[{"intvolume":"        30","month":"04","language":[{"iso":"eng"}],"issue":"4","_id":"7744","page":"124-132","oa_version":"None","doi":"10.1016/j.tig.2014.02.003","title":"Explaining additional genetic variation in complex traits","publication_identifier":{"issn":["0168-9525"]},"publisher":"Elsevier","author":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson"},{"last_name":"Wray","full_name":"Wray, Naomi R.","first_name":"Naomi R."},{"full_name":"Visscher, Peter M.","first_name":"Peter M.","last_name":"Visscher"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-04-01T00:00:00Z","volume":30,"day":"01","article_processing_charge":"No","article_type":"original","publication_status":"published","date_created":"2020-04-30T10:58:58Z","extern":"1","year":"2014","date_updated":"2021-01-12T08:15:14Z","quality_controlled":"1","publication":"Trends in Genetics","citation":{"ista":"Robinson MR, Wray NR, Visscher PM. 2014. Explaining additional genetic variation in complex traits. Trends in Genetics. 30(4), 124–132.","ama":"Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation in complex traits. <i>Trends in Genetics</i>. 2014;30(4):124-132. doi:<a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">10.1016/j.tig.2014.02.003</a>","short":"M.R. Robinson, N.R. Wray, P.M. Visscher, Trends in Genetics 30 (2014) 124–132.","ieee":"M. R. Robinson, N. R. Wray, and P. M. Visscher, “Explaining additional genetic variation in complex traits,” <i>Trends in Genetics</i>, vol. 30, no. 4. Elsevier, pp. 124–132, 2014.","chicago":"Robinson, Matthew Richard, Naomi R. Wray, and Peter M. Visscher. “Explaining Additional Genetic Variation in Complex Traits.” <i>Trends in Genetics</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">https://doi.org/10.1016/j.tig.2014.02.003</a>.","apa":"Robinson, M. R., Wray, N. R., &#38; Visscher, P. M. (2014). Explaining additional genetic variation in complex traits. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">https://doi.org/10.1016/j.tig.2014.02.003</a>","mla":"Robinson, Matthew Richard, et al. “Explaining Additional Genetic Variation in Complex Traits.” <i>Trends in Genetics</i>, vol. 30, no. 4, Elsevier, 2014, pp. 124–32, doi:<a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">10.1016/j.tig.2014.02.003</a>."},"type":"journal_article","status":"public"},{"date_updated":"2023-02-23T13:16:18Z","year":"2014","extern":"1","date_created":"2018-12-11T11:48:26Z","abstract":[{"text":"The long-lived renaming problem appears in shared-memory systems where a set of threads need to register and deregister frequently from the computation, while concurrent operations scan the set of currently registered threads. Instances of this problem show up in concurrent implementations of transactional memory, flat combining, thread barriers, and memory reclamation schemes for lock-free data structures. In this paper, we analyze a randomized solution for long-lived renaming. The algorithmic technique we consider, called the Level Array, has previously been used for hashing and one-shot (single-use) renaming. Our main contribution is to prove that, in long-lived executions, where processes may register and deregister polynomially many times, the technique guarantees constant steps on average and O (log log n) steps with high probability for registering, unit cost for deregistering, and O (n) steps for collect queries, where n is an upper bound on the number of processes that may be active at any point in time. We also show that the algorithm has the surprising property that it is self-healing: under reasonable assumptions on the schedule, operations running while the data structure is in a degraded state implicitly help the data structure re-balance itself. This subtle mechanism obviates the need for expensive periodic rebuilding procedures. Our benchmarks validate this approach, showing that, for typical use parameters, the average number of steps a process takes to register is less than two and the worst-case number of steps is bounded by six, even in executions with billions of operations. We contrast this with other randomized implementations, whose worst-case behavior we show to be unreliable, and with deterministic implementations, whose cost is linear in n.","lang":"eng"}],"publication_status":"published","status":"public","citation":{"ista":"Alistarh D-A, Kopinsky J, Matveev A, Shavit N. 2014. The levelarray: A fast, practical long-lived renaming algorithm. ICDCS: International Conference on Distributed Computing Systems, 348–357.","ama":"Alistarh D-A, Kopinsky J, Matveev A, Shavit N. The levelarray: A fast, practical long-lived renaming algorithm. In: IEEE; 2014:348-357. doi:<a href=\"https://doi.org/10.1109/ICDCS.2014.43\">10.1109/ICDCS.2014.43</a>","short":"D.-A. Alistarh, J. Kopinsky, A. Matveev, N. Shavit, in:, IEEE, 2014, pp. 348–357.","ieee":"D.-A. Alistarh, J. Kopinsky, A. Matveev, and N. Shavit, “The levelarray: A fast, practical long-lived renaming algorithm,” presented at the ICDCS: International Conference on Distributed Computing Systems, 2014, pp. 348–357.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Alexander Matveev, and Nir Shavit. “The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm,” 348–57. IEEE, 2014. <a href=\"https://doi.org/10.1109/ICDCS.2014.43\">https://doi.org/10.1109/ICDCS.2014.43</a>.","apa":"Alistarh, D.-A., Kopinsky, J., Matveev, A., &#38; Shavit, N. (2014). The levelarray: A fast, practical long-lived renaming algorithm (pp. 348–357). Presented at the ICDCS: International Conference on Distributed Computing Systems, IEEE. <a href=\"https://doi.org/10.1109/ICDCS.2014.43\">https://doi.org/10.1109/ICDCS.2014.43</a>","mla":"Alistarh, Dan-Adrian, et al. <i>The Levelarray: A Fast, Practical Long-Lived Renaming Algorithm</i>. IEEE, 2014, pp. 348–57, doi:<a href=\"https://doi.org/10.1109/ICDCS.2014.43\">10.1109/ICDCS.2014.43</a>."},"type":"conference","date_published":"2014-08-29T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"},{"last_name":"Kopinsky","full_name":"Kopinsky, Justin","first_name":"Justin"},{"last_name":"Matveev","first_name":"Alexander","full_name":"Matveev, Alexander"},{"last_name":"Shavit","full_name":"Shavit, Nir","first_name":"Nir"}],"arxiv":1,"article_processing_charge":"No","day":"29","oa":1,"oa_version":"Preprint","page":"348 - 357","_id":"775","conference":{"name":"ICDCS: International Conference on Distributed Computing Systems"},"publist_id":"6883","title":"The levelarray: A fast, practical long-lived renaming algorithm","doi":"10.1109/ICDCS.2014.43","month":"08","external_id":{"arxiv":["1405.5461"]},"main_file_link":[{"url":"https://arxiv.org/abs/1405.5461","open_access":"1"}],"language":[{"iso":"eng"}]},{"year":"2014","quality_controlled":"1","date_updated":"2021-01-12T08:15:24Z","publication_status":"published","abstract":[{"lang":"eng","text":"We investigate the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions as a function of packing fraction. Certain properties of the vibrational density of states (vDOS) are shown to correlate with the density and structure of the samples (i.e., in sparsely versus densely packed samples). Specifically, a crossover from dense glassy to sparse gel-like states is suggested by an excess of phonon modes at low frequency and by a variation in the slope of the vDOS with frequency at low frequency. This change in phonon mode distribution is demonstrated to arise largely from localized vibrations that involve individual and/or small clusters of particles with few local bonds. Conventional order parameters and void statistics did not exhibit obvious gel-glass signatures as a function of volume fraction. These mode behaviors and accompanying structural insights offer a potentially new set of indicators for identification of glass-gel transitions and for assignment of gel-like versus glass-like character to a disordered solid material."}],"date_created":"2020-04-30T11:41:54Z","extern":"1","status":"public","citation":{"ieee":"M. A. Lohr <i>et al.</i>, “Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings,” <i>Physical Review E</i>, vol. 90, no. 6. American Physical Society, 2014.","ama":"Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. <i>Physical Review E</i>. 2014;90(6). doi:<a href=\"https://doi.org/10.1103/physreve.90.062305\">10.1103/physreve.90.062305</a>","short":"M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz, C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014).","ista":"Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. 90(6), 062305.","mla":"Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” <i>Physical Review E</i>, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.062305\">10.1103/physreve.90.062305</a>.","apa":"Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz, K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.062305\">https://doi.org/10.1103/physreve.90.062305</a>","chicago":"Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson, Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.062305\">https://doi.org/10.1103/physreve.90.062305</a>."},"type":"journal_article","publication":"Physical Review E","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-12-05T00:00:00Z","author":[{"full_name":"Lohr, Matthew A.","first_name":"Matthew A.","last_name":"Lohr"},{"last_name":"Still","first_name":"Tim","full_name":"Still, Tim"},{"first_name":"Raman","full_name":"Ganti, Raman","last_name":"Ganti"},{"full_name":"Gratale, Matthew D.","first_name":"Matthew D.","last_name":"Gratale"},{"full_name":"Davidson, Zoey S.","first_name":"Zoey S.","last_name":"Davidson"},{"last_name":"Aptowicz","full_name":"Aptowicz, Kevin B.","first_name":"Kevin B."},{"last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter"},{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"full_name":"Yodh, A. G.","first_name":"A. G.","last_name":"Yodh"}],"publisher":"American Physical Society","day":"05","article_processing_charge":"No","article_type":"original","volume":90,"oa_version":"None","_id":"7768","publication_identifier":{"issn":["1539-3755","1550-2376"]},"title":"Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings","doi":"10.1103/physreve.90.062305","month":"12","intvolume":"        90","article_number":"062305","issue":"6","language":[{"iso":"eng"}]},{"month":"08","intvolume":"        90","issue":"2","article_number":"022138","language":[{"iso":"eng"}],"oa_version":"None","_id":"7769","publication_identifier":{"issn":["1539-3755","1550-2376"]},"title":"Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling","doi":"10.1103/physreve.90.022138","date_published":"2014-08-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","last_name":"Goodrich"},{"last_name":"Dagois-Bohy","full_name":"Dagois-Bohy, Simon","first_name":"Simon"},{"first_name":"Brian P.","full_name":"Tighe, Brian P.","last_name":"Tighe"},{"full_name":"van Hecke, Martin","first_name":"Martin","last_name":"van Hecke"},{"first_name":"Andrea J.","full_name":"Liu, Andrea J.","last_name":"Liu"},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"publisher":"American Physical Society","article_processing_charge":"No","article_type":"original","day":"27","volume":90,"quality_controlled":"1","date_updated":"2021-01-12T08:15:24Z","year":"2014","extern":"1","date_created":"2020-04-30T11:42:09Z","publication_status":"published","abstract":[{"lang":"eng","text":"Athermal packings of soft repulsive spheres exhibit a sharp jamming transition in the thermodynamic limit. Upon further compression, various structural and mechanical properties display clean power-law behavior over many decades in pressure. As with any phase transition, the rounding of such behavior in finite systems close to the transition plays an important role in understanding the nature of the transition itself. The situation for jamming is surprisingly rich: the assumption that jammed packings are isotropic is only strictly true in the large-size limit, and finite-size has a profound effect on the very meaning of jamming. Here, we provide a comprehensive numerical study of finite-size effects in sphere packings above the jamming transition, focusing on stability as well as the scaling of the contact number and the elastic response."}],"status":"public","publication":"Physical Review E","type":"journal_article","citation":{"ama":"Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. <i>Physical Review E</i>. 2014;90(2). doi:<a href=\"https://doi.org/10.1103/physreve.90.022138\">10.1103/physreve.90.022138</a>","short":"C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).","ista":"Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical Review E. 90(2), 022138.","ieee":"C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling,” <i>Physical Review E</i>, vol. 90, no. 2. American Physical Society, 2014.","apa":"Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J., &#38; Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.022138\">https://doi.org/10.1103/physreve.90.022138</a>","chicago":"Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke, Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.022138\">https://doi.org/10.1103/physreve.90.022138</a>.","mla":"Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” <i>Physical Review E</i>, vol. 90, no. 2, 022138, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.022138\">10.1103/physreve.90.022138</a>."}},{"author":[{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"first_name":"Sidney R.","full_name":"Nagel, Sidney R.","last_name":"Nagel"}],"publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-08-04T00:00:00Z","volume":90,"day":"04","article_type":"original","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"Packings of frictionless athermal particles that interact only when they overlap experience a jamming transition as a function of packing density. Such packings provide the foundation for the theory of jamming. This theory rests on the observation that, despite the multitude of disordered configurations, the mechanical response to linear order depends only on the distance to the transition. We investigate the validity and utility of such measurements that invoke the harmonic approximation and show that, despite particles coming in and out of contact, there is a well-defined linear regime in the thermodynamic limit."}],"extern":"1","date_created":"2020-04-30T11:42:24Z","year":"2014","date_updated":"2021-01-12T08:15:25Z","quality_controlled":"1","citation":{"ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response in jammed particulate packings. Physical Review E. 90(2), 022201.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).","ama":"Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in jammed particulate packings. <i>Physical Review E</i>. 2014;90(2). doi:<a href=\"https://doi.org/10.1103/physreve.90.022201\">10.1103/physreve.90.022201</a>","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear response in jammed particulate packings,” <i>Physical Review E</i>, vol. 90, no. 2. American Physical Society, 2014.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.022201\">https://doi.org/10.1103/physreve.90.022201</a>.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Contact nonlinearities and linear response in jammed particulate packings. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.022201\">https://doi.org/10.1103/physreve.90.022201</a>","mla":"Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” <i>Physical Review E</i>, vol. 90, no. 2, 022201, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.022201\">10.1103/physreve.90.022201</a>."},"type":"journal_article","publication":"Physical Review E","status":"public","intvolume":"        90","month":"08","language":[{"iso":"eng"}],"article_number":"022201","issue":"2","_id":"7770","oa_version":"None","title":"Contact nonlinearities and linear response in jammed particulate packings","doi":"10.1103/physreve.90.022201","publication_identifier":{"issn":["1539-3755","1550-2376"]}},{"issue":"4","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1306.1285"}],"external_id":{"arxiv":["1306.1285"]},"doi":"10.1103/physrevlett.112.049801","title":"Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”","oa_version":"Preprint","day":"20","article_processing_charge":"No","date_published":"2014-04-20T00:00:00Z","arxiv":1,"author":[{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"Sidney R.","full_name":"Nagel, Sidney R.","last_name":"Nagel"}],"publisher":"American Physical Society","status":"public","year":"2014","abstract":[{"lang":"eng","text":"In their Letter, Schreck, Bertrand, O'Hern and Shattuck [Phys. Rev. Lett. 107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise when contacts are altered. They conclude that there is \"no harmonic regime in the large system limit for all compressions\" and \"at jamming onset for any system size.\" Their argument rests on the claim that for finite-range repulsive potentials, of the form used in studies of jamming, the breaking or forming of a single contact is sufficient to destroy the linear regime. We dispute these conclusions and argue that linear response is both justified and essential for understanding the nature of the jammed solid. "}],"publication_status":"published","article_number":"049801 ","language":[{"iso":"eng"}],"month":"04","intvolume":"       112","publication_identifier":{"issn":["0031-9007","1079-7114"]},"_id":"7771","article_type":"letter_note","volume":112,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publication":"Physical Review Letters","citation":{"ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact interactions make jammed particulate systems inherently nonharmonic,’” <i>Physical Review Letters</i>, vol. 112, no. 4. American Physical Society, 2014.","ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic”. Physical Review Letters. 112(4), 049801.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).","ama":"Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” <i>Physical Review Letters</i>. 2014;112(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.112.049801\">10.1103/physrevlett.112.049801</a>","mla":"Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” <i>Physical Review Letters</i>, vol. 112, no. 4, 049801, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physrevlett.112.049801\">10.1103/physrevlett.112.049801</a>.","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physrevlett.112.049801\">https://doi.org/10.1103/physrevlett.112.049801</a>.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Comment on “Repulsive contact interactions make jammed particulate systems inherently nonharmonic.” <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.112.049801\">https://doi.org/10.1103/physrevlett.112.049801</a>"},"date_updated":"2021-01-12T08:15:26Z","date_created":"2020-04-30T11:42:39Z","extern":"1"},{"abstract":[{"lang":"eng","text":"Particle tracking and displacement covariance matrix techniques are employed to investigate the phonon dispersion relations of two-dimensional colloidal glasses composed of soft, thermoresponsive microgel particles whose temperature-sensitive size permits in situ variation of particle packing fraction. Bulk, B, and shear, G, moduli of the colloidal glasses are extracted from the dispersion relations as a function of packing fraction, and variation of the ratio G/B with packing fraction is found to agree quantitatively with predictions for jammed packings of frictional soft particles. In addition, G and B individually agree with numerical predictions for frictional particles. This remarkable level of agreement enabled us to extract an energy scale for the interparticle interaction from the individual elastic constants and to derive an approximate estimate for the interparticle friction coefficient."}],"publication_status":"published","extern":"1","date_created":"2020-04-30T11:43:02Z","year":"2014","quality_controlled":"1","date_updated":"2021-01-12T08:15:26Z","publication":"Physical Review E","type":"journal_article","citation":{"chicago":"Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz, Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.012301\">https://doi.org/10.1103/physreve.89.012301</a>.","apa":"Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A. J., &#38; Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.012301\">https://doi.org/10.1103/physreve.89.012301</a>","mla":"Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional Disordered Colloidal Packings of Soft Particles with Frictional Interactions.” <i>Physical Review E</i>, vol. 89, no. 1, 012301, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.012301\">10.1103/physreve.89.012301</a>.","ista":"Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. Physical Review E. 89(1), 012301.","ama":"Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions. <i>Physical Review E</i>. 2014;89(1). doi:<a href=\"https://doi.org/10.1103/physreve.89.012301\">10.1103/physreve.89.012301</a>","short":"T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G. Yodh, Physical Review E 89 (2014).","ieee":"T. Still <i>et al.</i>, “Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions,” <i>Physical Review E</i>, vol. 89, no. 1. American Physical Society, 2014."},"status":"public","author":[{"full_name":"Still, Tim","first_name":"Tim","last_name":"Still"},{"last_name":"Goodrich","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"full_name":"Chen, Ke","first_name":"Ke","last_name":"Chen"},{"first_name":"Peter J.","full_name":"Yunker, Peter J.","last_name":"Yunker"},{"last_name":"Schoenholz","first_name":"Samuel","full_name":"Schoenholz, Samuel"},{"first_name":"Andrea J.","full_name":"Liu, Andrea J.","last_name":"Liu"},{"first_name":"A. G.","full_name":"Yodh, A. G.","last_name":"Yodh"}],"publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-01-03T00:00:00Z","volume":89,"day":"03","article_processing_charge":"No","article_type":"original","_id":"7772","oa_version":"None","title":"Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings of soft particles with frictional interactions","doi":"10.1103/physreve.89.012301","publication_identifier":{"issn":["1539-3755","1550-2376"]},"intvolume":"        89","month":"01","language":[{"iso":"eng"}],"issue":"1","article_number":"012301"},{"citation":{"chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between the Mechanical Extremes of Order and Disorder.” <i>Nature Physics</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1038/nphys3006\">https://doi.org/10.1038/nphys3006</a>.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Solids between the mechanical extremes of order and disorder. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nphys3006\">https://doi.org/10.1038/nphys3006</a>","mla":"Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order and Disorder.” <i>Nature Physics</i>, vol. 10, no. 8, Springer Nature, 2014, pp. 578–81, doi:<a href=\"https://doi.org/10.1038/nphys3006\">10.1038/nphys3006</a>.","ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes of order and disorder. Nature Physics. 10(8), 578–581.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.","ama":"Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order and disorder. <i>Nature Physics</i>. 2014;10(8):578-581. doi:<a href=\"https://doi.org/10.1038/nphys3006\">10.1038/nphys3006</a>","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical extremes of order and disorder,” <i>Nature Physics</i>, vol. 10, no. 8. Springer Nature, pp. 578–581, 2014."},"type":"journal_article","publication":"Nature Physics","status":"public","abstract":[{"lang":"eng","text":"For more than a century, physicists have described real solids in terms of perturbations about perfect crystalline order1. Such an approach takes us only so far: a glass, another ubiquitous form of rigid matter, cannot be described in any meaningful sense as a defected crystal2. Is there an opposite extreme to a crystal—a solid with complete disorder—that forms an alternative starting point for understanding real materials? Here, we argue that the solid comprising particles with finite-ranged interactions at the jamming transition3,4,5 constitutes such a limit. It has been shown that the physics associated with this transition can be extended to interactions that are long ranged6. We demonstrate that jamming physics is not restricted to amorphous systems, but dominates the behaviour of solids with surprisingly high order. Just as the free-electron and tight-binding models represent two idealized cases from which to understand electronic structure1, we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming can be set side by side with the physics of crystals to provide an organizing structure for understanding the mechanical properties of solids over the entire spectrum of disorder."}],"publication_status":"published","date_created":"2020-04-30T11:43:29Z","extern":"1","year":"2014","quality_controlled":"1","date_updated":"2021-01-12T08:15:26Z","volume":10,"day":"06","article_processing_charge":"No","article_type":"original","publisher":"Springer Nature","author":[{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"last_name":"Liu","full_name":"Liu, Andrea J.","first_name":"Andrea J."},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2014-07-06T00:00:00Z","doi":"10.1038/nphys3006","title":"Solids between the mechanical extremes of order and disorder","publication_identifier":{"issn":["1745-2473","1745-2481"]},"_id":"7773","oa_version":"None","page":"578-581","language":[{"iso":"eng"}],"issue":"8","intvolume":"        10","month":"07"},{"external_id":{"pmid":["24982196"]},"issue":"28","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/","open_access":"1"}],"oa_version":"Published Version","doi":"10.1073/pnas.1321869111","title":"Activity-dependent dendritic spine neck changes are correlated with synaptic strength","date_published":"2014-07-15T00:00:00Z","pmid":1,"publisher":"Proceedings of the National Academy of Sciences","author":[{"last_name":"Araya","first_name":"R.","full_name":"Araya, R."},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","first_name":"Tim P","last_name":"Vogels"},{"full_name":"Yuste, R.","first_name":"R.","last_name":"Yuste"}],"day":"15","article_processing_charge":"No","year":"2014","abstract":[{"text":"Most excitatory inputs in the mammalian brain are made on dendritic spines, rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical isolation can underlie input-specific synaptic plasticity, providing a raison d'etre for spines. However, recent results indicate that the spine can experience a membrane potential different from that in the parent dendrite, as though the spine neck electrically isolated the spine. Here we use two-photon calcium imaging of mouse neocortical pyramidal neurons to analyze the correlation between the morphologies of spines activated under minimal synaptic stimulation and the excitatory postsynaptic potentials they generate. We find that excitatory postsynaptic potential amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike timing-dependent plasticity protocol, in which two-photon glutamate uncaging over a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine neck and concomitant increases in the amplitude of the evoked spine potentials. Using numerical simulations, we explore the parameter regimes for the spine neck resistance and synaptic conductance changes necessary to explain our observations. Our data, directly correlating synaptic and morphological plasticity, imply that long-necked spines have small or negligible somatic voltage contributions, but that, upon synaptic stimulation paired with postsynaptic activity, they can shorten their necks and increase synaptic efficacy, thus changing the input/output gain of pyramidal neurons. ","lang":"eng"}],"publication_status":"published","status":"public","month":"07","intvolume":"       111","language":[{"iso":"eng"}],"page":"E2895-E2904","_id":"8021","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_type":"original","volume":111,"oa":1,"date_updated":"2021-01-12T08:16:34Z","quality_controlled":"1","extern":"1","date_created":"2020-06-25T13:06:24Z","type":"journal_article","citation":{"ista":"Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. Proceedings of the National Academy of Sciences. 111(28), E2895–E2904.","short":"R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences 111 (2014) E2895–E2904.","ama":"Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(28):E2895-E2904. doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>","ieee":"R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine neck changes are correlated with synaptic strength,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28. Proceedings of the National Academy of Sciences, pp. E2895–E2904, 2014.","chicago":"Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>.","apa":"Araya, R., Vogels, T. P., &#38; Yuste, R. (2014). Activity-dependent dendritic spine neck changes are correlated with synaptic strength. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1321869111\">https://doi.org/10.1073/pnas.1321869111</a>","mla":"Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated with Synaptic Strength.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904, doi:<a href=\"https://doi.org/10.1073/pnas.1321869111\">10.1073/pnas.1321869111</a>."},"publication":"Proceedings of the National Academy of Sciences"},{"publisher":"Elsevier","author":[{"first_name":"Guillaume","full_name":"Hennequin, Guillaume","last_name":"Hennequin"},{"last_name":"Vogels","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P"},{"first_name":"Wulfram","full_name":"Gerstner, Wulfram","last_name":"Gerstner"}],"pmid":1,"date_published":"2014-06-18T00:00:00Z","article_processing_charge":"No","day":"18","publication_status":"published","abstract":[{"text":"Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex.","lang":"eng"}],"year":"2014","status":"public","external_id":{"pmid":["24945778"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/","open_access":"1"}],"issue":"6","oa_version":"Submitted Version","title":"Optimal control of transient dynamics in balanced networks supports generation of complex movements","doi":"10.1016/j.neuron.2014.04.045","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa":1,"volume":82,"article_type":"original","date_created":"2020-06-25T13:07:37Z","extern":"1","quality_controlled":"1","date_updated":"2021-01-12T08:16:35Z","citation":{"mla":"Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” <i>Neuron</i>, vol. 82, no. 6, Elsevier, 2014, pp. 1394–406, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">10.1016/j.neuron.2014.04.045</a>.","chicago":"Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">https://doi.org/10.1016/j.neuron.2014.04.045</a>.","apa":"Hennequin, G., Vogels, T. P., &#38; Gerstner, W. (2014). Optimal control of transient dynamics in balanced networks supports generation of complex movements. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">https://doi.org/10.1016/j.neuron.2014.04.045</a>","ieee":"G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient dynamics in balanced networks supports generation of complex movements,” <i>Neuron</i>, vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.","ista":"Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics in balanced networks supports generation of complex movements. Neuron. 82(6), 1394–1406.","ama":"Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in balanced networks supports generation of complex movements. <i>Neuron</i>. 2014;82(6):1394-1406. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.04.045\">10.1016/j.neuron.2014.04.045</a>","short":"G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406."},"type":"journal_article","publication":"Neuron","intvolume":"        82","month":"06","language":[{"iso":"eng"}],"_id":"8022","page":"1394-1406","publication_identifier":{"issn":["0896-6273"]}},{"publication":"Journal of Neurophysiology","citation":{"ama":"Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific biases make uniform random network models consistent with cortical recordings. <i>Journal of Neurophysiology</i>. 2014;112(8):1801-1814. doi:<a href=\"https://doi.org/10.1152/jn.00629.2013\">10.1152/jn.00629.2013</a>","short":"C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology 112 (2014) 1801–1814.","ista":"Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific biases make uniform random network models consistent with cortical recordings. Journal of Neurophysiology. 112(8), 1801–1814.","ieee":"C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific biases make uniform random network models consistent with cortical recordings,” <i>Journal of Neurophysiology</i>, vol. 112, no. 8. American Physiological Society, pp. 1801–1814, 2014.","apa":"Tomm, C., Avermann, M., Petersen, C., Gerstner, W., &#38; Vogels, T. P. (2014). Connection-type-specific biases make uniform random network models consistent with cortical recordings. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00629.2013\">https://doi.org/10.1152/jn.00629.2013</a>","chicago":"Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1152/jn.00629.2013\">https://doi.org/10.1152/jn.00629.2013</a>.","mla":"Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random Network Models Consistent with Cortical Recordings.” <i>Journal of Neurophysiology</i>, vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:<a href=\"https://doi.org/10.1152/jn.00629.2013\">10.1152/jn.00629.2013</a>."},"type":"journal_article","file_date_updated":"2020-07-16T10:12:13Z","quality_controlled":"1","date_updated":"2021-01-12T08:16:35Z","date_created":"2020-06-25T13:08:30Z","extern":"1","article_type":"original","volume":112,"oa":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication_identifier":{"eissn":["1522-1598"],"issn":["0022-3077"]},"page":"1801-1814","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/3.0/","_id":"8023","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"language":[{"iso":"eng"}],"month":"10","ddc":["570"],"intvolume":"       112","status":"public","year":"2014","abstract":[{"lang":"eng","text":"Uniform random sparse network architectures are ubiquitous in computational neuroscience, but the implicit hypothesis that they are a good representation of real neuronal networks has been met with skepticism. Here we used two experimental data sets, a study of triplet connectivity statistics and a data set measuring neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands of model networks. Network architectures comprised three neuron types (excitatory, fast spiking, and nonfast spiking inhibitory) and were created from a set of rules that govern the statistics of the resulting connection types. In a high-dimensional parameter scan, we varied the degree distributions (i.e., how many cells each neuron connects with) and the synaptic weight correlations of synapses from or onto the same neuron. These variations converted initially uniform random and homogeneously connected networks, in which every neuron sent and received equal numbers of synapses with equal synaptic strength distributions, to highly heterogeneous networks in which the number of synapses per neuron, as well as average synaptic strength of synapses from or to a neuron were variable. By evaluating the impact of each variable on the network structure and dynamics, and their similarity to the experimental data, we could falsify the uniform random sparse connectivity hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis in 8 cases. Twenty-one parameters had no substantial impact on the results of the test protocols we used."}],"publication_status":"published","day":"15","article_processing_charge":"No","file":[{"access_level":"open_access","success":1,"checksum":"7c06a086da6f924342650de6dc555c3f","file_id":"8122","file_size":1632295,"date_created":"2020-07-16T10:12:13Z","content_type":"application/pdf","date_updated":"2020-07-16T10:12:13Z","file_name":"2014_JNeurophysiol_Tomm.pdf","relation":"main_file","creator":"cziletti"}],"pmid":1,"date_published":"2014-10-15T00:00:00Z","publisher":"American Physiological Society","author":[{"first_name":"Christian","full_name":"Tomm, Christian","last_name":"Tomm"},{"full_name":"Avermann, Michael","first_name":"Michael","last_name":"Avermann"},{"first_name":"Carl","full_name":"Petersen, Carl","last_name":"Petersen"},{"last_name":"Gerstner","full_name":"Gerstner, Wulfram","first_name":"Wulfram"},{"last_name":"Vogels","full_name":"Vogels, Tim P","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"}],"title":"Connection-type-specific biases make uniform random network models consistent with cortical recordings","doi":"10.1152/jn.00629.2013","oa_version":"Published Version","issue":"8","external_id":{"pmid":["24944218"]}},{"OA_type":"free access","title":"Structure of the excitation spectrum for many-body quantum systems","oa_version":"Published Version","main_file_link":[{"url":"http://www.icm2014.org/en/vod/proceedings.html","open_access":"1"}],"status":"public","corr_author":"1","scopus_import":"1","year":"2014","abstract":[{"text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.","lang":"eng"}],"publication_status":"published","OA_place":"publisher","article_processing_charge":"No","day":"01","date_published":"2014-08-01T00:00:00Z","publisher":"International Congress of Mathematicians","author":[{"full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"publication_identifier":{"isbn":["9788961058063"]},"page":"1175-1194","_id":"8044","department":[{"_id":"RoSe"}],"conference":{"name":"ICM: International Congress of Mathematicans","end_date":"2014-08-21","start_date":"2014-08-13","location":"Seoul, South Korea"},"language":[{"iso":"eng"}],"month":"08","intvolume":"         3","type":"conference","citation":{"ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in <i>Proceeding of the International Congress of Mathematicans</i>, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.","ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194.","ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: <i>Proceeding of the International Congress of Mathematicans</i>. Vol 3. International Congress of Mathematicians; 2014:1175-1194.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” <i>Proceeding of the International Congress of Mathematicans</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In <i>Proceeding of the International Congress of Mathematicans</i>, 3:1175–94. International Congress of Mathematicians, 2014.","apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In <i>Proceeding of the International Congress of Mathematicans</i> (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians."},"publication":"Proceeding of the International Congress of Mathematicans","date_updated":"2025-07-15T08:39:50Z","quality_controlled":"1","date_created":"2020-06-29T07:59:35Z","oa":1,"volume":3,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"03","volume":111,"date_published":"2014-06-03T00:00:00Z","author":[{"last_name":"Bharata","full_name":"Bharata, Tanmay A","first_name":"Tanmay"},{"last_name":"Menendez","full_name":"Menendez, Luis R","first_name":"Luis"},{"full_name":"Hagena, Wim J","first_name":"Wim","last_name":"Hagena"},{"last_name":"Luxd","first_name":"Vanda","full_name":"Luxd, Vanda"},{"first_name":"Sebastien","full_name":"Igonete, Sebastien","last_name":"Igonete"},{"first_name":"Martin","full_name":"Schorba, Martin","last_name":"Schorba"},{"full_name":"Florian Schur","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"last_name":"Kraüsslich","full_name":"Kraüsslich, Hans Georg","first_name":"Hans"},{"last_name":"Briggsa","first_name":"John","full_name":"Briggsa, John A"}],"publisher":"National Academy of Sciences","status":"public","publication":"PNAS","type":"journal_article","citation":{"chicago":"Bharata, Tanmay, Luis Menendez, Wim Hagena, Vanda Luxd, Sebastien Igonete, Martin Schorba, Florian KM Schur, Hans Kraüsslich, and John Briggsa. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1401455111\">https://doi.org/10.1073/pnas.1401455111</a>.","apa":"Bharata, T., Menendez, L., Hagena, W., Luxd, V., Igonete, S., Schorba, M., … Briggsa, J. (2014). Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1401455111\">https://doi.org/10.1073/pnas.1401455111</a>","mla":"Bharata, Tanmay, et al. “Cryo Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.” <i>PNAS</i>, vol. 111, no. 22, National Academy of Sciences, 2014, pp. 8233–38, doi:<a href=\"https://doi.org/10.1073/pnas.1401455111\">10.1073/pnas.1401455111</a>.","ista":"Bharata T, Menendez L, Hagena W, Luxd V, Igonete S, Schorba M, Schur FK, Kraüsslich H, Briggsa J. 2014. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. PNAS. 111(22), 8233–8238.","short":"T. Bharata, L. Menendez, W. Hagena, V. Luxd, S. Igonete, M. Schorba, F.K. Schur, H. Kraüsslich, J. Briggsa, PNAS 111 (2014) 8233–8238.","ama":"Bharata T, Menendez L, Hagena W, et al. Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly. <i>PNAS</i>. 2014;111(22):8233-8238. doi:<a href=\"https://doi.org/10.1073/pnas.1401455111\">10.1073/pnas.1401455111</a>","ieee":"T. Bharata <i>et al.</i>, “Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly,” <i>PNAS</i>, vol. 111, no. 22. National Academy of Sciences, pp. 8233–8238, 2014."},"year":"2014","quality_controlled":0,"date_updated":"2021-01-12T08:16:50Z","publication_status":"published","abstract":[{"text":"The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position.","lang":"eng"}],"date_created":"2018-12-11T11:48:37Z","extern":1,"issue":"22","tmp":{"image":"/images/cc_by_nc_nd.png","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)"},"month":"06","intvolume":"       111","title":"Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly","doi":"10.1073/pnas.1401455111","page":"8233 - 8238","acknowledgement":"The authors thank Leonardo Trabuco for help with running MDFF, Maria Anders for preparing amprenavir-inhibited virus, Marie-Christine Vaney for help with X-ray data processing and structure refinement, Ahmed Haouz and Patrick Weber (robotized crystallization facility Proteopole, Institut Pasteur) for help in crystal screening, and the European Molecular Biology Laboratory (EMBL) Information Technology Services Unit and Frank Thommen for technical support. This study was supported by Deutsche Forschungsgemeinschaft Grants BR 3635/2-1 (to J.A.G.B.) and KR 906/7-1 (to H.-G.K.) and a Federation of European Biochemical Societies long-term fellowship (to T.A.M.B.). The laboratory of J.A.G.B. acknowledges financial support from EMBL and the Chica und Heinz Schaller Stiftung. ","publist_id":"6838","_id":"809"},{"issue":"7","language":[{"iso":"eng"}],"month":"07","intvolume":"        13","publication_identifier":{"issn":["1535-7163","1538-8514"]},"doi":"10.1158/1535-7163.mct-13-0288","title":"Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients","oa_version":"None","page":"1777-1790","_id":"8244","article_type":"original","article_processing_charge":"No","day":"01","volume":13,"date_published":"2014-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for Cancer Research","author":[{"first_name":"J.","full_name":"Singer, J.","last_name":"Singer"},{"last_name":"Fazekas","full_name":"Fazekas, Judit","first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"full_name":"Wang, W.","first_name":"W.","last_name":"Wang"},{"full_name":"Weichselbaumer, M.","first_name":"M.","last_name":"Weichselbaumer"},{"last_name":"Matz","full_name":"Matz, M.","first_name":"M."},{"full_name":"Mader, A.","first_name":"A.","last_name":"Mader"},{"first_name":"W.","full_name":"Steinfellner, W.","last_name":"Steinfellner"},{"first_name":"S.","full_name":"Meitz, S.","last_name":"Meitz"},{"last_name":"Mechtcheriakova","full_name":"Mechtcheriakova, D.","first_name":"D."},{"first_name":"Y.","full_name":"Sobanov, Y.","last_name":"Sobanov"},{"full_name":"Willmann, M.","first_name":"M.","last_name":"Willmann"},{"last_name":"Stockner","full_name":"Stockner, T.","first_name":"T."},{"last_name":"Spillner","first_name":"E.","full_name":"Spillner, E."},{"full_name":"Kunert, R.","first_name":"R.","last_name":"Kunert"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, E.","first_name":"E."}],"status":"public","type":"journal_article","publication":"Molecular Cancer Therapeutics","citation":{"ieee":"J. Singer <i>et al.</i>, “Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients,” <i>Molecular Cancer Therapeutics</i>, vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014.","ista":"Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E, Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics. 13(7), 1777–1790.","short":"J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner, R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790.","ama":"Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. <i>Molecular Cancer Therapeutics</i>. 2014;13(7):1777-1790. doi:<a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">10.1158/1535-7163.mct-13-0288</a>","mla":"Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” <i>Molecular Cancer Therapeutics</i>, vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:<a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">10.1158/1535-7163.mct-13-0288</a>.","chicago":"Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for Passive Immunotherapy in Dog Cancer Patients.” <i>Molecular Cancer Therapeutics</i>. American Association for Cancer Research, 2014. <a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">https://doi.org/10.1158/1535-7163.mct-13-0288</a>.","apa":"Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A., … Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients. <i>Molecular Cancer Therapeutics</i>. American Association for Cancer Research. <a href=\"https://doi.org/10.1158/1535-7163.mct-13-0288\">https://doi.org/10.1158/1535-7163.mct-13-0288</a>"},"quality_controlled":"1","date_updated":"2021-01-12T08:17:42Z","year":"2014","date_created":"2020-08-10T11:54:29Z","extern":"1","abstract":[{"text":"Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer.","lang":"eng"}],"publication_status":"published"},{"year":"2014","date_updated":"2021-01-12T08:19:21Z","quality_controlled":0,"publication_status":"published","abstract":[{"lang":"eng","text":"Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena."}],"extern":1,"date_created":"2018-12-11T11:48:48Z","status":"public","publication":"Molecular Biology and Evolution","type":"journal_article","citation":{"chicago":"Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/msu242\">https://doi.org/10.1093/molbev/msu242</a>.","apa":"Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N., … James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msu242\">https://doi.org/10.1093/molbev/msu242</a>","mla":"Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” <i>Molecular Biology and Evolution</i>, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:<a href=\"https://doi.org/10.1093/molbev/msu242\">10.1093/molbev/msu242</a>.","ista":"Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025.","ama":"Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. <i>Molecular Biology and Evolution</i>. 2014;31(11):3016-3025. doi:<a href=\"https://doi.org/10.1093/molbev/msu242\">10.1093/molbev/msu242</a>","short":"V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025.","ieee":"V. Seplyarskiy <i>et al.</i>, “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” <i>Molecular Biology and Evolution</i>, vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014."},"date_published":"2014-11-01T00:00:00Z","author":[{"last_name":"Seplyarskiy","first_name":"Vladimir","full_name":"Seplyarskiy, Vladimir B"},{"first_name":"Maria","full_name":"Logacheva, Maria D","last_name":"Logacheva"},{"first_name":"Aleksey","full_name":"Penin, Aleksey A","last_name":"Penin"},{"last_name":"Baranová","first_name":"Maria","full_name":"Baranová, Maria A"},{"first_name":"Evgeny","full_name":"Leushkin, Evgeny V","last_name":"Leushkin"},{"last_name":"Demidenko","first_name":"Natalia","full_name":"Demidenko, Natalia V"},{"last_name":"Klepikova","full_name":"Klepikova, Anna V","first_name":"Anna"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"},{"first_name":"Timothy","full_name":"James, Timothy Y","last_name":"James"}],"publisher":"Oxford University Press","day":"01","volume":31,"page":"3016 - 3025","acknowledgement":"The authors are grateful to Georgii Bazykin for valuable discussion and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology for Sanger sequencing. This study was supported by the Russian government grant No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute International Early Career Scientist Award and EMBO Young Investigator Program, and core funds provided by the University of Michigan.","publist_id":"6801","_id":"845","title":"Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity","doi":"10.1093/molbev/msu242","month":"11","intvolume":"        31","issue":"11","tmp":{"image":"/images/cc_by.png","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)"}},{"intvolume":"       136","month":"11","language":[{"iso":"eng"}],"issue":"51","_id":"8458","oa_version":"None","page":"17852-17860","title":"Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan","doi":"10.1021/ja5105987","publication_identifier":{"issn":["0002-7863","1520-5126"]},"author":[{"first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"},{"last_name":"Triboulet","full_name":"Triboulet, Sébastien","first_name":"Sébastien"},{"first_name":"Cédric","full_name":"Laguri, Cédric","last_name":"Laguri"},{"first_name":"Catherine M.","full_name":"Bougault, Catherine M.","last_name":"Bougault"},{"full_name":"Ayala, Isabel","first_name":"Isabel","last_name":"Ayala"},{"full_name":"Callon, Morgane","first_name":"Morgane","last_name":"Callon"},{"full_name":"Arthur, Michel","first_name":"Michel","last_name":"Arthur"},{"first_name":"Jean-Pierre","full_name":"Simorre, Jean-Pierre","last_name":"Simorre"}],"publisher":"American Chemical Society","date_published":"2014-11-27T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":136,"article_processing_charge":"No","article_type":"original","day":"27","date_created":"2020-09-18T10:07:52Z","extern":"1","publication_status":"published","abstract":[{"text":"The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis.","lang":"eng"}],"quality_controlled":"1","date_updated":"2021-01-12T08:19:24Z","year":"2014","publication":"Journal of the American Chemical Society","type":"journal_article","citation":{"mla":"Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60, doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>.","apa":"Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon, M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>","chicago":"Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>.","ieee":"P. Schanda <i>et al.</i>, “Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan,” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51. American Chemical Society, pp. 17852–17860, 2014.","short":"P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon, M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014) 17852–17860.","ama":"Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. 2014;136(51):17852-17860. doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>","ista":"Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 136(51), 17852–17860."},"status":"public"},{"issue":"15","oa_version":"None","doi":"10.1093/bioinformatics/btu166","title":"Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data","author":[{"last_name":"Morin","first_name":"Sébastien","full_name":"Morin, Sébastien"},{"last_name":"Linnet","full_name":"Linnet, Troels E","first_name":"Troels E"},{"last_name":"Lescanne","full_name":"Lescanne, Mathilde","first_name":"Mathilde"},{"full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"last_name":"Thompson","first_name":"Gary S","full_name":"Thompson, Gary S"},{"last_name":"Tollinger","first_name":"Martin","full_name":"Tollinger, Martin"},{"last_name":"Teilum","first_name":"Kaare","full_name":"Teilum, Kaare"},{"first_name":"Stéphane","full_name":"Gagné, Stéphane","last_name":"Gagné"},{"full_name":"Marion, Dominique","first_name":"Dominique","last_name":"Marion"},{"last_name":"Griesinger","full_name":"Griesinger, Christian","first_name":"Christian"},{"last_name":"Blackledge","first_name":"Martin","full_name":"Blackledge, Martin"},{"full_name":"d’Auvergne, Edward J","first_name":"Edward J","last_name":"d’Auvergne"}],"publisher":"Oxford University Press","date_published":"2014-08-01T00:00:00Z","article_processing_charge":"No","day":"01","publication_status":"published","abstract":[{"text":"Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis.","lang":"eng"}],"year":"2014","status":"public","intvolume":"        30","month":"08","language":[{"iso":"eng"}],"_id":"8459","page":"2219-2220","publication_identifier":{"issn":["1367-4803","1460-2059"]},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/bioinformatics/btz397"}]},"keyword":["Statistics and Probability","Computational Theory and Mathematics","Biochemistry","Molecular Biology","Computational Mathematics","Computer Science Applications"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":30,"article_type":"original","extern":"1","date_created":"2020-09-18T10:08:07Z","date_updated":"2021-01-12T08:19:25Z","quality_controlled":"1","publication":"Bioinformatics","type":"journal_article","citation":{"mla":"Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>.","chicago":"Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>.","apa":"Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>","ieee":"S. Morin <i>et al.</i>, “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” <i>Bioinformatics</i>, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.","ista":"Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.","ama":"Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. 2014;30(15):2219-2220. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>","short":"S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220."}},{"_id":"8460","oa_version":"None","page":"4312-4317","doi":"10.1002/anie.201311275","title":"Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy","publication_identifier":{"issn":["1433-7851"]},"intvolume":"        53","month":"03","language":[{"iso":"eng"}],"issue":"17","date_created":"2020-09-18T10:08:53Z","extern":"1","abstract":[{"lang":"eng","text":"The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states."}],"publication_status":"published","date_updated":"2021-01-12T08:19:25Z","quality_controlled":"1","year":"2014","publication":"Angewandte Chemie International Edition","citation":{"chicago":"Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>.","apa":"Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>","mla":"Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>.","ista":"Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317.","ama":"Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. 2014;53(17):4312-4317. doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>","short":"P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.","ieee":"P. Ma <i>et al.</i>, “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014."},"type":"journal_article","status":"public","publisher":"Wiley","author":[{"last_name":"Ma","first_name":"Peixiang","full_name":"Ma, Peixiang"},{"full_name":"Haller, Jens D.","first_name":"Jens D.","last_name":"Haller"},{"last_name":"Zajakala","full_name":"Zajakala, Jérémy","first_name":"Jérémy"},{"last_name":"Macek","full_name":"Macek, Pavel","first_name":"Pavel"},{"full_name":"Sivertsen, Astrid C.","first_name":"Astrid C.","last_name":"Sivertsen"},{"last_name":"Willbold","full_name":"Willbold, Dieter","first_name":"Dieter"},{"full_name":"Boisbouvier, Jérôme","first_name":"Jérôme","last_name":"Boisbouvier"},{"first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"}],"date_published":"2014-03-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":53,"article_type":"original","article_processing_charge":"No","day":"18"},{"title":"Arnol′d diffusion in a pendulum lattice","doi":"10.1002/cpa.21509","publication_identifier":{"issn":["0010-3640"]},"_id":"8500","oa_version":"None","page":"748-775","language":[{"iso":"eng"}],"issue":"5","intvolume":"        67","month":"05","citation":{"ama":"Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. 2014;67(5):748-775. doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>","short":"V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775.","ista":"Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775.","ieee":"V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5. Wiley, pp. 748–775, 2014.","apa":"Kaloshin, V., Levi, M., &#38; Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>","chicago":"Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>.","mla":"Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>."},"publication":"Communications on Pure and Applied Mathematics","type":"journal_article","status":"public","date_created":"2020-09-18T10:47:01Z","extern":"1","publication_status":"published","abstract":[{"text":"The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way.","lang":"eng"}],"quality_controlled":"1","date_updated":"2022-08-25T13:58:13Z","year":"2014","volume":67,"article_type":"original","article_processing_charge":"No","day":"01","author":[{"full_name":"Kaloshin, Vadim","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"last_name":"Levi","first_name":"Mark","full_name":"Levi, Mark"},{"last_name":"Saprykina","first_name":"Maria","full_name":"Saprykina, Maria"}],"publisher":"Wiley","date_published":"2014-05-01T00:00:00Z","keyword":["Applied Mathematics","General Mathematics"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"issue":"2","external_id":{"arxiv":["1304.3050"]},"title":"Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom","doi":"10.17323/1609-4514-2014-14-2-181-203","oa_version":"Preprint","day":"01","article_processing_charge":"No","date_published":"2014-04-01T00:00:00Z","arxiv":1,"publisher":"Independent University of Moscow","author":[{"last_name":"Bounemoura","first_name":"Abed","full_name":"Bounemoura, Abed"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin"}],"status":"public","year":"2014","abstract":[{"text":"In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"month":"04","intvolume":"        14","publication_identifier":{"issn":["1609-3321","1609-4514"]},"page":"181-203","_id":"8501","article_type":"original","volume":14,"keyword":["General Mathematics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Moscow Mathematical Journal","citation":{"ieee":"A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.","ista":"Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203.","short":"A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.","ama":"Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. 2014;14(2):181-203. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>","mla":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>.","apa":"Bounemoura, A., &#38; Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>"},"type":"journal_article","quality_controlled":"1","date_updated":"2021-01-12T08:19:43Z","extern":"1","date_created":"2020-09-18T10:47:09Z"}]