[{"citation":{"chicago":"Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2015. https://doi.org/10.1002/2015jd023137.","ista":"Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.","mla":"Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8, American Geophysical Union, 2015, pp. 3139–57, doi:10.1002/2015jd023137.","apa":"Ayala, A., Pellicciotti, F., & Shea, J. M. (2015). Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/2015jd023137","ama":"Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 2015;120(8):3139-3157. doi:10.1002/2015jd023137","short":"A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres 120 (2015) 3139–3157.","ieee":"A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming,” Journal of Geophysical Research: Atmospheres, vol. 120, no. 8. American Geophysical Union, pp. 3139–3157, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"A.","full_name":"Ayala, A.","last_name":"Ayala"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"},{"last_name":"Shea","full_name":"Shea, J. M.","first_name":"J. M."}],"article_processing_charge":"No","title":"Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming","year":"2015","day":"18","publication":"Journal of Geophysical Research: Atmospheres","page":"3139-3157","date_published":"2015-04-18T00:00:00Z","doi":"10.1002/2015jd023137","date_created":"2023-02-20T08:16:28Z","quality_controlled":"1","publisher":"American Geophysical Union","date_updated":"2023-02-24T09:16:26Z","extern":"1","_id":"12631","type":"journal_article","article_type":"original","status":"public","keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"publication_identifier":{"eissn":["2169-8996"],"issn":["2169-897X"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"8","volume":120,"abstract":[{"lang":"eng","text":"Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 120"},{"quality_controlled":"1","publisher":"Taylor & Francis","oa":1,"page":"174-200","date_published":"2015-04-18T00:00:00Z","doi":"10.1080/07900627.2015.1020417","date_created":"2023-02-20T08:16:17Z","year":"2015","day":"18","publication":"International Journal of Water Resources Development","author":[{"last_name":"Shea","full_name":"Shea, J.M.","first_name":"J.M."},{"first_name":"P.","last_name":"Wagnon","full_name":"Wagnon, P."},{"last_name":"Immerzeel","full_name":"Immerzeel, W.W.","first_name":"W.W."},{"first_name":"R.","last_name":"Biron","full_name":"Biron, R."},{"first_name":"F.","full_name":"Brun, F.","last_name":"Brun"},{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"}],"article_processing_charge":"No","title":"A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya","citation":{"mla":"Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development, vol. 31, no. 2, Taylor & Francis, 2015, pp. 174–200, doi:10.1080/07900627.2015.1020417.","ieee":"J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” International Journal of Water Resources Development, vol. 31, no. 2. Taylor & Francis, pp. 174–200, 2015.","short":"J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200.","apa":"Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., & Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. Taylor & Francis. https://doi.org/10.1080/07900627.2015.1020417","ama":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 2015;31(2):174-200. doi:10.1080/07900627.2015.1020417","chicago":"Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” International Journal of Water Resources Development. Taylor & Francis, 2015. https://doi.org/10.1080/07900627.2015.1020417.","ista":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1080/07900627.2015.1020417","open_access":"1"}],"month":"04","intvolume":" 31","abstract":[{"text":"Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region.","lang":"eng"}],"oa_version":"Published Version","issue":"2","volume":31,"publication_identifier":{"eissn":["1360-0648"],"issn":["0790-0627"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","keyword":["Water Science and Technology","Development"],"_id":"12629","date_updated":"2023-02-24T09:30:42Z","extern":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Steiner, Jakob F., Francesca Pellicciotti, Pascal Buri, Evan S. Miles, Walter W. Immerzeel, and Tim D. Reid. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j194.","ista":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. 2015. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 61(229), 889–907.","mla":"Steiner, Jakob F., et al. “Modelling Ice-Cliff Backwasting on a Debris-Covered Glacier in the Nepalese Himalaya.” Journal of Glaciology, vol. 61, no. 229, International Glaciological Society, 2015, pp. 889–907, doi:10.3189/2015jog14j194.","ieee":"J. F. Steiner, F. Pellicciotti, P. Buri, E. S. Miles, W. W. Immerzeel, and T. D. Reid, “Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya,” Journal of Glaciology, vol. 61, no. 229. International Glaciological Society, pp. 889–907, 2015.","short":"J.F. Steiner, F. Pellicciotti, P. Buri, E.S. Miles, W.W. Immerzeel, T.D. Reid, Journal of Glaciology 61 (2015) 889–907.","ama":"Steiner JF, Pellicciotti F, Buri P, Miles ES, Immerzeel WW, Reid TD. Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. 2015;61(229):889-907. doi:10.3189/2015jog14j194","apa":"Steiner, J. F., Pellicciotti, F., Buri, P., Miles, E. S., Immerzeel, W. W., & Reid, T. D. (2015). Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j194"},"title":"Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya","author":[{"last_name":"Steiner","full_name":"Steiner, Jakob F.","first_name":"Jakob F."},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"},{"first_name":"Pascal","last_name":"Buri","full_name":"Buri, Pascal"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"first_name":"Walter W.","full_name":"Immerzeel, Walter W.","last_name":"Immerzeel"},{"first_name":"Tim D.","last_name":"Reid","full_name":"Reid, Tim D."}],"article_processing_charge":"No","day":"01","publication":"Journal of Glaciology","year":"2015","doi":"10.3189/2015jog14j194","date_published":"2015-07-01T00:00:00Z","date_created":"2023-02-20T08:16:01Z","page":"889-907","quality_controlled":"1","publisher":"International Glaciological Society","oa":1,"extern":"1","date_updated":"2023-02-24T09:43:14Z","_id":"12626","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"publication_status":"published","volume":61,"issue":"229","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%."}],"month":"07","intvolume":" 61","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.3189/2015JoG14J194","open_access":"1"}]},{"_id":"12627","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-02-24T09:40:30Z","extern":"1","abstract":[{"lang":"eng","text":"Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3189/2015JoG14J227"}],"scopus_import":"1","intvolume":" 61","month":"05","publication_status":"published","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"language":[{"iso":"eng"}],"volume":61,"issue":"227","citation":{"chicago":"Herreid, Sam, Francesca Pellicciotti, Alvaro Ayala, Anna Chesnokova, Christian Kienholz, Joseph Shea, and Arun Shrestha. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology. International Glaciological Society, 2015. https://doi.org/10.3189/2015jog14j227.","ista":"Herreid S, Pellicciotti F, Ayala A, Chesnokova A, Kienholz C, Shea J, Shrestha A. 2015. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 61(227), 524–536.","mla":"Herreid, Sam, et al. “Satellite Observations Show No Net Change in the Percentage of Supraglacial Debris-Covered Area in Northern Pakistan from 1977 to 2014.” Journal of Glaciology, vol. 61, no. 227, International Glaciological Society, 2015, pp. 524–36, doi:10.3189/2015jog14j227.","ieee":"S. Herreid et al., “Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014,” Journal of Glaciology, vol. 61, no. 227. International Glaciological Society, pp. 524–536, 2015.","short":"S. Herreid, F. Pellicciotti, A. Ayala, A. Chesnokova, C. Kienholz, J. Shea, A. Shrestha, Journal of Glaciology 61 (2015) 524–536.","apa":"Herreid, S., Pellicciotti, F., Ayala, A., Chesnokova, A., Kienholz, C., Shea, J., & Shrestha, A. (2015). Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. International Glaciological Society. https://doi.org/10.3189/2015jog14j227","ama":"Herreid S, Pellicciotti F, Ayala A, et al. Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014. Journal of Glaciology. 2015;61(227):524-536. doi:10.3189/2015jog14j227"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Sam","full_name":"Herreid, Sam","last_name":"Herreid"},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"last_name":"Ayala","full_name":"Ayala, Alvaro","first_name":"Alvaro"},{"first_name":"Anna","last_name":"Chesnokova","full_name":"Chesnokova, Anna"},{"first_name":"Christian","last_name":"Kienholz","full_name":"Kienholz, Christian"},{"first_name":"Joseph","full_name":"Shea, Joseph","last_name":"Shea"},{"full_name":"Shrestha, Arun","last_name":"Shrestha","first_name":"Arun"}],"title":"Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014","oa":1,"publisher":"International Glaciological Society","quality_controlled":"1","year":"2015","publication":"Journal of Glaciology","day":"01","page":"524-536","date_created":"2023-02-20T08:16:06Z","doi":"10.3189/2015jog14j227","date_published":"2015-05-01T00:00:00Z"},{"department":[{"_id":"MiSi"}],"date_updated":"2023-03-30T11:32:57Z","status":"public","type":"journal_article","_id":"1618","ec_funded":1,"issue":"27","volume":54,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 54","month":"06","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed."}],"title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","article_processing_charge":"No","external_id":{"pmid":["26115234"]},"publist_id":"5548","author":[{"full_name":"Veldkamp, Christopher","last_name":"Veldkamp","first_name":"Christopher"},{"last_name":"Kiermaier","full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","first_name":"Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Skylar","full_name":"Gabel Eissens, Skylar","last_name":"Gabel Eissens"},{"first_name":"Miranda","full_name":"Gillitzer, Miranda","last_name":"Gillitzer"},{"full_name":"Lippner, David","last_name":"Lippner","first_name":"David"},{"full_name":"Disilvio, Frank","last_name":"Disilvio","first_name":"Frank"},{"first_name":"Casey","last_name":"Mueller","full_name":"Mueller, Casey"},{"first_name":"Paeton","last_name":"Wantuch","full_name":"Wantuch, Paeton"},{"last_name":"Chaffee","full_name":"Chaffee, Gary","first_name":"Gary"},{"last_name":"Famiglietti","full_name":"Famiglietti, Michael","first_name":"Michael"},{"first_name":"Danielle","last_name":"Zgoba","full_name":"Zgoba, Danielle"},{"full_name":"Bailey, Asha","last_name":"Bailey","first_name":"Asha"},{"last_name":"Bah","full_name":"Bah, Yaya","first_name":"Yaya"},{"last_name":"Engebretson","full_name":"Engebretson, Samantha","first_name":"Samantha"},{"first_name":"David","full_name":"Graupner, David","last_name":"Graupner"},{"full_name":"Lackner, Emily","last_name":"Lackner","first_name":"Emily"},{"first_name":"Vincent","last_name":"Larosa","full_name":"Larosa, Vincent"},{"first_name":"Tysha","full_name":"Medeiros, Tysha","last_name":"Medeiros"},{"first_name":"Michael","last_name":"Olson","full_name":"Olson, Michael"},{"first_name":"Andrew","last_name":"Phillips","full_name":"Phillips, Andrew"},{"last_name":"Pyles","full_name":"Pyles, Harley","first_name":"Harley"},{"first_name":"Amanda","full_name":"Richard, Amanda","last_name":"Richard"},{"last_name":"Schoeller","full_name":"Schoeller, Scott","first_name":"Scott"},{"first_name":"Boris","last_name":"Touzeau","full_name":"Touzeau, Boris"},{"last_name":"Williams","full_name":"Williams, Larry","first_name":"Larry"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Peterson","full_name":"Peterson, Francis","first_name":"Francis"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:10.1021/acs.biochem.5b00560.","ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 2015;54(27):4163-4166. doi:10.1021/acs.biochem.5b00560","apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. American Chemical Society. https://doi.org/10.1021/acs.biochem.5b00560","ieee":"C. Veldkamp et al., “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” Biochemistry, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.","chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” Biochemistry. American Chemical Society, 2015. https://doi.org/10.1021/acs.biochem.5b00560.","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166."},"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"}],"date_created":"2018-12-11T11:53:03Z","doi":"10.1021/acs.biochem.5b00560","date_published":"2015-06-26T00:00:00Z","page":"4163 - 4166","publication":"Biochemistry","day":"26","year":"2015","oa":1,"publisher":"American Chemical Society","quality_controlled":"1"},{"ec_funded":1,"file":[{"date_created":"2023-05-02T07:02:59Z","file_name":"2015_ECAL_Martius.pdf","creator":"dernst","date_updated":"2023-05-02T07:02:59Z","file_size":1674241,"file_id":"12882","checksum":"880eabe59c9df12f06a882aa1bc4e600","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9780262330275"]},"publication_status":"published","month":"07","scopus_import":"1","oa_version":"Published Version","file_date_updated":"2023-05-02T07:02:59Z","department":[{"_id":"ChLa"}],"ddc":["000"],"date_updated":"2023-05-02T07:06:21Z","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"ECAL: European Conference on Artificial Life","start_date":"2015-07-20","location":"York, United Kingdom","end_date":"2015-07-24"},"_id":"12881","date_published":"2015-07-01T00:00:00Z","doi":"10.7551/978-0-262-33027-5-ch018","date_created":"2023-04-30T22:01:07Z","page":"78","day":"01","publication":"Proceedings of the 13th European Conference on Artificial Life","has_accepted_license":"1","year":"2015","quality_controlled":"1","publisher":"MIT Press","oa":1,"acknowledgement":"This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734).","title":"Quantifying self-organizing behavior of autonomous robots","author":[{"last_name":"Martius","full_name":"Martius, Georg S","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eckehard","full_name":"Olbrich, Eckehard","last_name":"Olbrich"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018.","ama":"Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: Proceedings of the 13th European Conference on Artificial Life. MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In Proceedings of the 13th European Conference on Artificial Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018","ieee":"G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in Proceedings of the 13th European Conference on Artificial Life, York, United Kingdom, 2015, p. 78.","short":"G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78.","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018.","ista":"Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78."},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcv087","ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623. doi:10.1093/pcp/pcv087","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623.","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.","ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.","chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087."},"title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","article_processing_charge":"No","external_id":{"pmid":["26063389"]},"author":[{"first_name":"Kaeli C.M.","full_name":"Johnson, Kaeli C.M.","last_name":"Johnson"},{"first_name":"Shitou","last_name":"Xia","full_name":"Xia, Shitou"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Li, Xin","last_name":"Li","first_name":"Xin"}],"publication":"Plant and Cell Physiology","year":"2015","date_created":"2023-01-16T09:20:22Z","doi":"10.1093/pcp/pcv087","date_published":"2015-08-01T00:00:00Z","page":"1616-1623","acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","publisher":"Oxford University Press","quality_controlled":"1","extern":"1","date_updated":"2023-05-08T11:03:23Z","department":[{"_id":"XiFe"}],"_id":"12196","keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0032-0781","1471-9053"]},"volume":56,"issue":"8","pmid":1,"oa_version":"None","abstract":[{"text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity.","lang":"eng"}],"intvolume":" 56","month":"08","scopus_import":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zhao, Hui, et al. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology, vol. 11, Springer Nature, 2015, pp. 82–88, doi:10.1038/nnano.2015.256.","apa":"Zhao, H., Sen, S., Udayabhaskararao, T., Sawczyk, M., Kučanda, K., Manna, D., … Klajn, R. (2015). Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/nnano.2015.256","ama":"Zhao H, Sen S, Udayabhaskararao T, et al. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 2015;11:82-88. doi:10.1038/nnano.2015.256","short":"H. Zhao, S. Sen, T. Udayabhaskararao, M. Sawczyk, K. Kučanda, D. Manna, P.K. Kundu, J.-W. Lee, P. Král, R. Klajn, Nature Nanotechnology 11 (2015) 82–88.","ieee":"H. Zhao et al., “Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks,” Nature Nanotechnology, vol. 11. Springer Nature, pp. 82–88, 2015.","chicago":"Zhao, Hui, Soumyo Sen, T. Udayabhaskararao, Michał Sawczyk, Kristina Kučanda, Debasish Manna, Pintu K. Kundu, Ji-Woong Lee, Petr Král, and Rafal Klajn. “Reversible Trapping and Reaction Acceleration within Dynamically Self-Assembling Nanoflasks.” Nature Nanotechnology. Springer Nature, 2015. https://doi.org/10.1038/nnano.2015.256.","ista":"Zhao H, Sen S, Udayabhaskararao T, Sawczyk M, Kučanda K, Manna D, Kundu PK, Lee J-W, Král P, Klajn R. 2015. Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks. Nature Nanotechnology. 11, 82–88."},"title":"Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks","external_id":{"pmid":["26595335"]},"article_processing_charge":"No","author":[{"first_name":"Hui","last_name":"Zhao","full_name":"Zhao, Hui"},{"last_name":"Sen","full_name":"Sen, Soumyo","first_name":"Soumyo"},{"last_name":"Udayabhaskararao","full_name":"Udayabhaskararao, T.","first_name":"T."},{"first_name":"Michał","last_name":"Sawczyk","full_name":"Sawczyk, Michał"},{"last_name":"Kučanda","full_name":"Kučanda, Kristina","first_name":"Kristina"},{"first_name":"Debasish","full_name":"Manna, Debasish","last_name":"Manna"},{"first_name":"Pintu K.","full_name":"Kundu, Pintu K.","last_name":"Kundu"},{"last_name":"Lee","full_name":"Lee, Ji-Woong","first_name":"Ji-Woong"},{"last_name":"Král","full_name":"Král, Petr","first_name":"Petr"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature Nanotechnology","day":"23","year":"2015","date_created":"2023-08-01T09:44:04Z","date_published":"2015-11-23T00:00:00Z","doi":"10.1038/nnano.2015.256","page":"82-88","_id":"13392","keyword":["Electrical and Electronic Engineering","Condensed Matter Physics","General Materials Science","Biomedical Engineering","Atomic and Molecular Physics","and Optics","Bioengineering"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-07T12:55:46Z","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution."}],"intvolume":" 11","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"volume":11},{"volume":7,"publication_status":"published","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 7","month":"07","abstract":[{"text":"The ability to guide the assembly of nanosized objects reversibly with external stimuli, in particular light, is of fundamental importance, and it contributes to the development of applications as diverse as nanofabrication and controlled drug delivery. However, all the systems described to date are based on nanoparticles (NPs) that are inherently photoresponsive, which makes their preparation cumbersome and can markedly hamper their performance. Here we describe a conceptually new methodology to assemble NPs reversibly using light that does not require the particles to be functionalized with light-responsive ligands. Our strategy is based on the use of a photoswitchable medium that responds to light in such a way that it modulates the interparticle interactions. NP assembly proceeds quantitatively and without apparent fatigue, both in solution and in gels. Exposing the gels to light in a spatially controlled manner allowed us to draw images that spontaneously disappeared after a specific period of time.","lang":"eng"}],"pmid":1,"oa_version":"None","date_updated":"2023-08-07T13:00:15Z","extern":"1","type":"journal_article","article_type":"original","keyword":["General Chemical Engineering","General Chemistry"],"status":"public","_id":"13394","page":"646-652","date_created":"2023-08-01T09:44:33Z","date_published":"2015-07-20T00:00:00Z","doi":"10.1038/nchem.2303","year":"2015","publication":"Nature Chemistry","day":"20","publisher":"Springer Nature","quality_controlled":"1","article_processing_charge":"No","external_id":{"pmid":["26201741"]},"author":[{"full_name":"Kundu, Pintu K.","last_name":"Kundu","first_name":"Pintu K."},{"last_name":"Samanta","full_name":"Samanta, Dipak","first_name":"Dipak"},{"first_name":"Ron","full_name":"Leizrowice, Ron","last_name":"Leizrowice"},{"full_name":"Margulis, Baruch","last_name":"Margulis","first_name":"Baruch"},{"last_name":"Zhao","full_name":"Zhao, Hui","first_name":"Hui"},{"last_name":"Börner","full_name":"Börner, Martin","first_name":"Martin"},{"full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao","first_name":"T."},{"first_name":"Debasish","last_name":"Manna","full_name":"Manna, Debasish"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"}],"title":"Light-controlled self-assembly of non-photoresponsive nanoparticles","citation":{"apa":"Kundu, P. K., Samanta, D., Leizrowice, R., Margulis, B., Zhao, H., Börner, M., … Klajn, R. (2015). Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. Springer Nature. https://doi.org/10.1038/nchem.2303","ama":"Kundu PK, Samanta D, Leizrowice R, et al. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 2015;7:646-652. doi:10.1038/nchem.2303","short":"P.K. Kundu, D. Samanta, R. Leizrowice, B. Margulis, H. Zhao, M. Börner, T. Udayabhaskararao, D. Manna, R. Klajn, Nature Chemistry 7 (2015) 646–652.","ieee":"P. K. Kundu et al., “Light-controlled self-assembly of non-photoresponsive nanoparticles,” Nature Chemistry, vol. 7. Springer Nature, pp. 646–652, 2015.","mla":"Kundu, Pintu K., et al. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry, vol. 7, Springer Nature, 2015, pp. 646–52, doi:10.1038/nchem.2303.","ista":"Kundu PK, Samanta D, Leizrowice R, Margulis B, Zhao H, Börner M, Udayabhaskararao T, Manna D, Klajn R. 2015. Light-controlled self-assembly of non-photoresponsive nanoparticles. Nature Chemistry. 7, 646–652.","chicago":"Kundu, Pintu K., Dipak Samanta, Ron Leizrowice, Baruch Margulis, Hui Zhao, Martin Börner, T. Udayabhaskararao, Debasish Manna, and Rafal Klajn. “Light-Controlled Self-Assembly of Non-Photoresponsive Nanoparticles.” Nature Chemistry. Springer Nature, 2015. https://doi.org/10.1038/nchem.2303."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes","author":[{"first_name":"Debasish","full_name":"Manna, Debasish","last_name":"Manna"},{"full_name":"Udayabhaskararao, Thumu","last_name":"Udayabhaskararao","first_name":"Thumu"},{"first_name":"Hui","full_name":"Zhao, Hui","last_name":"Zhao"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["25959725"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. 2015. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 54(42), 12394–12397.","chicago":"Manna, Debasish, Thumu Udayabhaskararao, Hui Zhao, and Rafal Klajn. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition. Wiley, 2015. https://doi.org/10.1002/anie.201502419.","apa":"Manna, D., Udayabhaskararao, T., Zhao, H., & Klajn, R. (2015). Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201502419","ama":"Manna D, Udayabhaskararao T, Zhao H, Klajn R. Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes. Angewandte Chemie International Edition. 2015;54(42):12394-12397. doi:10.1002/anie.201502419","ieee":"D. Manna, T. Udayabhaskararao, H. Zhao, and R. Klajn, “Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes,” Angewandte Chemie International Edition, vol. 54, no. 42. Wiley, pp. 12394–12397, 2015.","short":"D. Manna, T. Udayabhaskararao, H. Zhao, R. Klajn, Angewandte Chemie International Edition 54 (2015) 12394–12397.","mla":"Manna, Debasish, et al. “Orthogonal Light-Induced Self-Assembly of Nanoparticles Using Differently Substituted Azobenzenes.” Angewandte Chemie International Edition, vol. 54, no. 42, Wiley, 2015, pp. 12394–97, doi:10.1002/anie.201502419."},"doi":"10.1002/anie.201502419","date_published":"2015-10-01T00:00:00Z","date_created":"2023-08-01T09:44:19Z","page":"12394-12397","day":"01","publication":"Angewandte Chemie International Edition","year":"2015","publisher":"Wiley","quality_controlled":"1","extern":"1","date_updated":"2023-08-07T12:58:29Z","status":"public","keyword":["General Chemistry","Catalysis"],"type":"journal_article","article_type":"original","_id":"13393","volume":54,"issue":"42","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"publication_status":"published","month":"10","intvolume":" 54","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials (“frustrated” nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light."}]},{"citation":{"ista":"Lee J-W, Klajn R. 2015. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 51(11), 2036–2039.","chicago":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4cc08541h.","ama":"Lee J-W, Klajn R. Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. 2015;51(11):2036-2039. doi:10.1039/c4cc08541h","apa":"Lee, J.-W., & Klajn, R. (2015). Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/c4cc08541h","short":"J.-W. Lee, R. Klajn, Chemical Communications 51 (2015) 2036–2039.","ieee":"J.-W. Lee and R. Klajn, “Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2,” Chemical Communications, vol. 51, no. 11. Royal Society of Chemistry, pp. 2036–2039, 2015.","mla":"Lee, Ji-Woong, and Rafal Klajn. “Dual-Responsive Nanoparticles That Aggregate under the Simultaneous Action of Light and CO2.” Chemical Communications, vol. 51, no. 11, Royal Society of Chemistry, 2015, pp. 2036–39, doi:10.1039/c4cc08541h."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["25417754"]},"author":[{"first_name":"Ji-Woong","full_name":"Lee, Ji-Woong","last_name":"Lee"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"title":"Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","year":"2015","publication":"Chemical Communications","day":"18","page":"2036-2039","date_created":"2023-08-01T09:44:48Z","doi":"10.1039/c4cc08541h","date_published":"2015-11-18T00:00:00Z","_id":"13395","article_type":"original","type":"journal_article","keyword":["Materials Chemistry","Metals and Alloys","Surfaces","Coatings and Films","General Chemistry","Ceramics and Composites","Electronic","Optical and Magnetic Materials","Catalysis"],"status":"public","date_updated":"2023-08-07T13:01:53Z","extern":"1","abstract":[{"lang":"eng","text":"Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate."}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1039/C4CC08541H","open_access":"1"}],"scopus_import":"1","intvolume":" 51","month":"11","publication_status":"published","publication_identifier":{"eissn":["1364-548X"],"issn":["1359-7345"]},"language":[{"iso":"eng"}],"volume":51,"issue":"11"},{"publisher":"American Chemical Society","quality_controlled":"1","date_created":"2023-08-01T09:45:02Z","date_published":"2015-01-27T00:00:00Z","doi":"10.1021/la504291n","page":"1048-1057","publication":"Langmuir","day":"27","year":"2015","title":"Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature","article_processing_charge":"No","external_id":{"pmid":["25544061"]},"author":[{"first_name":"Thomas","full_name":"Moldt, Thomas","last_name":"Moldt"},{"last_name":"Brete","full_name":"Brete, Daniel","first_name":"Daniel"},{"first_name":"Daniel","last_name":"Przyrembel","full_name":"Przyrembel, Daniel"},{"full_name":"Das, Sanjib","last_name":"Das","first_name":"Sanjib"},{"last_name":"Goldman","full_name":"Goldman, Joel R.","first_name":"Joel R."},{"full_name":"Kundu, Pintu K.","last_name":"Kundu","first_name":"Pintu K."},{"full_name":"Gahl, Cornelius","last_name":"Gahl","first_name":"Cornelius"},{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"},{"last_name":"Weinelt","full_name":"Weinelt, Martin","first_name":"Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Moldt, Thomas, Daniel Brete, Daniel Przyrembel, Sanjib Das, Joel R. Goldman, Pintu K. Kundu, Cornelius Gahl, Rafal Klajn, and Martin Weinelt. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504291n.","ista":"Moldt T, Brete D, Przyrembel D, Das S, Goldman JR, Kundu PK, Gahl C, Klajn R, Weinelt M. 2015. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 31(3), 1048–1057.","mla":"Moldt, Thomas, et al. “Tailoring the Properties of Surface-Immobilized Azobenzenes by Monolayer Dilution and Surface Curvature.” Langmuir, vol. 31, no. 3, American Chemical Society, 2015, pp. 1048–57, doi:10.1021/la504291n.","ama":"Moldt T, Brete D, Przyrembel D, et al. Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. 2015;31(3):1048-1057. doi:10.1021/la504291n","apa":"Moldt, T., Brete, D., Przyrembel, D., Das, S., Goldman, J. R., Kundu, P. K., … Weinelt, M. (2015). Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature. Langmuir. American Chemical Society. https://doi.org/10.1021/la504291n","ieee":"T. Moldt et al., “Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature,” Langmuir, vol. 31, no. 3. American Chemical Society, pp. 1048–1057, 2015.","short":"T. Moldt, D. Brete, D. Przyrembel, S. Das, J.R. Goldman, P.K. Kundu, C. Gahl, R. Klajn, M. Weinelt, Langmuir 31 (2015) 1048–1057."},"intvolume":" 31","month":"01","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs."}],"volume":31,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5827"],"issn":["0743-7463"]},"keyword":["Electrochemistry","Spectroscopy","Surfaces and Interfaces","Condensed Matter Physics","General Materials Science"],"status":"public","type":"journal_article","article_type":"original","_id":"13396","extern":"1","date_updated":"2023-08-07T13:05:04Z"},{"_id":"13397","keyword":["Physical and Theoretical Chemistry"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2023-08-07T13:06:23Z","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light.","lang":"eng"}],"intvolume":" 181","month":"01","main_file_link":[{"url":"https://doi.org/10.1039/C4FD00265B","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"volume":181,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"G. Singh et al., “Magnetic field-induced self-assembly of iron oxide nanocubes,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 403–421, 2015.","short":"G. Singh, H. Chan, T. Udayabhaskararao, E. Gelman, D. Peddis, A. Baskin, G. Leitus, P. Král, R. Klajn, Faraday Discussions 181 (2015) 403–421.","apa":"Singh, G., Chan, H., Udayabhaskararao, T., Gelman, E., Peddis, D., Baskin, A., … Klajn, R. (2015). Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c4fd00265b","ama":"Singh G, Chan H, Udayabhaskararao T, et al. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 2015;181:403-421. doi:10.1039/c4fd00265b","mla":"Singh, Gurvinder, et al. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 403–21, doi:10.1039/c4fd00265b.","ista":"Singh G, Chan H, Udayabhaskararao T, Gelman E, Peddis D, Baskin A, Leitus G, Král P, Klajn R. 2015. Magnetic field-induced self-assembly of iron oxide nanocubes. Faraday Discussions. 181, 403–421.","chicago":"Singh, Gurvinder, Henry Chan, T. Udayabhaskararao, Elijah Gelman, Davide Peddis, Artem Baskin, Gregory Leitus, Petr Král, and Rafal Klajn. “Magnetic Field-Induced Self-Assembly of Iron Oxide Nanocubes.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4fd00265b."},"title":"Magnetic field-induced self-assembly of iron oxide nanocubes","external_id":{"pmid":["25920522"]},"article_processing_charge":"No","author":[{"first_name":"Gurvinder","full_name":"Singh, Gurvinder","last_name":"Singh"},{"full_name":"Chan, Henry","last_name":"Chan","first_name":"Henry"},{"first_name":"T.","full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao"},{"last_name":"Gelman","full_name":"Gelman, Elijah","first_name":"Elijah"},{"full_name":"Peddis, Davide","last_name":"Peddis","first_name":"Davide"},{"full_name":"Baskin, Artem","last_name":"Baskin","first_name":"Artem"},{"full_name":"Leitus, Gregory","last_name":"Leitus","first_name":"Gregory"},{"first_name":"Petr","full_name":"Král, Petr","last_name":"Král"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"oa":1,"quality_controlled":"1","publisher":"Royal Society of Chemistry","publication":"Faraday Discussions","day":"02","year":"2015","date_created":"2023-08-01T09:45:17Z","date_published":"2015-01-02T00:00:00Z","doi":"10.1039/c4fd00265b","page":"403-421"},{"date_updated":"2023-08-08T07:16:20Z","extern":"1","article_type":"letter_note","type":"journal_article","keyword":["Physical and Theoretical Chemistry"],"status":"public","_id":"13398","volume":181,"publication_status":"published","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]},"language":[{"iso":"eng"}],"scopus_import":"1","intvolume":" 181","month":"07","oa_version":"None","pmid":1,"article_processing_charge":"No","external_id":{"pmid":["26149295"]},"author":[{"full_name":"Sun, Yugang","last_name":"Sun","first_name":"Yugang"},{"first_name":"Leonardo","last_name":"Scarabelli","full_name":"Scarabelli, Leonardo"},{"first_name":"Nicholas","last_name":"Kotov","full_name":"Kotov, Nicholas"},{"first_name":"Moritz","last_name":"Tebbe","full_name":"Tebbe, Moritz"},{"first_name":"Xiao-Min","full_name":"Lin, Xiao-Min","last_name":"Lin"},{"full_name":"Brullot, Ward","last_name":"Brullot","first_name":"Ward"},{"first_name":"Lucio","full_name":"Isa, Lucio","last_name":"Isa"},{"first_name":"Peter","last_name":"Schurtenberger","full_name":"Schurtenberger, Peter"},{"first_name":"Helmuth","last_name":"Moehwald","full_name":"Moehwald, Helmuth"},{"full_name":"Fedin, Igor","last_name":"Fedin","first_name":"Igor"},{"first_name":"Orlin","full_name":"Velev, Orlin","last_name":"Velev"},{"first_name":"Damien","last_name":"Faivre","full_name":"Faivre, Damien"},{"last_name":"Sorensen","full_name":"Sorensen, Christopher","first_name":"Christopher"},{"last_name":"Perzynski","full_name":"Perzynski, Régine","first_name":"Régine"},{"last_name":"Chanana","full_name":"Chanana, Munish","first_name":"Munish"},{"full_name":"Li, Zhihai","last_name":"Li","first_name":"Zhihai"},{"full_name":"Bresme, Fernando","last_name":"Bresme","first_name":"Fernando"},{"first_name":"Petr","last_name":"Král","full_name":"Král, Petr"},{"last_name":"Firlar","full_name":"Firlar, Emre","first_name":"Emre"},{"last_name":"Schiffrin","full_name":"Schiffrin, David","first_name":"David"},{"last_name":"Souza Junior","full_name":"Souza Junior, Joao Batista","first_name":"Joao Batista"},{"full_name":"Fery, Andreas","last_name":"Fery","first_name":"Andreas"},{"first_name":"Elena","last_name":"Shevchenko","full_name":"Shevchenko, Elena"},{"first_name":"Ozgur","full_name":"Tarhan, Ozgur","last_name":"Tarhan"},{"first_name":"Armand Paul","last_name":"Alivisatos","full_name":"Alivisatos, Armand Paul"},{"first_name":"Sabrina","full_name":"Disch, Sabrina","last_name":"Disch"},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"last_name":"Ghosh","full_name":"Ghosh, Suvojit","first_name":"Suvojit"}],"title":"Field-assisted self-assembly process: General discussion","citation":{"chicago":"Sun, Yugang, Leonardo Scarabelli, Nicholas Kotov, Moritz Tebbe, Xiao-Min Lin, Ward Brullot, Lucio Isa, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c5fd90041g.","ista":"Sun Y, Scarabelli L, Kotov N, Tebbe M, Lin X-M, Brullot W, Isa L, Schurtenberger P, Moehwald H, Fedin I, Velev O, Faivre D, Sorensen C, Perzynski R, Chanana M, Li Z, Bresme F, Král P, Firlar E, Schiffrin D, Souza Junior JB, Fery A, Shevchenko E, Tarhan O, Alivisatos AP, Disch S, Klajn R, Ghosh S. 2015. Field-assisted self-assembly process: General discussion. Faraday Discussions. 181, 463–479.","mla":"Sun, Yugang, et al. “Field-Assisted Self-Assembly Process: General Discussion.” Faraday Discussions, vol. 181, Royal Society of Chemistry, 2015, pp. 463–79, doi:10.1039/c5fd90041g.","short":"Y. Sun, L. Scarabelli, N. Kotov, M. Tebbe, X.-M. Lin, W. Brullot, L. Isa, P. Schurtenberger, H. Moehwald, I. Fedin, O. Velev, D. Faivre, C. Sorensen, R. Perzynski, M. Chanana, Z. Li, F. Bresme, P. Král, E. Firlar, D. Schiffrin, J.B. Souza Junior, A. Fery, E. Shevchenko, O. Tarhan, A.P. Alivisatos, S. Disch, R. Klajn, S. Ghosh, Faraday Discussions 181 (2015) 463–479.","ieee":"Y. Sun et al., “Field-assisted self-assembly process: General discussion,” Faraday Discussions, vol. 181. Royal Society of Chemistry, pp. 463–479, 2015.","ama":"Sun Y, Scarabelli L, Kotov N, et al. Field-assisted self-assembly process: General discussion. Faraday Discussions. 2015;181:463-479. doi:10.1039/c5fd90041g","apa":"Sun, Y., Scarabelli, L., Kotov, N., Tebbe, M., Lin, X.-M., Brullot, W., … Ghosh, S. (2015). Field-assisted self-assembly process: General discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/c5fd90041g"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"463-479","date_created":"2023-08-01T09:45:29Z","date_published":"2015-07-07T00:00:00Z","doi":"10.1039/c5fd90041g","year":"2015","publication":"Faraday Discussions","day":"07","publisher":"Royal Society of Chemistry","quality_controlled":"1"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","year":"2015","publication":"Physical Review A","day":"19","date_created":"2023-08-10T06:38:10Z","date_published":"2015-02-19T00:00:00Z","doi":"10.1103/physreva.91.023421","article_number":"023421","citation":{"chicago":"Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/physreva.91.023421.","ista":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 91(2), 023421.","mla":"Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” Physical Review A, vol. 91, no. 2, 023421, American Physical Society, 2015, doi:10.1103/physreva.91.023421.","short":"S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical Review A 91 (2015).","ieee":"S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer, “Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation,” Physical Review A, vol. 91, no. 2. American Physical Society, 2015.","ama":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 2015;91(2). doi:10.1103/physreva.91.023421","apa":"Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., & Rohringer, N. (2015). Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.91.023421"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1504.03933"]},"author":[{"first_name":"Song Bin","last_name":"Zhang","full_name":"Zhang, Song Bin"},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"first_name":"Peter M.","full_name":"Kraus, Peter M.","last_name":"Kraus"},{"last_name":"Wörner","full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob"},{"first_name":"Nina","last_name":"Rohringer","full_name":"Rohringer, Nina"}],"title":"Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation","abstract":[{"lang":"eng","text":"The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.03933"}],"scopus_import":"1","intvolume":" 91","month":"02","publication_status":"published","publication_identifier":{"issn":["1050-2947"],"eissn":["1094-1622"]},"language":[{"iso":"eng"}],"issue":"2","volume":91,"_id":"14017","type":"journal_article","article_type":"original","keyword":["Atomic and Molecular Physics","and Optics"],"status":"public","date_updated":"2023-08-22T08:56:34Z","extern":"1"},{"status":"public","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"type":"journal_article","article_type":"original","_id":"14016","extern":"1","date_updated":"2023-08-22T08:52:56Z","month":"05","intvolume":" 6","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms8039"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies."}],"volume":6,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","article_number":"7039","title":"Observation of laser-induced electronic structure in oriented polyatomic molecules","author":[{"first_name":"P. M.","last_name":"Kraus","full_name":"Kraus, P. M."},{"last_name":"Tolstikhin","full_name":"Tolstikhin, O. I.","first_name":"O. I."},{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"first_name":"A.","last_name":"Rupenyan","full_name":"Rupenyan, A."},{"last_name":"Schneider","full_name":"Schneider, J.","first_name":"J."},{"last_name":"Bisgaard","full_name":"Bisgaard, C. Z.","first_name":"C. Z."},{"first_name":"T.","last_name":"Morishita","full_name":"Morishita, T."},{"first_name":"F.","full_name":"Jensen, F.","last_name":"Jensen"},{"first_name":"L. B.","last_name":"Madsen","full_name":"Madsen, L. B."},{"first_name":"H. J.","full_name":"Wörner, H. J.","last_name":"Wörner"}],"external_id":{"pmid":["25940229"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications, vol. 6, 7039, Springer Nature, 2015, doi:10.1038/ncomms8039.","short":"P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015).","ieee":"P. M. Kraus et al., “Observation of laser-induced electronic structure in oriented polyatomic molecules,” Nature Communications, vol. 6. Springer Nature, 2015.","apa":"Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms8039","ama":"Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 2015;6. doi:10.1038/ncomms8039","chicago":"Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” Nature Communications. Springer Nature, 2015. https://doi.org/10.1038/ncomms8039.","ista":"Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. 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A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 350","month":"10","date_updated":"2023-08-22T08:47:39Z","extern":"1","_id":"14013","article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","year":"2015","publication":"Science","day":"22","page":"790-795","date_created":"2023-08-10T06:37:35Z","date_published":"2015-10-22T00:00:00Z","doi":"10.1126/science.aab2160","quality_controlled":"1","publisher":"American Association for the Advancement of Science","citation":{"mla":"Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” Science, vol. 350, no. 6262, American Association for the Advancement of Science, 2015, pp. 790–95, doi:10.1126/science.aab2160.","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, G. Grassi, O.I. Tolstikhin, J. 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Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Kraus","full_name":"Kraus, P M","first_name":"P M"},{"first_name":"B","last_name":"Mignolet","full_name":"Mignolet, B"},{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"first_name":"A","full_name":"Rupenyan, A","last_name":"Rupenyan"},{"first_name":"L","last_name":"Horný","full_name":"Horný, L"},{"first_name":"E F","last_name":"Penka","full_name":"Penka, E F"},{"first_name":"O I","full_name":"Tolstikhin, O I","last_name":"Tolstikhin"},{"first_name":"J","full_name":"Schneider, J","last_name":"Schneider"},{"last_name":"Jensen","full_name":"Jensen, F","first_name":"F"},{"last_name":"Madsen","full_name":"Madsen, L B","first_name":"L B"},{"first_name":"A D","full_name":"Bandrauk, A D","last_name":"Bandrauk"},{"first_name":"F","last_name":"Remacle","full_name":"Remacle, F"},{"first_name":"H J","last_name":"Wörner","full_name":"Wörner, H J"}],"title":"Attosecond charge migration and its laser control","citation":{"mla":"Kraus, P. 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We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons.","lang":"eng"}],"title":"Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography","article_processing_charge":"No","author":[{"last_name":"Walt","full_name":"Walt, Samuel G","first_name":"Samuel G"},{"last_name":"Ram","full_name":"Ram, N Bhargava","first_name":"N Bhargava"},{"first_name":"Aaron","full_name":"von Conta, Aaron","last_name":"von Conta"},{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"first_name":"Marcos","full_name":"Atala, Marcos","last_name":"Atala"},{"last_name":"Wörner","full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” Journal of Physics: Conference Series, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:10.1088/1742-6596/635/11/112135.","apa":"Walt, S. 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We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"oa_version":"Published Version","author":[{"first_name":"Sébastien","last_name":"Wielgoss","full_name":"Wielgoss, Sébastien"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Anna M.","last_name":"Bischofberger","full_name":"Bischofberger, Anna M."},{"first_name":"Alex R.","full_name":"Hall, Alex R.","last_name":"Hall"}],"article_processing_charge":"No","title":"Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria","department":[{"_id":"CaGu"}],"citation":{"short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).","ieee":"S. Wielgoss, T. Bergmiller, A. 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Institute of Science and Technology Austria."},"title":"Learning with attributes for object recognition: Parametric and non-parametrics views","article_processing_charge":"No","author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia","orcid":"0000-0003-0192-9308"}],"publist_id":"5806","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:51:48Z","doi":"10.15479/at:ista:1401","date_published":"2015-04-01T00:00:00Z","page":"144","acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["000"],"date_updated":"2023-09-07T11:40:11Z","supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"file_date_updated":"2021-11-17T13:47:24Z","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"_id":"1401","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"9177","checksum":"3605b402bb6934e09ae4cf672c84baf7","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2015_Thesis_Sharmanska.pdf","date_created":"2021-02-22T11:33:17Z","creator":"dernst","file_size":7964342,"date_updated":"2021-02-22T11:33:17Z"},{"date_updated":"2021-11-17T13:47:24Z","file_size":7372241,"creator":"cchlebak","date_created":"2021-11-16T14:40:45Z","file_name":"2015_Thesis_Sharmanska_pdfa.pdf","content_type":"application/pdf","access_level":"closed","relation":"main_file","file_id":"10297","checksum":"e37593b3ee75bf3180629df2d6ca8f4e"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","abstract":[{"text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views.","lang":"eng"}],"month":"04","main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"alternative_title":["ISTA Thesis"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rspb.2015.1041.","ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812).","mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812, Royal Society, 2015, doi:10.1098/rspb.2015.1041.","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., & Chatterjee, K. (2015). Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society. https://doi.org/10.1098/rspb.2015.1041","ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 2015;282(1812). doi:10.1098/rspb.2015.1041","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 282, no. 1812. Royal Society, 2015.","short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015)."},"title":"Biological auctions with multiple rewards","author":[{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kanodia","full_name":"Kanodia, Ayush","first_name":"Ayush"},{"last_name":"Gupta","full_name":"Gupta, Raghav","first_name":"Raghav"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5425","external_id":{"pmid":["26180069"]},"article_processing_charge":"No","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"day":"15","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","year":"2015","date_published":"2015-07-15T00:00:00Z","doi":"10.1098/rspb.2015.1041","date_created":"2018-12-11T11:53:35Z","acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.","publisher":"Royal Society","quality_controlled":"1","oa":1,"date_updated":"2023-09-07T11:40:43Z","department":[{"_id":"KrCh"}],"_id":"1709","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","issue":"1812","volume":282,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1400"}]},"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards."}],"month":"07","intvolume":" 282","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/"}]},{"status":"public","type":"dissertation","_id":"1400","department":[{"_id":"KrCh"}],"title":"The subclonal evolution of cancer","publist_id":"5807","author":[{"first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"citation":{"chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria.","mla":"Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science and Technology Austria, 2015.","apa":"Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science and Technology Austria.","ama":"Reiter J. The subclonal evolution of cancer. 2015.","short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015."},"date_updated":"2023-09-07T11:40:44Z","month":"04","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","oa_version":"None","abstract":[{"text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease.","lang":"eng"}],"date_published":"2015-04-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"1709","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2000"},{"relation":"part_of_dissertation","status":"public","id":"2247"},{"relation":"part_of_dissertation","status":"public","id":"2816"},{"id":"2858","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"3157","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"3260","status":"public"}]},"date_created":"2018-12-11T11:51:48Z","page":"183","day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"year":"2015","degree_awarded":"PhD","publication_status":"published"},{"doi":"10.1016/j.jco.2015.06.002","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1399"}]},"volume":31,"issue":"6","date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:54:02Z","page":"773 - 797","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Complexity","year":"2015","publication_status":"published","month":"12","intvolume":" 31","scopus_import":1,"quality_controlled":"1","publisher":"Academic Press","oa_version":"None","acknowledgement":"F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation.","abstract":[{"lang":"eng","text":"Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology."}],"title":"A Koksma-Hlawka inequality for general discrepancy systems","department":[{"_id":"HeEd"}],"publist_id":"5320","author":[{"last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Anne","full_name":"Svane, Anne","last_name":"Svane"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” Journal of Complexity, vol. 31, no. 6. Academic Press, pp. 773–797, 2015.","short":"F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.","apa":"Pausinger, F., & Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.06.002","ama":"Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 2015;31(6):773-797. doi:10.1016/j.jco.2015.06.002","mla":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:10.1016/j.jco.2015.06.002.","ista":"Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797.","chicago":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” Journal of Complexity. Academic Press, 2015. https://doi.org/10.1016/j.jco.2015.06.002."},"date_updated":"2023-09-07T11:41:25Z","status":"public","type":"journal_article","_id":"1792"},{"day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","year":"2015","date_published":"2015-06-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"1662","relation":"part_of_dissertation"},{"id":"1792","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"2255","relation":"part_of_dissertation"}]},"date_created":"2018-12-11T11:51:48Z","page":"144","oa_version":"None","abstract":[{"text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold.","lang":"eng"}],"month":"06","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"citation":{"chicago":"Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute of Science and Technology Austria, 2015.","ista":"Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","mla":"Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute of Science and Technology Austria, 2015.","short":"F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015.","ieee":"F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science and Technology Austria, 2015.","apa":"Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute of Science and Technology Austria.","ama":"Pausinger F. On the approximation of intrinsic volumes. 2015."},"date_updated":"2023-09-07T11:41:25Z","department":[{"_id":"HeEd"}],"title":"On the approximation of intrinsic volumes","author":[{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pausinger","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian"}],"publist_id":"5808","article_processing_charge":"No","_id":"1399","status":"public","type":"dissertation"},{"_id":"1666","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"463","status":"public","date_updated":"2023-09-07T11:53:49Z","ddc":["576"],"file_date_updated":"2020-07-14T12:45:10Z","department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 11","month":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:07:58Z","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","creator":"system","date_updated":"2020-07-14T12:45:10Z","file_size":2580778,"file_id":"4657","checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":11,"related_material":{"record":[{"id":"9712","status":"public","relation":"research_data"},{"id":"1131","status":"public","relation":"dissertation_contains"}]},"issue":"11","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"citation":{"chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639","apa":"Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. 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Complete Composition Operators for IOCO-Testing Theory. ACM, 2015, pp. 101–10, doi:10.1145/2737166.2737175.","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110.","short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:10.1145/2737166.2737175","apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., & Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. https://doi.org/10.1145/2737166.2737175","chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. https://doi.org/10.1145/2737166.2737175.","ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Beneš","full_name":"Beneš, Nikola","first_name":"Nikola"},{"first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"}],"publist_id":"5676","title":"Complete composition operators for IOCO-testing theory","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2015","day":"01","page":"101 - 110","date_published":"2015-05-01T00:00:00Z","doi":"10.1145/2737166.2737175","date_created":"2018-12-11T11:52:24Z","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer). Jan Křetínský has been partially supported by the Czech Science Foundation, grant No. P202/12/G061. Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","publisher":"ACM","quality_controlled":"1","oa":1,"date_updated":"2023-09-07T11:58:33Z","ddc":["000"],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:59Z","_id":"1502","type":"conference","conference":{"start_date":"2015-05-04","end_date":"2015-05-08","location":"Montreal, QC, Canada","name":"CBSE: Component-Based Software Engineering "},"status":"public","pubrep_id":"625","publication_identifier":{"isbn":["978-1-4503-3471-6"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5303","checksum":"c6ce681035c163a158751f240cb7d389","date_updated":"2020-07-14T12:44:59Z","file_size":467561,"creator":"system","date_created":"2018-12-12T10:17:46Z","file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system."}],"oa_version":"Submitted Version","alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"scopus_import":1,"month":"05"},{"title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca","full_name":"Daca, Przemyslaw"}],"publist_id":"5677","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:10.1007/s10703-015-0235-2.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 2015;47(2):230-264. doi:10.1007/s10703-015-0235-2","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-015-0235-2","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” Formal Methods in System Design, vol. 47, no. 2. Springer, pp. 230–264, 2015.","short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” Formal Methods in System Design. Springer, 2015. https://doi.org/10.1007/s10703-015-0235-2.","ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264."},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"date_published":"2015-10-01T00:00:00Z","doi":"10.1007/s10703-015-0235-2","date_created":"2018-12-11T11:52:23Z","page":"230 - 264","day":"01","publication":"Formal Methods in System Design","year":"2015","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-07T11:58:33Z","status":"public","type":"journal_article","_id":"1501","related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"issue":"2","volume":47,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 47","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.0835"}],"oa_version":"Preprint","abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. ","lang":"eng"}]},{"day":"01","publication":"ACM SIGPLAN Notices","year":"2015","date_published":"2015-01-01T00:00:00Z","doi":"10.1145/2676726.2676979","date_created":"2018-12-11T11:52:58Z","page":"97 - 109","acknowledgement":"We thank anonymous reviewers for helpful comments to improve the presentation of the paper.","publisher":"ACM","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms for algebraic path properties in recursive state machines with constant treewidth,” ACM SIGPLAN Notices, vol. 50, no. 1. ACM, pp. 97–109, 2015.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices 50 (2015) 97–109.","apa":"Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., & Goyal, P. (2015). Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676979","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 2015;50(1):97-109. doi:10.1145/2676726.2676979","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices, vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:10.1145/2676726.2676979.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 50(1), 97–109.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” ACM SIGPLAN Notices. ACM, 2015. https://doi.org/10.1145/2676726.2676979."},"title":"Faster algorithms for algebraic path properties in recursive state machines with constant treewidth","publist_id":"5565","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"last_name":"Goyal","full_name":"Goyal, Prateesh","first_name":"Prateesh"}],"external_id":{"arxiv":["1410.7724"]},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":50,"issue":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"821"}]},"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks."}],"month":"01","intvolume":" 50","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1410.7724"}],"date_updated":"2023-09-07T12:01:58Z","department":[{"_id":"KrCh"}],"_id":"1602","status":"public","type":"journal_article","conference":{"end_date":"2015-01-17","location":"Mumbai, India","start_date":"2015-01-15","name":"SIGPLAN: Symposium on Principles of Programming Languages"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . ACM, 2015. https://doi.org/10.1145/2676726.2676968.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51, doi:10.1145/2676726.2676968.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1. ACM, pp. 539–551, 2015.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT 50 (2015) 539–551.","ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551. doi:10.1145/2676726.2676968","apa":"Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India: ACM. https://doi.org/10.1145/2676726.2676968"},"title":"Quantitative interprocedural analysis","publist_id":"5563","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","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"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"day":"01","publication":"Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT ","year":"2015","doi":"10.1145/2676726.2676968","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:52:59Z","page":"539 - 551","publisher":"ACM","quality_controlled":"1","date_updated":"2023-09-07T12:01:59Z","department":[{"_id":"KrCh"}],"_id":"1604","status":"public","pubrep_id":"523","type":"journal_article","conference":{"location":"Mumbai, India","end_date":"2015-01-17","start_date":"2015-01-15","name":"SIGPLAN: Symposium on Principles of Programming Languages"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-1-4503-3300-9"]},"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5445"},{"relation":"dissertation_contains","status":"public","id":"821"}]},"volume":50,"issue":"1","ec_funded":1,"oa_version":"None","abstract":[{"lang":"eng","text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs."}],"month":"01","intvolume":" 50","scopus_import":1},{"department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T12:01:59Z","status":"public","conference":{"start_date":"2015-07-18","location":"San Francisco, CA, USA","end_date":"2015-07-24","name":"CAV: Computer Aided Verification"},"type":"conference","_id":"1607","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5430"},{"id":"5437","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","id":"821","status":"public"}]},"volume":9206,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 9206","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.07384"}],"alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Preprint","abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.","lang":"eng"}],"title":"Faster algorithms for quantitative verification in constant treewidth graphs","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"}],"publist_id":"5560","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157. doi:10.1007/978-3-319-21690-4_9","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157). Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-21690-4_9","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp. 140–157.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in constant treewidth graphs,” presented at the CAV: Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification, LNCS, vol. 9206, 140–157.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,” 9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9."},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"date_created":"2018-12-11T11:52:59Z","date_published":"2015-07-16T00:00:00Z","doi":"10.1007/978-3-319-21690-4_9","page":"140 - 157","day":"16","year":"2015","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award."},{"article_processing_charge":"No","publist_id":"5417","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"full_name":"Kößler, Alexander","last_name":"Kößler","first_name":"Alexander"},{"first_name":"Ulrich","full_name":"Schmid, Ulrich","last_name":"Schmid"}],"title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","citation":{"mla":"Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” Real-Time Systems Symposium, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:10.1109/RTSS.2014.9.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127.","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in Real-Time Systems Symposium, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127.","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: Real-Time Systems Symposium. Vol 2015. IEEE; 2015:118-127. doi:10.1109/RTSS.2014.9","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In Real-Time Systems Symposium (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. https://doi.org/10.1109/RTSS.2014.9","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In Real-Time Systems Symposium, 2015:118–27. IEEE, 2015. https://doi.org/10.1109/RTSS.2014.9.","ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","quality_controlled":"1","page":"118 - 127","date_created":"2018-12-11T11:53:37Z","doi":"10.1109/RTSS.2014.9","date_published":"2015-01-15T00:00:00Z","year":"2015","publication":"Real-Time Systems Symposium","day":"15","conference":{"end_date":"2014-12-05","location":"Rome, Italy","start_date":"2014-12-02","name":"RTSS: Real-Time Systems Symposium"},"type":"conference","status":"public","_id":"1714","department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T12:01:59Z","scopus_import":1,"intvolume":" 2015","month":"01","abstract":[{"lang":"eng","text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application."}],"oa_version":"None","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5423"},{"id":"821","status":"public","relation":"dissertation_contains"}]},"volume":2015,"issue":"January","publication_status":"published","language":[{"iso":"eng"}]},{"_id":"1633","type":"conference","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2015-08-09","end_date":"2015-08-13","location":"Los Angeles, CA, United States"},"status":"public","pubrep_id":"609","date_updated":"2023-09-07T12:02:56Z","ddc":["000"],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:07Z","abstract":[{"text":"We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.\r\n\r\nOur system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.\r\n\r\nSeparating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"07","intvolume":" 34","publication_status":"published","file":[{"checksum":"955aee971983f6b6152bcc1c9b4a7c20","file_id":"5131","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-609-v1+1_FractureBEM.pdf","date_created":"2018-12-12T10:15:13Z","file_size":20154270,"date_updated":"2020-07-14T12:45:07Z","creator":"system"}],"language":[{"iso":"eng"}],"volume":34,"related_material":{"record":[{"id":"839","status":"public","relation":"dissertation_contains"}]},"issue":"4","ec_funded":1,"article_number":"151","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"mla":"Hahn, David, and Chris Wojtan. High-Resolution Brittle Fracture Simulation with Boundary Elements. Vol. 34, no. 4, 151, ACM, 2015, doi:10.1145/2766896.","ama":"Hahn D, Wojtan C. High-resolution brittle fracture simulation with boundary elements. In: Vol 34. ACM; 2015. doi:10.1145/2766896","apa":"Hahn, D., & Wojtan, C. (2015). High-resolution brittle fracture simulation with boundary elements (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766896","short":"D. Hahn, C. Wojtan, in:, ACM, 2015.","ieee":"D. Hahn and C. Wojtan, “High-resolution brittle fracture simulation with boundary elements,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.","chicago":"Hahn, David, and Chris Wojtan. “High-Resolution Brittle Fracture Simulation with Boundary Elements,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766896.","ista":"Hahn D, Wojtan C. 2015. High-resolution brittle fracture simulation with boundary elements. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 151."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hahn","full_name":"Hahn, David","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"publist_id":"5522","title":"High-resolution brittle fracture simulation with boundary elements","publisher":"ACM","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2015","day":"27","doi":"10.1145/2766896","date_published":"2015-07-27T00:00:00Z","date_created":"2018-12-11T11:53:09Z"},{"project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","grant_number":"T 560-B17","_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I 812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation"}],"title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","author":[{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"last_name":"Wieser","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"last_name":"Callan Jones","full_name":"Callan Jones, Andrew","first_name":"Andrew"},{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny"},{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi","full_name":"Morita, Hitoshi","last_name":"Morita"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke","last_name":"Sako"},{"last_name":"Barone","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa"},{"first_name":"Monika","last_name":"Ritsch Marte","full_name":"Ritsch Marte, Monika"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Voituriez","full_name":"Voituriez, Raphaël","first_name":"Raphaël"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5634","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:10.1016/j.cell.2015.01.008.","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 2015;160(4):673-685. doi:10.1016/j.cell.2015.01.008","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.01.008","short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","ieee":"V. Ruprecht et al., “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” Cell, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.01.008.","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685."},"publisher":"Cell Press","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","doi":"10.1016/j.cell.2015.01.008","date_published":"2015-02-12T00:00:00Z","date_created":"2018-12-11T11:52:35Z","page":"673 - 685","day":"12","publication":"Cell","has_accepted_license":"1","year":"2015","status":"public","pubrep_id":"484","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1537","file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"ddc":["570"],"date_updated":"2023-09-07T12:05:08Z","month":"02","intvolume":" 160","scopus_import":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype.","lang":"eng"}],"issue":"4","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"}]},"volume":160,"file":[{"file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","date_created":"2018-12-12T10:13:21Z","file_size":4362653,"date_updated":"2020-07-14T12:45:01Z","creator":"system","file_id":"5003","checksum":"228d3edf40627d897b3875088a0ac51f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"citation":{"ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32.","chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874","apa":"Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874","short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5580","external_id":{"pmid":["25604445"]},"title":"PIN-dependent auxin transport: Action, regulation, and evolution","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"year":"2015","day":"20","publication":"Plant Cell","page":"20 - 32","doi":"10.1105/tpc.114.134874","date_published":"2015-01-20T00:00:00Z","date_created":"2018-12-11T11:52:54Z","_id":"1591","type":"journal_article","status":"public","date_updated":"2023-09-07T12:06:09Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/","open_access":"1"}],"month":"01","intvolume":" 27","publication_status":"published","language":[{"iso":"eng"}],"issue":"1","related_material":{"record":[{"status":"public","id":"938","relation":"dissertation_contains"}]},"volume":27},{"year":"2015","day":"09","publication":"Journal of Mathematical Physics","doi":"10.1063/1.4932606","date_published":"2015-10-09T00:00:00Z","date_created":"2018-12-11T11:53:25Z","publisher":"American Institute of Physics","quality_controlled":"1","oa":1,"citation":{"ista":"Alt J. 2015. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 56(10), 103301.","chicago":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4932606.","short":"J. Alt, Journal of Mathematical Physics 56 (2015).","ieee":"J. Alt, “The local semicircle law for random matrices with a fourfold symmetry,” Journal of Mathematical Physics, vol. 56, no. 10. American Institute of Physics, 2015.","ama":"Alt J. The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. 2015;56(10). doi:10.1063/1.4932606","apa":"Alt, J. (2015). The local semicircle law for random matrices with a fourfold symmetry. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4932606","mla":"Alt, Johannes. “The Local Semicircle Law for Random Matrices with a Fourfold Symmetry.” Journal of Mathematical Physics, vol. 56, no. 10, 103301, American Institute of Physics, 2015, doi:10.1063/1.4932606."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","full_name":"Alt, Johannes"}],"publist_id":"5472","title":"The local semicircle law for random matrices with a fourfold symmetry","article_number":"103301","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"issue":"10","volume":56,"related_material":{"record":[{"relation":"dissertation_contains","id":"149","status":"public"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.04683"}],"month":"10","intvolume":" 56","date_updated":"2023-09-07T12:38:08Z","department":[{"_id":"LaEr"}],"_id":"1677","type":"journal_article","status":"public"},{"acknowledgement":"This work was supported by grants from the European Union Seventh Framework Programme (CIG-303564 to H.J. and ERC-StG-311166 to S.M.B.N.), the Human Frontier Science Program (RGY0084_2012 to H.J.) and the Herzfelder Foundation (to M.G.). A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W 1232) and a FemTech fellowship (3580812 Austrian Research Promotion Agency).","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"Nature Chemical Biology","day":"12","page":"952 - 954","date_created":"2018-12-11T11:53:25Z","date_published":"2015-10-12T00:00:00Z","doi":"10.1038/nchembio.1933","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"citation":{"ama":"Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, et al. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 2015;11(12):952-954. doi:10.1038/nchembio.1933","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Muellner, M., Nowak, M., Nijman, S., Grusch, M., & Janovjak, H. L. (2015). Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.1933","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, M. Muellner, M. Nowak, S. Nijman, M. Grusch, H.L. Janovjak, Nature Chemical Biology 11 (2015) 952–954.","ieee":"Á. Inglés Prieto et al., “Light-assisted small-molecule screening against protein kinases,” Nature Chemical Biology, vol. 11, no. 12. Nature Publishing Group, pp. 952–954, 2015.","mla":"Inglés Prieto, Álvaro, et al. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 952–54, doi:10.1038/nchembio.1933.","ista":"Inglés Prieto Á, Gschaider-Reichhart E, Muellner M, Nowak M, Nijman S, Grusch M, Janovjak HL. 2015. Light-assisted small-molecule screening against protein kinases. Nature Chemical Biology. 11(12), 952–954.","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Markus Muellner, Matthias Nowak, Sebastian Nijman, Michael Grusch, and Harald L Janovjak. “Light-Assisted Small-Molecule Screening against Protein Kinases.” Nature Chemical Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nchembio.1933."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto"},{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart"},{"first_name":"Markus","last_name":"Muellner","full_name":"Muellner, Markus"},{"id":"30845DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Nowak","full_name":"Nowak, Matthias"},{"first_name":"Sebastian","last_name":"Nijman","full_name":"Nijman, Sebastian"},{"first_name":"Michael","full_name":"Grusch, Michael","last_name":"Grusch"},{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5471","title":"Light-assisted small-molecule screening against protein kinases","abstract":[{"text":"High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that avoids the need for chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small-molecule screen against human protein kinases, including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 11","month":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:10:51Z","file_name":"IST-2017-837-v1+1_ingles-prieto.pdf","creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":1308364,"checksum":"e9fb251dfcb7cd209b83f17867e61321","file_id":"4842","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"issue":"12","related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"}]},"volume":11,"_id":"1678","type":"journal_article","pubrep_id":"837","status":"public","date_updated":"2023-09-07T12:49:09Z","ddc":["571"],"file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"HaJa"},{"_id":"LifeSc"}]},{"date_updated":"2023-09-07T12:55:21Z","department":[{"_id":"GaTk"}],"_id":"1576","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"volume":115,"issue":"24","ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state."}],"month":"12","intvolume":" 115","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.05716"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.","ama":"Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101","apa":"Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101","short":"S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).","ieee":"S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015.","chicago":"Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101.","ista":"Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101."},"title":"Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation","author":[{"last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A"},{"full_name":"Rieckh, Georg","last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publist_id":"5595","article_number":"248101","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"day":"08","publication":"Physical Review Letters","year":"2015","date_published":"2015-12-08T00:00:00Z","doi":"10.1103/PhysRevLett.115.248101","date_created":"2018-12-11T11:52:49Z","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"external_id":{"arxiv":["1511.03501"]},"article_processing_charge":"No","author":[{"last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"full_name":"Mabillard, Isaac","last_name":"Mabillard","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"A.","last_name":"Skopenkov","full_name":"Skopenkov, A."},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"title":"Eliminating higher-multiplicity intersections, III. Codimension 2","department":[{"_id":"UlWa"}],"citation":{"chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, n.d.","ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” ArXiv, 1511.03501.","short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” arXiv. .","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., & Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv.","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv."},"date_updated":"2023-09-07T13:12:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","status":"public","_id":"8183","article_number":"1511.03501","date_created":"2020-07-30T10:45:19Z","related_material":{"record":[{"relation":"later_version","id":"9308","status":"public"},{"relation":"later_version","id":"10220","status":"public"},{"id":"8156","status":"public","relation":"dissertation_contains"}]},"date_published":"2015-11-15T00:00:00Z","year":"2015","publication_status":"submitted","publication":"arXiv","language":[{"iso":"eng"}],"day":"15","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"month":"11","abstract":[{"lang":"eng","text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample."}],"acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","oa_version":"Preprint"},{"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir","orcid":"0000-0003-1702-6584"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:56Z","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","date_updated":"2023-09-19T14:36:19Z","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-340-v1-1.","ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 24p.","mla":"Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015, doi:10.15479/AT:IST-2015-340-v1-1.","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., & Pavlogiannis, A. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria. https://doi.org/10.15479/AT:IST-2015-340-v1-1","ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015. doi:10.15479/AT:IST-2015-340-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015.","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","pubrep_id":"340","status":"public","_id":"5441","page":"24","date_created":"2018-12-12T11:39:21Z","date_published":"2015-07-11T00:00:00Z","doi":"10.15479/AT:IST-2015-340-v1-1","related_material":{"record":[{"id":"1437","status":"public","relation":"later_version"},{"relation":"earlier_version","status":"public","id":"5442"},{"status":"public","id":"6009","relation":"later_version"}]},"year":"2015","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"file_id":"5531","checksum":"df383dc62c94d7b2ea639aba088a76c6","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2015-340-v1+1_main.pdf","date_created":"2018-12-12T11:54:09Z","creator":"system","file_size":861396,"date_updated":"2020-07-14T12:46:56Z"}],"day":"11","oa":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","month":"07","abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 22p.","mla":"Anonymous, 1, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria."},"date_updated":"2023-09-19T14:36:19Z","file_date_updated":"2020-07-14T12:46:57Z","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","author":[{"first_name":"1","last_name":"Anonymous","full_name":"Anonymous, 1"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"last_name":"Anonymous","full_name":"Anonymous, 3","first_name":"3"},{"first_name":"4","last_name":"Anonymous","full_name":"Anonymous, 4"}],"_id":"5442","status":"public","pubrep_id":"344","type":"technical_report","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5498","checksum":"98fd936102f3e057fc321ef6d316001d","creator":"system","file_size":658747,"date_updated":"2020-07-14T12:46:57Z","file_name":"IST-2015-343-v2+1_main.pdf","date_created":"2018-12-12T11:53:37Z"},{"creator":"dernst","file_size":139,"date_updated":"2020-07-14T12:46:57Z","file_name":"IST-2015-343-v2+2_anonymous.txt","date_created":"2019-04-16T12:36:08Z","relation":"main_file","access_level":"closed","content_type":"text/plain","checksum":"b31d09b1241b59c75e1f42dadf09d258","file_id":"6316"}],"day":"14","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","publication_status":"published","year":"2015","related_material":{"record":[{"id":"1437","status":"public","relation":"later_version"},{"status":"public","id":"5441","relation":"later_version"},{"status":"public","id":"6009","relation":"later_version"}]},"date_published":"2015-07-14T00:00:00Z","date_created":"2018-12-12T11:39:21Z","page":"22","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural properties that arise in program analysis.\r\nWe consider that each component of the concurrent system is a graph with constant treewidth, and it is known that the controlflow graphs of most programs have constant treewidth. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis problems (e.g., alias analysis). The study of multiple queries allows us to consider the tradeoff between the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual} query. The traditional approaches construct the product graph of all components and apply the best-known graph algorithm on the product. In the traditional approach, even the answer to a single query requires the transitive closure computation (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\n\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, \r\neach subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results that show that the worst-case running times of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (such as improving \r\nthe worst-case bounds for the shortest path problem in general graphs whose current best-known bound has not been improved in five decades). Finally, we provide a prototype implementation of our algorithms which significantly outperforms the existing algorithmic methods on several benchmarks."}],"month":"07","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","scopus_import":1,"oa":1},{"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publist_id":"5456","author":[{"full_name":"Svoreňová, Mária","last_name":"Svoreňová","first_name":"Mária"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Cěrná, Ivana","last_name":"Cěrná","first_name":"Ivana"},{"full_name":"Belta, Cǎlin","last_name":"Belta","first_name":"Cǎlin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-20T09:43:09Z","citation":{"short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–268.","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,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 259–268.","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 259–268). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728608","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. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:259-268. doi:10.1145/2728606.2728608","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–68, doi:10.1145/2728606.2728608.","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 259–268.","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.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 259–68. ACM, 2015. https://doi.org/10.1145/2728606.2728608."},"status":"public","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"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","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"}],"type":"conference","conference":{"end_date":"2015-04-16","location":"Seattle, WA, United States","start_date":"2015-04-14","name":"HSCC: Hybrid Systems - Computation and Control"},"_id":"1689","doi":"10.1145/2728606.2728608","related_material":{"record":[{"relation":"later_version","id":"1407","status":"public"}]},"date_published":"2015-04-14T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:53:29Z","page":"259 - 268","day":"14","publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","language":[{"iso":"eng"}],"publication_status":"published","year":"2015","month":"04","publisher":"ACM","scopus_import":1,"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.5387"}],"oa_version":"Preprint","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 satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study.","lang":"eng"}]},{"quality_controlled":"1","publisher":"Springer","page":"180 - 197","doi":"10.1007/978-3-319-21668-3_11","date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:53:42Z","has_accepted_license":"1","year":"2015","day":"01","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Clarke","full_name":"Clarke, Edmund","first_name":"Edmund"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","last_name":"Samanta","full_name":"Samanta, Roopsha"},{"first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tarrach","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten"}],"publist_id":"5398","title":"From non-preemptive to preemptive scheduling using synchronization synthesis","citation":{"apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2015). From non-preemptive to preemptive scheduling using synchronization synthesis. Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21668-3_11","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. 2015;9207:180-197. doi:10.1007/978-3-319-21668-3_11","ieee":"P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015.","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, 9207 (2015) 180–197.","mla":"Cerny, Pavol, et al. From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis. Vol. 9207, Springer, 2015, pp. 180–97, doi:10.1007/978-3-319-21668-3_11.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis. 9207, 180–197.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-21668-3_11."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"scopus_import":1,"month":"07","intvolume":" 9207","abstract":[{"lang":"eng","text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions."}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"dissertation_contains","id":"1130","status":"public"},{"status":"public","id":"1338","relation":"later_version"}]},"volume":9207,"ec_funded":1,"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"local","relation":"main_file","file_id":"4715","checksum":"6ff58ac220e2f20cb001ba35d4924495","date_updated":"2020-07-14T12:45:13Z","file_size":481922,"creator":"system","date_created":"2018-12-12T10:08:53Z","file_name":"IST-2015-336-v1+1_long_version.pdf"}],"language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2015-07-24","location":"San Francisco, CA, United States","start_date":"2015-07-18","name":"CAV: Computer Aided Verification"},"status":"public","pubrep_id":"336","_id":"1729","series_title":"Lecture Notes in Computer Science","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:13Z","date_updated":"2023-09-20T11:13:50Z","ddc":["000"]},{"oa_version":"Preprint","abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"intvolume":" 9035","month":"04","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.7704"}],"alternative_title":["LNCS"],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"1351"}]},"volume":9035,"_id":"1835","series_title":"Lecture Notes in Computer Science","status":"public","conference":{"start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"type":"conference","date_updated":"2023-09-20T11:06:03Z","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","oa":1,"publisher":"Springer","quality_controlled":"1","day":"01","year":"2015","date_created":"2018-12-11T11:54:16Z","doi":"10.1007/978-3-662-46681-0_47","date_published":"2015-04-01T00:00:00Z","page":"469 - 483","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47","mla":"Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47."},"title":"Model checking gene regulatory networks","publist_id":"5267","author":[{"full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","last_name":"Gupta"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1.","ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol. 4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1.","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” F1000 Research , vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4 (2015).","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 2015;4. doi:10.12688/f1000research.7143.1"},"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","publist_id":"5668","author":[{"first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","full_name":"Michalko, Jaroslav"},{"orcid":"0000-0002-2519-8004","full_name":"Dravecka, Marta","last_name":"Dravecka","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"article_processing_charge":"No","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"day":"01","publication":"F1000 Research ","has_accepted_license":"1","year":"2015","doi":"10.12688/f1000research.7143.1","date_published":"2015-10-01T00:00:00Z","date_created":"2018-12-11T11:52:26Z","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","publisher":"F1000 Research","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2023-10-10T14:10:24Z","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:44:59Z","_id":"1509","status":"public","pubrep_id":"497","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","date_created":"2018-12-12T10:16:12Z","file_size":4414248,"date_updated":"2020-07-14T12:44:59Z","creator":"system","file_id":"5198","checksum":"8beae5cbe988e1060265ae7de2ee8306","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":4,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.","lang":"eng"}],"month":"10","intvolume":" 4","scopus_import":"1"},{"ddc":["000"],"date_updated":"2023-10-17T11:42:52Z","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:12Z","_id":"1681","pubrep_id":"448","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:41Z","file_name":"IST-2016-448-v1+1_games-06-00413.pdf","creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":518832,"checksum":"912e1acbaf201100f447a43e4d5958bd","file_id":"4959","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2073-4336"]},"ec_funded":1,"volume":6,"issue":"4","oa_version":"Published Version","abstract":[{"text":"In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game.","lang":"eng"}],"intvolume":" 6","month":"09","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413.","ieee":"T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015.","short":"T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.","apa":"Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413","ama":"Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413","chicago":"Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413.","ista":"Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437."},"title":"Evolution of decisions in population games with sequentially searching individuals","article_processing_charge":"No","publist_id":"5467","author":[{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"publication":"Games","day":"29","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:26Z","date_published":"2015-09-29T00:00:00Z","doi":"10.3390/g6040413","page":"413 - 437","oa":1,"publisher":"MDPI","quality_controlled":"1"},{"ddc":["000"],"date_updated":"2023-10-17T11:42:00Z","file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"_id":"1655","pubrep_id":"464","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"945d99631a96e0315acb26dc8541dcf9","file_id":"4943","file_size":6455007,"date_updated":"2020-07-14T12:45:08Z","creator":"system","file_name":"IST-2016-464-v1+1_entropy-17-07266.pdf","date_created":"2018-12-12T10:12:25Z"}],"publication_status":"published","ec_funded":1,"volume":17,"issue":"10","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration."}],"intvolume":" 17","month":"10","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy. MDPI, 2015. https://doi.org/10.3390/e17107266.","ista":"Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297.","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:10.3390/e17107266.","ieee":"G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” Entropy, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015.","short":"G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297.","apa":"Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. Entropy. MDPI. https://doi.org/10.3390/e17107266","ama":"Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266"},"title":"Quantifying emergent behavior of autonomous robots","article_processing_charge":"No","publist_id":"5495","author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"},{"full_name":"Olbrich, Eckehard","last_name":"Olbrich","first_name":"Eckehard"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Entropy","day":"23","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:53:17Z","date_published":"2015-10-23T00:00:00Z","doi":"10.3390/e17107266","page":"7266 - 7297","acknowledgement":"This work was supported by the DFG priority program 1527 (Autonomous Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","oa":1,"publisher":"MDPI","quality_controlled":"1"},{"volume":7,"issue":"2","license":"https://creativecommons.org/licenses/by/3.0/","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"53e16bd3fc2ae2c0d7de9164626c37aa","file_id":"5057","file_size":1146814,"date_updated":"2020-07-14T12:45:18Z","creator":"system","file_name":"IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf","date_created":"2018-12-12T10:14:08Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"04","intvolume":" 7","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks.","lang":"eng"}],"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:18Z","ddc":["570"],"date_updated":"2023-10-18T06:47:30Z","status":"public","pubrep_id":"456","type":"journal_article","article_type":"original","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"_id":"1834","doi":"10.1177/1759091415575845","date_published":"2015-04-13T00:00:00Z","date_created":"2018-12-11T11:54:16Z","day":"13","publication":"ASN Neuro","has_accepted_license":"1","year":"2015","publisher":"SAGE Publications","quality_controlled":"1","oa":1,"title":"Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats","publist_id":"5269","author":[{"last_name":"Chen","full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong"},{"first_name":"Chao","full_name":"Wang, Chao","last_name":"Wang"},{"first_name":"Xuan","last_name":"Zhao","full_name":"Zhao, Xuan"},{"first_name":"Tao","last_name":"Zhou","full_name":"Zhou, Tao"},{"full_name":"Xu, Dao","last_name":"Xu","first_name":"Dao"},{"first_name":"Zhi","full_name":"Wang, Zhi","last_name":"Wang"},{"full_name":"Wang, Ying","last_name":"Wang","first_name":"Ying"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 7(2).","chicago":"Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro. SAGE Publications, 2015. https://doi.org/10.1177/1759091415575845.","short":"C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7 (2015).","ieee":"C. Chen et al., “Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats,” ASN Neuro, vol. 7, no. 2. SAGE Publications, 2015.","apa":"Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., & Wang, Y. (2015). Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. SAGE Publications. https://doi.org/10.1177/1759091415575845","ama":"Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 2015;7(2). doi:10.1177/1759091415575845","mla":"Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro, vol. 7, no. 2, SAGE Publications, 2015, doi:10.1177/1759091415575845."}},{"oa":1,"publisher":"Faculté des sciences de Toulouse","quality_controlled":"1","year":"2015","publication":"Annales de la faculté des sciences de Toulouse","day":"01","page":"781 - 800","date_created":"2018-12-11T11:53:10Z","doi":"10.5802/afst.1464","date_published":"2015-01-01T00:00:00Z","citation":{"ieee":"M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” Annales de la faculté des sciences de Toulouse, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015.","short":"M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800.","ama":"Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 2015;24(4):781-800. doi:10.5802/afst.1464","apa":"Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464","mla":"Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464.","ista":"Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800.","chicago":"Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015. https://doi.org/10.5802/afst.1464."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1409.8605"]},"author":[{"last_name":"Erbar","full_name":"Erbar, Matthias","first_name":"Matthias"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tetali","full_name":"Tetali, Prasad","first_name":"Prasad"}],"publist_id":"5520","title":"Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models","abstract":[{"text":"We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1409.8605","open_access":"1"}],"intvolume":" 24","month":"01","publication_status":"published","language":[{"iso":"eng"}],"volume":24,"issue":"4","_id":"1635","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-10-18T07:48:28Z","department":[{"_id":"JaMa"}]},{"status":"public","type":"journal_article","article_type":"letter_note","_id":"14303","extern":"1","date_updated":"2023-11-07T11:56:32Z","intvolume":" 15","month":"06","main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.5b01461","open_access":"1"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale."}],"issue":"7","volume":15,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"title":"Efficient production of single-stranded phage DNA as scaffolds for DNA origami","article_processing_charge":"No","external_id":{"pmid":["26028443"]},"author":[{"full_name":"Kick, B","last_name":"Kick","first_name":"B"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"},{"first_name":"H","last_name":"Dietz","full_name":"Dietz, H"},{"first_name":"D","last_name":"Weuster-Botz","full_name":"Weuster-Botz, D"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676. doi:10.1021/acs.nanolett.5b01461","apa":"Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461","ieee":"B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015.","short":"B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676.","mla":"Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:10.1021/acs.nanolett.5b01461.","ista":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676.","chicago":"Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461."},"oa":1,"publisher":"ACS Publications","quality_controlled":"1","date_created":"2023-09-06T12:52:47Z","date_published":"2015-06-01T00:00:00Z","doi":"10.1021/acs.nanolett.5b01461","page":"4672-4676","publication":"Nano Letters","day":"01","year":"2015"}]