[{"extern":1,"abstract":[{"lang":"eng","text":"Tampering attacks are cryptanalytic attacks on the implementation of cryptographic algorithms (e.g., smart cards), where an adversary introduces faults with the hope that the tampered device will reveal secret information. Inspired by the work of Ishai et al. [Eurocrypt'06], we propose a compiler that transforms any circuit into a new circuit with the same functionality, but which is resilient against a well-defined and powerful tampering adversary. More concretely, our transformed circuits remain secure even if the adversary can adaptively tamper with every wire in the circuit as long as the tampering fails with some probability δ>0. This additional requirement is motivated by practical tampering attacks, where it is often difficult to guarantee the success of a specific attack. Formally, we show that a q-query tampering attack against the transformed circuit can be "simulated" with only black-box access to the original circuit and log(q) bits of additional auxiliary information. Thus, if the implemented cryptographic scheme is secure against log(q) bits of leakage, then our implementation is tamper-proof in the above sense. Surprisingly, allowing for this small amount of information leakage allows for much more efficient compilers, which moreover do not require randomness during evaluation. Similar to earlier works our compiler requires small, stateless and computation-independent tamper-proof gadgets. Thus, our result can be interpreted as reducing the problem of shielding arbitrary complex computation to protecting simple components. © 2011 Springer-Verlag."}],"publist_id":"3441","issue":"Part 1","alternative_title":["LNCS"],"type":"conference","date_created":"2018-12-11T12:02:12Z","date_updated":"2021-01-12T07:42:02Z","volume":"6755 ","author":[{"last_name":"Faust","first_name":"Sebastian","full_name":"Faust, Sebastian"},{"full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Venturi, Daniele","first_name":"Daniele","last_name":"Venturi"}],"title":"Tamper proof circuits How to trade leakage for tamper resilience","status":"public","publication_status":"published","publisher":"Springer","_id":"3239","year":"2011","day":"01","month":"01","conference":{"name":"ICALP: Automata, Languages and Programming"},"doi":"10.1007/978-3-642-22006-7_33","date_published":"2011-01-01T00:00:00Z","quality_controlled":0,"page":"391 - 402","citation":{"ama":"Faust S, Pietrzak KZ, Venturi D. Tamper proof circuits How to trade leakage for tamper resilience. In: Vol 6755. Springer; 2011:391-402. doi:10.1007/978-3-642-22006-7_33","apa":"Faust, S., Pietrzak, K. Z., & Venturi, D. (2011). Tamper proof circuits How to trade leakage for tamper resilience (Vol. 6755, pp. 391–402). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-642-22006-7_33","ieee":"S. Faust, K. Z. Pietrzak, and D. Venturi, “Tamper proof circuits How to trade leakage for tamper resilience,” presented at the ICALP: Automata, Languages and Programming, 2011, vol. 6755, no. Part 1, pp. 391–402.","ista":"Faust S, Pietrzak KZ, Venturi D. 2011. Tamper proof circuits How to trade leakage for tamper resilience. ICALP: Automata, Languages and Programming, LNCS, vol. 6755, 391–402.","short":"S. Faust, K.Z. Pietrzak, D. Venturi, in:, Springer, 2011, pp. 391–402.","mla":"Faust, Sebastian, et al. Tamper Proof Circuits How to Trade Leakage for Tamper Resilience. Vol. 6755, no. Part 1, Springer, 2011, pp. 391–402, doi:10.1007/978-3-642-22006-7_33.","chicago":"Faust, Sebastian, Krzysztof Z Pietrzak, and Daniele Venturi. “Tamper Proof Circuits How to Trade Leakage for Tamper Resilience,” 6755:391–402. Springer, 2011. https://doi.org/10.1007/978-3-642-22006-7_33."}},{"month":"01","day":"01","conference":{"name":"TCC: Theory of Cryptography Conference"},"doi":"10.1007/978-3-642-19571-6_5","date_published":"2011-01-01T00:00:00Z","quality_controlled":0,"page":"58 - 69","citation":{"short":"A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.","mla":"Jain, Abhishek, and Krzysztof Z. Pietrzak. Parallel Repetition for Leakage Resilience Amplification Revisited. Vol. 6597, Springer, 2011, pp. 58–69, doi:10.1007/978-3-642-19571-6_5.","chicago":"Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. https://doi.org/10.1007/978-3-642-19571-6_5.","ama":"Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification revisited. In: Vol 6597. Springer; 2011:58-69. doi:10.1007/978-3-642-19571-6_5","apa":"Jain, A., & Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-19571-6_5","ieee":"A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol. 6597, pp. 58–69.","ista":"Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69."},"extern":1,"abstract":[{"lang":"eng","text":"If a cryptographic primitive remains secure even if ℓ bits about the secret key are leaked to the adversary, one would expect that at least one of n independent instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition has been proven true for schemes satisfying some special information-theoretic properties by Alwen et al. [Eurocrypt'10]. On the negative side, Lewko and Waters [FOCS'10] construct a CPA secure public-key encryption scheme for which this intuition fails. The counterexample of Lewko and Waters leaves open the interesting possibility that for any scheme there exists a constant c>0, such that n fold repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample requires the n copies of the encryption scheme to share a common reference parameter, leaving open the possibility that the intuition is true for all schemes without common setup. In this work we give a stronger counterexample ruling out these possibilities. We construct a signature scheme such that: 1. a single instantiation remains secure given ℓ = log(k) bits of leakage where k is a security parameter. 2. any polynomial number of independent instantiations can be broken (in the strongest sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not depend on the number of instances. The computational assumption underlying our counterexample is that non-interactive computationally sound proofs exist. Moreover, under a stronger (non-standard) assumption about such proofs, our counterexample does not require a common reference parameter. The underlying idea of our counterexample is rather generic and can be applied to other primitives like encryption schemes. © 2011 International Association for Cryptologic Research."}],"publist_id":"3443","alternative_title":["LNCS"],"type":"conference","date_updated":"2021-01-12T07:42:00Z","date_created":"2018-12-11T12:02:11Z","volume":"6597 ","author":[{"full_name":"Jain, Abhishek","first_name":"Abhishek","last_name":"Jain"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Krzysztof Pietrzak"}],"publication_status":"published","title":"Parallel repetition for leakage resilience amplification revisited","status":"public","publisher":"Springer","year":"2011","_id":"3236"},{"month":"07","day":"20","date_published":"2011-07-20T00:00:00Z","doi":"10.1371/journal.pone.0019884","quality_controlled":0,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"chicago":"Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian, and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0019884.","short":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011).","mla":"Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884.","ieee":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.","apa":"Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., & Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0019884","ista":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 6(7).","ama":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0019884"},"oa":1,"publication":"PLoS One","extern":1,"publist_id":"3370","issue":"7","file_date_updated":"2020-07-14T12:46:06Z","abstract":[{"lang":"eng","text":"We present an algorithm to identify individual neural spikes observed on high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers of distinct neural units, even when spikes overlap, and accounts for intrinsic variability of spikes from each unit. As MEAs grow larger, it is important to find spike-identification methods that are scalable, that is, the computational cost of spike fitting should scale well with the number of units observed. Our algorithm accomplishes this goal, and is fast, because it exploits the spatial locality of each unit and the basic biophysics of extracellular signal propagation. Human interaction plays a key role in our method; but effort is minimized and streamlined via a graphical interface. We illustrate our method on data from guinea pig retinal ganglion cells and document its performance on simulated data consisting of spikes added to experimentally measured background noise. We present several tests demonstrating that the algorithm is highly accurate: it exhibits low error rates on fits to synthetic data, low refractory violation rates, good receptive field coverage, and consistency across users."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"IST-2015-381-v1+1_journal.pone.0019884.pdf","file_size":885464,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4894","checksum":"654464e99683b55a699734213d5356f1","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:11:38Z"}],"volume":6,"date_updated":"2021-01-12T07:42:19Z","date_created":"2018-12-11T12:02:24Z","pubrep_id":"381","author":[{"full_name":"Prentice, Jason S","first_name":"Jason","last_name":"Prentice"},{"last_name":"Homann","first_name":"Jan","full_name":"Homann, Jan"},{"last_name":"Simmons","first_name":"Kristina","full_name":"Simmons, Kristina D"},{"full_name":"Gasper Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"},{"last_name":"Balasubramanian","first_name":"Vijay","full_name":"Balasubramanian, Vijay"},{"full_name":"Nelson, Philip C","last_name":"Nelson","first_name":"Philip"}],"publisher":"Public Library of Science","intvolume":" 6","publication_status":"published","status":"public","title":"Fast, scalable, Bayesian spike identification for multi-electrode arrays","year":"2011","_id":"3276","acknowledgement":"This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04.\n\nMichael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior.\n\n"},{"author":[{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert"},{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"first_name":"Erald","last_name":"Vuçini","full_name":"Vuçini, Erald"}],"oa_version":"None","date_created":"2018-12-11T12:02:23Z","date_updated":"2021-01-12T07:42:18Z","year":"2011","_id":"3271","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","editor":[{"full_name":"Peikert, Ronald","first_name":"Ronald","last_name":"Peikert"},{"full_name":"Hauser, Helwig","first_name":"Helwig","last_name":"Hauser"},{"full_name":"Carr, Hamish","first_name":"Hamish","last_name":"Carr"},{"first_name":"Raphael","last_name":"Fuchs","full_name":"Fuchs, Raphael"}],"department":[{"_id":"HeEd"}],"publisher":"Springer","status":"public","publication_status":"published","title":"Efficient computation of persistent homology for cubical data","publist_id":"3375","abstract":[{"text":"In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets.","lang":"eng"}],"type":"book_chapter","alternative_title":["Theory, Algorithms, and Applications"],"date_published":"2011-11-14T00:00:00Z","doi":"10.1007/978-3-642-23175-9_7","language":[{"iso":"eng"}],"citation":{"ama":"Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. Topological Methods in Data Analysis and Visualization II. Springer; 2011:91-106. doi:10.1007/978-3-642-23175-9_7","ieee":"H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology for cubical data,” in Topological Methods in Data Analysis and Visualization II, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp. 91–106.","apa":"Wagner, H., Chen, C., & Vuçini, E. (2011). Efficient computation of persistent homology for cubical data. In R. Peikert, H. Hauser, H. Carr, & R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II (pp. 91–106). Springer. https://doi.org/10.1007/978-3-642-23175-9_7","ista":"Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology for cubical data. In: Topological Methods in Data Analysis and Visualization II. Theory, Algorithms, and Applications, , 91–106.","short":"H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106.","mla":"Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical Data.” Topological Methods in Data Analysis and Visualization II, edited by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:10.1007/978-3-642-23175-9_7.","chicago":"Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of Persistent Homology for Cubical Data.” In Topological Methods in Data Analysis and Visualization II, edited by Ronald Peikert, Helwig Hauser, Hamish Carr, and Raphael Fuchs, 91–106. Springer, 2011. https://doi.org/10.1007/978-3-642-23175-9_7."},"publication":"Topological Methods in Data Analysis and Visualization II","page":"91 - 106","quality_controlled":"1","month":"11","day":"14","scopus_import":1},{"month":"10","day":"01","date_published":"2011-10-01T00:00:00Z","doi":"10.1016/j.ympev.2011.05.016","quality_controlled":0,"page":"237 - 243","publication":"Molecular Phylogenetics and Evolution","citation":{"short":"R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution 61 (2011) 237–243.","mla":"Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:10.1016/j.ympev.2011.05.016.","chicago":"Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” Molecular Phylogenetics and Evolution. Elsevier, 2011. https://doi.org/10.1016/j.ympev.2011.05.016.","ama":"Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 2011;61(1):237-243. doi:10.1016/j.ympev.2011.05.016","apa":"Vila, R., Pierce, N., Nash, D., & Ugelvig, L. V. (2011). A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. Elsevier. https://doi.org/10.1016/j.ympev.2011.05.016","ieee":"R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade,” Molecular Phylogenetics and Evolution, vol. 61, no. 1. Elsevier, pp. 237–243, 2011.","ista":"Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 61(1), 237–243."},"extern":1,"abstract":[{"lang":"eng","text":"Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species.\nWe find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies."}],"publist_id":"3368","issue":"1","type":"journal_article","date_updated":"2021-01-12T07:42:20Z","date_created":"2018-12-11T12:02:25Z","volume":61,"author":[{"full_name":"Vila, Roger","first_name":"Roger","last_name":"Vila"},{"first_name":"Naomi","last_name":"Pierce","full_name":"Pierce, Naomi E"},{"full_name":"Nash, David R","last_name":"Nash","first_name":"David"},{"full_name":"Line Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","first_name":"Line V","last_name":"Ugelvig"}],"title":"A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade","status":"public","publication_status":"published","intvolume":" 61","publisher":"Elsevier","_id":"3278","year":"2011"},{"page":"197 - 200","quality_controlled":"1","citation":{"chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.","mla":"Chen, Chao, and Michael Kerber. Persistent Homology Computation with a Twist. TU Dortmund, 2011, pp. 197–200.","ieee":"C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland, 2011, pp. 197–200.","apa":"Chen, C., & Kerber, M. (2011). Persistent homology computation with a twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland: TU Dortmund.","ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200."},"language":[{"iso":"eng"}],"date_published":"2011-01-01T00:00:00Z","conference":{"name":"EuroCG: European Workshop on Computational Geometry","location":"Morschach, Switzerland","start_date":"2011-03-28","end_date":"2011-03-30"},"month":"01","day":"01","department":[{"_id":"HeEd"}],"publisher":"TU Dortmund","title":"Persistent homology computation with a twist","publication_status":"published","status":"public","year":"2011","_id":"3270","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2018-12-11T12:02:22Z","date_updated":"2021-01-12T07:42:17Z","author":[{"last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"first_name":"Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"}],"type":"conference","publist_id":"3376","abstract":[{"lang":"eng","text":"The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions."}]},{"type":"conference","abstract":[{"text":"We present a new algorithm for enforcing incompressibility for Smoothed Particle Hydrodynamics (SPH) by preserving uniform density across the domain. We propose a hybrid method that uses a Poisson solve on a coarse grid to enforce a divergence free velocity field, followed by a local density correction of the particles. This avoids typical grid artifacts and maintains the Lagrangian nature of SPH by directly transferring pressures onto particles. Our method can be easily integrated with existing SPH techniques such as the incompressible PCISPH method as well as weakly compressible SPH by adding an additional force term. We show that this hybrid method accelerates convergence towards uniform density and permits a significantly larger time step compared to earlier approaches while producing similar results. We demonstrate our approach in a variety of scenarios with significant pressure gradients such as splashing liquids.","lang":"eng"}],"status":"public","ddc":["000"],"title":"Hybrid smoothed particle hydrodynamics","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3298","file":[{"file_id":"4769","relation":"main_file","checksum":"6579d27709946e0eefbfa60a456b4913","date_created":"2018-12-12T10:09:44Z","date_updated":"2020-07-14T12:46:06Z","access_level":"open_access","file_name":"IST-2016-598-v1+1_HybridSPH_Preprint.pdf","creator":"system","file_size":2536216,"content_type":"application/pdf"}],"oa_version":"Submitted Version","pubrep_id":"598","scopus_import":1,"has_accepted_license":"1","day":"05","page":"33 - 42","citation":{"short":"K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp. 33–42.","mla":"Raveendran, Karthik, et al. Hybrid Smoothed Particle Hydrodynamics. Edited by Stephen Spencer, ACM, 2011, pp. 33–42, doi:10.1145/2019406.2019411.","chicago":"Raveendran, Karthik, Chris Wojtan, and Greg Turk. “Hybrid Smoothed Particle Hydrodynamics.” edited by Stephen Spencer, 33–42. ACM, 2011. https://doi.org/10.1145/2019406.2019411.","ama":"Raveendran K, Wojtan C, Turk G. Hybrid smoothed particle hydrodynamics. In: Spencer S, ed. ACM; 2011:33-42. doi:10.1145/2019406.2019411","apa":"Raveendran, K., Wojtan, C., & Turk, G. (2011). Hybrid smoothed particle hydrodynamics. In S. Spencer (Ed.) (pp. 33–42). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada: ACM. https://doi.org/10.1145/2019406.2019411","ieee":"K. Raveendran, C. Wojtan, and G. Turk, “Hybrid smoothed particle hydrodynamics,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada, 2011, pp. 33–42.","ista":"Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42."},"date_published":"2011-08-05T00:00:00Z","publist_id":"3343","file_date_updated":"2020-07-14T12:46:06Z","publisher":"ACM","editor":[{"full_name":"Spencer, Stephen","last_name":"Spencer","first_name":"Stephen"}],"department":[{"_id":"ChWo"}],"publication_status":"published","year":"2011","date_created":"2018-12-11T12:02:32Z","date_updated":"2023-02-23T11:21:05Z","author":[{"full_name":"Raveendran, Karthik","first_name":"Karthik","last_name":"Raveendran"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"first_name":"Greg","last_name":"Turk","full_name":"Turk, Greg"}],"month":"08","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2019406.2019411","conference":{"location":"Vancouver, Canada","start_date":"2011-08-05","end_date":"2011-08-07","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation"}},{"oa":1,"quality_controlled":"1","doi":"10.1145/2037636.2037644","conference":{"end_date":"2011-08-11","location":"Vancouver, BC, Canada","start_date":"2011-08-07","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"language":[{"iso":"eng"}],"month":"08","year":"2011","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","author":[{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"},{"full_name":"Müller Fischer, Matthias","last_name":"Müller Fischer","first_name":"Matthias"},{"last_name":"Brochu","first_name":"Tyson","full_name":"Brochu, Tyson"}],"date_updated":"2023-02-23T11:21:02Z","date_created":"2018-12-11T12:02:31Z","article_number":"8","publist_id":"3344","file_date_updated":"2020-07-14T12:46:06Z","citation":{"short":"C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.","mla":"Wojtan, Chris, et al. Liquid Simulation with Mesh-Based Surface Tracking. 8, ACM, 2011, doi:10.1145/2037636.2037644.","chicago":"Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation with Mesh-Based Surface Tracking.” ACM, 2011. https://doi.org/10.1145/2037636.2037644.","ama":"Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface tracking. In: ACM; 2011. doi:10.1145/2037636.2037644","apa":"Wojtan, C., Müller Fischer, M., & Brochu, T. (2011). Liquid simulation with mesh-based surface tracking. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada: ACM. https://doi.org/10.1145/2037636.2037644","ieee":"C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011.","ista":"Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 8."},"date_published":"2011-08-07T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"07","_id":"3297","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"status":"public","title":"Liquid simulation with mesh-based surface tracking","pubrep_id":"599","oa_version":"Published Version","file":[{"checksum":"8d508ad7c82f50978acbaa4170ee0a75","date_created":"2018-12-12T10:13:34Z","date_updated":"2020-07-14T12:46:06Z","file_id":"5018","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":34672096,"access_level":"open_access","file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf"}],"type":"conference","abstract":[{"text":"Animating detailed liquid surfaces has always been a challenge for computer graphics researchers and visual effects artists. Over the past few years, researchers in this field have focused on mesh-based surface tracking to synthesize extremely detailed liquid surfaces as efficiently as possible. This course provides a solid understanding of the steps required to create a fluid simulator with a mesh-based liquid surface.\r\n\r\nThe course begins with an overview of several existing liquid-surface-tracking techniques and the pros and cons of each method. Then it explains how to embed a triangle mesh into a finite-difference-based fluid simulator and describes several methods for allowing the liquid surface to merge together or break apart. The final section showcases the benefits and further applications of a mesh-based liquid surface, highlighting state-of-the-art methods for tracking colors and textures, maintaining liquid volume, preserving small surface features, and simulating realistic surface-tension waves.","lang":"eng"}]},{"volume":189,"date_updated":"2021-01-12T07:42:26Z","date_created":"2018-12-11T12:02:29Z","author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"last_name":"Harrison","first_name":"Richard","full_name":"Harrison, Richard"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2011","publist_id":"3355","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.111.129569","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/"}],"month":"11","oa_version":"Submitted Version","intvolume":" 189","status":"public","title":"A general method for calculating likelihoods under the coalescent process","_id":"3290","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"text":"Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small.","lang":"eng"}],"type":"journal_article","date_published":"2011-11-01T00:00:00Z","page":"977 - 987","citation":{"apa":"Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.111.129569","ieee":"K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987.","ama":"Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569","chicago":"Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics Society of America, 2011. https://doi.org/10.1534/genetics.111.129569.","short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","mla":"Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:10.1534/genetics.111.129569."},"publication":"Genetics","day":"01","scopus_import":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3312","status":"public","title":"Detailed reconstruction of 3D plant root shape","ddc":["000"],"pubrep_id":"541","file":[{"checksum":"30a33564b7b45a7ee31610898267fd0e","date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:09:04Z","relation":"main_file","file_id":"4727","content_type":"application/pdf","file_size":5622728,"creator":"system","access_level":"open_access","file_name":"IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf"}],"oa_version":"Submitted Version","type":"conference_poster","abstract":[{"text":"We study the 3D reconstruction of plant roots from multiple 2D images. To meet the challenge caused by the delicate nature of thin branches, we make three innovations to cope with the sensitivity to image quality and calibration. First, we model the background as a harmonic function to improve the segmentation of the root in each 2D image. Second, we develop the concept of the regularized visual hull which reduces the effect of jittering and refraction by ensuring consistency with one 2D image. Third, we guarantee connectedness through adjustments to the 3D reconstruction that minimize global error. Our software is part of a biological phenotype/genotype study of agricultural root systems. It has been tested on more than 40 plant roots and results are promising in terms of reconstruction quality and efficiency.","lang":"eng"}],"publication":"Proceedings of the IEEE International Conference on Computer Vision","citation":{"ista":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction of 3D plant root shape, IEEE,p.","apa":"Zheng, Y., Gu, S., Edelsbrunner, H., Tomasi, C., & Benfey, P. (2011). Detailed reconstruction of 3D plant root shape. Proceedings of the IEEE International Conference on Computer Vision. Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126475","ieee":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey, Detailed reconstruction of 3D plant root shape. IEEE, 2011.","ama":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. Detailed Reconstruction of 3D Plant Root Shape. IEEE; 2011. doi:10.1109/ICCV.2011.6126475","chicago":"Zheng, Ying, Steve Gu, Herbert Edelsbrunner, Carlo Tomasi, and Philip Benfey. Detailed Reconstruction of 3D Plant Root Shape. Proceedings of the IEEE International Conference on Computer Vision. IEEE, 2011. https://doi.org/10.1109/ICCV.2011.6126475.","mla":"Zheng, Ying, et al. “Detailed Reconstruction of 3D Plant Root Shape.” Proceedings of the IEEE International Conference on Computer Vision, 6126475, IEEE, 2011, doi:10.1109/ICCV.2011.6126475.","short":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, P. Benfey, Detailed Reconstruction of 3D Plant Root Shape, IEEE, 2011."},"date_published":"2011-12-31T00:00:00Z","day":"31","article_processing_charge":"No","has_accepted_license":"1","year":"2011","acknowledgement":"This research is supported by the National Science Foundation (NSF) under grant DBI-0820624.","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"IEEE","author":[{"first_name":"Ying","last_name":"Zheng","full_name":"Zheng, Ying"},{"first_name":"Steve","last_name":"Gu","full_name":"Gu, Steve"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"last_name":"Tomasi","first_name":"Carlo","full_name":"Tomasi, Carlo"},{"first_name":"Philip","last_name":"Benfey","full_name":"Benfey, Philip"}],"date_created":"2018-12-11T12:02:36Z","date_updated":"2020-07-14T23:03:43Z","article_number":"6126475","file_date_updated":"2020-07-14T12:46:07Z","publist_id":"3328","oa":1,"quality_controlled":"1","conference":{"start_date":"2011-11-06","location":"Barcelona, Spain","end_date":"2011-11-13","name":"ICCV: International Conference on Computer Vision"},"doi":"10.1109/ICCV.2011.6126475","language":[{"iso":"eng"}],"month":"12"}]