--- _id: '1827' abstract: - lang: eng text: Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved. article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham full_name: Mayo, Avraham last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055 apa: Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055 chicago: Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055. ieee: T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015. ista: Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3). mla: Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055. short: T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:54:14Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T14:07:51Z day: '23' ddc: - '576' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055 ec_funded: 1 file: - access_level: open_access checksum: b8aa66f450ff8de393014b87ec7d2efb content_type: application/pdf creator: system date_created: 2018-12-12T10:15:39Z date_updated: 2020-07-14T12:45:17Z file_id: '5161' file_name: IST-2016-452-v1+1_journal.pcbi.1004055.pdf file_size: 1811647 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 11' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '03' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5278' pubrep_id: '452' quality_controlled: '1' related_material: record: - id: '9718' relation: research_data status: public - id: '9773' relation: research_data status: public scopus_import: 1 status: public title: Evolution of bow-tie architectures in biology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '1809' abstract: - lang: eng text: 'Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.' author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager citation: ama: Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907 apa: Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907 chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907. ieee: B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015. ista: Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5). mla: Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907. short: B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015). date_created: 2018-12-11T11:54:07Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T14:07:48Z day: '18' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1371/journal.pone.0126907 file: - access_level: open_access checksum: d3a4a58ef4bd3b3e2f32b7fd7af4a743 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:07Z date_updated: 2020-07-14T12:45:17Z file_id: '4730' file_name: IST-2016-453-v1+1_journal.pone.0126907.pdf file_size: 2748982 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 10' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5299' pubrep_id: '453' quality_controlled: '1' related_material: record: - id: '9715' relation: research_data status: public - id: '9772' relation: research_data status: public scopus_import: 1 status: public title: Indirect genetic effects and the dynamics of social interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2015' ... --- _id: '9772' article_processing_charge: No author: - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Reinmar full_name: Hager, Reinmar last_name: Hager citation: ama: Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003 apa: Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003 chicago: Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003. ieee: B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015. ista: Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003. mla: Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003. short: B. Trubenova, S. Novak, R. Hager, (2015). date_created: 2021-08-05T12:55:20Z date_published: 2015-05-18T00:00:00Z date_updated: 2023-02-23T10:15:25Z day: '18' department: - _id: NiBa doi: 10.1371/journal.pone.0126907.s003 month: '05' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1809' relation: used_in_publication status: public status: public title: Description of the agent based simulations type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9773' article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham E. full_name: Mayo, Avraham E. last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002 apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002 chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002. ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015. ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002. mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002. short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015). date_created: 2021-08-05T12:58:07Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T10:16:13Z day: '23' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055.s002 month: '03' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1827' relation: used_in_publication status: public status: public title: Evolutionary simulation code type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '981' abstract: - lang: eng text: The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials. acknowledgement: We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004. author: - first_name: Ilija full_name: Zeljkovic, Ilija last_name: Zeljkovic - first_name: Yoshinori full_name: Okada, Yoshinori last_name: Okada - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Raman full_name: Sankar, Raman last_name: Sankar - first_name: Daniel full_name: Walkup, Daniel last_name: Walkup - first_name: Wenwen full_name: Zhou, Wenwen last_name: Zhou - first_name: Junwei full_name: Liu, Junwei last_name: Liu - first_name: Guoqing full_name: Chang, Guoqing last_name: Chang - first_name: Yungjui full_name: Wang, Yungjui last_name: Wang - first_name: Md full_name: Hasan, Md Z last_name: Hasan - first_name: Fangcheng full_name: Chou, Fangcheng last_name: Chou - first_name: Hsin full_name: Lin, Hsin last_name: Lin - first_name: Arun full_name: Bansil, Arun last_name: Bansil - first_name: Liang full_name: Fu, Liang last_name: Fu - first_name: Vidya full_name: Madhavan, Vidya last_name: Madhavan citation: ama: Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 2015;14(3):318-324. doi:10.1038/nmat4215 apa: Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. Nature Publishing Group. https://doi.org/10.1038/nmat4215 chicago: Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials. Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215. ieee: I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” Nature Materials, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015. ista: Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324. mla: Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215. short: I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324. date_created: 2018-12-11T11:49:31Z date_published: 2015-03-01T00:00:00Z date_updated: 2021-01-12T08:22:24Z day: '01' doi: 10.1038/nmat4215 extern: 1 intvolume: ' 14' issue: '3' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.4906 month: '03' oa: 1 page: 318 - 324 publication: Nature Materials publication_status: published publisher: Nature Publishing Group publist_id: '6419' quality_controlled: 0 status: public title: Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators type: journal_article volume: 14 year: '2015' ... --- _id: '982' abstract: - lang: eng text: We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions. acknowledgement: We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić - first_name: Dmitry full_name: Abanin, Dmitry A last_name: Abanin citation: ama: Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047 apa: Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047 chicago: Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047. ieee: M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015. ista: Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4). mla: Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047. short: M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015). date_created: 2018-12-11T11:49:32Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T08:22:25Z day: '01' doi: 10.1103/PhysRevX.5.041047 extern: 1 intvolume: ' 5' issue: '4' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.01635 month: '01' oa: 1 publication: Physical Review X publication_status: published publisher: American Physical Society publist_id: '6418' quality_controlled: 0 status: public title: Criterion for many-body localization-delocalization phase transition type: journal_article volume: 5 year: '2015' ... --- _id: '99' abstract: - lang: eng text: Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms. acknowledgement: Research support by Microsoft Project Q, the Danish National Research Foundation, the Lundbeck Foundation, the Carlsberg Foundation, and the European Commission. A.P.H. acknowledges support from the US Department of Energy, C.M.M. acknowledges support from the Villum Foundation. author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: S M full_name: Albrecht, S M last_name: Albrecht - first_name: Gediminas full_name: Kiršanskas, Gediminas last_name: Kiršanskas - first_name: W full_name: Chang, W last_name: Chang - first_name: Ferdinand full_name: Kuemmeth, Ferdinand last_name: Kuemmeth - first_name: Peter full_name: Krogstrup, Peter last_name: Krogstrup - first_name: Thomas full_name: Jespersen, Thomas last_name: Jespersen - first_name: Jesper full_name: Nygård, Jesper last_name: Nygård - first_name: Karsten full_name: Flensberg, Karsten last_name: Flensberg - first_name: Charles full_name: Marcus, Charles last_name: Marcus citation: ama: Higginbotham AP, Albrecht SM, Kiršanskas G, et al. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 2015;11(12):1017-1021. doi:10.1038/nphys3461 apa: Higginbotham, A. P., Albrecht, S. M., Kiršanskas, G., Chang, W., Kuemmeth, F., Krogstrup, P., … Marcus, C. (2015). Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys3461 chicago: Higginbotham, Andrew P, S M Albrecht, Gediminas Kiršanskas, W Chang, Ferdinand Kuemmeth, Peter Krogstrup, Thomas Jespersen, Jesper Nygård, Karsten Flensberg, and Charles Marcus. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics. Nature Publishing Group, 2015. https://doi.org/10.1038/nphys3461. ieee: A. P. Higginbotham et al., “Parity lifetime of bound states in a proximitized semiconductor nanowire,” Nature Physics, vol. 11, no. 12. Nature Publishing Group, pp. 1017–1021, 2015. ista: Higginbotham AP, Albrecht SM, Kiršanskas G, Chang W, Kuemmeth F, Krogstrup P, Jespersen T, Nygård J, Flensberg K, Marcus C. 2015. Parity lifetime of bound states in a proximitized semiconductor nanowire. Nature Physics. 11(12), 1017–1021. mla: Higginbotham, Andrew P., et al. “Parity Lifetime of Bound States in a Proximitized Semiconductor Nanowire.” Nature Physics, vol. 11, no. 12, Nature Publishing Group, 2015, pp. 1017–21, doi:10.1038/nphys3461. short: A.P. Higginbotham, S.M. Albrecht, G. Kiršanskas, W. Chang, F. Kuemmeth, P. Krogstrup, T. Jespersen, J. Nygård, K. Flensberg, C. Marcus, Nature Physics 11 (2015) 1017–1021. date_created: 2018-12-11T11:44:37Z date_published: 2015-09-14T00:00:00Z date_updated: 2021-01-12T08:22:28Z day: '14' doi: 10.1038/nphys3461 extern: '1' external_id: arxiv: - '1501.05155' intvolume: ' 11' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1501.05155 month: '09' oa: 1 oa_version: Preprint page: 1017 - 1021 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7955' quality_controlled: '1' status: public title: Parity lifetime of bound states in a proximitized semiconductor nanowire type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '8495' abstract: - lang: eng text: 'In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'''': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting.' article_processing_charge: No article_type: letter_note author: - first_name: Abed full_name: Bounemoura, Abed last_name: Bounemoura - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Bounemoura A, Kaloshin V. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 2015;144(4):1553-1560. doi:10.1090/proc/12796 apa: Bounemoura, A., & Kaloshin, V. (2015). A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12796 chicago: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/proc/12796. ieee: A. Bounemoura and V. Kaloshin, “A note on micro-instability for Hamiltonian systems close to integrable,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1553–1560, 2015. ista: Bounemoura A, Kaloshin V. 2015. A note on micro-instability for Hamiltonian systems close to integrable. Proceedings of the American Mathematical Society. 144(4), 1553–1560. mla: Bounemoura, Abed, and Vadim Kaloshin. “A Note on Micro-Instability for Hamiltonian Systems Close to Integrable.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2015, pp. 1553–60, doi:10.1090/proc/12796. short: A. Bounemoura, V. Kaloshin, Proceedings of the American Mathematical Society 144 (2015) 1553–1560. date_created: 2020-09-18T10:46:14Z date_published: 2015-12-21T00:00:00Z date_updated: 2021-01-12T08:19:40Z day: '21' doi: 10.1090/proc/12796 extern: '1' intvolume: ' 144' issue: '4' language: - iso: eng month: '12' oa_version: None page: 1553-1560 publication: Proceedings of the American Mathematical Society publication_identifier: issn: - 0002-9939 - 1088-6826 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: A note on micro-instability for Hamiltonian systems close to integrable type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 144 year: '2015' ... --- _id: '866' abstract: - lang: eng text: Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF. acknowledgement: | We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist. author: - first_name: Colin full_name: Kretz, Colin A last_name: Kretz - first_name: Manhong full_name: Dai, Manhong last_name: Dai - first_name: Onuralp full_name: Soylemez, Onuralp last_name: Soylemez - first_name: Andrew full_name: Yee, Andrew last_name: Yee - first_name: Karl full_name: Desch, Karl C last_name: Desch - first_name: David full_name: Siemieniak, David R last_name: Siemieniak - first_name: Kärt full_name: Tomberg, Kärt last_name: Tomberg - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Fan full_name: Meng, Fan last_name: Meng - first_name: David full_name: Ginsburg, David B last_name: Ginsburg citation: ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 2015;112(30):9328-9333. doi:10.1073/pnas.1511328112 apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg, D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511328112 chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112. ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112, no. 30. National Academy of Sciences, pp. 9328–9333, 2015. ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333. mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112, no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112. short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg, F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333. date_created: 2018-12-11T11:48:55Z date_published: 2015-07-28T00:00:00Z date_updated: 2021-01-12T08:20:26Z day: '28' doi: 10.1073/pnas.1511328112 extern: 1 intvolume: ' 112' issue: '30' month: '07' page: 9328 - 9333 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6783' quality_controlled: 0 status: public title: Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13 type: journal_article volume: 112 year: '2015' ... --- _id: '886' abstract: - lang: eng text: The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space. acknowledgement: 'This work has been supported by a grant from the HHMI International Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional Development Fund (ERDF), the European Union, and the European Research Council under grant agreement no 335980_EinME.' author: - first_name: Dmitry full_name: Kondrashov, Dmitry A last_name: Kondrashov - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009 apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009 chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015. https://doi.org/10.1016/j.tig.2014.09.009. ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33, 2015. ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes in sequence space. Trends in Genetics. 31(1), 24–33. mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no. 1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009. short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33. date_created: 2018-12-11T11:49:01Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T08:21:16Z day: '01' doi: 10.1016/j.tig.2014.09.009 extern: 1 intvolume: ' 31' issue: '1' month: '01' page: 24 - 33 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6764' quality_controlled: 0 status: public title: Topological features of rugged fitness landscapes in sequence space type: journal_article volume: 31 year: '2015' ...