>."},"page":"1088-1095","date_published":"2017-03-27T00:00:00Z","_id":"17943","abstract":[{"lang":"eng","text":"This Account provides an overview of our recent efforts to uncover the fundamental charge transport properties of Si–Si and Ge–Ge single bonds and introduce useful functions into group 14 molecular wires. We utilize the tools of chemical synthesis and a scanning tunneling microscopy-based break-junction technique to study the mechanism of charge transport in these molecular systems. We evaluated the fundamental ability of silicon, germanium, and carbon molecular wires to transport charge by comparing conductances within families of well-defined structures, the members of which differ only in the number of Si (or Ge or C) atoms in the wire. For each family, this procedure yielded a length-dependent conductance decay parameter, β. Comparison of the different β values demonstrates that Si–Si and Ge–Ge σ bonds are more conductive than the analogous C–C σ bonds. These molecular trends mirror what is seen in the bulk.\r\n\r\nThe conductance decay of Si and Ge-based wires is similar in magnitude to those from π-based molecular wires such as paraphenylenes However, the chemistry of the linkers that attach the molecular wires to the electrodes has a large influence on the resulting β value. For example, Si- and Ge-based wires of many different lengths connected with a methyl–thiomethyl linker give β values of 0.36–0.39 Å–1, whereas Si- and Ge-based wires connected with aryl–thiomethyl groups give drastically different β values for short and long wires. This observation inspired us to study molecular wires that are composed of both π- and σ-orbitals. The sequence and composition of group 14 atoms in the σ chain modulates the electronic coupling between the π end-groups and dictates the molecular conductance. The conductance behavior originates from the coupling between the subunits, which can be understood by considering periodic trends such as bond length, polarizability, and bond polarity.\r\n\r\nWe found that the same periodic trends determine the electric field-induced breakdown properties of individual Si–Si, Ge–Ge, Si–O, Si–C, and C–C bonds. Building from these studies, we have prepared a system that has two different, alternative conductance pathways. In this wire, we can intentionally break a labile, strained silicon–silicon bond and thereby shunt the current through the secondary conduction pathway. This type of in situ bond-rupture provides a new tool to study single molecule reactions that are induced by electric fields. Moreover, these studies provide guidance for designing dielectric materials as well as molecular devices that require stability under high voltage bias.\r\n\r\nThe fundamental studies on the structure/function relationships of the molecular wires have guided the design of new functional systems based on the Si- and Ge-based wires. For example, we exploited the principle of strain-induced Lewis acidity from reaction chemistry to design a single molecule switch that can be controllably switched between two conductive states by varying the distance between the tip and substrate electrodes. We found that the strain intrinsic to the disilaacenaphthene scaffold also creates two state conductance switching. Finally, we demonstrate the first example of a stereoelectronic conductance switch, and we demonstrate that the switching relies crucially on the electronic delocalization in Si–Si and Ge–Ge wire backbones. These studies illustrate the untapped potential in using Si- and Ge-based wires to design and control charge transport at the nanoscale and to allow quantum mechanics to be used as a tool to design ultraminiaturized switches."}],"date_updated":"2024-12-18T07:41:16Z","article_type":"original","intvolume":"        50","author":[{"full_name":"Su, Timothy A.","first_name":"Timothy A.","last_name":"Su"},{"last_name":"Li","first_name":"Haixing","full_name":"Li, Haixing"},{"last_name":"Klausen","first_name":"Rebekka S.","full_name":"Klausen, Rebekka S."},{"first_name":"Nathaniel T.","last_name":"Kim","full_name":"Kim, Nathaniel T."},{"first_name":"Madhav","last_name":"Neupane","full_name":"Neupane, Madhav"},{"first_name":"James L.","last_name":"Leighton","full_name":"Leighton, James L."},{"last_name":"Steigerwald","first_name":"Michael L.","full_name":"Steigerwald, Michael L."},{"orcid":"0000-0002-6957-6089","last_name":"Venkataraman","first_name":"Latha","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"first_name":"Colin","last_name":"Nuckolls","full_name":"Nuckolls, Colin"}],"extern":"1","year":"2017","article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Silane and Germane molecular electronics","OA_type":"closed access","doi":"10.1021/acs.accounts.7b00059","month":"03","external_id":{"pmid":["28345881"]},"quality_controlled":"1","publication_identifier":{"issn":["0001-4842"],"eissn":["1520-4898"]},"day":"27","pmid":1,"status":"public","publisher":"American Chemical Society","publication_status":"published","publication":"Accounts of Chemical Research","volume":50},{"quality_controlled":"1","volume":146,"publication":"The Journal of Chemical Physics","publication_status":"published","publisher":"AIP Publishing","status":"public","day":"07","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"month":"03","doi":"10.1063/1.4977469","OA_type":"closed access","article_processing_charge":"No","year":"2017","extern":"1","intvolume":"       146","author":[{"full_name":"Evers, Ferdinand","first_name":"Ferdinand","last_name":"Evers"},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","first_name":"Latha","last_name":"Venkataraman","orcid":"0000-0002-6957-6089"}],"article_type":"letter_note","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Preface: Special topic on Frontiers in Molecular Scale Electronics","scopus_import":"1","date_created":"2024-09-09T08:52:10Z","oa_version":"None","article_number":"092101","type":"journal_article","issue":"9","date_updated":"2024-12-18T07:44:28Z","_id":"17944","abstract":[{"text":"The electronic, mechanical, and thermoelectric properties of molecular scale devices have fascinated scientists across several disciplines in natural sciences and engineering. The interest is partially technological, driven by the fast miniaturization of integrated circuits that now have reached characteristic features at the nanometer scale. Equally important, a very strong incentive also exists to elucidate the fundamental aspects of structure-function relations for nanoscale devices, which utilize molecular building blocks as functional units. Thus motivated, a rich research field has established itself, broadly termed “Molecular Electronics,” that hosts a plethora of activities devoted to this goal in chemistry, physics, and electrical engineering. This Special Topic on Frontiers of Molecular Scale Electronics captures recent theoretical and experimental advances in the field.","lang":"eng"}],"citation":{"chicago":"Evers, Ferdinand, and Latha Venkataraman. “Preface: Special Topic on Frontiers in Molecular Scale Electronics.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4977469\">https://doi.org/10.1063/1.4977469</a>.","ista":"Evers F, Venkataraman L. 2017. Preface: Special topic on Frontiers in Molecular Scale Electronics. The Journal of Chemical Physics. 146(9), 092101.","ieee":"F. Evers and L. Venkataraman, “Preface: Special topic on Frontiers in Molecular Scale Electronics,” <i>The Journal of Chemical Physics</i>, vol. 146, no. 9. AIP Publishing, 2017.","ama":"Evers F, Venkataraman L. Preface: Special topic on Frontiers in Molecular Scale Electronics. <i>The Journal of Chemical Physics</i>. 2017;146(9). doi:<a href=\"https://doi.org/10.1063/1.4977469\">10.1063/1.4977469</a>","apa":"Evers, F., &#38; Venkataraman, L. (2017). Preface: Special topic on Frontiers in Molecular Scale Electronics. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4977469\">https://doi.org/10.1063/1.4977469</a>","short":"F. Evers, L. Venkataraman, The Journal of Chemical Physics 146 (2017).","mla":"Evers, Ferdinand, and Latha Venkataraman. “Preface: Special Topic on Frontiers in Molecular Scale Electronics.” <i>The Journal of Chemical Physics</i>, vol. 146, no. 9, 092101, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4977469\">10.1063/1.4977469</a>."},"date_published":"2017-03-07T00:00:00Z","language":[{"iso":"eng"}]}]