[{"title":"Richard Hudson and Norman Kaplan on the coalescent process","pubrep_id":"768","type":"journal_article","status":"public","citation":{"ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” <i>Genetics</i>, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","short":"N.H. Barton, Genetics 202 (2016) 865–866.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. 2016;202(3):865-866. doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>.","apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.187542\">https://doi.org/10.1534/genetics.116.187542</a>","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” <i>Genetics</i>, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:<a href=\"https://doi.org/10.1534/genetics.116.187542\">10.1534/genetics.116.187542</a>."},"quality_controlled":"1","department":[{"_id":"NiBa"}],"doi":"10.1534/genetics.116.187542","intvolume":"       202","_id":"1357","page":"865 - 866","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["576"],"date_updated":"2021-01-12T06:50:07Z","month":"03","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5888","scopus_import":1,"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","access_level":"open_access","file_size":130779,"file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","file_id":"5127","checksum":"b2174bab2de1d1142900062a150f35c9","relation":"main_file","creator":"system","date_created":"2018-12-12T10:15:09Z"}],"publisher":"Genetics Society of America","date_created":"2018-12-11T11:51:33Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"date_published":"2016-03-01T00:00:00Z","volume":202,"file_date_updated":"2020-07-14T12:44:46Z","issue":"3","publication":"Genetics","year":"2016","language":[{"iso":"eng"}],"day":"01"},{"day":"04","language":[{"iso":"eng"}],"year":"2016","publication":"Nature Communications","ec_funded":1,"file_date_updated":"2020-07-14T12:44:46Z","abstract":[{"text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.","lang":"eng"}],"volume":7,"date_published":"2016-08-04T00:00:00Z","author":[{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roshan","last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"date_created":"2018-12-11T11:51:34Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"}],"publisher":"Nature Publishing Group","file":[{"relation":"main_file","checksum":"fe3f3a1526d180b29fe691ab11435b78","date_created":"2018-12-12T10:12:01Z","creator":"system","file_id":"4919","access_level":"open_access","file_size":861805,"file_name":"IST-2016-627-v1+1_ncomms12307.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z"},{"date_updated":"2020-07-14T12:44:46Z","content_type":"application/pdf","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","file_size":1084703,"access_level":"open_access","file_id":"4920","date_created":"2018-12-12T10:12:02Z","creator":"system","checksum":"164864a1a675f3ad80e9917c27aba07f","relation":"main_file"}],"scopus_import":1,"publist_id":"5887","related_material":{"record":[{"id":"6071","relation":"dissertation_contains","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"08","oa_version":"Published Version","date_updated":"2023-09-07T12:53:49Z","ddc":["576"],"publication_status":"published","oa":1,"has_accepted_license":"1","article_number":"12307","_id":"1358","intvolume":"         7","doi":"10.1038/ncomms12307","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"quality_controlled":"1","citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016."},"status":"public","type":"journal_article","pubrep_id":"627","title":"Intrinsic limits to gene regulation by global crosstalk","tmp":{"short":"CC BY (4.0)","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)"}},{"quality_controlled":"1","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"external_id":{"pmid":["27044080"]},"doi":"10.1073/pnas.1518830113","intvolume":"       113","page":"4422 - 4427","_id":"1359","title":"The effect of gene interactions on the long-term response to selection","type":"journal_article","status":"public","article_processing_charge":"No","citation":{"ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” <i>PNAS</i>, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. 2016;113(16):4422-4427. doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” <i>PNAS</i>, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:<a href=\"https://doi.org/10.1073/pnas.1518830113\">10.1073/pnas.1518830113</a>.","apa":"Paixao, T., &#38; Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1518830113\">https://doi.org/10.1073/pnas.1518830113</a>"},"oa":1,"publication_status":"published","date_updated":"2021-01-12T06:50:08Z","oa_version":"Published Version","month":"04","publist_id":"5886","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7"}],"date_created":"2018-12-11T11:51:34Z","article_type":"original","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"pmid":1,"publisher":"National Academy of Sciences","ec_funded":1,"publication":"PNAS","language":[{"iso":"eng"}],"year":"2016","day":"19","author":[{"orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2016-04-19T00:00:00Z","volume":113,"abstract":[{"text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population.","lang":"eng"}],"issue":"16"},{"citation":{"ama":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed billiard trajectories in asymmetric normed spaces. <i>Proceedings of the American Mathematical Society</i>. 2016;144(10):4501-4513. doi:<a href=\"https://doi.org/10.1090/proc/13062\">10.1090/proc/13062</a>","short":"A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American Mathematical Society 144 (2016) 4501–4513.","chicago":"Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/proc/13062\">https://doi.org/10.1090/proc/13062</a>.","apa":"Akopyan, A., Balitskiy, A., Karasev, R., &#38; Sharipova, A. (2016). Elementary approach to closed billiard trajectories in asymmetric normed spaces. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/13062\">https://doi.org/10.1090/proc/13062</a>","mla":"Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:<a href=\"https://doi.org/10.1090/proc/13062\">10.1090/proc/13062</a>.","ista":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 144(10), 4501–4513.","ieee":"A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach to closed billiard trajectories in asymmetric normed spaces,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 10. American Mathematical Society, pp. 4501–4513, 2016."},"article_processing_charge":"No","status":"public","type":"journal_article","title":"Elementary approach to closed billiard trajectories in asymmetric normed spaces","intvolume":"       144","page":"4501 - 4513","_id":"1360","doi":"10.1090/proc/13062","department":[{"_id":"HeEd"}],"quality_controlled":"1","acknowledgement":"The first and third authors were supported by the Dynasty Foundation. The first, second and third authors were supported by the Russian Foundation for Basic Re- search grant 15-31-20403 (mol a ved).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5885","oa_version":"Preprint","month":"10","date_updated":"2021-01-12T06:50:09Z","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.0442"}],"publisher":"American Mathematical Society","scopus_import":1,"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"date_created":"2018-12-11T11:51:34Z","issue":"10","date_published":"2016-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. "}],"volume":144,"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Balitskiy, Alexey","last_name":"Balitskiy","first_name":"Alexey"},{"first_name":"Roman","last_name":"Karasev","full_name":"Karasev, Roman"},{"last_name":"Sharipova","first_name":"Anastasia","full_name":"Sharipova, Anastasia"}],"language":[{"iso":"eng"}],"year":"2016","day":"01","publication":"Proceedings of the American Mathematical Society","ec_funded":1},{"scopus_import":1,"file":[{"file_id":"4660","checksum":"6d662893bd447d4f575b4961a2247811","relation":"main_file","creator":"system","date_created":"2018-12-12T10:08:01Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","file_size":10561865,"access_level":"open_access","file_name":"IST-2016-637-v1+1_2016_Da_SOL.pdf"}],"publisher":"ACM","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"}],"date_created":"2018-12-11T11:51:35Z","author":[{"full_name":"Da, Fang","first_name":"Fang","last_name":"Da"},{"last_name":"Hahn","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David"},{"last_name":"Batty","first_name":"Christopher","full_name":"Batty, Christopher"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"},{"full_name":"Grinspun, Eitan","last_name":"Grinspun","first_name":"Eitan"}],"date_published":"2016-07-11T00:00:00Z","abstract":[{"text":"We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes.","lang":"eng"}],"volume":35,"file_date_updated":"2020-07-14T12:44:46Z","issue":"4","ec_funded":1,"language":[{"iso":"eng"}],"year":"2016","day":"11","title":"Surface only liquids","pubrep_id":"637","status":"public","type":"conference","citation":{"mla":"Da, Fang, et al. <i>Surface Only Liquids</i>. Vol. 35, no. 4, a78, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925899\">10.1145/2897824.2925899</a>.","apa":"Da, F., Hahn, D., Batty, C., Wojtan, C., &#38; Grinspun, E. (2016). Surface only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925899\">https://doi.org/10.1145/2897824.2925899</a>","short":"F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016.","chicago":"Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Surface Only Liquids,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925899\">https://doi.org/10.1145/2897824.2925899</a>.","ama":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925899\">10.1145/2897824.2925899</a>","ista":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. 2016. Surface only liquids. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78.","ieee":"F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4."},"quality_controlled":"1","department":[{"_id":"ChWo"}],"doi":"10.1145/2897824.2925899","intvolume":"        35","_id":"1361","article_number":"a78","has_accepted_license":"1","alternative_title":["ACM Transactions on Graphics"],"conference":{"name":"ACM SIGGRAPH","start_date":"2016-07-24","end_date":"2016-07-28","location":"Anaheim, CA, USA"},"publication_status":"published","oa":1,"ddc":["000"],"date_updated":"2023-02-21T10:36:07Z","month":"07","oa_version":"Published Version","publist_id":"5881","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"file":[{"access_level":"open_access","file_size":12453704,"file_name":"IST-2016-632-v1+2_a104-hahn.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:46Z","relation":"main_file","checksum":"943712d9c9dc8bb5048d4adc561d7d38","creator":"system","date_created":"2018-12-12T10:15:04Z","file_id":"5121"}],"publisher":"ACM","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"}],"date_created":"2018-12-11T11:51:35Z","abstract":[{"text":"We present a boundary element based method for fast simulation of brittle fracture. By introducing simplifying assumptions that allow us to quickly estimate stress intensities and opening displacements during crack propagation, we build a fracture algorithm where the cost of each time step scales linearly with the length of the crackfront. The transition from a full boundary element method to our faster variant is possible at the beginning of any time step. This allows us to build a hybrid method, which uses the expensive but more accurate BEM while the number of degrees of freedom is low, and uses the fast method once that number exceeds a given threshold as the crack geometry becomes more complicated. Furthermore, we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body coupling solves a Neumann boundary value problem by carefully separating translational, rotational and deformational components of the collision forces and then applying a Tikhonov regularizer to the resulting linear system. We show that our method produces physically reasonable results in standard test cases and is capable of dealing with complex scenes faster than previous finite- or boundary element approaches.","lang":"eng"}],"volume":35,"date_published":"2016-07-01T00:00:00Z","author":[{"last_name":"Hahn","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David"},{"first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"issue":"4","file_date_updated":"2020-07-14T12:44:46Z","ec_funded":1,"day":"01","year":"2016","language":[{"iso":"eng"}],"type":"conference","status":"public","pubrep_id":"632","tmp":{"short":"CC BY (4.0)","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)"},"title":"Fast approximations for boundary element based brittle fracture simulation","citation":{"ieee":"D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.","short":"D. Hahn, C. Wojtan, in:, ACM, 2016.","chicago":"Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>.","ama":"Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>","mla":"Hahn, David, and Chris Wojtan. <i>Fast Approximations for Boundary Element Based Brittle Fracture Simulation</i>. Vol. 35, no. 4, 104, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925902\">10.1145/2897824.2925902</a>.","apa":"Hahn, D., &#38; Wojtan, C. (2016). Fast approximations for boundary element based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925902\">https://doi.org/10.1145/2897824.2925902</a>"},"department":[{"_id":"ChWo"}],"quality_controlled":"1","_id":"1362","intvolume":"        35","doi":"10.1145/2897824.2925902","article_number":"104","alternative_title":["ACM Transactions on Graphics"],"has_accepted_license":"1","date_updated":"2023-09-07T12:02:56Z","ddc":["000"],"publication_status":"published","oa":1,"conference":{"start_date":"2016-07-24","name":"ACM SIGGRAPH","end_date":"2016-07-28","location":"Anaheim, CA, USA"},"related_material":{"record":[{"relation":"dissertation_contains","id":"839","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5880","oa_version":"Published Version","month":"07"},{"publisher":"ACM","file":[{"file_id":"4981","checksum":"140b5532f0a2a006a0149cab7c73c17c","relation":"main_file","date_created":"2018-12-12T10:13:00Z","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:44:47Z","access_level":"open_access","file_size":12422760,"file_name":"IST-2016-631-v1+2_a96-bojsen-hansen.pdf"}],"project":[{"call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"date_created":"2018-12-11T11:51:35Z","issue":"4","file_date_updated":"2020-07-14T12:44:47Z","volume":35,"abstract":[{"text":"When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special &quot;non-reflecting&quot; boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation.","lang":"eng"}],"date_published":"2016-07-11T00:00:00Z","author":[{"first_name":"Morten","last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}],"day":"11","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"ieee":"M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2016). Generalized non-reflecting boundaries for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. <i>Generalized Non-Reflecting Boundaries for Fluid Re-Simulation</i>. Vol. 35, no. 4, 96, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>.","short":"M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>.","ama":"Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid re-simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>"},"type":"conference","status":"public","pubrep_id":"631","tmp":{"short":"CC BY (4.0)","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)"},"title":"Generalized non-reflecting boundaries for fluid re-simulation","_id":"1363","intvolume":"        35","doi":"10.1145/2897824.2925963","department":[{"_id":"ChWo"}],"acknowledgement":"We thank the IST Austria Visual Computing group for helpful feedback throughout the project. ","quality_controlled":"1","alternative_title":["ACM Transactions on Graphics"],"has_accepted_license":"1","article_number":"96","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5879","month":"07","oa_version":"Published Version","ddc":["000"],"date_updated":"2023-02-21T10:36:12Z","publication_status":"published","oa":1,"conference":{"location":"Anaheim, CA, USA","name":"ACM SIGGRAPH","start_date":"2016-07-24","end_date":"2016-07-28"}},{"file":[{"access_level":"open_access","file_size":44766392,"file_name":"IST-2017-763-v1+1_wirebending.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:47Z","checksum":"d00c2664a43d945df8876ea0193734e3","relation":"main_file","date_created":"2018-12-12T10:11:01Z","creator":"system","file_id":"4853"}],"publisher":"ACM","scopus_import":1,"date_created":"2018-12-11T11:51:36Z","project":[{"call_identifier":"H2020","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation","_id":"25082902-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:44:47Z","issue":"4","author":[{"full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba"},{"full_name":"Lepoutre, Mathias","first_name":"Mathias","last_name":"Lepoutre"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated."}],"volume":35,"date_published":"2016-07-01T00:00:00Z","day":"01","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"citation":{"ama":"Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod structures. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>","chicago":"Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>.","short":"E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.","apa":"Miguel Villalba, E., Lepoutre, M., &#38; Bickel, B. (2016). Computational design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925978\">https://doi.org/10.1145/2897824.2925978</a>","mla":"Miguel Villalba, Eder, et al. <i>Computational Design of Stable Planar-Rod Structures</i>. Vol. 35, no. 4, 86, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925978\">10.1145/2897824.2925978</a>.","ieee":"E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ista":"Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86."},"title":"Computational design of stable planar-rod structures","status":"public","type":"conference","pubrep_id":"763","doi":"10.1145/2897824.2925978","_id":"1364","intvolume":"        35","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 645599.","quality_controlled":"1","department":[{"_id":"BeBi"}],"has_accepted_license":"1","alternative_title":["ACM Transactions on Graphics"],"article_number":"86","oa_version":"Preprint","month":"07","publist_id":"5878","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"conference":{"location":"Anaheim, CA, USA","start_date":"2016-07-24","name":"ACM SIGGRAPH","end_date":"2016-07-28"},"date_updated":"2021-01-12T06:50:10Z","ddc":["006"]},{"volume":9815,"abstract":[{"text":"A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε &gt; 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest.","lang":"eng"}],"date_published":"2016-08-01T00:00:00Z","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F"},{"full_name":"Blocki, Jeremiah","last_name":"Blocki","first_name":"Jeremiah"}],"alternative_title":["LNCS"],"date_updated":"2021-01-12T06:50:11Z","publication_status":"published","oa":1,"conference":{"end_date":"2016-08-18","name":"CRYPTO: International Cryptology Conference","start_date":"2016-08-14","location":"Santa Barbara, CA, USA"},"day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5876","year":"2016","language":[{"iso":"eng"}],"oa_version":"Preprint","month":"08","status":"public","type":"conference","title":"Efficiently computing data-independent memory-hard functions","scopus_import":1,"publisher":"Springer","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2016/115"}],"citation":{"ieee":"J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard functions,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.","ista":"Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.","mla":"Alwen, Joel F., and Jeremiah Blocki. <i>Efficiently Computing Data-Independent Memory-Hard Functions</i>. Vol. 9815, Springer, 2016, pp. 241–71, doi:<a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">10.1007/978-3-662-53008-5_9</a>.","apa":"Alwen, J. F., &#38; Blocki, J. (2016). Efficiently computing data-independent memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">https://doi.org/10.1007/978-3-662-53008-5_9</a>","short":"J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271.","chicago":"Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent Memory-Hard Functions,” 9815:241–71. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">https://doi.org/10.1007/978-3-662-53008-5_9</a>.","ama":"Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions. In: Vol 9815. Springer; 2016:241-271. doi:<a href=\"https://doi.org/10.1007/978-3-662-53008-5_9\">10.1007/978-3-662-53008-5_9</a>"},"department":[{"_id":"KrPi"}],"quality_controlled":"1","page":"241 - 271","_id":"1365","intvolume":"      9815","date_created":"2018-12-11T11:51:36Z","doi":"10.1007/978-3-662-53008-5_9"},{"author":[{"first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tessaro, Stefano","first_name":"Stefano","last_name":"Tessaro"}],"date_published":"2016-05-01T00:00:00Z","abstract":[{"text":"We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions.","lang":"eng"}],"volume":9665,"ec_funded":1,"year":"2016","language":[{"iso":"eng"}],"day":"01","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/169/20160219:201940"}],"publisher":"Springer","project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668"}],"date_created":"2018-12-11T11:51:36Z","alternative_title":["LNCS"],"conference":{"start_date":"2016-05-08","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","end_date":"2016-05-12","location":"Vienna, Austria"},"publication_status":"published","oa":1,"date_updated":"2021-01-12T06:50:11Z","month":"05","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5872","title":"Provably robust sponge-based PRNGs and KDFs","type":"conference","status":"public","citation":{"ista":"Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.","ieee":"P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9665, pp. 87–116.","chicago":"Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and KDFs,” 9665:87–116. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">https://doi.org/10.1007/978-3-662-49890-3_4</a>.","short":"P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.","ama":"Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665. Springer; 2016:87-116. doi:<a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">10.1007/978-3-662-49890-3_4</a>","mla":"Gazi, Peter, and Stefano Tessaro. <i>Provably Robust Sponge-Based PRNGs and KDFs</i>. Vol. 9665, Springer, 2016, pp. 87–116, doi:<a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">10.1007/978-3-662-49890-3_4</a>.","apa":"Gazi, P., &#38; Tessaro, S. (2016). Provably robust sponge-based PRNGs and KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49890-3_4\">https://doi.org/10.1007/978-3-662-49890-3_4</a>"},"quality_controlled":"1","department":[{"_id":"KrPi"}],"doi":"10.1007/978-3-662-49890-3_4","intvolume":"      9665","page":"87 - 116","_id":"1366"},{"article_number":"024517","oa":1,"publication_status":"published","date_updated":"2021-01-12T06:50:12Z","month":"07","oa_version":"Preprint","publist_id":"5844","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Correlation driven d wave superconductivity in Anderson lattice model: Two gaps","type":"journal_article","status":"public","citation":{"ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 94(2), 024517.","ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 2. American Physical Society, 2016.","apa":"Wysokiński, M., Kaczmarczyk, J., &#38; Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>","mla":"Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>.","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">https://doi.org/10.1103/PhysRevB.94.024517</a>.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2016;94(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.94.024517\">10.1103/PhysRevB.94.024517</a>"},"acknowledgement":"The  work  has  been  supported  by  the  National Science  Center  (NCN)  under  the  Grant  MAESTRO,  No.\r\nDEC-2012/04/A/ST3/00342. ","quality_controlled":"1","department":[{"_id":"MiLe"}],"doi":"10.1103/PhysRevB.94.024517","_id":"1368","intvolume":"        94","author":[{"full_name":"Wysokiński, Marcin","first_name":"Marcin","last_name":"Wysokiński"},{"orcid":"0000-0002-1629-3675","first_name":"Jan","last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarczyk, Jan"},{"first_name":"Jozef","last_name":"Spałek","full_name":"Spałek, Jozef"}],"volume":94,"abstract":[{"lang":"eng","text":"Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5."}],"date_published":"2016-07-01T00:00:00Z","issue":"2","ec_funded":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","day":"01","language":[{"iso":"eng"}],"year":"2016","scopus_import":1,"publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/abs/1510.00224","open_access":"1"}],"date_created":"2018-12-11T11:51:37Z","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}]},{"ec_funded":1,"language":[{"iso":"eng"}],"year":"2016","day":"15","date_published":"2016-09-15T00:00:00Z","abstract":[{"text":"We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations.","lang":"eng"}],"volume":9908,"author":[{"first_name":"Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"project":[{"grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"date_created":"2018-12-11T11:51:37Z","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1603.06098","open_access":"1"}],"publisher":"Springer","date_updated":"2021-01-12T06:50:12Z","conference":{"end_date":"2016-10-14","name":"ECCV: European Conference on Computer Vision","start_date":"2016-10-11","location":"Amsterdam, The Netherlands"},"publication_status":"published","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5842","oa_version":"Preprint","month":"09","alternative_title":["LNCS"],"department":[{"_id":"ChLa"}],"quality_controlled":"1","intvolume":"      9908","_id":"1369","page":"695 - 711","doi":"10.1007/978-3-319-46493-0_42","type":"conference","status":"public","title":"Seed, expand and constrain: Three principles for weakly-supervised image segmentation","citation":{"mla":"Kolesnikov, Alexander, and Christoph Lampert. <i>Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation</i>. Vol. 9908, Springer, 2016, pp. 695–711, doi:<a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">10.1007/978-3-319-46493-0_42</a>.","apa":"Kolesnikov, A., &#38; Lampert, C. (2016). Seed, expand and constrain: Three principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711). Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands: Springer. <a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">https://doi.org/10.1007/978-3-319-46493-0_42</a>","short":"A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711.","ama":"Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:<a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">10.1007/978-3-319-46493-0_42</a>","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-46493-0_42\">https://doi.org/10.1007/978-3-319-46493-0_42</a>.","ieee":"A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles for weakly-supervised image segmentation,” presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.","ista":"Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 9908, 695–711."}},{"issue":"3","author":[{"first_name":"Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"full_name":"Vitali, David","first_name":"David","last_name":"Vitali"}],"date_published":"2016-03-28T00:00:00Z","volume":93,"abstract":[{"text":"We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction.","lang":"eng"}],"publication":"Physical Review A - Atomic, Molecular, and Optical Physics","language":[{"iso":"eng"}],"year":"2016","day":"28","main_file_link":[{"url":"http://arxiv.org/abs/1601.01818","open_access":"1"}],"publisher":"American Physical Society","scopus_import":1,"date_created":"2018-12-11T11:51:38Z","article_number":"033846","oa_version":"Preprint","month":"03","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5841","publication_status":"published","oa":1,"date_updated":"2023-02-21T10:36:32Z","citation":{"ista":"Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 033846.","ieee":"S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3. American Physical Society, 2016.","chicago":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>.","short":"S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","ama":"Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;93(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>","apa":"Barzanjeh, S., &#38; Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">https://doi.org/10.1103/PhysRevA.93.033846</a>","mla":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.033846\">10.1103/PhysRevA.93.033846</a>."},"title":"Phonon Josephson junction with nanomechanical resonators","type":"journal_article","status":"public","doi":"10.1103/PhysRevA.93.033846","intvolume":"        93","_id":"1370","quality_controlled":"1","acknowledgement":"The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation.  ","department":[{"_id":"JoFi"}]},{"author":[{"first_name":"Olivier","last_name":"Martin","full_name":"Martin, Olivier"},{"last_name":"Krzywicki","first_name":"André","full_name":"Krzywicki, André"},{"id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","first_name":"Marcin P"}],"volume":17,"abstract":[{"text":"Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent &quot;motifs&quot;, that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure.","lang":"eng"}],"date_published":"2016-07-01T00:00:00Z","oa_version":"None","publication":"Physics of Life Reviews","month":"07","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5840","day":"01","language":[{"iso":"eng"}],"year":"2016","publication_status":"published","date_updated":"2021-01-12T06:50:13Z","ec_funded":1,"publisher":"Elsevier","citation":{"short":"O. Martin, A. Krzywicki, M.P. Zagórski, Physics of Life Reviews 17 (2016) 124–158.","chicago":"Martin, Olivier, André Krzywicki, and Marcin P Zagórski. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">https://doi.org/10.1016/j.plrev.2016.06.002</a>.","ama":"Martin O, Krzywicki A, Zagórski MP. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. <i>Physics of Life Reviews</i>. 2016;17:124-158. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">10.1016/j.plrev.2016.06.002</a>","apa":"Martin, O., Krzywicki, A., &#38; Zagórski, M. P. (2016). Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">https://doi.org/10.1016/j.plrev.2016.06.002</a>","mla":"Martin, Olivier, et al. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 124–58, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.002\">10.1016/j.plrev.2016.06.002</a>.","ista":"Martin O, Krzywicki A, Zagórski MP. 2016. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 17, 124–158.","ieee":"O. Martin, A. Krzywicki, and M. P. Zagórski, “Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 124–158, 2016."},"scopus_import":1,"title":"Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function","status":"public","type":"journal_article","doi":"10.1016/j.plrev.2016.06.002","date_created":"2018-12-11T11:51:38Z","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"_id":"1371","page":"124 - 158","intvolume":"        17","acknowledgement":"MZ has been supported by Polish National Science Centre Grant No. DEC-2012/07/N/NZ2/00107 and by Foundation of Polish Science award START. ","quality_controlled":"1","department":[{"_id":"AnKi"}]},{"pubrep_id":"1006","type":"journal_article","status":"public","title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","citation":{"ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. <i>New Phytologist</i>. 2016;212(2):497-509. doi:<a href=\"https://doi.org/10.1111/nph.14049\">10.1111/nph.14049</a>","chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” <i>New Phytologist</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1111/nph.14049\">https://doi.org/10.1111/nph.14049</a>.","short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. <i>New Phytologist</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/nph.14049\">https://doi.org/10.1111/nph.14049</a>","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” <i>New Phytologist</i>, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:<a href=\"https://doi.org/10.1111/nph.14049\">10.1111/nph.14049</a>.","ieee":"M. Pernisová <i>et al.</i>, “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” <i>New Phytologist</i>, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509."},"department":[{"_id":"JiFr"}],"quality_controlled":"1","acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P","intvolume":"       212","page":"497 - 509","_id":"1372","doi":"10.1111/nph.14049","has_accepted_license":"1","date_updated":"2021-01-12T06:50:13Z","ddc":["581"],"oa":1,"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5839","month":"10","oa_version":"Submitted Version","scopus_import":1,"publisher":"Wiley-Blackwell","file":[{"file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","access_level":"open_access","file_size":972763,"date_updated":"2020-07-14T12:44:47Z","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:14:53Z","relation":"main_file","checksum":"27fd841ceaf0403559d7048ef51500f9","file_id":"5108"}],"date_created":"2018-12-11T11:51:38Z","date_published":"2016-10-01T00:00:00Z","abstract":[{"text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism.","lang":"eng"}],"volume":212,"author":[{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","full_name":"Prat, Tomas","first_name":"Tomas","last_name":"Prat"},{"last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Haruštiaková, Danka","first_name":"Danka","last_name":"Haruštiaková"},{"full_name":"Matonohova, Martina","last_name":"Matonohova","first_name":"Martina"},{"last_name":"Spíchal","first_name":"Lukáš","full_name":"Spíchal, Lukáš"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"}],"issue":"2","file_date_updated":"2020-07-14T12:44:47Z","year":"2016","language":[{"iso":"eng"}],"day":"01","publication":"New Phytologist"},{"author":[{"first_name":"Olivier","last_name":"Martin","full_name":"Martin, Olivier"},{"orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"}],"volume":17,"date_published":"2016-07-01T00:00:00Z","month":"07","publication":"Physics of Life Reviews","oa_version":"Preprint","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5838","language":[{"iso":"eng"}],"year":"2016","publication_status":"published","oa":1,"date_updated":"2022-08-26T09:39:27Z","publisher":"Elsevier","article_processing_charge":"No","citation":{"ista":"Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; Physics of Life Reviews. 17, 168–171.","ieee":"O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot;,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 168–171, 2016.","short":"O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.","ama":"Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; <i>Physics of Life Reviews</i>. 2016;17:168-171. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">10.1016/j.plrev.2016.06.006</a>","chicago":"Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot;” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">https://doi.org/10.1016/j.plrev.2016.06.006</a>.","apa":"Martin, O., &#38; Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">https://doi.org/10.1016/j.plrev.2016.06.006</a>","mla":"Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot;” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 168–71, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.006\">10.1016/j.plrev.2016.06.006</a>."},"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01531698"}],"title":"Network architectures and operating principles. Reply to comments on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot;","scopus_import":"1","status":"public","type":"journal_article","doi":"10.1016/j.plrev.2016.06.006","date_created":"2018-12-11T11:51:39Z","page":"168 - 171","_id":"1373","intvolume":"        17","quality_controlled":"1","department":[{"_id":"AnKi"}]},{"date_updated":"2021-01-12T06:50:15Z","oa":1,"publication_status":"published","publist_id":"5834","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"05","oa_version":"Preprint","department":[{"_id":"VlKo"}],"quality_controlled":"1","intvolume":"         9","page":"605 - 636","_id":"1377","doi":"10.1137/15M1010257","type":"journal_article","status":"public","title":"Total variation on a tree","citation":{"ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” <i>SIAM Journal on Imaging Sciences</i>, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016.","ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636.","apa":"Kolmogorov, V., Pock, T., &#38; Rolinek, M. (2016). Total variation on a tree. <i>SIAM Journal on Imaging Sciences</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/15M1010257\">https://doi.org/10.1137/15M1010257</a>","mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” <i>SIAM Journal on Imaging Sciences</i>, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:<a href=\"https://doi.org/10.1137/15M1010257\">10.1137/15M1010257</a>.","ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. <i>SIAM Journal on Imaging Sciences</i>. 2016;9(2):605-636. doi:<a href=\"https://doi.org/10.1137/15M1010257\">10.1137/15M1010257</a>","short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636.","chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” <i>SIAM Journal on Imaging Sciences</i>. Society for Industrial and Applied Mathematics , 2016. <a href=\"https://doi.org/10.1137/15M1010257\">https://doi.org/10.1137/15M1010257</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"year":"2016","day":"03","publication":"SIAM Journal on Imaging Sciences","date_published":"2016-05-03T00:00:00Z","abstract":[{"text":"We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.","lang":"eng"}],"volume":9,"author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"},{"last_name":"Pock","first_name":"Thomas","full_name":"Pock, Thomas"},{"first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"issue":"2","date_created":"2018-12-11T11:51:40Z","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160"}],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1502.07770","open_access":"1"}],"publisher":"Society for Industrial and Applied Mathematics "},{"quality_controlled":"1","department":[{"_id":"UlWa"}],"doi":"10.4230/LIPIcs.SoCG.2016.35","intvolume":"        51","page":"35.1 - 35.10","_id":"1378","tmp":{"short":"CC BY (4.0)","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)"},"title":"On expansion and topological overlap","pubrep_id":"623","status":"public","type":"conference","citation":{"ista":"Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.","ieee":"D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 35.1-35.10.","mla":"Dotterrer, Dominic, et al. <i>On Expansion and Topological Overlap</i>. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">10.4230/LIPIcs.SoCG.2016.35</a>.","apa":"Dotterrer, D., Kaufman, T., &#38; Wagner, U. (2016). On expansion and topological overlap (Vol. 51, p. 35.1-35.10). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">https://doi.org/10.4230/LIPIcs.SoCG.2016.35</a>","chicago":"Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological Overlap,” 51:35.1-35.10. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">https://doi.org/10.4230/LIPIcs.SoCG.2016.35</a>.","short":"D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10.","ama":"Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:35.1-35.10. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.35\">10.4230/LIPIcs.SoCG.2016.35</a>"},"conference":{"location":"Medford, MA, USA","start_date":"2016-06-14","name":"SoCG: Symposium on Computational Geometry","end_date":"2016-06-17"},"publication_status":"published","oa":1,"ddc":["510"],"date_updated":"2023-09-27T12:29:56Z","oa_version":"Published Version","month":"06","related_material":{"record":[{"status":"public","relation":"later_version","id":"742"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5833","has_accepted_license":"1","alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:51:41Z","project":[{"_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","grant_number":"PP00P2_138948"}],"scopus_import":1,"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","file":[{"access_level":"open_access","file_size":536923,"file_name":"IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:47Z","checksum":"cee65b0e722d50f9d1cc70c90ec1d59b","relation":"main_file","date_created":"2018-12-12T10:08:38Z","creator":"system","file_id":"4699"}],"language":[{"iso":"eng"}],"year":"2016","day":"01","author":[{"full_name":"Dotterrer, Dominic","last_name":"Dotterrer","first_name":"Dominic"},{"full_name":"Kaufman, Tali","last_name":"Kaufman","first_name":"Tali"},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2016-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ &gt; 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M."}],"volume":51,"file_date_updated":"2020-07-14T12:44:47Z"},{"date_created":"2018-12-11T11:51:41Z","file":[{"file_name":"IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf","file_size":574770,"access_level":"open_access","date_updated":"2020-07-14T12:44:47Z","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:12:12Z","relation":"main_file","checksum":"f04248a61c24297cfabd30c5f8e0deb9","file_id":"4930"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","scopus_import":1,"year":"2016","language":[{"iso":"eng"}],"day":"01","file_date_updated":"2020-07-14T12:44:47Z","date_published":"2016-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case."}],"volume":51,"author":[{"full_name":"Burton, Benjamin","first_name":"Benjamin","last_name":"Burton"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","full_name":"De Mesmay, Arnaud N","first_name":"Arnaud N","last_name":"De Mesmay"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"intvolume":"        51","_id":"1379","page":"24.1 - 24.15","doi":"10.4230/LIPIcs.SoCG.2016.24","department":[{"_id":"UlWa"}],"quality_controlled":"1","citation":{"apa":"Burton, B., de Mesmay, A. N., &#38; Wagner, U. (2016). Finding non-orientable surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">https://doi.org/10.4230/LIPIcs.SoCG.2016.24</a>","mla":"Burton, Benjamin, et al. <i>Finding Non-Orientable Surfaces in 3-Manifolds</i>. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">10.4230/LIPIcs.SoCG.2016.24</a>.","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:24.1-24.15. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">10.4230/LIPIcs.SoCG.2016.24</a>","short":"B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2016.24\">https://doi.org/10.4230/LIPIcs.SoCG.2016.24</a>.","ista":"Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15.","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 24.1-24.15."},"pubrep_id":"622","type":"conference","status":"public","title":"Finding non-orientable surfaces in 3-manifolds","tmp":{"short":"CC BY (4.0)","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)"},"publist_id":"5832","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","id":"534","status":"public"}]},"month":"06","oa_version":"Published Version","date_updated":"2023-02-23T12:23:20Z","ddc":["510"],"conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2016-06-14","end_date":"2016-06-17","location":"Medford, MA, USA"},"publication_status":"published","oa":1,"alternative_title":["LIPIcs"],"has_accepted_license":"1"},{"year":"2016","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5831","day":"01","oa_version":"Preprint","month":"06","publication":"Journal of the ACM","date_updated":"2021-01-12T06:50:17Z","publication_status":"published","oa":1,"issue":"3","date_published":"2016-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP."}],"volume":63,"article_number":"23","author":[{"first_name":"Ventsislav K","last_name":"Chonev","full_name":"Chonev, Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ouaknine, Joël","last_name":"Ouaknine","first_name":"Joël"},{"full_name":"Worrell, James","last_name":"Worrell","first_name":"James"}],"intvolume":"        63","_id":"1380","date_created":"2018-12-11T11:51:41Z","doi":"10.1145/2857050","department":[{"_id":"KrCh"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.2981"}],"citation":{"short":"V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016).","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” <i>Journal of the ACM</i>. ACM, 2016. <a href=\"https://doi.org/10.1145/2857050\">https://doi.org/10.1145/2857050</a>.","ama":"Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. <i>Journal of the ACM</i>. 2016;63(3). doi:<a href=\"https://doi.org/10.1145/2857050\">10.1145/2857050</a>","mla":"Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” <i>Journal of the ACM</i>, vol. 63, no. 3, 23, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2857050\">10.1145/2857050</a>.","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the complexity of the orbit problem. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2857050\">https://doi.org/10.1145/2857050</a>","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” <i>Journal of the ACM</i>, vol. 63, no. 3. ACM, 2016."},"publisher":"ACM","type":"journal_article","status":"public","title":"On the complexity of the orbit problem","scopus_import":1}]