[{"citation":{"short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:1573-1580. doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>","mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 1573–80, doi:<a href=\"https://doi.org/10.1145/2463372.2463568\">10.1145/2463372.2463568</a>.","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.","apa":"Barton, N. H., &#38; Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 1573–1580). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 1573–1580.","chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 1573–80. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463568\">https://doi.org/10.1145/2463372.2463568</a>."},"conference":{"end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference","location":"Amsterdam, Netherlands","start_date":"2013-07-06"},"has_accepted_license":"1","oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","date_updated":"2024-10-09T20:55:12Z","abstract":[{"lang":"eng","text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C."}],"language":[{"iso":"eng"}],"page":"1573 - 1580","_id":"2718","day":"01","publisher":"ACM","file":[{"file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-12T10:15:38Z","content_type":"application/pdf","creator":"system","file_id":"5159","file_size":475844,"checksum":"9d9be9090ce5c20766e0eb076ace5b98","relation":"main_file"}],"file_date_updated":"2020-07-14T12:45:45Z","oa_version":"Submitted Version","doi":"10.1145/2463372.2463568","ddc":["570"],"scopus_import":1,"title":"Can quantitative and population genetics help us understand evolutionary computation?","quality_controlled":"1","publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","publication_status":"published","pubrep_id":"564","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"corr_author":"1","ec_funded":1,"date_published":"2013-07-01T00:00:00Z","year":"2013","status":"public","month":"07","date_created":"2018-12-11T11:59:14Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}],"publist_id":"4174"},{"oa_version":"None","citation":{"mla":"Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2013, pp. 845–52, doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>.","ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2013:845-852. doi:<a href=\"https://doi.org/10.1145/2463372.2463470\">10.1145/2463372.2463470</a>","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i>, Amsterdam, Netherlands, 2013, pp. 845–852.","chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In <i>Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation</i>, 845–52. ACM, 2013. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>.","apa":"Paixao, T., &#38; Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In <i>Proceedings of the 15th annual conference on Genetic and evolutionary computation</i> (pp. 845–852). Amsterdam, Netherlands: ACM. <a href=\"https://doi.org/10.1145/2463372.2463470\">https://doi.org/10.1145/2463372.2463470</a>","ista":"Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852."},"doi":"10.1145/2463372.2463470","quality_controlled":"1","title":"A variance decomposition approach to the analysis of genetic algorithms","conference":{"start_date":"2013-07-06","location":"Amsterdam, Netherlands","end_date":"2013-07-10","name":"GECCO: Genetic and evolutionary computation conference"},"scopus_import":1,"type":"conference","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","abstract":[{"lang":"eng","text":"Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation."}],"date_updated":"2024-10-09T20:55:12Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"page":"845 - 852","publication_status":"published","date_published":"2013-07-01T00:00:00Z","ec_funded":1,"corr_author":"1","month":"07","_id":"2719","status":"public","year":"2013","publist_id":"4173","author":[{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"publisher":"ACM","day":"01","date_created":"2018-12-11T11:59:15Z"},{"_id":"2720","day":"01","publisher":"Genetics Society of America","page":"527-540","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":195,"type":"journal_article","date_updated":"2025-09-29T14:08:19Z","language":[{"iso":"eng"}],"abstract":[{"text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is &lt;10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.","lang":"eng"}],"citation":{"ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","apa":"Long, H., Paixao, T., Azevedo, R., &#38; Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>. Genetics Society of America, 2013. <a href=\"https://doi.org/10.1534/genetics.113.153536\">https://doi.org/10.1534/genetics.113.153536</a>.","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” <i>Genetics</i>, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. <i>Genetics</i>. 2013;195(2):527-540. doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>","mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” <i>Genetics</i>, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:<a href=\"https://doi.org/10.1534/genetics.113.153536\">10.1534/genetics.113.153536</a>."},"issue":"2","year":"2013","month":"10","status":"public","isi":1,"date_created":"2018-12-11T11:59:15Z","publist_id":"4172","intvolume":"       195","author":[{"full_name":"Long, Hongan","first_name":"Hongan","last_name":"Long"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Azevedo, Ricardo","first_name":"Ricardo","last_name":"Azevedo"},{"full_name":"Zufall, Rebecca","last_name":"Zufall","first_name":"Rebecca"}],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_published":"2013-10-01T00:00:00Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/","open_access":"1"}],"ec_funded":1,"article_processing_charge":"No","pmid":1,"publication":"Genetics","doi":"10.1534/genetics.113.153536","oa_version":"Submitted Version","external_id":{"pmid":["23934880"],"isi":["000325286200020"]},"scopus_import":"1","quality_controlled":"1","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila"},{"page":"1837 - 1926","publication_status":"published","date_published":"2013-12-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.5664"}],"year":"2013","status":"public","_id":"2780","month":"12","date_created":"2018-12-11T11:59:33Z","publisher":"Birkhäuser","day":"01","author":[{"last_name":"Erdös","first_name":"László","full_name":"László Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"},{"full_name":"Yau, Horng-Tzer","first_name":"Horng","last_name":"Yau"}],"extern":1,"intvolume":"        14","publist_id":"4110","citation":{"short":"L. Erdös, A. Knowles, H. Yau, Annales Henri Poincare 14 (2013) 1837–1926.","ama":"Erdös L, Knowles A, Yau H. Averaging fluctuations in resolvents of random band matrices. <i>Annales Henri Poincare</i>. 2013;14(8):1837-1926. doi:<a href=\"https://doi.org/10.1007/s00023-013-0235-y\">10.1007/s00023-013-0235-y</a>","mla":"Erdös, László, et al. “Averaging Fluctuations in Resolvents of Random Band Matrices.” <i>Annales Henri Poincare</i>, vol. 14, no. 8, Birkhäuser, 2013, pp. 1837–926, doi:<a href=\"https://doi.org/10.1007/s00023-013-0235-y\">10.1007/s00023-013-0235-y</a>.","ista":"Erdös L, Knowles A, Yau H. 2013. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 14(8), 1837–1926.","apa":"Erdös, L., Knowles, A., &#38; Yau, H. (2013). Averaging fluctuations in resolvents of random band matrices. <i>Annales Henri Poincare</i>. Birkhäuser. <a href=\"https://doi.org/10.1007/s00023-013-0235-y\">https://doi.org/10.1007/s00023-013-0235-y</a>","ieee":"L. Erdös, A. Knowles, and H. Yau, “Averaging fluctuations in resolvents of random band matrices,” <i>Annales Henri Poincare</i>, vol. 14, no. 8. Birkhäuser, pp. 1837–1926, 2013.","chicago":"Erdös, László, Antti Knowles, and Horng Yau. “Averaging Fluctuations in Resolvents of Random Band Matrices.” <i>Annales Henri Poincare</i>. Birkhäuser, 2013. <a href=\"https://doi.org/10.1007/s00023-013-0235-y\">https://doi.org/10.1007/s00023-013-0235-y</a>."},"doi":"10.1007/s00023-013-0235-y","issue":"8","title":"Averaging fluctuations in resolvents of random band matrices","quality_controlled":0,"oa":1,"volume":14,"type":"journal_article","date_updated":"2021-01-12T06:59:40Z","abstract":[{"text":"We consider a general class of random matrices whose entries are centred random variables, independent up to a symmetry constraint. We establish precise high-probability bounds on the averages of arbitrary monomials in the resolvent matrix entries. Our results generalize the previous results of Erdős et al. (Ann Probab, arXiv:1103.1919, 2013; Commun Math Phys, arXiv:1103.3869, 2013; J Combin 1(2):15-85, 2011) which constituted a key step in the proof of the local semicircle law with optimal error bound in mean-field random matrix models. Our bounds apply to random band matrices and improve previous estimates from order 2 to order 4 in the cases relevant to applications. In particular, they lead to a proof of the diffusion approximation for the magnitude of the resolvent of random band matrices. This, in turn, implies new delocalization bounds on the eigenvectors. The applications are presented in a separate paper (Erdős et al., arXiv:1205.5669, 2013).","lang":"eng"}],"publication":"Annales Henri Poincare"},{"oa":1,"type":"journal_article","volume":41,"date_updated":"2021-01-12T06:59:41Z","abstract":[{"text":"We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, that is, graphs on N vertices where every edge is chosen independently and with probability p = p(N). We rescale the matrix so that its bulk eigenvalues are of order one. We prove that, as long as pN→∞(with a speed at least logarithmic in N), the density of eigenvalues of the Erdős-Rényi ensemble is given by the Wigner semicircle law for spectral windows of length larger than N-1 (up to logarithmic corrections). As a consequence, all eigenvectors are proved to be completely delocalized in the sense that the ℓ∞-norms of the ℓ2-normalized eigenvectors are at most of order N-1/2 with a very high probability. The estimates in this paper will be used in the companion paper [Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues (2011) Preprint] to prove the universality of eigenvalue distributions both in the bulk and at the spectral edges under the further restriction that pN »N2/3.","lang":"eng"}],"publication":"Annals of Probability","doi":"10.1214/11-AOP734","citation":{"ama":"Erdös L, Knowles A, Yau H, Yin J. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. <i>Annals of Probability</i>. 2013;41(3 B):2279-2375. doi:<a href=\"https://doi.org/10.1214/11-AOP734\">10.1214/11-AOP734</a>","short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Annals of Probability 41 (2013) 2279–2375.","mla":"Erdös, László, et al. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” <i>Annals of Probability</i>, vol. 41, no. 3 B, Institute of Mathematical Statistics, 2013, pp. 2279–375, doi:<a href=\"https://doi.org/10.1214/11-AOP734\">10.1214/11-AOP734</a>.","ista":"Erdös L, Knowles A, Yau H, Yin J. 2013. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. 41(3 B), 2279–2375.","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/11-AOP734\">https://doi.org/10.1214/11-AOP734</a>.","ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “Spectral statistics of Erdős-Rényi graphs I: Local semicircle law,” <i>Annals of Probability</i>, vol. 41, no. 3 B. Institute of Mathematical Statistics, pp. 2279–2375, 2013.","apa":"Erdös, L., Knowles, A., Yau, H., &#38; Yin, J. (2013). Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/11-AOP734\">https://doi.org/10.1214/11-AOP734</a>"},"issue":"3 B","quality_controlled":0,"title":"Spectral statistics of Erdős-Rényi graphs I: Local semicircle law","year":"2013","month":"05","_id":"2781","status":"public","publisher":"Institute of Mathematical Statistics","day":"01","date_created":"2018-12-11T11:59:34Z","intvolume":"        41","publist_id":"4109","extern":1,"author":[{"last_name":"Erdös","first_name":"László","full_name":"László Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng-Tzer"},{"last_name":"Yin","first_name":"Jun","full_name":"Yin, Jun"}],"page":"2279 - 2375","publication_status":"published","date_published":"2013-05-01T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1103.1919","open_access":"1"}]},{"abstract":[{"text":"We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-09-29T14:07:43Z","type":"journal_article","volume":152,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"6","citation":{"apa":"Erdös, L., &#38; Farrell, B. (2013). Local eigenvalue density for general MANOVA matrices. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-013-0807-8\">https://doi.org/10.1007/s10955-013-0807-8</a>","chicago":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” <i>Journal of Statistical Physics</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10955-013-0807-8\">https://doi.org/10.1007/s10955-013-0807-8</a>.","ieee":"L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,” <i>Journal of Statistical Physics</i>, vol. 152, no. 6. Springer, pp. 1003–1032, 2013.","ista":"Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 152(6), 1003–1032.","mla":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” <i>Journal of Statistical Physics</i>, vol. 152, no. 6, Springer, 2013, pp. 1003–32, doi:<a href=\"https://doi.org/10.1007/s10955-013-0807-8\">10.1007/s10955-013-0807-8</a>.","short":"L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032.","ama":"Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. <i>Journal of Statistical Physics</i>. 2013;152(6):1003-1032. doi:<a href=\"https://doi.org/10.1007/s10955-013-0807-8\">10.1007/s10955-013-0807-8</a>"},"publisher":"Springer","day":"18","_id":"2782","page":"1003 - 1032","publication":"Journal of Statistical Physics","article_processing_charge":"No","title":"Local eigenvalue density for general MANOVA matrices","quality_controlled":"1","scopus_import":"1","doi":"10.1007/s10955-013-0807-8","oa_version":"Preprint","external_id":{"arxiv":["1207.0031"],"isi":["000323203800001"]},"author":[{"last_name":"Erdös","first_name":"László","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Farrell","first_name":"Brendan","full_name":"Farrell, Brendan"}],"intvolume":"       152","publist_id":"4107","isi":1,"date_created":"2018-12-11T11:59:34Z","arxiv":1,"status":"public","month":"07","year":"2013","date_published":"2013-07-18T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1207.0031","open_access":"1"}],"corr_author":"1","department":[{"_id":"LaEr"}],"publication_status":"published"},{"date_published":"2013-05-01T00:00:00Z","page":"140 - 162","publication_status":"published","extern":1,"author":[{"full_name":"Holzner, Markus","last_name":"Holzner","first_name":"Markus"},{"full_name":"Song, Baofang","first_name":"Baofang","last_name":"Song"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Björn Hof"}],"intvolume":"       723","publist_id":"4084","date_created":"2018-12-11T11:59:41Z","publisher":"Cambridge University Press","day":"01","status":"public","month":"05","_id":"2805","year":"2013","title":"Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow","quality_controlled":0,"doi":"10.1017/jfm.2013.127","citation":{"ama":"Holzner M, Song B, Avila M, Hof B. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. <i>Journal of Fluid Mechanics</i>. 2013;723:140-162. doi:<a href=\"https://doi.org/10.1017/jfm.2013.127\">10.1017/jfm.2013.127</a>","short":"M. Holzner, B. Song, M. Avila, B. Hof, Journal of Fluid Mechanics 723 (2013) 140–162.","mla":"Holzner, Markus, et al. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 723, Cambridge University Press, 2013, pp. 140–62, doi:<a href=\"https://doi.org/10.1017/jfm.2013.127\">10.1017/jfm.2013.127</a>.","ista":"Holzner M, Song B, Avila M, Hof B. 2013. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. 723, 140–162.","ieee":"M. Holzner, B. Song, M. Avila, and B. Hof, “Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 723. Cambridge University Press, pp. 140–162, 2013.","chicago":"Holzner, Markus, Baofang Song, Marc Avila, and Björn Hof. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2013. <a href=\"https://doi.org/10.1017/jfm.2013.127\">https://doi.org/10.1017/jfm.2013.127</a>.","apa":"Holzner, M., Song, B., Avila, M., &#38; Hof, B. (2013). Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2013.127\">https://doi.org/10.1017/jfm.2013.127</a>"},"abstract":[{"text":"Transition in shear flows is characterized by localized turbulent regions embedded in the surrounding laminar flow. These so-called turbulent spots or puffs are observed in a variety of shear flows and in certain Reynolds-number regimes, and they are advected by the flow while keeping their characteristic length. We show here for the case of pipe flow that this seemingly passive advection of turbulent puffs involves continuous entrainment and relaminarization of laminar and turbulent fluid across strongly convoluted interfaces. Surprisingly, interface areas are almost two orders of magnitude larger than the pipe cross-section, while local entrainment velocities are much smaller than the mean speed. Even though these velocities were shown to be small and proportional to the Kolmogorov velocity scale (in agreement with a prediction by Corrsin) in a flow without mean shear before, we find that, in pipe flow, local entrainment velocities are about an order of magnitude smaller than this scale. The Lagrangian method used to study the dynamics of the laminar-turbulent interfaces allows accurate determination of the leading and trailing edge speeds. However, to resolve the highly complex interface dynamics requires much higher numerical resolutions than for ordinary turbulent flows. This method also reveals that the volume flux across the leading edge has the same radial dependence but the opposite sign as that across the trailing edge, and it is this symmetry that is responsible for the puff shape remaining constant.","lang":"eng"}],"publication":"Journal of Fluid Mechanics","date_updated":"2021-01-12T06:59:50Z","type":"journal_article","volume":723},{"external_id":{"isi":["000321273500052"]},"doi":"10.1063/1.4807704","oa_version":"None","scopus_import":"1","title":"High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects","quality_controlled":"1","article_processing_charge":"No","publication":"Review of Scientific Instruments","publication_status":"published","department":[{"_id":"BjHo"}],"date_published":"2013-06-06T00:00:00Z","year":"2013","status":"public","month":"06","date_created":"2018-12-11T11:59:42Z","isi":1,"author":[{"first_name":"Kerstin","last_name":"Avila","full_name":"Avila, Kerstin"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn"}],"intvolume":"        84","publist_id":"4081","citation":{"ama":"Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. <i>Review of Scientific Instruments</i>. 2013;84(6). doi:<a href=\"https://doi.org/10.1063/1.4807704\">10.1063/1.4807704</a>","short":"K. Avila, B. Hof, Review of Scientific Instruments 84 (2013).","mla":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” <i>Review of Scientific Instruments</i>, vol. 84, no. 6, 065106, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1063/1.4807704\">10.1063/1.4807704</a>.","ista":"Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 84(6), 065106.","ieee":"K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects,” <i>Review of Scientific Instruments</i>, vol. 84, no. 6. American Institute of Physics, 2013.","chicago":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” <i>Review of Scientific Instruments</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1063/1.4807704\">https://doi.org/10.1063/1.4807704</a>.","apa":"Avila, K., &#38; Hof, B. (2013). High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. <i>Review of Scientific Instruments</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4807704\">https://doi.org/10.1063/1.4807704</a>"},"issue":"6","article_number":"065106","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","volume":84,"date_updated":"2025-09-29T14:07:11Z","abstract":[{"text":"A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 101-106). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η &lt; 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities.","lang":"eng"}],"language":[{"iso":"eng"}],"_id":"2806","publisher":"American Institute of Physics","day":"06"},{"page":"595 - 604","_id":"2807","publisher":"ACM","day":"01","citation":{"apa":"Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., &#38; Wagner, U. (2013). Extending continuous maps: Polynomiality and undecidability. In <i>45th Annual ACM Symposium on theory of computing</i> (pp. 595–604). Palo Alto, CA, United States: ACM. <a href=\"https://doi.org/10.1145/2488608.2488683\">https://doi.org/10.1145/2488608.2488683</a>","chicago":"Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner. “Extending Continuous Maps: Polynomiality and Undecidability.” In <i>45th Annual ACM Symposium on Theory of Computing</i>, 595–604. ACM, 2013. <a href=\"https://doi.org/10.1145/2488608.2488683\">https://doi.org/10.1145/2488608.2488683</a>.","ieee":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous maps: Polynomiality and undecidability,” in <i>45th Annual ACM Symposium on theory of computing</i>, Palo Alto, CA, United States, 2013, pp. 595–604.","ista":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of computing. STOC: Symposium on the Theory of Computing, 595–604.","mla":"Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.” <i>45th Annual ACM Symposium on Theory of Computing</i>, ACM, 2013, pp. 595–604, doi:<a href=\"https://doi.org/10.1145/2488608.2488683\">10.1145/2488608.2488683</a>.","short":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604.","ama":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps: Polynomiality and undecidability. In: <i>45th Annual ACM Symposium on Theory of Computing</i>. ACM; 2013:595-604. doi:<a href=\"https://doi.org/10.1145/2488608.2488683\">10.1145/2488608.2488683</a>"},"conference":{"end_date":"2013-06-04","name":"STOC: Symposium on the Theory of Computing","location":"Palo Alto, CA, United States","start_date":"2013-06-01"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"conference","date_updated":"2021-01-12T06:59:51Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \\no holes up to dimension k-1&quot; (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. "}],"publication_status":"published","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"pubrep_id":"533","date_published":"2013-06-01T00:00:00Z","year":"2013","month":"06","status":"public","date_created":"2018-12-11T11:59:42Z","publist_id":"4078","author":[{"full_name":"Čadek, Martin","first_name":"Martin","last_name":"Čadek"},{"last_name":"Krcál","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"},{"full_name":"Matoušek, Jiří","first_name":"Jiří","last_name":"Matoušek"},{"full_name":"Vokřínek, Lukáš","last_name":"Vokřínek","first_name":"Lukáš"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli"}],"file":[{"checksum":"06c2ce5c1135fbc1f71ca15eeb242dcf","file_size":447945,"file_id":"5081","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:14:29Z","date_updated":"2020-07-14T12:45:48Z","access_level":"open_access","file_name":"IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf","relation":"main_file"}],"ddc":["510"],"doi":"10.1145/2488608.2488683","file_date_updated":"2020-07-14T12:45:48Z","oa_version":"Submitted Version","scopus_import":1,"quality_controlled":"1","title":"Extending continuous maps: Polynomiality and undecidability","publication":"45th Annual ACM Symposium on theory of computing"},{"pmid":1,"publication":"Plant Physiology","article_processing_charge":"No","quality_controlled":"1","title":"The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain","scopus_import":"1","doi":"10.1104/pp.113.214023","external_id":{"isi":["000321325700015"],"pmid":["23669745"]},"oa_version":"Submitted Version","publist_id":"4079","intvolume":"       162","author":[{"full_name":"Landberg, Katarina","last_name":"Landberg","first_name":"Katarina"},{"first_name":"Eric","last_name":"Pederson","full_name":"Pederson, Eric"},{"full_name":"Viaene, Tom","first_name":"Tom","last_name":"Viaene"},{"full_name":"Bozorg, Behruz","last_name":"Bozorg","first_name":"Behruz"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Jönsson, Henrik","first_name":"Henrik","last_name":"Jönsson"},{"full_name":"Thelander, Mattias","first_name":"Mattias","last_name":"Thelander"},{"first_name":"Eva","last_name":"Sundberg","full_name":"Sundberg, Eva"}],"isi":1,"date_created":"2018-12-11T11:59:42Z","month":"07","status":"public","year":"2013","date_published":"2013-07-03T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/"}],"department":[{"_id":"JiFr"}],"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"text":"In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.","lang":"eng"}],"date_updated":"2025-09-29T14:06:13Z","volume":162,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"issue":"3","citation":{"mla":"Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” <i>Plant Physiology</i>, vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:<a href=\"https://doi.org/10.1104/pp.113.214023\">10.1104/pp.113.214023</a>.","ama":"Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. <i>Plant Physiology</i>. 2013;162(3):1406-1419. doi:<a href=\"https://doi.org/10.1104/pp.113.214023\">10.1104/pp.113.214023</a>","short":"K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M. Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419.","ieee":"K. Landberg <i>et al.</i>, “The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain,” <i>Plant Physiology</i>, vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013.","chicago":"Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml, Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1104/pp.113.214023\">https://doi.org/10.1104/pp.113.214023</a>.","apa":"Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H., … Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.113.214023\">https://doi.org/10.1104/pp.113.214023</a>","ista":"Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419."},"day":"03","publisher":"American Society of Plant Biologists","_id":"2808","page":"1406 - 1419"},{"citation":{"mla":"de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” <i>PLoS Genetics</i>, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003580\">10.1371/journal.pgen.1003580</a>.","ama":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence of genetic constraint. <i>PLoS Genetics</i>. 2013;9(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1003580\">10.1371/journal.pgen.1003580</a>","short":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).","ieee":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental dependence of genetic constraint,” <i>PLoS Genetics</i>, vol. 9, no. 6. Public Library of Science, 2013.","chicago":"Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander Tans. “Environmental Dependence of Genetic Constraint.” <i>PLoS Genetics</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pgen.1003580\">https://doi.org/10.1371/journal.pgen.1003580</a>.","apa":"de Vos, M., Poelwijk, F., Battich, N., Ndika, J., &#38; Tans, S. (2013). Environmental dependence of genetic constraint. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1003580\">https://doi.org/10.1371/journal.pgen.1003580</a>","ista":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580."},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","issue":"6","article_number":"e1003580","type":"journal_article","volume":9,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data."}],"language":[{"iso":"eng"}],"date_updated":"2025-09-29T14:05:09Z","_id":"2810","day":"27","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:48Z","doi":"10.1371/journal.pgen.1003580","oa_version":"Published Version","external_id":{"isi":["000321222600053"]},"ddc":["570"],"file":[{"relation":"main_file","content_type":"application/pdf","creator":"system","file_id":"4713","file_size":474655,"checksum":"7a4736dd80496d29ff6908b6f2329b4e","file_name":"IST-2016-412-v1+1_journal.pgen.1003580.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:48Z","date_created":"2018-12-12T10:08:51Z"}],"title":"Environmental dependence of genetic constraint","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","publication":"PLoS Genetics","pubrep_id":"412","department":[{"_id":"ToBo"}],"publication_status":"published","date_published":"2013-06-27T00:00:00Z","status":"public","month":"06","year":"2013","author":[{"last_name":"De Vos","first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","full_name":"De Vos, Marjon"},{"last_name":"Poelwijk","first_name":"Frank","full_name":"Poelwijk, Frank"},{"full_name":"Battich, Nico","first_name":"Nico","last_name":"Battich"},{"first_name":"Joseph","last_name":"Ndika","full_name":"Ndika, Joseph"},{"full_name":"Tans, Sander","last_name":"Tans","first_name":"Sander"}],"intvolume":"         9","publist_id":"4075","isi":1,"date_created":"2018-12-11T11:59:43Z"},{"article_number":"063012","issue":"6","citation":{"apa":"Avila, M., &#38; Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>","chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>. American Institute of Physics, 2013. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>.","ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” <i>Physical Review E</i>, vol. 87, no. 6. American Institute of Physics, 2013.","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>, vol. 87, no. 6, 063012, American Institute of Physics, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>.","short":"M. Avila, B. Hof, Physical Review E 87 (2013).","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. 2013;87(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>"},"date_updated":"2025-09-29T14:04:31Z","language":[{"iso":"eng"}],"abstract":[{"text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.","lang":"eng"}],"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"type":"journal_article","volume":87,"day":"18","publisher":"American Institute of Physics","_id":"2811","scopus_import":"1","quality_controlled":"1","title":"Nature of laminar-turbulence intermittency in shear flows","oa_version":"Preprint","external_id":{"isi":["000320645700009"],"arxiv":["1306.5890"]},"doi":"10.1103/PhysRevE.87.063012","publication":"Physical Review E","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1306.5890"}],"date_published":"2013-06-18T00:00:00Z","ec_funded":1,"publication_status":"published","department":[{"_id":"BjHo"}],"arxiv":1,"date_created":"2018-12-11T11:59:43Z","isi":1,"publist_id":"4074","intvolume":"        87","author":[{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"year":"2013","month":"06","status":"public"},{"date_updated":"2025-09-23T09:18:30Z","acknowledgement":"Some of the authors were partially supported by the GIGA ANR grant (contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827).","abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"publication":"Proceedings of the 29th annual symposium on Computational Geometry","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","scopus_import":1,"conference":{"start_date":"2013-06-17","name":"SoCG: Symposium on Computational Geometry","end_date":"2013-06-20","location":"Rio de Janeiro, Brazil"},"title":"Homological reconstruction and simplification in R3","quality_controlled":"1","oa_version":"Submitted Version","citation":{"ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>. ACM; 2013:117-125. doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125.","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, ACM, 2013, pp. 117–25, doi:<a href=\"https://doi.org/10.1145/2462356.2462373\">10.1145/2462356.2462373</a>.","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction and simplification in R3. Proceedings of the 29th annual symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 117–125.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In <i>Proceedings of the 29th Annual Symposium on Computational Geometry</i>, 117–25. ACM, 2013. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in <i>Proceedings of the 29th annual symposium on Computational Geometry</i>, Rio de Janeiro, Brazil, 2013, pp. 117–125.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2013). Homological reconstruction and simplification in R3. In <i>Proceedings of the 29th annual symposium on Computational Geometry</i> (pp. 117–125). Rio de Janeiro, Brazil: ACM. <a href=\"https://doi.org/10.1145/2462356.2462373\">https://doi.org/10.1145/2462356.2462373</a>"},"doi":"10.1145/2462356.2462373","date_created":"2018-12-11T11:59:44Z","day":"01","publisher":"ACM","author":[{"full_name":"Attali, Dominique","first_name":"Dominique","last_name":"Attali"},{"first_name":"Ulrich","last_name":"Bauer","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"last_name":"Devillers","first_name":"Olivier","full_name":"Devillers, Olivier"},{"full_name":"Glisse, Marc","last_name":"Glisse","first_name":"Marc"},{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"1805"}]},"publist_id":"4072","year":"2013","status":"public","month":"06","_id":"2812","main_file_link":[{"open_access":"1","url":"http://hal.archives-ouvertes.fr/hal-00833791/"}],"date_published":"2013-06-01T00:00:00Z","page":"117 - 125","publication_status":"published","department":[{"_id":"HeEd"}]},{"_id":"2813","day":"25","publisher":"National Academy of Sciences","page":"10557 - 10562","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","volume":110,"date_updated":"2025-09-29T14:03:43Z","abstract":[{"lang":"eng","text":"Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called &quot;maximum drag reduction&quot; asymptote, which is exhibited by a wide range of viscoelastic fluids."}],"language":[{"iso":"eng"}],"citation":{"mla":"Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” <i>PNAS</i>, vol. 110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>.","ama":"Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. <i>PNAS</i>. 2013;110(26):10557-10562. doi:<a href=\"https://doi.org/10.1073/pnas.1219666110\">10.1073/pnas.1219666110</a>","short":"D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B. Hof, PNAS 110 (2013) 10557–10562.","chicago":"Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>.","ieee":"D. Samanta <i>et al.</i>, “Elasto-inertial turbulence,” <i>PNAS</i>, vol. 110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.","apa":"Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C., &#38; Hof, B. (2013). Elasto-inertial turbulence. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1219666110\">https://doi.org/10.1073/pnas.1219666110</a>","ista":"Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013. Elasto-inertial turbulence. PNAS. 110(26), 10557–10562."},"issue":"26","year":"2013","status":"public","month":"06","isi":1,"date_created":"2018-12-11T11:59:44Z","author":[{"full_name":"Samanta, Devranjan","first_name":"Devranjan","last_name":"Samanta"},{"full_name":"Dubief, Yves","first_name":"Yves","last_name":"Dubief"},{"full_name":"Holzner, Markus","first_name":"Markus","last_name":"Holzner"},{"last_name":"Schäfer","first_name":"Christof","full_name":"Schäfer, Christof"},{"full_name":"Morozov, Alexander","last_name":"Morozov","first_name":"Alexander"},{"last_name":"Wagner","first_name":"Christian","full_name":"Wagner, Christian"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn"}],"intvolume":"       110","publist_id":"4073","publication_status":"published","department":[{"_id":"BjHo"}],"corr_author":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/","open_access":"1"}],"date_published":"2013-06-25T00:00:00Z","article_processing_charge":"No","pmid":1,"publication":"PNAS","external_id":{"pmid":["23757498"],"isi":["000321503700035"]},"doi":"10.1073/pnas.1219666110","oa_version":"Submitted Version","scopus_import":"1","title":"Elasto-inertial turbulence","quality_controlled":"1"},{"_id":"2814","publisher":"World Scientific Publishing","day":"01","page":"165 - 185","volume":24,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing &quot;reset&quot; action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems."}],"date_updated":"2025-09-29T14:02:41Z","citation":{"ista":"Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International Journal of Foundations of Computer Science. 24(2), 165–185.","apa":"Chatterjee, K., Alfaro, L., &#38; Majumdar, R. (2013). The complexity of coverage. <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054113400066\">https://doi.org/10.1142/S0129054113400066</a>","ieee":"K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” <i>International Journal of Foundations of Computer Science</i>, vol. 24, no. 2. World Scientific Publishing, pp. 165–185, 2013.","chicago":"Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity of Coverage.” <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2013. <a href=\"https://doi.org/10.1142/S0129054113400066\">https://doi.org/10.1142/S0129054113400066</a>.","short":"K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations of Computer Science 24 (2013) 165–185.","ama":"Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. <i>International Journal of Foundations of Computer Science</i>. 2013;24(2):165-185. doi:<a href=\"https://doi.org/10.1142/S0129054113400066\">10.1142/S0129054113400066</a>","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” <i>International Journal of Foundations of Computer Science</i>, vol. 24, no. 2, World Scientific Publishing, 2013, pp. 165–85, doi:<a href=\"https://doi.org/10.1142/S0129054113400066\">10.1142/S0129054113400066</a>."},"issue":"2","month":"02","status":"public","year":"2013","intvolume":"        24","publist_id":"4070","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Alfaro, Luca","first_name":"Luca","last_name":"Alfaro"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar"}],"arxiv":1,"date_created":"2018-12-11T11:59:44Z","isi":1,"department":[{"_id":"KrCh"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0804.4525"}],"date_published":"2013-02-01T00:00:00Z","ec_funded":1,"article_processing_charge":"No","publication":"International Journal of Foundations of Computer Science","external_id":{"arxiv":["0804.4525"],"isi":["000319838100002"]},"oa_version":"Preprint","doi":"10.1142/S0129054113400066","quality_controlled":"1","title":"The complexity of coverage","scopus_import":"1"},{"corr_author":"1","main_file_link":[{"url":"https://doi.org/10.1007/s00454-013-9517-x","open_access":"1"}],"date_published":"2013-06-01T00:00:00Z","publication_status":"published","department":[{"_id":"HeEd"}],"date_created":"2018-12-11T11:59:44Z","isi":1,"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Fasy, Brittany Terese","id":"F65D502E-E68D-11E9-9252-C644099818F6","first_name":"Brittany Terese","last_name":"Fasy"},{"last_name":"Rote","first_name":"Günter","full_name":"Rote, Günter"}],"publist_id":"3991","intvolume":"        49","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"year":"2013","status":"public","month":"06","scopus_import":"1","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","quality_controlled":"1","external_id":{"isi":["000320672400005"]},"oa_version":"Published Version","doi":"10.1007/s00454-013-9517-x","acknowledgement":"This research is partially supported by the National Science Foundation (NSF) under Grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.","publication":"Discrete & Computational Geometry","article_processing_charge":"No","page":"797 - 822","day":"01","publisher":"Springer","related_material":{"record":[{"relation":"earlier_version","id":"3134","status":"public"}]},"article_type":"original","_id":"2815","issue":"4","citation":{"apa":"Edelsbrunner, H., Fasy, B. T., &#38; Rote, G. (2013). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-013-9517-x\">https://doi.org/10.1007/s00454-013-9517-x</a>","chicago":"Edelsbrunner, Herbert, Brittany Terese Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00454-013-9517-x\">https://doi.org/10.1007/s00454-013-9517-x</a>.","ieee":"H. Edelsbrunner, B. T. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” <i>Discrete &#38; Computational Geometry</i>, vol. 49, no. 4. Springer, pp. 797–822, 2013.","ista":"Edelsbrunner H, Fasy BT, Rote G. 2013. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Discrete &#38; Computational Geometry. 49(4), 797–822.","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” <i>Discrete &#38; Computational Geometry</i>, vol. 49, no. 4, Springer, 2013, pp. 797–822, doi:<a href=\"https://doi.org/10.1007/s00454-013-9517-x\">10.1007/s00454-013-9517-x</a>.","short":"H. Edelsbrunner, B.T. Fasy, G. Rote, Discrete &#38; Computational Geometry 49 (2013) 797–822.","ama":"Edelsbrunner H, Fasy BT, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. <i>Discrete &#38; Computational Geometry</i>. 2013;49(4):797-822. doi:<a href=\"https://doi.org/10.1007/s00454-013-9517-x\">10.1007/s00454-013-9517-x</a>"},"date_updated":"2025-09-29T14:02:00Z","abstract":[{"lang":"eng","text":"The fact that a sum of isotropic Gaussian kernels can have more modes than kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally not well studied in higher dimensions. We study a configuration of n+1 Gaussian kernels for which there are exactly n+2 modes. We show that all modes lie on a finite set of lines, which we call axes, and study the restriction of the Gaussian mixture to these axes in order to discover that there are an exponential number of critical points in this configuration. Although the existence of ghost modes remained unknown due to the difficulty of finding examples in ℝ2, we show that the resilience of ghost modes grows like the square root of the dimension. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","volume":49},{"article_processing_charge":"No","publication":"Journal of Theoretical Biology","ddc":["000"],"file_date_updated":"2020-07-14T12:45:49Z","doi":"10.1016/j.jtbi.2013.05.029","external_id":{"isi":["000323629500003"]},"oa_version":"Published Version","file":[{"relation":"main_file","creator":"system","file_id":"5110","content_type":"application/pdf","file_size":834604,"checksum":"3c29059ab03a4b8f97a07646b817ddbb","file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:49Z","date_created":"2018-12-12T10:14:54Z"}],"quality_controlled":"1","title":"Density games","scopus_import":"1","month":"10","status":"public","year":"2013","publist_id":"3984","intvolume":"       334","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"date_created":"2018-12-11T11:59:45Z","isi":1,"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"pubrep_id":"400","publication_status":"published","date_published":"2013-10-07T00:00:00Z","ec_funded":1,"corr_author":"1","volume":334,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle."}],"date_updated":"2025-09-29T13:59:11Z","citation":{"apa":"Novak, S., Chatterjee, K., &#38; Nowak, M. (2013). Density games. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>","chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” <i>Journal of Theoretical Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">https://doi.org/10.1016/j.jtbi.2013.05.029</a>.","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” <i>Journal of Theoretical Biology</i>, vol. 334. Elsevier, pp. 26–34, 2013.","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34.","mla":"Novak, Sebastian, et al. “Density Games.” <i>Journal of Theoretical Biology</i>, vol. 334, Elsevier, 2013, pp. 26–34, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>.","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","ama":"Novak S, Chatterjee K, Nowak M. Density games. <i>Journal of Theoretical Biology</i>. 2013;334:26-34. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2013.05.029\">10.1016/j.jtbi.2013.05.029</a>"},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"_id":"2817","publisher":"Elsevier","day":"07","page":"26 - 34"},{"page":"1661 - 1692","_id":"2818","publisher":"MIT Press ","day":"01","citation":{"mla":"Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>.","short":"K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.","ama":"Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. 2013;25(7):1661-1692. doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>","apa":"Rajan, K., Marre, O., &#38; Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. MIT Press . <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>","ieee":"K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” <i>Neural Computation</i>, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013.","chicago":"Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>. MIT Press , 2013. <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>.","ista":"Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692."},"issue":"7","type":"journal_article","volume":25,"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus."}],"language":[{"iso":"eng"}],"date_updated":"2025-09-29T13:58:36Z","department":[{"_id":"GaTk"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0121"}],"date_published":"2013-07-01T00:00:00Z","status":"public","month":"07","year":"2013","author":[{"full_name":"Rajan, Kanaka","first_name":"Kanaka","last_name":"Rajan"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper"}],"publist_id":"3983","intvolume":"        25","date_created":"2018-12-11T11:59:45Z","isi":1,"arxiv":1,"doi":"10.1162/NECO_a_00463","external_id":{"arxiv":["1209.0121"],"isi":["000319903700001"]},"oa_version":"Preprint","title":"Learning quadratic receptive fields from neural responses to natural stimuli","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","publication":"Neural Computation"},{"day":"01","publisher":"Springer","_id":"2819","page":"273 - 282","language":[{"iso":"eng"}],"abstract":[{"text":"We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the &quot;steady-state&quot; maximum timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. ","lang":"eng"}],"date_updated":"2025-06-11T08:04:41Z","type":"conference","volume":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1,"conference":{"start_date":"2013-04-08","location":"Philadelphia, PA USA","name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2013-04-11"},"citation":{"ista":"Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and refinement metrics for real-time systems. Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 1, 273–282.","ieee":"K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and refinement metrics for real-time systems,” in <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, Philadelphia, PA USA, 2013, vol. 1, pp. 273–282.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, 1:273–82. Springer, 2013. <a href=\"https://doi.org/10.1145/2461328.2461370\">https://doi.org/10.1145/2461328.2461370</a>.","apa":"Chatterjee, K., &#38; Prabhu, V. (2013). Quantitative timed simulation functions and refinement metrics for real-time systems. In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i> (Vol. 1, pp. 273–282). Philadelphia, PA USA: Springer. <a href=\"https://doi.org/10.1145/2461328.2461370\">https://doi.org/10.1145/2461328.2461370</a>","ama":"Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement metrics for real-time systems. In: <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>. Vol 1. Springer; 2013:273-282. doi:<a href=\"https://doi.org/10.1145/2461328.2461370\">10.1145/2461328.2461370</a>","short":"K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, vol. 1, Springer, 2013, pp. 273–82, doi:<a href=\"https://doi.org/10.1145/2461328.2461370\">10.1145/2461328.2461370</a>."},"publist_id":"3982","intvolume":"         1","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Vinayak","last_name":"Prabhu","full_name":"Prabhu, Vinayak"}],"arxiv":1,"date_created":"2018-12-11T11:59:46Z","month":"04","status":"public","year":"2013","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.6556"}],"date_published":"2013-04-01T00:00:00Z","ec_funded":1,"department":[{"_id":"KrCh"}],"publication_status":"published","publication":"Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control","acknowledgement":"This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOP-TILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); and the Microsoft faculty fellows award","article_processing_charge":"No","quality_controlled":"1","title":"Quantitative timed simulation functions and refinement metrics for real-time systems","scopus_import":"1","doi":"10.1145/2461328.2461370","external_id":{"arxiv":["1212.6556"]},"oa_version":"Preprint"},{"date_published":"2013-04-01T00:00:00Z","ec_funded":1,"department":[{"_id":"KrCh"}],"publication_status":"published","page":"163 - 172","related_material":{"record":[{"relation":"later_version","id":"738","status":"public"}]},"publist_id":"3981","publication_identifier":{"isbn":["978-1-4503-1567-8 "]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Kößler, Alexander","last_name":"Kößler","first_name":"Alexander"},{"first_name":"Ulrich","last_name":"Schmid","full_name":"Schmid, Ulrich"}],"day":"01","publisher":"ACM","date_created":"2018-12-11T11:59:46Z","_id":"2820","month":"04","status":"public","year":"2013","quality_controlled":"1","title":"Automated analysis of real-time scheduling using graph games","conference":{"start_date":"2013-04-08","location":"Philadelphia, PA, United States","end_date":"2013-04-11","name":"HSCC: Hybrid Systems - Computation and Control"},"scopus_import":1,"doi":"10.1145/2461328.2461356","citation":{"chicago":"Chatterjee, Krishnendu, Alexander Kößler, and Ulrich Schmid. “Automated Analysis of Real-Time Scheduling Using Graph Games.” In <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, 163–72. ACM, 2013. <a href=\"https://doi.org/10.1145/2461328.2461356\">https://doi.org/10.1145/2461328.2461356</a>.","ieee":"K. Chatterjee, A. Kößler, and U. Schmid, “Automated analysis of real-time scheduling using graph games,” in <i>Proceedings of the 16th International conference on Hybrid systems: Computation and control</i>, Philadelphia, PA, United States, 2013, pp. 163–172.","apa":"Chatterjee, K., Kößler, A., &#38; Schmid, U. (2013). Automated analysis of real-time scheduling using graph games. In <i>Proceedings of the 16th International conference on Hybrid systems: Computation and control</i> (pp. 163–172). Philadelphia, PA, United States: ACM. <a href=\"https://doi.org/10.1145/2461328.2461356\">https://doi.org/10.1145/2461328.2461356</a>","ista":"Chatterjee K, Kößler A, Schmid U. 2013. Automated analysis of real-time scheduling using graph games. Proceedings of the 16th International conference on Hybrid systems: Computation and control. HSCC: Hybrid Systems - Computation and Control, 163–172.","mla":"Chatterjee, Krishnendu, et al. “Automated Analysis of Real-Time Scheduling Using Graph Games.” <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2013, pp. 163–72, doi:<a href=\"https://doi.org/10.1145/2461328.2461356\">10.1145/2461328.2461356</a>.","ama":"Chatterjee K, Kößler A, Schmid U. Automated analysis of real-time scheduling using graph games. In: <i>Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2013:163-172. doi:<a href=\"https://doi.org/10.1145/2461328.2461356\">10.1145/2461328.2461356</a>","short":"K. Chatterjee, A. Kößler, U. Schmid, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–172."},"oa_version":"None","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this paper, we introduce the powerful framework of graph games for the analysis of real-time scheduling with firm deadlines. We introduce a novel instance of a partial-observation game that is suitable for this purpose, and prove decidability of all the involved decision problems. We derive a graph game that allows the automated computation of the competitive ratio (along with an optimal witness algorithm for the competitive ratio) and establish an NP-completeness proof for the graph game problem. For a given on-line algorithm, we present polynomial time solution for computing (i) the worst-case utility; (ii) the worst-case utility ratio w.r.t. a clairvoyant off-line algorithm; and (iii) the competitive ratio. A major strength of the proposed approach lies in its flexibility w.r.t. incorporating additional constraints on the adversary and/or the algorithm, including limited maximum or average load, finiteness of periods of overload, etc., which are easily added by means of additional instances of standard objective functions for graph games. "}],"publication":"Proceedings of the 16th International conference on Hybrid systems: Computation and control","date_updated":"2025-04-15T08:12:28Z","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]}]