[{"doi":"10.1111/cgf.12826","date_published":"2016-05-27T00:00:00Z","department":[{"_id":"ChWo"}],"acknowledgement":"This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ","language":[{"iso":"eng"}],"file":[{"file_id":"5000","content_type":"application/pdf","checksum":"8e61387ee2e3bd0e776fbe301629bfd9","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:13:18Z","date_updated":"2020-07-14T12:44:53Z","relation":"main_file","file_size":15873858,"file_name":"IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf"}],"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020"}],"article_processing_charge":"No","has_accepted_license":"1","author":[{"full_name":"Goldade, Ryan","last_name":"Goldade","first_name":"Ryan"},{"full_name":"Batty, Christopher","last_name":"Batty","first_name":"Christopher"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"_id":"1412","isi":1,"ddc":["000"],"publication":"Computer Graphics Forum","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"intvolume":" 35","quality_controlled":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods."}],"date_updated":"2025-09-18T14:26:23Z","month":"05","external_id":{"isi":["000377222200022"]},"publist_id":"5795","ec_funded":1,"scopus_import":"1","pubrep_id":"612","day":"27","citation":{"chicago":"Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826.","mla":"Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 233–42, doi:10.1111/cgf.12826.","short":"R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242.","ama":"Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826","apa":"Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826","ista":"Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242.","ieee":"R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 233–242, 2016."},"date_created":"2018-12-11T11:51:52Z","volume":35,"type":"journal_article","file_date_updated":"2020-07-14T12:44:53Z","title":"A practical method for high-resolution embedded liquid surfaces","issue":"2","publication_status":"published","publisher":"Wiley-Blackwell","year":"2016","page":"233 - 242"},{"date_created":"2018-12-11T11:51:53Z","volume":35,"citation":{"ieee":"S. Jeschke, “Generalized diffusion curves: An improved vector representation for smooth-shaded images,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 71–79, 2016.","mla":"Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 71–79, doi:10.1111/cgf.12812.","chicago":"Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12812.","apa":"Jeschke, S. (2016). Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12812","ista":"Jeschke S. 2016. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 35(2), 71–79.","short":"S. Jeschke, Computer Graphics Forum 35 (2016) 71–79.","ama":"Jeschke S. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 2016;35(2):71-79. doi:10.1111/cgf.12812"},"day":"01","scopus_import":"1","corr_author":"1","page":"71 - 79","year":"2016","publication_status":"published","publisher":"Wiley-Blackwell","issue":"2","type":"journal_article","title":"Generalized diffusion curves: An improved vector representation for smooth-shaded images","publication":"Computer Graphics Forum","author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"}],"_id":"1413","isi":1,"project":[{"grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","doi":"10.1111/cgf.12812","department":[{"_id":"ChWo"}],"date_published":"2016-05-01T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000377222200008"]},"publist_id":"5794","abstract":[{"text":"This paper generalizes the well-known Diffusion Curves Images (DCI), which are composed of a set of Bezier curves with colors specified on either side. These colors are diffused as Laplace functions over the image domain, which results in smooth color gradients interrupted by the Bezier curves. Our new formulation allows for more color control away from the boundary, providing a similar expressive power as recent Bilaplace image models without introducing associated issues and computational costs. The new model is based on a special Laplace function blending and a new edge blur formulation. We demonstrate that given some user-defined boundary curves over an input raster image, fitting colors and edge blur from the image to the new model and subsequent editing and animation is equally convenient as with DCIs. Numerous examples and comparisons to DCIs are presented.","lang":"eng"}],"date_updated":"2025-09-18T14:25:33Z","month":"05","quality_controlled":"1","oa_version":"None","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 35"},{"publication":"Computer Graphics Forum","isi":1,"_id":"1414","author":[{"first_name":"Eder","last_name":"Miguel Villalba","orcid":"0000-0001-5665-0430","full_name":"Miguel Villalba, Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Miraut","full_name":"Miraut, David"},{"full_name":"Otaduy, Miguel","first_name":"Miguel","last_name":"Otaduy"}],"article_processing_charge":"No","acknowledgement":"This work was funded in part by grants from the Spanish Ministry of Economy (TIN2012-35840), the European Research Council (ERC Starting Grant no. 280135 Animetrics), and the EU FP7 (project no. 601165 WEARHAP).","language":[{"iso":"eng"}],"date_published":"2016-05-01T00:00:00Z","department":[{"_id":"BeBi"}],"doi":"10.1111/cgf.12840","external_id":{"isi":["000377222200036"]},"publist_id":"5792","month":"05","date_updated":"2025-09-18T14:24:28Z","abstract":[{"lang":"eng","text":"In this paper, we present a method to model hyperelasticity that is well suited for representing the nonlinearity of real-world objects, as well as for estimating it from deformation examples. Previous approaches suffer several limitations, such as lack of integrability of elastic forces, failure to enforce energy convexity, lack of robustness of parameter estimation, or difficulty to model cross-modal effects. Our method avoids these problems by relying on a general energy-based definition of elastic properties. The accuracy of the resulting elastic model is maximized by defining an additive model of separable energy terms, which allow progressive parameter estimation. In addition, our method supports efficient modeling of extreme nonlinearities thanks to energy-limiting constraints. We combine our energy-based model with an optimization method to estimate model parameters from force-deformation examples, and we show successful modeling of diverse deformable objects, including cloth, human finger skin, and internal human anatomy in a medical imaging application."}],"oa_version":"None","quality_controlled":"1","intvolume":" 35","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","volume":35,"date_created":"2018-12-11T11:51:53Z","citation":{"mla":"Miguel Villalba, Eder, et al. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 385–96, doi:10.1111/cgf.12840.","chicago":"Miguel Villalba, Eder, David Miraut, and Miguel Otaduy. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12840.","ista":"Miguel Villalba E, Miraut D, Otaduy M. 2016. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 35(2), 385–396.","apa":"Miguel Villalba, E., Miraut, D., & Otaduy, M. (2016). Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12840","ama":"Miguel Villalba E, Miraut D, Otaduy M. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 2016;35(2):385-396. doi:10.1111/cgf.12840","short":"E. Miguel Villalba, D. Miraut, M. Otaduy, Computer Graphics Forum 35 (2016) 385–396.","ieee":"E. Miguel Villalba, D. Miraut, and M. Otaduy, “Modeling and estimation of energy-based hyperelastic objects,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 385–396, 2016."},"day":"01","scopus_import":"1","year":"2016","page":"385 - 396","publisher":"Wiley-Blackwell","publication_status":"published","issue":"2","title":"Modeling and estimation of energy-based hyperelastic objects","type":"journal_article"},{"citation":{"ieee":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, and N. Thuerey, “Narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 225–232, 2016.","mla":"Ferstl, Florian, et al. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 225–32, doi:10.1111/cgf.12825.","chicago":"Ferstl, Florian, Ryoichi Ando, Chris Wojtan, Rüdiger Westermann, and Nils Thuerey. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12825.","apa":"Ferstl, F., Ando, R., Wojtan, C., Westermann, R., & Thuerey, N. (2016). Narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12825","ista":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. 2016. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 35(2), 225–232.","short":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232.","ama":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 2016;35(2):225-232. doi:10.1111/cgf.12825"},"volume":35,"date_created":"2018-12-11T11:51:53Z","pubrep_id":"611","scopus_import":"1","day":"01","publisher":"Wiley-Blackwell","publication_status":"published","year":"2016","page":"225 - 232","title":"Narrow band FLIP for liquid simulations","file_date_updated":"2020-07-14T12:44:53Z","type":"journal_article","issue":"2","isi":1,"_id":"1415","author":[{"full_name":"Ferstl, Florian","last_name":"Ferstl","first_name":"Florian"},{"full_name":"Ando, Ryoichi","last_name":"Ando","first_name":"Ryoichi"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"},{"full_name":"Westermann, Rüdiger","last_name":"Westermann","first_name":"Rüdiger"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"}],"has_accepted_license":"1","publication":"Computer Graphics Forum","ddc":["000"],"language":[{"iso":"eng"}],"date_published":"2016-05-01T00:00:00Z","department":[{"_id":"ChWo"}],"doi":"10.1111/cgf.12825","article_processing_charge":"No","file":[{"access_level":"open_access","date_created":"2018-12-12T10:12:22Z","creator":"system","checksum":"984afbe510ed48019025dff1dcc7baad","file_id":"4940","content_type":"application/pdf","file_size":5938324,"date_updated":"2020-07-14T12:44:53Z","relation":"main_file","file_name":"IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf"}],"month":"05","date_updated":"2025-09-18T14:25:04Z","abstract":[{"text":"The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation.","lang":"eng"}],"publist_id":"5793","external_id":{"isi":["000377222200021"]},"intvolume":" 35","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"status":"public","oa_version":"Submitted Version","quality_controlled":"1"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"intvolume":" 211","status":"public","quality_controlled":"1","oa_version":"Submitted Version","month":"07","date_updated":"2025-09-18T14:23:21Z","abstract":[{"text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.","lang":"eng"}],"publist_id":"5790","external_id":{"isi":["000379212800008"]},"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","language":[{"iso":"eng"}],"doi":"10.1111/nph.14019","date_published":"2016-07-01T00:00:00Z","department":[{"_id":"JiFr"}],"file":[{"date_updated":"2020-07-14T12:44:53Z","relation":"main_file","file_size":3828383,"checksum":"23522ced3508ffe7a4f247c4230e6493","content_type":"application/pdf","file_id":"5016","creator":"system","date_created":"2018-12-12T10:13:32Z","access_level":"open_access","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf"}],"article_processing_charge":"No","_id":"1417","isi":1,"has_accepted_license":"1","author":[{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"full_name":"Viaene, Tom","first_name":"Tom","last_name":"Viaene"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"full_name":"Klíma, Petr","first_name":"Petr","last_name":"Klíma"},{"last_name":"Čarná","first_name":"Mária","full_name":"Čarná, Mária"},{"full_name":"Rolčík, Jakub","first_name":"Jakub","last_name":"Rolčík"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"full_name":"Moreno, Ignacio","first_name":"Ignacio","last_name":"Moreno"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"full_name":"Orellana, Ariel","first_name":"Ariel","last_name":"Orellana"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication":"New Phytologist","ddc":["581"],"type":"journal_article","title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","file_date_updated":"2020-07-14T12:44:53Z","issue":"1","publisher":"Wiley-Blackwell","publication_status":"published","corr_author":"1","year":"2016","page":"65 - 74","pubrep_id":"1004","scopus_import":"1","day":"01","citation":{"ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019."},"date_created":"2018-12-11T11:51:54Z","volume":211},{"quality_controlled":"1","oa_version":"None","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 28","publist_id":"5788","external_id":{"isi":["000374393100011"]},"date_updated":"2025-09-18T14:22:40Z","abstract":[{"lang":"eng","text":"We study the superconducting phase of the Hubbard model using the Gutzwiller variational wave function (GWF) and the recently proposed diagrammatic expansion technique (DE-GWF). The DE-GWF method works on the level of the full GWF and in the thermodynamic limit. Here, we consider a finite-size system to study the accuracy of the results as a function of the system size (which is practically unrestricted). We show that the finite-size scaling used, e.g. in the variational Monte Carlo method can lead to significant, uncontrolled errors. The presented research is the first step towards applying the DE-GWF method in studies of inhomogeneous situations, including systems with impurities, defects, inhomogeneous phases, or disorder."}],"month":"03","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"article_processing_charge":"No","doi":"10.1088/0953-8984/28/17/175701","date_published":"2016-03-29T00:00:00Z","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"publication":"Journal of Physics: Condensed Matter","author":[{"first_name":"Andrzej","last_name":"Tomski","full_name":"Tomski, Andrzej"},{"id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kaczmarczyk","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675"}],"_id":"1419","isi":1,"issue":"17","type":"journal_article","title":"Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model","year":"2016","publication_status":"published","publisher":"IOP Publishing","day":"29","scopus_import":"1","ec_funded":1,"date_created":"2018-12-11T11:51:55Z","volume":28,"article_number":"175701","citation":{"short":"A. Tomski, J. Kaczmarczyk, Journal of Physics: Condensed Matter 28 (2016).","ama":"Tomski A, Kaczmarczyk J. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 2016;28(17). doi:10.1088/0953-8984/28/17/175701","ista":"Tomski A, Kaczmarczyk J. 2016. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 28(17), 175701.","apa":"Tomski, A., & Kaczmarczyk, J. (2016). Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. IOP Publishing. https://doi.org/10.1088/0953-8984/28/17/175701","chicago":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter. IOP Publishing, 2016. https://doi.org/10.1088/0953-8984/28/17/175701.","mla":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter, vol. 28, no. 17, 175701, IOP Publishing, 2016, doi:10.1088/0953-8984/28/17/175701.","ieee":"A. Tomski and J. Kaczmarczyk, “Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model,” Journal of Physics: Condensed Matter, vol. 28, no. 17. IOP Publishing, 2016."}},{"publication_status":"published","publisher":"Genetics Society of America","year":"2016","page":"1523 - 1548","corr_author":"1","title":"A general approximation for the dynamics of quantitative traits","type":"journal_article","issue":"4","citation":{"ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016."},"main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"volume":202,"date_created":"2018-12-11T11:51:55Z","scopus_import":"1","ec_funded":1,"day":"06","date_updated":"2025-09-18T14:22:05Z","abstract":[{"text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. ","lang":"eng"}],"month":"04","external_id":{"arxiv":["1510.08344"],"isi":["000373959100022"]},"publist_id":"5787","status":"public","intvolume":" 202","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","quality_controlled":"1","arxiv":1,"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","first_name":"Katarína","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"_id":"1420","publication":"Genetics","date_published":"2016-04-06T00:00:00Z","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"doi":"10.1534/genetics.115.184127","language":[{"iso":"eng"}],"article_processing_charge":"No","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}]},{"page":"155 - 164","year":"2016","publist_id":"5786","external_id":{"isi":["000390844400018"]},"publisher":"Springer","month":"04","publication_status":"published","date_updated":"2025-09-18T14:21:28Z","abstract":[{"text":"Hybridization methods enable the analysis of hybrid automata with complex, nonlinear dynamics through a sound abstraction process. Complex dynamics are converted to simpler ones with added noise, and then analysis is done using a reachability method for the simpler dynamics. Several such recent approaches advocate that only "dynamic" hybridization techniquesi.e., those where the dynamics are abstracted on-The-fly during a reachability computation are effective. In this paper, we demonstrate this is not the case, and create static hybridization methods that are more scalable than earlier approaches. The main insight in our approach is that quick, numeric simulations can be used to guide the process, eliminating the need for an exponential number of hybridization domains. Transitions between domains are generally timetriggered, avoiding accumulated error from geometric intersections. We enhance our static technique by combining time-Triggered transitions with occasional space-Triggered transitions, and demonstrate the benefits of the combined approach in what we call mixed-Triggered hybridization. Finally, error modes are inserted to confirm that the reachable states stay within the hybridized regions. The developed techniques can scale to higher dimensions than previous static approaches, while enabling the parallelization of the main performance bottleneck for many dynamic hybridization approaches: The nonlinear optimization required for sound dynamics abstraction. We implement our method as a model transformation pass in the HYST tool, and perform reachability analysis and evaluation using an unmodified version of SpaceEx on nonlinear models with up to six dimensions.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Scalable static hybridization methods for analysis of nonlinear systems","status":"public","type":"conference","date_created":"2018-12-11T11:51:55Z","isi":1,"citation":{"ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, T. Johnson, and P. Prakash, “Scalable static hybridization methods for analysis of nonlinear systems,” presented at the HSCC: Hybrid Systems - Computation and Control, Vienna, Austria, 2016, pp. 155–164.","mla":"Bak, Stanley, et al. Scalable Static Hybridization Methods for Analysis of Nonlinear Systems. Springer, 2016, pp. 155–64, doi:10.1145/2883817.2883837.","chicago":"Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, Taylor Johnson, and Pradyot Prakash. “Scalable Static Hybridization Methods for Analysis of Nonlinear Systems,” 155–64. Springer, 2016. https://doi.org/10.1145/2883817.2883837.","ista":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. 2016. Scalable static hybridization methods for analysis of nonlinear systems. HSCC: Hybrid Systems - Computation and Control, 155–164.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., Johnson, T., & Prakash, P. (2016). Scalable static hybridization methods for analysis of nonlinear systems (pp. 155–164). Presented at the HSCC: Hybrid Systems - Computation and Control, Vienna, Austria: Springer. https://doi.org/10.1145/2883817.2883837","short":"S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164.","ama":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. Scalable static hybridization methods for analysis of nonlinear systems. In: Springer; 2016:155-164. doi:10.1145/2883817.2883837"},"_id":"1421","author":[{"last_name":"Bak","first_name":"Stanley","full_name":"Bak, Stanley"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Johnson","first_name":"Taylor","full_name":"Johnson, Taylor"},{"full_name":"Prakash, Pradyot","last_name":"Prakash","first_name":"Pradyot"}],"article_processing_charge":"No","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"day":"11","conference":{"start_date":"2016-04-12","location":"Vienna, Austria","name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2016-04-14"},"language":[{"iso":"eng"}],"ec_funded":1,"scopus_import":"1","date_published":"2016-04-11T00:00:00Z","department":[{"_id":"ToHe"}],"doi":"10.1145/2883817.2883837"},{"date_updated":"2025-09-18T14:20:53Z","abstract":[{"text":"We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior.","lang":"eng"}],"month":"07","publist_id":"5785","external_id":{"isi":["000378844700002"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","intvolume":" 106","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"}],"has_accepted_license":"1","isi":1,"_id":"1422","publication":"Letters in Mathematical Physics","ddc":["510","530"],"department":[{"_id":"RoSe"}],"date_published":"2016-07-01T00:00:00Z","doi":"10.1007/s11005-016-0847-5","language":[{"iso":"eng"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file":[{"file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","date_created":"2018-12-12T10:15:57Z","creator":"system","access_level":"open_access","checksum":"fb404923d8ca9a1faeb949561f26cbea","content_type":"application/pdf","file_id":"5181","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","file_size":458968}],"publication_status":"published","publisher":"Springer","year":"2016","page":"913 - 923","corr_author":"1","file_date_updated":"2020-07-14T12:44:53Z","title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","type":"journal_article","issue":"7","citation":{"ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5","ista":"Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 106(7), 913–923.","apa":"Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5","chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.","mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5."},"volume":106,"date_created":"2018-12-11T11:51:56Z","pubrep_id":"591","scopus_import":"1","day":"01"},{"type":"journal_article","file_date_updated":"2020-07-14T12:44:53Z","title":"Comparing reactive and memory-one strategies of direct reciprocity","corr_author":"1","year":"2016","publisher":"Nature Publishing Group","publication_status":"published","day":"10","pubrep_id":"590","scopus_import":"1","date_created":"2018-12-11T11:51:56Z","volume":6,"article_number":"25676","citation":{"ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","apa":"Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep25676","ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group, 2016, doi:10.1038/srep25676.","chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676."},"quality_controlled":"1","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"intvolume":" 6","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"external_id":{"isi":["000375448500002"]},"publist_id":"5784","month":"05","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation."}],"date_updated":"2025-09-18T14:15:33Z","file":[{"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:18:08Z","checksum":"ee17c482370d2e1b3add393710d3c696","file_id":"5327","content_type":"application/pdf","file_size":1349915,"relation":"main_file","date_updated":"2020-07-14T12:44:53Z","file_name":"IST-2016-590-v1+1_srep25676.pdf"}],"article_processing_charge":"No","acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","language":[{"iso":"eng"}],"doi":"10.1038/srep25676","department":[{"_id":"KrCh"}],"date_published":"2016-05-10T00:00:00Z","ddc":["000"],"publication":"Scientific Reports","_id":"1423","isi":1,"has_accepted_license":"1","author":[{"last_name":"Baek","first_name":"Seung","full_name":"Baek, Seung"},{"full_name":"Jeong, Hyeongchai","last_name":"Jeong","first_name":"Hyeongchai"},{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}]},{"issue":"3","type":"journal_article","file_date_updated":"2020-07-14T12:44:53Z","title":"Epistatic interactions in the arabinose cis-regulatory element","corr_author":"1","year":"2016","page":"761 - 769","publication_status":"published","publisher":"Oxford University Press","day":"01","ec_funded":1,"pubrep_id":"588","scopus_import":"1","date_created":"2018-12-11T11:51:57Z","volume":33,"citation":{"mla":"Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.","chicago":"Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269.","apa":"Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269","ista":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769.","ama":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269","short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.","ieee":"M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016."},"quality_controlled":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"intvolume":" 33","publist_id":"5772","external_id":{"isi":["000371219500014"]},"abstract":[{"text":"Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.","lang":"eng"}],"date_updated":"2025-09-18T14:11:47Z","month":"03","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"file":[{"file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf","file_size":648115,"relation":"main_file","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:09:27Z","creator":"system","access_level":"open_access","file_id":"4751","checksum":"1f456ce1d2aa2f67176a1709f9702ecf","content_type":"application/pdf"}],"article_processing_charge":"No","doi":"10.1093/molbev/msv269","date_published":"2016-03-01T00:00:00Z","department":[{"_id":"CaGu"},{"_id":"JoBo"}],"language":[{"iso":"eng"}],"ddc":["570","576"],"publication":"Molecular Biology and Evolution","has_accepted_license":"1","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Igler","first_name":"Claudia","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anaisa","last_name":"Moreno","full_name":"Moreno, Anaisa"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback"}],"_id":"1427","isi":1},{"month":"03","date_updated":"2025-09-18T14:04:23Z","abstract":[{"text":"We report on a mathematically rigorous analysis of the superfluid properties of a Bose- Einstein condensate in the many-body ground state of a one-dimensional model of interacting bosons in a random potential.","lang":"eng"}],"external_id":{"isi":["000402374100016"]},"publist_id":"5770","intvolume":" 691","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","oa_version":"Published Version","quality_controlled":"1","isi":1,"_id":"1428","author":[{"full_name":"Könenberg, Martin","first_name":"Martin","last_name":"Könenberg"},{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas","first_name":"Thomas","last_name":"Moser"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"},{"first_name":"Jakob","last_name":"Yngvason","full_name":"Yngvason, Jakob"}],"has_accepted_license":"1","ddc":["510","530"],"publication":"Journal of Physics: Conference Series","language":[{"iso":"eng"}],"date_published":"2016-03-07T00:00:00Z","department":[{"_id":"RoSe"}],"doi":"10.1088/1742-6596/691/1/012016","article_processing_charge":"No","file":[{"file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf","file_size":1434688,"date_updated":"2020-07-14T12:44:53Z","relation":"main_file","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:10:55Z","checksum":"109db801749072c3f6c8f1a1848700fa","content_type":"application/pdf","file_id":"4847"}],"project":[{"call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"publisher":"IOP Publishing","publication_status":"published","year":"2016","title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential","file_date_updated":"2020-07-14T12:44:53Z","type":"conference","issue":"1","citation":{"short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing, 2016.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In: Journal of Physics: Conference Series. Vol 691. IOP Publishing; 2016. doi:10.1088/1742-6596/691/1/012016","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2016. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. Journal of Physics: Conference Series. 24th International Laser Physics Workshop (LPHYS’15) vol. 691, 012016.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2016). Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In Journal of Physics: Conference Series (Vol. 691). Shanghai, China: IOP Publishing. https://doi.org/10.1088/1742-6596/691/1/012016","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” In Journal of Physics: Conference Series, Vol. 691. IOP Publishing, 2016. https://doi.org/10.1088/1742-6596/691/1/012016.","mla":"Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” Journal of Physics: Conference Series, vol. 691, no. 1, 012016, IOP Publishing, 2016, doi:10.1088/1742-6596/691/1/012016.","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential,” in Journal of Physics: Conference Series, Shanghai, China, 2016, vol. 691, no. 1."},"article_number":"012016","volume":691,"date_created":"2018-12-11T11:51:58Z","pubrep_id":"585","scopus_import":"1","day":"07","conference":{"end_date":"2015-08-25","location":"Shanghai, China","name":"24th International Laser Physics Workshop (LPHYS'15)","start_date":"2015-08-21"}},{"publist_id":"5769","external_id":{"isi":["000374127800001"]},"month":"04","abstract":[{"lang":"eng","text":"Solitons are localized waves formed by a balance of focusing and defocusing effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar properties including stability, periodic recurrence and particle-like trajectories. One important property is soliton fission, a process by which an energetic higher-order soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate through both experiment and theory that nonlinear photocarrier generation can induce soliton fission. Using near-field measurements, we directly observe the nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic semiconductor waveguide. We develop an analytic formalism describing the free-carrier dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold by an order of magnitude. We confirm these observations with a numerical nonlinear Schrödinger equation model. These results provide a fundamental explanation and physical scaling of optical pulse evolution in free-carrier media and could enable improved supercontinuum sources in gas based and integrated semiconductor waveguides."}],"date_updated":"2025-09-18T14:02:55Z","oa_version":"Published Version","quality_controlled":"1","intvolume":" 7","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication":"Nature Communications","ddc":["530"],"isi":1,"_id":"1429","author":[{"full_name":"Husko, Chad","first_name":"Chad","last_name":"Husko"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","last_name":"Wulf","first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","last_name":"Lefrançois","full_name":"Lefrançois, Simon"},{"last_name":"Combrié","first_name":"Sylvain","full_name":"Combrié, Sylvain"},{"full_name":"Lehoucq, Gaëlle","last_name":"Lehoucq","first_name":"Gaëlle"},{"first_name":"Alfredo","last_name":"De Rossi","full_name":"De Rossi, Alfredo"},{"full_name":"Eggleton, Benjamin","last_name":"Eggleton","first_name":"Benjamin"},{"last_name":"Kuipers","first_name":"Laurens","full_name":"Kuipers, Laurens"}],"has_accepted_license":"1","article_processing_charge":"No","file":[{"relation":"main_file","date_updated":"2020-07-14T12:44:53Z","file_size":965176,"content_type":"application/pdf","file_id":"5177","checksum":"6484fa81a2e52e4fdd7935e1ae6091d4","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:15:53Z","file_name":"IST-2016-583-v1+1_ncomms11332.pdf"}],"acknowledgement":"This research was supported by the Australian Research Council (ARC) Center of Excellence CUDOS (CE110001018), ARC Laureate Fellowship (FL120100029), ARC Discovery Early Career Researcher Award (DECRA DE120102069), the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO). L.K. acknowledges funding from ERC Advanced Investigator Grant (no. 240438-CONSTANS). A.D.R, S.C., and G.L. acknowledge financial support from the ERC-Pharos programme lead by A. P. Mosk.","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"date_published":"2016-04-15T00:00:00Z","doi":"10.1038/ncomms11332","year":"2016","corr_author":"1","publisher":"Nature Publishing Group","publication_status":"published","title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","file_date_updated":"2020-07-14T12:44:53Z","type":"journal_article","volume":7,"date_created":"2018-12-11T11:51:58Z","article_number":"11332 (2016)","citation":{"short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016).","ama":"Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 2016;7. doi:10.1038/ncomms11332","apa":"Husko, C., Wulf, M., Lefrançois, S., Combrié, S., Lehoucq, G., De Rossi, A., … Kuipers, L. (2016). Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11332","ista":"Husko C, Wulf M, Lefrançois S, Combrié S, Lehoucq G, De Rossi A, Eggleton B, Kuipers L. 2016. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 7, 11332 (2016).","chicago":"Husko, Chad, Matthias Wulf, Simon Lefrançois, Sylvain Combrié, Gaëlle Lehoucq, Alfredo De Rossi, Benjamin Eggleton, and Laurens Kuipers. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11332.","mla":"Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications, vol. 7, 11332 (2016), Nature Publishing Group, 2016, doi:10.1038/ncomms11332.","ieee":"C. Husko et al., “Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides,” Nature Communications, vol. 7. Nature Publishing Group, 2016."},"day":"15","pubrep_id":"583","scopus_import":"1"},{"publisher":"PeerJ","publication_status":"published","year":"2016","title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","file_date_updated":"2020-07-14T12:44:53Z","type":"journal_article","issue":"3","article_number":"1865","citation":{"short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016;2016(3). doi:10.7717/peerj.1865","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.","apa":"Tartally, A., Kelager, A., Fürst, M., & Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. PeerJ. https://doi.org/10.7717/peerj.1865","chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ. PeerJ, 2016. https://doi.org/10.7717/peerj.1865.","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:10.7717/peerj.1865.","ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” PeerJ, vol. 2016, no. 3. PeerJ, 2016."},"volume":2016,"date_created":"2018-12-11T11:51:59Z","pubrep_id":"584","scopus_import":"1","day":"01","month":"01","abstract":[{"text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow.","lang":"eng"}],"date_updated":"2025-09-18T14:01:56Z","publist_id":"5767","external_id":{"isi":["000374159800006"]},"intvolume":" 2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","quality_controlled":"1","isi":1,"_id":"1431","author":[{"first_name":"András","last_name":"Tartally","full_name":"Tartally, András"},{"full_name":"Kelager, Andreas","first_name":"Andreas","last_name":"Kelager"},{"first_name":"Matthias","last_name":"Fürst","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nash, David","last_name":"Nash","first_name":"David"}],"has_accepted_license":"1","publication":"PeerJ","ddc":["570"],"language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"date_published":"2016-01-01T00:00:00Z","doi":"10.7717/peerj.1865","article_processing_charge":"No","file":[{"date_updated":"2020-07-14T12:44:53Z","relation":"main_file","file_size":1216360,"checksum":"c27d898598a1e3d7f629607a309254e1","file_id":"5272","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:17:19Z","access_level":"open_access","file_name":"IST-2016-584-v1+1_peerj-1865.pdf"}]},{"publist_id":"5764","external_id":{"arxiv":["1508.05905"],"isi":["000378013400009"]},"month":"08","abstract":[{"text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B on scales down to N−2/3N−2/3.","lang":"eng"}],"date_updated":"2025-09-18T14:00:03Z","arxiv":1,"oa_version":"Preprint","quality_controlled":"1","intvolume":" 271","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"status":"public","publication":"Journal of Functional Analysis","isi":1,"_id":"1434","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","first_name":"Kevin","last_name":"Schnelli"}],"article_processing_charge":"No","project":[{"grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"language":[{"iso":"eng"}],"date_published":"2016-08-01T00:00:00Z","department":[{"_id":"LaEr"}],"doi":"10.1016/j.jfa.2016.04.006","year":"2016","page":"672 - 719","corr_author":"1","publisher":"Academic Press","publication_status":"published","issue":"3","title":"Local stability of the free additive convolution","type":"journal_article","volume":271,"date_created":"2018-12-11T11:52:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.05905"}],"citation":{"ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” Journal of Functional Analysis, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2016). Local stability of the free additive convolution. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2016.04.006","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. Journal of Functional Analysis. 2016;271(3):672-719. doi:10.1016/j.jfa.2016.04.006","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:10.1016/j.jfa.2016.04.006.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2016.04.006."},"day":"01","scopus_import":"1","ec_funded":1},{"ddc":["570"],"publication":"Neural Plasticity","has_accepted_license":"1","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242","last_name":"Guzmán","first_name":"José"},{"last_name":"Gerevich","first_name":"Zoltan","full_name":"Gerevich, Zoltan"}],"_id":"1435","isi":1,"file":[{"date_updated":"2020-07-14T12:44:54Z","relation":"main_file","file_size":1395180,"checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","file_id":"4740","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:09:17Z","creator":"system","file_name":"IST-2016-580-v1+1_1207393.pdf"}],"article_processing_charge":"No","doi":"10.1155/2016/1207393","date_published":"2016-01-01T00:00:00Z","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000374056200001"]},"publist_id":"5762","date_updated":"2025-09-18T11:45:18Z","abstract":[{"lang":"eng","text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states."}],"month":"01","quality_controlled":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"intvolume":" 2016","date_created":"2018-12-11T11:52:00Z","volume":2016,"citation":{"ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” Neural Plasticity, vol. 2016. Hindawi Publishing Corporation, 2016.","chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity. Hindawi Publishing Corporation, 2016. https://doi.org/10.1155/2016/1207393.","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:10.1155/2016/1207393.","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016;2016. doi:10.1155/2016/1207393","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","apa":"Guzmán, J., & Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. Hindawi Publishing Corporation. https://doi.org/10.1155/2016/1207393"},"article_number":"1207393","day":"01","pubrep_id":"580","scopus_import":"1","year":"2016","publication_status":"published","publisher":"Hindawi Publishing Corporation","type":"journal_article","file_date_updated":"2020-07-14T12:44:54Z","title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction"},{"author":[{"first_name":"Volker","last_name":"Bach","full_name":"Bach, Volker"},{"last_name":"Breteaux","first_name":"Sébastien","full_name":"Breteaux, Sébastien"},{"last_name":"Petrat","first_name":"Sören P","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"},{"last_name":"Tzaneteas","first_name":"Tim","full_name":"Tzaneteas, Tim"}],"has_accepted_license":"1","isi":1,"_id":"1436","publication":"Journal de Mathématiques Pures et Appliquées","ddc":["510","530"],"department":[{"_id":"RoSe"}],"date_published":"2016-01-01T00:00:00Z","doi":"10.1016/j.matpur.2015.09.003","language":[{"iso":"eng"}],"article_processing_charge":"No","file":[{"file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","file_size":658491,"relation":"main_file","date_updated":"2020-07-14T12:44:54Z","creator":"system","date_created":"2018-12-12T10:10:36Z","access_level":"open_access","content_type":"application/pdf","file_id":"4825","checksum":"c5afe1f6935bc7f2b546adbde1d31a35"}],"project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-09-18T12:31:28Z","abstract":[{"text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system.","lang":"eng"}],"month":"01","external_id":{"isi":["000366773900001"]},"publist_id":"5763","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"status":"public","intvolume":" 105","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"oa_version":"Published Version","quality_controlled":"1","citation":{"mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:10.1016/j.matpur.2015.09.003.","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2016. https://doi.org/10.1016/j.matpur.2015.09.003.","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., & Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2015.09.003","ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 2016;105(1):1-30. doi:10.1016/j.matpur.2015.09.003","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30.","ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1. Elsevier, pp. 1–30, 2016."},"volume":105,"date_created":"2018-12-11T11:52:00Z","ec_funded":1,"scopus_import":"1","pubrep_id":"581","day":"01","publication_status":"published","publisher":"Elsevier","year":"2016","page":"1 - 30","file_date_updated":"2020-07-14T12:44:54Z","title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","type":"journal_article","issue":"1"},{"abstract":[{"text":"In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.","lang":"eng"}],"date_updated":"2025-04-15T08:12:22Z","month":"01","publist_id":"5760","external_id":{"arxiv":["1510.08517"]},"status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","status":"public","id":"5993"}]},"oa_version":"Preprint","quality_controlled":"1","arxiv":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hasheminezhad","first_name":"Rouzbeh","full_name":"Hasheminezhad, Rouzbeh"}],"alternative_title":["POPL"],"_id":"1438","department":[{"_id":"KrCh"}],"date_published":"2016-01-11T00:00:00Z","doi":"10.1145/2837614.2837639","language":[{"iso":"eng"}],"acknowledgement":"Supported by the Natural Science Foundation of China (NSFC) under Grant No. 61532019 ","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"publication_status":"published","publisher":"ACM","year":"2016","page":"327 - 342","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","type":"conference","citation":{"ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 327–342.","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.","apa":"Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2016). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837639","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. In: Vol 20-22. ACM; 2016:327-342. doi:10.1145/2837614.2837639","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.","mla":"Chatterjee, Krishnendu, et al. Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs. Vol. 20–22, ACM, 2016, pp. 327–42, doi:10.1145/2837614.2837639.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. https://doi.org/10.1145/2837614.2837639."},"main_file_link":[{"url":"http://arxiv.org/abs/1510.08517","open_access":"1"}],"volume":"20-22","date_created":"2018-12-11T11:52:01Z","scopus_import":1,"ec_funded":1,"conference":{"end_date":"2016-01-22","start_date":"2016-01-20","name":"POPL: Principles of Programming Languages","location":"St. Petersburg, FL, USA"},"day":"11"},{"publication_status":"published","publisher":"ACM","year":"2016","page":"400 - 415","title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","type":"conference","citation":{"ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415.","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:10.1145/2837614.2837650","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837650","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. https://doi.org/10.1145/2837614.2837650.","mla":"Dragoi, Cezara, et al. PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms. Vol. 20–22, ACM, 2016, pp. 400–15, doi:10.1145/2837614.2837650."},"main_file_link":[{"url":"https://hal.inria.fr/hal-01251199/","open_access":"1"}],"volume":"20-22","date_created":"2018-12-11T11:52:01Z","scopus_import":"1","ec_funded":1,"conference":{"end_date":"2016-01-22","location":"St. Petersburg, FL, USA","start_date":"2016-01-20","name":"POPL: Principles of Programming Languages"},"day":"11","abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification."}],"date_updated":"2025-09-18T11:44:23Z","month":"01","external_id":{"isi":["000374053600033"]},"publist_id":"5759","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"oa_version":"Preprint","quality_controlled":"1","author":[{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi","full_name":"Dragoi, Cezara"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"alternative_title":["ACM SIGPLAN Notices"],"_id":"1439","date_published":"2016-01-11T00:00:00Z","department":[{"_id":"ToHe"}],"doi":"10.1145/2837614.2837650","language":[{"iso":"eng"}],"acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","article_processing_charge":"No","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"}]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 24","status":"public","quality_controlled":"1","oa_version":"None","month":"02","date_updated":"2025-09-18T11:43:50Z","external_id":{"isi":["000373567700001"]},"publist_id":"5756","acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).","language":[{"iso":"eng"}],"doi":"10.1016/j.str.2016.01.002","date_published":"2016-02-02T00:00:00Z","department":[{"_id":"HaJa"}],"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","grant_number":"RGY0084/2012"},{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24"}],"article_processing_charge":"No","_id":"1440","isi":1,"author":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"}],"publication":"Structure","type":"journal_article","title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","issue":"2","publisher":"Cell Press","publication_status":"published","corr_author":"1","year":"2016","page":"213 - 215","ec_funded":1,"scopus_import":"1","day":"02","citation":{"ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” Structure, vol. 24, no. 2. Cell Press, pp. 213–215, 2016.","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure. Cell Press, 2016. https://doi.org/10.1016/j.str.2016.01.002.","mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:10.1016/j.str.2016.01.002.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 2016;24(2):213-215. doi:10.1016/j.str.2016.01.002","short":"H.L. Janovjak, Structure 24 (2016) 213–215.","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. Cell Press. https://doi.org/10.1016/j.str.2016.01.002","ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215."},"date_created":"2018-12-11T11:52:02Z","volume":24}]