[{"OA_type":"closed access","article_type":"letter_note","month":"05","oa_version":"None","publication_status":"published","type":"journal_article","publisher":"American Chemical Society","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"pmid":1,"_id":"17970","title":"Flicker noise as a probe of electronic interaction at metal–single molecule interfaces","date_updated":"2024-12-18T11:32:55Z","status":"public","author":[{"last_name":"Adak","full_name":"Adak, Olgun","first_name":"Olgun"},{"full_name":"Rosenthal, Ethan","last_name":"Rosenthal","first_name":"Ethan"},{"first_name":"Jeffery","full_name":"Meisner, Jeffery","last_name":"Meisner"},{"first_name":"Erick F.","full_name":"Andrade, Erick F.","last_name":"Andrade"},{"last_name":"Pasupathy","full_name":"Pasupathy, Abhay N.","first_name":"Abhay N."},{"last_name":"Nuckolls","full_name":"Nuckolls, Colin","first_name":"Colin"},{"last_name":"Hybertsen","full_name":"Hybertsen, Mark S.","first_name":"Mark S."},{"first_name":"Latha","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"external_id":{"pmid":["25942441"]},"extern":"1","volume":15,"date_published":"2015-05-05T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","page":"4143-4149","language":[{"iso":"eng"}],"publication":"Nano Letters","year":"2015","day":"05","scopus_import":"1","date_created":"2024-09-09T09:45:50Z","citation":{"mla":"Adak, Olgun, et al. “Flicker Noise as a Probe of Electronic Interaction at Metal–Single Molecule Interfaces.” <i>Nano Letters</i>, vol. 15, no. 6, American Chemical Society, 2015, pp. 4143–49, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01270\">10.1021/acs.nanolett.5b01270</a>.","apa":"Adak, O., Rosenthal, E., Meisner, J., Andrade, E. F., Pasupathy, A. N., Nuckolls, C., … Venkataraman, L. (2015). Flicker noise as a probe of electronic interaction at metal–single molecule interfaces. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01270\">https://doi.org/10.1021/acs.nanolett.5b01270</a>","chicago":"Adak, Olgun, Ethan Rosenthal, Jeffery Meisner, Erick F. Andrade, Abhay N. Pasupathy, Colin Nuckolls, Mark S. Hybertsen, and Latha Venkataraman. “Flicker Noise as a Probe of Electronic Interaction at Metal–Single Molecule Interfaces.” <i>Nano Letters</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01270\">https://doi.org/10.1021/acs.nanolett.5b01270</a>.","ista":"Adak O, Rosenthal E, Meisner J, Andrade EF, Pasupathy AN, Nuckolls C, Hybertsen MS, Venkataraman L. 2015. Flicker noise as a probe of electronic interaction at metal–single molecule interfaces. Nano Letters. 15(6), 4143–4149.","ama":"Adak O, Rosenthal E, Meisner J, et al. Flicker noise as a probe of electronic interaction at metal–single molecule interfaces. <i>Nano Letters</i>. 2015;15(6):4143-4149. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01270\">10.1021/acs.nanolett.5b01270</a>","short":"O. Adak, E. Rosenthal, J. Meisner, E.F. Andrade, A.N. Pasupathy, C. Nuckolls, M.S. Hybertsen, L. Venkataraman, Nano Letters 15 (2015) 4143–4149.","ieee":"O. Adak <i>et al.</i>, “Flicker noise as a probe of electronic interaction at metal–single molecule interfaces,” <i>Nano Letters</i>, vol. 15, no. 6. American Chemical Society, pp. 4143–4149, 2015."},"quality_controlled":"1","doi":"10.1021/acs.nanolett.5b01270","intvolume":"        15","abstract":[{"text":"Charge transport properties of metal–molecule interfaces depend strongly on the character of molecule–electrode interactions. Although through-bond coupled systems have attracted the most attention, through-space coupling is important in molecular systems when, for example, through-bond coupling is suppressed due to quantum interference effects. To date, a probe that clearly distinguishes these two types of coupling has not yet been demonstrated. Here, we investigate the origin of flicker noise in single molecule junctions and demonstrate how the character of the molecule–electrode coupling influences the flicker noise behavior of single molecule junctions. Importantly, we find that flicker noise shows a power law dependence on conductance in all junctions studied with an exponent that can distinguish through-space and through-bond coupling. Our results provide a new and powerful tool for probing and understanding coupling at the metal-molecule interface.","lang":"eng"}],"article_processing_charge":"No"},{"year":"2015","issue":"6","publication":"Nano Letters","page":"3716-3722","language":[{"iso":"eng"}],"external_id":{"arxiv":["1504.00242"]},"author":[{"first_name":"Olgun","last_name":"Adak","full_name":"Adak, Olgun"},{"first_name":"Richard","full_name":"Korytár, Richard","last_name":"Korytár"},{"last_name":"Joe","full_name":"Joe, Andrew Y.","first_name":"Andrew Y."},{"last_name":"Evers","full_name":"Evers, Ferdinand","first_name":"Ferdinand"},{"orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","first_name":"Latha"}],"extern":"1","volume":15,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-05-28T00:00:00Z","status":"public","article_processing_charge":"No","oa":1,"abstract":[{"lang":"eng","text":"We study the impact of electrode band structure on transport through single-molecule junctions by measuring the conductance of pyridine-based molecules using Ag and Au electrodes. Our experiments are carried out using the scanning tunneling microscope based break-junction technique and are supported by density functional theory based calculations. We find from both experiments and calculations that the coupling of the dominant transport orbital to the metal is stronger for Au-based junctions when compared with Ag-based junctions. We attribute this difference to relativistic effects, which result in an enhanced density of d-states at the Fermi energy for Au compared with Ag. We further show that the alignment of the conducting orbital relative to the Fermi level does not follow the work function difference between two metals and is different for conjugated and saturated systems. We thus demonstrate that the details of the molecular level alignment and electronic coupling in metal–organic interfaces do not follow simple rules but are rather the consequence of subtle local interactions."}],"doi":"10.1021/acs.nanolett.5b01195","intvolume":"        15","day":"28","scopus_import":"1","citation":{"ama":"Adak O, Korytár R, Joe AY, Evers F, Venkataraman L. Impact of electrode density of states on transport through pyridine-linked single molecule junctions. <i>Nano Letters</i>. 2015;15(6):3716-3722. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01195\">10.1021/acs.nanolett.5b01195</a>","short":"O. Adak, R. Korytár, A.Y. Joe, F. Evers, L. Venkataraman, Nano Letters 15 (2015) 3716–3722.","ieee":"O. Adak, R. Korytár, A. Y. Joe, F. Evers, and L. Venkataraman, “Impact of electrode density of states on transport through pyridine-linked single molecule junctions,” <i>Nano Letters</i>, vol. 15, no. 6. American Chemical Society, pp. 3716–3722, 2015.","ista":"Adak O, Korytár R, Joe AY, Evers F, Venkataraman L. 2015. Impact of electrode density of states on transport through pyridine-linked single molecule junctions. Nano Letters. 15(6), 3716–3722.","chicago":"Adak, Olgun, Richard Korytár, Andrew Y. Joe, Ferdinand Evers, and Latha Venkataraman. “Impact of Electrode Density of States on Transport through Pyridine-Linked Single Molecule Junctions.” <i>Nano Letters</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01195\">https://doi.org/10.1021/acs.nanolett.5b01195</a>.","apa":"Adak, O., Korytár, R., Joe, A. Y., Evers, F., &#38; Venkataraman, L. (2015). Impact of electrode density of states on transport through pyridine-linked single molecule junctions. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01195\">https://doi.org/10.1021/acs.nanolett.5b01195</a>","mla":"Adak, Olgun, et al. “Impact of Electrode Density of States on Transport through Pyridine-Linked Single Molecule Junctions.” <i>Nano Letters</i>, vol. 15, no. 6, American Chemical Society, 2015, pp. 3716–22, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01195\">10.1021/acs.nanolett.5b01195</a>."},"date_created":"2024-09-09T10:02:07Z","quality_controlled":"1","oa_version":"Preprint","publication_status":"published","publisher":"American Chemical Society","type":"journal_article","arxiv":1,"article_type":"letter_note","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1504.00242","open_access":"1"}],"OA_type":"green","date_updated":"2024-12-18T11:37:35Z","title":"Impact of electrode density of states on transport through pyridine-linked single molecule junctions","_id":"17971","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"OA_place":"repository"},{"publication_status":"published","publisher":"Springer Nature","type":"journal_article","oa_version":"None","month":"06","article_type":"letter_note","OA_type":"closed access","date_updated":"2024-12-18T12:03:16Z","title":"Single-molecule diodes with high rectification ratios through environmental control","_id":"17972","pmid":1,"publication_identifier":{"issn":["1748-3387"],"eissn":["1748-3395"]},"year":"2015","publication":"Nature Nanotechnology","language":[{"iso":"eng"}],"page":"522-527","issue":"6","date_published":"2015-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":10,"external_id":{"pmid":["26005998"]},"author":[{"first_name":"Brian","full_name":"Capozzi, Brian","last_name":"Capozzi"},{"last_name":"Xia","full_name":"Xia, Jianlong","first_name":"Jianlong"},{"first_name":"Olgun","full_name":"Adak, Olgun","last_name":"Adak"},{"full_name":"Dell, Emma J.","last_name":"Dell","first_name":"Emma J."},{"last_name":"Liu","full_name":"Liu, Zhen-Fei","first_name":"Zhen-Fei"},{"full_name":"Taylor, Jeffrey C.","last_name":"Taylor","first_name":"Jeffrey C."},{"first_name":"Jeffrey B.","last_name":"Neaton","full_name":"Neaton, Jeffrey B."},{"last_name":"Campos","full_name":"Campos, Luis M.","first_name":"Luis M."},{"first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha"}],"status":"public","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Molecular electronics aims to miniaturize electronic devices by using subnanometre-scale active components1,2,3. A single-molecule diode, a circuit element that directs current flow4, was first proposed more than 40 years ago5 and consisted of an asymmetric molecule comprising a donor–bridge–acceptor architecture to mimic a semiconductor p–n junction. Several single-molecule diodes have since been realized in junctions featuring asymmetric molecular backbones6,7,8, molecule–electrode linkers9 or electrode materials10. Despite these advances, molecular diodes have had limited potential for applications due to their low conductance, low rectification ratios, extreme sensitivity to the junction structure and high operating voltages7,8,9,11,12. Here, we demonstrate a powerful approach to induce current rectification in symmetric single-molecule junctions using two electrodes of the same metal, but breaking symmetry by exposing considerably different electrode areas to an ionic solution. This allows us to control the junction's electrostatic environment in an asymmetric fashion by simply changing the bias polarity. With this method, we reliably and reproducibly achieve rectification ratios in excess of 200 at voltages as low as 370 mV using a symmetric oligomer of thiophene-1,1-dioxide13,14. By taking advantage of the changes in the junction environment induced by the presence of an ionic solution, this method provides a general route for tuning nonlinear nanoscale device phenomena, which could potentially be applied in systems beyond single-molecule junctions."}],"intvolume":"        10","doi":"10.1038/nnano.2015.97","quality_controlled":"1","citation":{"ista":"Capozzi B, Xia J, Adak O, Dell EJ, Liu Z-F, Taylor JC, Neaton JB, Campos LM, Venkataraman L. 2015. Single-molecule diodes with high rectification ratios through environmental control. Nature Nanotechnology. 10(6), 522–527.","mla":"Capozzi, Brian, et al. “Single-Molecule Diodes with High Rectification Ratios through Environmental Control.” <i>Nature Nanotechnology</i>, vol. 10, no. 6, Springer Nature, 2015, pp. 522–27, doi:<a href=\"https://doi.org/10.1038/nnano.2015.97\">10.1038/nnano.2015.97</a>.","apa":"Capozzi, B., Xia, J., Adak, O., Dell, E. J., Liu, Z.-F., Taylor, J. C., … Venkataraman, L. (2015). Single-molecule diodes with high rectification ratios through environmental control. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nnano.2015.97\">https://doi.org/10.1038/nnano.2015.97</a>","chicago":"Capozzi, Brian, Jianlong Xia, Olgun Adak, Emma J. Dell, Zhen-Fei Liu, Jeffrey C. Taylor, Jeffrey B. Neaton, Luis M. Campos, and Latha Venkataraman. “Single-Molecule Diodes with High Rectification Ratios through Environmental Control.” <i>Nature Nanotechnology</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nnano.2015.97\">https://doi.org/10.1038/nnano.2015.97</a>.","ama":"Capozzi B, Xia J, Adak O, et al. Single-molecule diodes with high rectification ratios through environmental control. <i>Nature Nanotechnology</i>. 2015;10(6):522-527. doi:<a href=\"https://doi.org/10.1038/nnano.2015.97\">10.1038/nnano.2015.97</a>","ieee":"B. Capozzi <i>et al.</i>, “Single-molecule diodes with high rectification ratios through environmental control,” <i>Nature Nanotechnology</i>, vol. 10, no. 6. Springer Nature, pp. 522–527, 2015.","short":"B. Capozzi, J. Xia, O. Adak, E.J. Dell, Z.-F. Liu, J.C. Taylor, J.B. Neaton, L.M. Campos, L. Venkataraman, Nature Nanotechnology 10 (2015) 522–527."},"date_created":"2024-09-09T10:03:23Z","scopus_import":"1","day":"01"},{"year":"2015","issue":"15","page":"5028-5033","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","author":[{"full_name":"Li, Haixing","last_name":"Li","first_name":"Haixing"},{"last_name":"Su","full_name":"Su, Timothy A.","first_name":"Timothy A."},{"last_name":"Zhang","full_name":"Zhang, Vivian","first_name":"Vivian"},{"last_name":"Steigerwald","full_name":"Steigerwald, Michael L.","first_name":"Michael L."},{"full_name":"Nuckolls, Colin","last_name":"Nuckolls","first_name":"Colin"},{"first_name":"Latha","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"external_id":{"pmid":["25675085"]},"extern":"1","volume":137,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-02-12T00:00:00Z","status":"public","article_processing_charge":"No","abstract":[{"text":"Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S–Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor–acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si–Si and Ge–Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si–Si, Si–C, and Si–O bonds and find that Si–C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level.","lang":"eng"}],"doi":"10.1021/ja512523r","intvolume":"       137","day":"12","scopus_import":"1","date_created":"2024-09-09T10:04:02Z","citation":{"ista":"Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. 2015. Electric field breakdown in single molecule junctions. Journal of the American Chemical Society. 137(15), 5028–5033.","apa":"Li, H., Su, T. A., Zhang, V., Steigerwald, M. L., Nuckolls, C., &#38; Venkataraman, L. (2015). Electric field breakdown in single molecule junctions. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja512523r\">https://doi.org/10.1021/ja512523r</a>","chicago":"Li, Haixing, Timothy A. Su, Vivian Zhang, Michael L. Steigerwald, Colin Nuckolls, and Latha Venkataraman. “Electric Field Breakdown in Single Molecule Junctions.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/ja512523r\">https://doi.org/10.1021/ja512523r</a>.","mla":"Li, Haixing, et al. “Electric Field Breakdown in Single Molecule Junctions.” <i>Journal of the American Chemical Society</i>, vol. 137, no. 15, American Chemical Society, 2015, pp. 5028–33, doi:<a href=\"https://doi.org/10.1021/ja512523r\">10.1021/ja512523r</a>.","ama":"Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. Electric field breakdown in single molecule junctions. <i>Journal of the American Chemical Society</i>. 2015;137(15):5028-5033. doi:<a href=\"https://doi.org/10.1021/ja512523r\">10.1021/ja512523r</a>","ieee":"H. Li, T. A. Su, V. Zhang, M. L. Steigerwald, C. Nuckolls, and L. Venkataraman, “Electric field breakdown in single molecule junctions,” <i>Journal of the American Chemical Society</i>, vol. 137, no. 15. American Chemical Society, pp. 5028–5033, 2015.","short":"H. Li, T.A. Su, V. Zhang, M.L. Steigerwald, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 137 (2015) 5028–5033."},"quality_controlled":"1","oa_version":"None","publisher":"American Chemical Society","publication_status":"published","type":"journal_article","article_type":"original","month":"02","OA_type":"closed access","date_updated":"2024-12-18T12:10:06Z","title":"Electric field breakdown in single molecule junctions","pmid":1,"_id":"17973","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]}},{"publication":"Chemical Society Reviews","language":[{"iso":"eng"}],"page":"842-844","issue":"4","year":"2015","status":"public","date_published":"2015-01-30T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":44,"extern":"1","author":[{"full_name":"Guldi, Dirk M.","last_name":"Guldi","first_name":"Dirk M."},{"first_name":"Hiroshi","full_name":"Nishihara, Hiroshi","last_name":"Nishihara"},{"first_name":"Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha"}],"external_id":{"pmid":["25636152"]},"abstract":[{"lang":"eng","text":"Guest editors Dirk M. Guldi, Hiroshi Nishihara and Latha Venkataraman introduce the Molecular Wires issue of \"Chemical Society Reviews\"."}],"article_processing_charge":"No","date_created":"2024-09-09T10:53:55Z","quality_controlled":"1","citation":{"ista":"Guldi DM, Nishihara H, Venkataraman L. 2015. Molecular wires. Chemical Society Reviews. 44(4), 842–844.","chicago":"Guldi, Dirk M., Hiroshi Nishihara, and Latha Venkataraman. “Molecular Wires.” <i>Chemical Society Reviews</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c5cs90010g\">https://doi.org/10.1039/c5cs90010g</a>.","apa":"Guldi, D. M., Nishihara, H., &#38; Venkataraman, L. (2015). Molecular wires. <i>Chemical Society Reviews</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c5cs90010g\">https://doi.org/10.1039/c5cs90010g</a>","mla":"Guldi, Dirk M., et al. “Molecular Wires.” <i>Chemical Society Reviews</i>, vol. 44, no. 4, Royal Society of Chemistry, 2015, pp. 842–44, doi:<a href=\"https://doi.org/10.1039/c5cs90010g\">10.1039/c5cs90010g</a>.","ieee":"D. M. Guldi, H. Nishihara, and L. Venkataraman, “Molecular wires,” <i>Chemical Society Reviews</i>, vol. 44, no. 4. Royal Society of Chemistry, pp. 842–844, 2015.","short":"D.M. Guldi, H. Nishihara, L. Venkataraman, Chemical Society Reviews 44 (2015) 842–844.","ama":"Guldi DM, Nishihara H, Venkataraman L. Molecular wires. <i>Chemical Society Reviews</i>. 2015;44(4):842-844. doi:<a href=\"https://doi.org/10.1039/c5cs90010g\">10.1039/c5cs90010g</a>"},"scopus_import":"1","day":"30","intvolume":"        44","doi":"10.1039/c5cs90010g","type":"journal_article","publisher":"Royal Society of Chemistry","publication_status":"published","oa_version":"None","OA_type":"closed access","month":"01","article_type":"letter_note","title":"Molecular wires","date_updated":"2025-01-02T13:26:36Z","publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"_id":"17974","pmid":1},{"day":"16","citation":{"mla":"Su, Timothy A., et al. “Stereoelectronic Switching in Single-Molecule Junctions.” <i>Nature Chemistry</i>, vol. 7, no. 3, Springer Nature, 2015, pp. 215–20, doi:<a href=\"https://doi.org/10.1038/nchem.2180\">10.1038/nchem.2180</a>.","chicago":"Su, Timothy A., Haixing Li, Michael L. Steigerwald, Latha Venkataraman, and Colin Nuckolls. “Stereoelectronic Switching in Single-Molecule Junctions.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2180\">https://doi.org/10.1038/nchem.2180</a>.","apa":"Su, T. A., Li, H., Steigerwald, M. L., Venkataraman, L., &#38; Nuckolls, C. (2015). Stereoelectronic switching in single-molecule junctions. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2180\">https://doi.org/10.1038/nchem.2180</a>","ista":"Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. 2015. Stereoelectronic switching in single-molecule junctions. Nature Chemistry. 7(3), 215–220.","ama":"Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. Stereoelectronic switching in single-molecule junctions. <i>Nature Chemistry</i>. 2015;7(3):215-220. doi:<a href=\"https://doi.org/10.1038/nchem.2180\">10.1038/nchem.2180</a>","short":"T.A. Su, H. Li, M.L. Steigerwald, L. Venkataraman, C. Nuckolls, Nature Chemistry 7 (2015) 215–220.","ieee":"T. A. Su, H. Li, M. L. Steigerwald, L. Venkataraman, and C. Nuckolls, “Stereoelectronic switching in single-molecule junctions,” <i>Nature Chemistry</i>, vol. 7, no. 3. Springer Nature, pp. 215–220, 2015."},"quality_controlled":"1","date_created":"2024-09-09T10:54:59Z","scopus_import":"1","doi":"10.1038/nchem.2180","intvolume":"         7","abstract":[{"text":"A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong σ conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur–methylene σ bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states.","lang":"eng"}],"article_processing_charge":"No","status":"public","extern":"1","volume":7,"author":[{"first_name":"Timothy A.","last_name":"Su","full_name":"Su, Timothy A."},{"first_name":"Haixing","last_name":"Li","full_name":"Li, Haixing"},{"first_name":"Michael L.","full_name":"Steigerwald, Michael L.","last_name":"Steigerwald"},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","first_name":"Latha"},{"first_name":"Colin","full_name":"Nuckolls, Colin","last_name":"Nuckolls"}],"external_id":{"pmid":["25698330"]},"date_published":"2015-02-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","publication":"Nature Chemistry","page":"215-220","language":[{"iso":"eng"}],"year":"2015","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"pmid":1,"_id":"17975","title":"Stereoelectronic switching in single-molecule junctions","date_updated":"2025-01-02T13:28:51Z","OA_type":"closed access","article_type":"original","month":"02","oa_version":"None","publisher":"Springer Nature","type":"journal_article","publication_status":"published"},{"scopus_import":"1","date_created":"2024-09-09T10:55:42Z","quality_controlled":"1","citation":{"ista":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. 2015. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. Nature Chemistry. 7(3), 209–214.","apa":"Dell, E. J., Capozzi, B., Xia, J., Venkataraman, L., &#38; Campos, L. M. (2015). Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>","chicago":"Dell, Emma J., Brian Capozzi, Jianlong Xia, Latha Venkataraman, and Luis M. Campos. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>.","mla":"Dell, Emma J., et al. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>, vol. 7, no. 3, Springer Nature, 2015, pp. 209–14, doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>.","ieee":"E. J. Dell, B. Capozzi, J. Xia, L. Venkataraman, and L. M. Campos, “Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes,” <i>Nature Chemistry</i>, vol. 7, no. 3. Springer Nature, pp. 209–214, 2015.","short":"E.J. Dell, B. Capozzi, J. Xia, L. Venkataraman, L.M. Campos, Nature Chemistry 7 (2015) 209–214.","ama":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. 2015;7(3):209-214. doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>"},"day":"02","intvolume":"         7","doi":"10.1038/nchem.2160","abstract":[{"lang":"eng","text":"To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials."}],"article_processing_charge":"No","status":"public","date_published":"2015-02-02T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Emma J.","last_name":"Dell","full_name":"Dell, Emma J."},{"first_name":"Brian","full_name":"Capozzi, Brian","last_name":"Capozzi"},{"first_name":"Jianlong","last_name":"Xia","full_name":"Xia, Jianlong"},{"first_name":"Latha","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","last_name":"Venkataraman"},{"last_name":"Campos","full_name":"Campos, Luis M.","first_name":"Luis M."}],"external_id":{"pmid":["25698329"]},"extern":"1","volume":7,"publication":"Nature Chemistry","page":"209-214","language":[{"iso":"eng"}],"issue":"3","year":"2015","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"_id":"17976","pmid":1,"title":"Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes","date_updated":"2025-01-02T13:35:46Z","OA_type":"closed access","month":"02","article_type":"original","publication_status":"published","publisher":"Springer Nature","type":"journal_article","oa_version":"None"},{"date_updated":"2021-01-12T06:53:18Z","title":"Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway","abstract":[{"text":"Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.","lang":"eng"}],"_id":"1803","intvolume":"       112","doi":"10.1073/pnas.1415845112","quality_controlled":0,"citation":{"ista":"Rei D, Mason X, Seo J, Gräff J, Rudenko A, Wang J, Rueda R, Siegert S, Cho S, Canter R, Mungenast A, Deisseroth K, Tsai L. 2015. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. PNAS. 112(23), 7291–7296.","apa":"Rei, D., Mason, X., Seo, J., Gräff, J., Rudenko, A., Wang, J., … Tsai, L. (2015). Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1415845112\">https://doi.org/10.1073/pnas.1415845112</a>","mla":"Rei, Damien, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” <i>PNAS</i>, vol. 112, no. 23, National Academy of Sciences, 2015, pp. 7291–96, doi:<a href=\"https://doi.org/10.1073/pnas.1415845112\">10.1073/pnas.1415845112</a>.","chicago":"Rei, Damien, Xenos Mason, Jinsoo Seo, Johannes Gräff, Andrii Rudenko, Jùn Wang, Richard Rueda, et al. “Basolateral Amygdala Bidirectionally Modulates Stress Induced Hippocampal Learning and Memory Deficits through a P25/Cdk5-Dependent Pathway.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1415845112\">https://doi.org/10.1073/pnas.1415845112</a>.","ama":"Rei D, Mason X, Seo J, et al. Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. <i>PNAS</i>. 2015;112(23):7291-7296. doi:<a href=\"https://doi.org/10.1073/pnas.1415845112\">10.1073/pnas.1415845112</a>","ieee":"D. Rei <i>et al.</i>, “Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway,” <i>PNAS</i>, vol. 112, no. 23. National Academy of Sciences, pp. 7291–7296, 2015.","short":"D. Rei, X. Mason, J. Seo, J. Gräff, A. Rudenko, J. Wang, R. Rueda, S. Siegert, S. Cho, R. Canter, A. Mungenast, K. Deisseroth, L. Tsai, PNAS 112 (2015) 7291–7296."},"date_created":"2018-12-11T11:54:06Z","day":"09","type":"journal_article","publication_status":"published","publisher":"National Academy of Sciences","year":"2015","publication":"PNAS","page":"7291 - 7296","issue":"23","date_published":"2015-06-09T00:00:00Z","month":"06","volume":112,"publist_id":"5307","extern":1,"author":[{"full_name":"Rei, Damien","last_name":"Rei","first_name":"Damien"},{"full_name":"Mason, Xenos","last_name":"Mason","first_name":"Xenos"},{"full_name":"Seo, Jinsoo","last_name":"Seo","first_name":"Jinsoo"},{"first_name":"Johannes","full_name":"Gräff, Johannes","last_name":"Gräff"},{"first_name":"Andrii","last_name":"Rudenko","full_name":"Rudenko, Andrii"},{"full_name":"Wang, Jùn","last_name":"Wang","first_name":"Jùn"},{"full_name":"Rueda, Richard","last_name":"Rueda","first_name":"Richard"},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","full_name":"Sandra Siegert","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cho","full_name":"Cho, Sukhee","first_name":"Sukhee"},{"full_name":"Canter, Rebecca G","last_name":"Canter","first_name":"Rebecca"},{"full_name":"Mungenast, Alison E","last_name":"Mungenast","first_name":"Alison"},{"first_name":"Karl","last_name":"Deisseroth","full_name":"Deisseroth, Karl A"},{"first_name":"Lihuei","last_name":"Tsai","full_name":"Tsai, Lihuei"}],"acknowledgement":"AG047661; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nNS051874; NIH; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung\nSNSF; Schweizerische Nationalfonds zur Förderung der Wissenschaftlichen Forschung","status":"public"},{"month":"06","type":"journal_article","publication_status":"published","publisher":"Nature Publishing Group","oa_version":"Published Version","isi":1,"_id":"1804","department":[{"_id":"BjHo"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","date_updated":"2025-09-29T10:58:13Z","status":"public","pubrep_id":"450","date_published":"2015-06-12T00:00:00Z","file":[{"date_created":"2018-12-12T10:17:26Z","access_level":"open_access","content_type":"application/pdf","checksum":"7716f582f8c9d82d8f2bf80bf896b440","file_size":2449723,"file_name":"IST-2016-450-v1+1_srep10781.pdf","relation":"main_file","file_id":"5280","creator":"system","date_updated":"2020-07-14T12:45:16Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Sebastian","orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"first_name":"Ying","full_name":"Lai, Ying","last_name":"Lai"}],"external_id":{"isi":["000356150200001"]},"publist_id":"5306","volume":5,"publication":"Scientific Reports","language":[{"iso":"eng"}],"year":"2015","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T11:54:06Z","citation":{"short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015.","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>","ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>.","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>, vol. 5, 10781, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>."},"corr_author":"1","day":"12","intvolume":"         5","doi":"10.1038/srep10781","license":"https://creativecommons.org/licenses/by/4.0/","ddc":["530"],"abstract":[{"lang":"eng","text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control."}],"file_date_updated":"2020-07-14T12:45:16Z","oa":1,"article_processing_charge":"No","article_number":"10781","has_accepted_license":"1"},{"oa_version":"Preprint","publisher":"EDP Sciences","type":"journal_article","publication_status":"published","arxiv":1,"month":"05","main_file_link":[{"url":"http://arxiv.org/abs/1401.1727","open_access":"1"}],"date_updated":"2025-09-23T10:45:09Z","title":"Sharp interface limit for two components Bose-Einstein condensates","department":[{"_id":"RoSe"}],"_id":"1807","isi":1,"year":"2015","issue":"3","publication":"ESAIM - Control, Optimisation and Calculus of Variations","language":[{"iso":"eng"}],"page":"603 - 624","volume":21,"publist_id":"5303","external_id":{"isi":["000356012000001"],"arxiv":["1401.1727"]},"author":[{"first_name":"Michael","last_name":"Goldman","full_name":"Goldman, Michael"},{"full_name":"Royo-Letelier, Jimena","last_name":"Royo-Letelier","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","first_name":"Jimena"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-05-01T00:00:00Z","status":"public","article_processing_charge":"No","oa":1,"abstract":[{"lang":"eng","text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential."}],"doi":"10.1051/cocv/2014040","intvolume":"        21","day":"01","corr_author":"1","citation":{"ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. 2015;21(3):603-624. doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>","ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624.","apa":"Goldman, M., &#38; Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences, 2015. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>.","mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>."},"date_created":"2018-12-11T11:54:07Z","quality_controlled":"1","scopus_import":"1"},{"external_id":{"isi":["000354789200001"]},"author":[{"full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"volume":25,"publist_id":"5302","month":"05","date_published":"2015-05-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","year":"2015","oa_version":"None","publisher":"ACM","publication_status":"published","type":"journal_article","issue":"2","language":[{"iso":"eng"}],"publication":"ACM Transactions on Modeling and Computer Simulation","doi":"10.1145/2745799","intvolume":"        25","_id":"1808","day":"01","isi":1,"scopus_import":"1","date_created":"2018-12-11T11:54:07Z","quality_controlled":"1","citation":{"ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 7, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>.","apa":"Gupta, A., &#38; Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>.","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7."},"article_processing_charge":"No","date_updated":"2025-09-23T09:11:51Z","article_number":"7","title":"Guest editors' introduction to special issue on computational methods in systems biology","department":[{"_id":"ToHe"}]},{"month":"05","publisher":"Public Library of Science","publication_status":"published","type":"journal_article","oa_version":"Published Version","_id":"1809","isi":1,"date_updated":"2025-09-23T09:21:54Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"NiBa"}],"title":"Indirect genetic effects and the dynamics of social interactions","date_published":"2015-05-18T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"creator":"system","file_id":"4730","relation":"main_file","date_updated":"2020-07-14T12:45:17Z","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:09:07Z","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","file_size":2748982}],"pubrep_id":"453","author":[{"first_name":"Barbora","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"external_id":{"isi":["000354917300064"]},"publist_id":"5299","volume":10,"status":"public","year":"2015","publication":"PLoS One","language":[{"iso":"eng"}],"issue":"5","intvolume":"        10","related_material":{"record":[{"relation":"research_data","status":"public","id":"9715"},{"status":"public","relation":"research_data","id":"9772"}]},"doi":"10.1371/journal.pone.0126907","scopus_import":"1","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>"},"date_created":"2018-12-11T11:54:07Z","quality_controlled":"1","day":"18","corr_author":"1","article_processing_charge":"No","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"ddc":["570","576"],"file_date_updated":"2020-07-14T12:45:17Z","oa":1},{"date_updated":"2025-09-23T07:55:38Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"ToBo"}],"title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","ec_funded":1,"_id":"1810","isi":1,"oa_version":"Published Version","publication_status":"published","type":"journal_article","publisher":"Elsevier","month":"06","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22"},{"grant_number":"303507","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2020-07-14T12:45:17Z","oa":1,"abstract":[{"text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.","lang":"eng"}],"ddc":["570"],"doi":"10.1016/j.mib.2015.05.008","intvolume":"        27","corr_author":"1","day":"01","scopus_import":"1","date_created":"2018-12-11T11:54:08Z","quality_controlled":"1","citation":{"mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>, vol. 27, Elsevier, 2015, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>.","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>.","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>","ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. 2015;27:1-9. doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>","ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” <i>Current Opinion in Microbiology</i>, vol. 27. Elsevier, pp. 1–9, 2015.","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9."},"year":"2015","page":"1 - 9","publication":"Current Opinion in Microbiology","language":[{"iso":"eng"}],"external_id":{"isi":["000365065400003"]},"author":[{"first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"volume":27,"publist_id":"5298","date_published":"2015-06-01T00:00:00Z","pubrep_id":"493","file":[{"checksum":"1683bb0f42ef892a5b3b71a050d65d25","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:17:23Z","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","file_size":1047255,"creator":"system","file_id":"5277","relation":"main_file","date_updated":"2020-07-14T12:45:17Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public"},{"publist_id":"5295","volume":56,"external_id":{"isi":["000355920800016"],"arxiv":["1409.0110"]},"author":[{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","full_name":"Safari, Laleh"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"},{"first_name":"Pedro","last_name":"Amaro","full_name":"Amaro, Pedro"},{"last_name":"Jänkälä","full_name":"Jänkälä, Kari","first_name":"Kari"},{"first_name":"Filippo","last_name":"Fratini","full_name":"Fratini, Filippo"}],"date_published":"2015-05-20T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","status":"public","year":"2015","issue":"5","language":[{"iso":"eng"}],"publication":"Journal of Mathematical Physics","doi":"10.1063/1.4921227","intvolume":"        56","day":"20","corr_author":"1","citation":{"ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5. American Institute of Physics, 2015.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. 2015;56(5). doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., &#38; Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>.","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>.","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105."},"date_created":"2018-12-11T11:54:08Z","scopus_import":"1","article_number":"052105","article_processing_charge":"No","oa":1,"abstract":[{"lang":"eng","text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms."}],"month":"05","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"oa_version":"Preprint","publication_status":"published","type":"journal_article","publisher":"American Institute of Physics","arxiv":1,"_id":"1811","ec_funded":1,"isi":1,"date_updated":"2025-09-23T07:53:00Z","title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","department":[{"_id":"MiLe"}]},{"_id":"1812","isi":1,"date_updated":"2025-09-23T08:45:19Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","department":[{"_id":"MiLe"}],"month":"04","oa_version":"Published Version","type":"journal_article","publisher":"IOP Publishing","publication_status":"published","doi":"10.1088/1367-2630/17/4/045005","intvolume":"        17","day":"01","scopus_import":"1","citation":{"ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” <i>New Journal of Physics</i>, vol. 17, no. 4. IOP Publishing, 2015.","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. 2015;17(4). doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>.","apa":"Lahrz, M., Lemeshko, M., &#38; Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>","mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>, vol. 17, no. 4, 045005, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>.","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005."},"date_created":"2018-12-11T11:54:09Z","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","article_number":"045005","file_date_updated":"2020-07-14T12:45:17Z","oa":1,"abstract":[{"text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n","lang":"eng"}],"ddc":["530"],"external_id":{"isi":["000354022400001"]},"author":[{"first_name":"Martin","full_name":"Lahrz, Martin","last_name":"Lahrz"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"first_name":"Ludwig","full_name":"Mathey, Ludwig","last_name":"Mathey"}],"publist_id":"5294","volume":17,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"446","date_published":"2015-04-01T00:00:00Z","file":[{"date_updated":"2020-07-14T12:45:17Z","file_id":"5184","creator":"system","relation":"main_file","file_name":"IST-2016-446-v1+1_document.pdf","file_size":1900925,"checksum":"551f751a75b39b89a1db2f7f498f9a49","date_created":"2018-12-12T10:15:59Z","content_type":"application/pdf","access_level":"open_access"}],"status":"public","year":"2015","issue":"4","language":[{"iso":"eng"}],"publication":"New Journal of Physics"},{"abstract":[{"text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.","lang":"eng"}],"oa":1,"article_number":"203001","article_processing_charge":"No","citation":{"ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. 2015;114(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>","short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” <i>Physical Review Letters</i>, vol. 114, no. 20. American Physical Society, 2015.","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>.","apa":"Schmidt, R., &#38; Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>.","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001."},"date_created":"2018-12-11T11:54:09Z","quality_controlled":"1","scopus_import":"1","day":"18","corr_author":"1","intvolume":"       114","doi":"10.1103/PhysRevLett.114.203001","publication":"Physical Review Letters","language":[{"iso":"eng"}],"issue":"20","year":"2015","status":"public","date_published":"2015-05-18T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5293","volume":114,"author":[{"last_name":"Schmidt","full_name":"Schmidt, Richard","first_name":"Richard"},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1502.03447"],"isi":["000354969900003"]},"title":"Rotation of quantum impurities in the presence of a many-body environment","department":[{"_id":"MiLe"}],"date_updated":"2025-09-23T10:40:28Z","isi":1,"_id":"1813","arxiv":1,"publisher":"American Physical Society","type":"journal_article","publication_status":"published","oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"month":"05"},{"_id":"1814","ec_funded":1,"isi":1,"date_updated":"2025-09-29T11:05:55Z","department":[{"_id":"ChWo"}],"title":"Water wave animation via wavefront parameter interpolation","project":[{"call_identifier":"FWF","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425"},{"grant_number":"638176","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"month":"04","oa_version":"Submitted Version","type":"journal_article","publication_status":"published","publisher":"ACM","doi":"10.1145/2714572","intvolume":"        34","corr_author":"1","day":"01","date_created":"2018-12-11T11:54:09Z","citation":{"short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3. ACM, 2015.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. 2015;34(3). doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3, 27, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>.","apa":"Jeschke, S., &#38; Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27."},"quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","article_number":"27","article_processing_charge":"No","oa":1,"file_date_updated":"2020-07-14T12:45:17Z","abstract":[{"text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.","lang":"eng"}],"ddc":["000"],"volume":34,"publist_id":"5292","external_id":{"isi":["000354800700004"]},"author":[{"first_name":"Stefan","full_name":"Jeschke, Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"pubrep_id":"575","date_published":"2015-04-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"relation":"main_file","file_id":"4933","creator":"system","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:12:15Z","content_type":"application/pdf","access_level":"open_access","checksum":"67c9f4fa370def68cdf31299e48bc91f","file_size":23712153,"file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf"}],"status":"public","year":"2015","issue":"3","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics"},{"title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","department":[{"_id":"CaHe"}],"date_updated":"2025-09-29T11:07:11Z","isi":1,"pmid":1,"_id":"1817","oa_version":"Submitted Version","publisher":"Nature Publishing Group","type":"journal_article","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"month":"03","oa":1,"abstract":[{"text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. ","lang":"eng"}],"article_processing_charge":"No","corr_author":"1","day":"16","scopus_import":"1","citation":{"short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","ieee":"S. Porazinski <i>et al.</i>, “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” <i>Nature</i>, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. 2015;521(7551):217-221. doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>.","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221."},"date_created":"2018-12-11T11:54:10Z","quality_controlled":"1","doi":"10.1038/nature14215","intvolume":"       521","issue":"7551","language":[{"iso":"eng"}],"publication":"Nature","page":"217 - 221","year":"2015","status":"public","author":[{"full_name":"Porazinski, Sean","last_name":"Porazinski","first_name":"Sean"},{"full_name":"Wang, Huijia","last_name":"Wang","first_name":"Huijia"},{"first_name":"Yoichi","full_name":"Asaoka, Yoichi","last_name":"Asaoka"},{"first_name":"Martin","full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Miyamoto, Tatsuo","last_name":"Miyamoto","first_name":"Tatsuo"},{"full_name":"Morita, Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi"},{"full_name":"Hata, Shoji","last_name":"Hata","first_name":"Shoji"},{"last_name":"Sasaki","full_name":"Sasaki, Takashi","first_name":"Takashi"},{"orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"first_name":"Yumi","full_name":"Osada, Yumi","last_name":"Osada"},{"first_name":"Satoshi","last_name":"Asaka","full_name":"Asaka, Satoshi"},{"first_name":"Akihiro","full_name":"Momoi, Akihiro","last_name":"Momoi"},{"first_name":"Sarah","full_name":"Linton, Sarah","last_name":"Linton"},{"last_name":"Miesfeld","full_name":"Miesfeld, Joel","first_name":"Joel"},{"last_name":"Link","full_name":"Link, Brian","first_name":"Brian"},{"full_name":"Senga, Takeshi","last_name":"Senga","first_name":"Takeshi"},{"full_name":"Castillo Morales, Atahualpa","last_name":"Castillo Morales","first_name":"Atahualpa"},{"last_name":"Urrutia","full_name":"Urrutia, Araxi","first_name":"Araxi"},{"full_name":"Shimizu, Nobuyoshi","last_name":"Shimizu","first_name":"Nobuyoshi"},{"first_name":"Hideaki","last_name":"Nagase","full_name":"Nagase, Hideaki"},{"full_name":"Matsuura, Shinya","last_name":"Matsuura","first_name":"Shinya"},{"full_name":"Bagby, Stefan","last_name":"Bagby","first_name":"Stefan"},{"first_name":"Hisato","last_name":"Kondoh","full_name":"Kondoh, Hisato"},{"last_name":"Nishina","full_name":"Nishina, Hiroshi","first_name":"Hiroshi"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Makoto","last_name":"Furutani Seiki","full_name":"Furutani Seiki, Makoto"}],"external_id":{"isi":["000354377800058"],"pmid":["25778702"]},"publist_id":"5289","volume":521,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-03-16T00:00:00Z"},{"isi":1,"pmid":1,"_id":"1818","ec_funded":1,"title":"Limits to adaptation along environmental gradients","department":[{"_id":"NiBa"}],"date_updated":"2025-09-23T09:27:16Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"month":"05","project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","publication_status":"published","publisher":"National Academy of Sciences","type":"journal_article","corr_author":"1","day":"19","citation":{"ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>.","apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406."},"date_created":"2018-12-11T11:54:11Z","quality_controlled":"1","scopus_import":"1","doi":"10.1073/pnas.1421515112","intvolume":"       112","oa":1,"abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"article_processing_charge":"No","status":"public","volume":112,"publist_id":"5288","external_id":{"pmid":["25941385"],"isi":["000354729500058"]},"author":[{"orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-05-19T00:00:00Z","issue":"20","publication":"PNAS","language":[{"iso":"eng"}],"page":"6401 - 6406","year":"2015"},{"abstract":[{"text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.","lang":"eng"}],"article_processing_charge":"No","date_created":"2018-12-11T11:54:11Z","quality_controlled":"1","citation":{"apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., &#38; Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>.","chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>.","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. 2015;8(8):1175-1187. doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187.","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” <i>Molecular Plant</i>, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015."},"scopus_import":"1","corr_author":"1","day":"03","intvolume":"         8","doi":"10.1016/j.molp.2015.03.007","publication":"Molecular Plant","page":"1175 - 1187","language":[{"iso":"eng"}],"issue":"8","year":"2015","status":"public","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-08-03T00:00:00Z","volume":8,"publist_id":"5287","author":[{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"first_name":"Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596"}],"external_id":{"isi":["000359136100006"]},"title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","department":[{"_id":"JiFr"}],"date_updated":"2025-09-23T09:47:17Z","isi":1,"_id":"1819","ec_funded":1,"publisher":"Elsevier","publication_status":"published","type":"journal_article","oa_version":"None","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"month":"08"}]