---
_id: '10067'
abstract:
- lang: eng
  text: The search for novel entangled phases of matter has lead to the recent discovery
    of a new class of “entanglement transitions,” exemplified by random tensor networks
    and monitored quantum circuits. Most known examples can be understood as some
    classical ordering transitions in an underlying statistical mechanics model, where
    entanglement maps onto the free-energy cost of inserting a domain wall. In this
    paper we study the possibility of entanglement transitions driven by physics beyond
    such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired
    variational Ansätze, we investigate under what conditions on the variational parameters
    these Ansätze can capture an entanglement transition. We study the entanglement
    scaling of short-range restricted Boltzmann machine (RBM) quantum states with
    random phases. For uncorrelated random phases, we analytically demonstrate the
    absence of an entanglement transition and reveal subtle finite-size effects in
    finite-size numerical simulations. Introducing phases with correlations decaying
    as 1/r^α in real space, we observe three regions with a different scaling of entanglement
    entropy depending on the exponent α. We study the nature of the transition between
    these regions, finding numerical evidence for critical behavior. Our work establishes
    the presence of long-range correlated phases in RBM-based wave functions as a
    required ingredient for entanglement transitions.
acknowledgement: We would like to thank S. De Nicola, P. Brighi, and V. Karle for
  fruitful discussions and valuable feedback on the manuscript. R.M. and M.S. acknowledge
  support by the European Research Council (ERC) under the European Union's Horizon
  2020 research and innovation program (Grant Agreement No. 850899). R.V. acknowledges
  support from the US Department of Energy, Office of Science, Basic Energy Sciences,
  under Early Career Award No. DE-SC0019168, and the Alfred P. Sloan Foundation through
  a Sloan Research Fellowship.
article_number: '104205'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Raimel A
  full_name: Medina Ramos, Raimel A
  id: CE680B90-D85A-11E9-B684-C920E6697425
  last_name: Medina Ramos
  orcid: 0000-0002-5383-2869
- first_name: Romain
  full_name: Vasseur, Romain
  last_name: Vasseur
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
citation:
  ama: Medina Ramos RA, Vasseur R, Serbyn M. Entanglement transitions from restricted
    Boltzmann machines. <i>Physical Review B</i>. 2021;104(10). doi:<a href="https://doi.org/10.1103/physrevb.104.104205">10.1103/physrevb.104.104205</a>
  apa: Medina Ramos, R. A., Vasseur, R., &#38; Serbyn, M. (2021). Entanglement transitions
    from restricted Boltzmann machines. <i>Physical Review B</i>. American Physical
    Society. <a href="https://doi.org/10.1103/physrevb.104.104205">https://doi.org/10.1103/physrevb.104.104205</a>
  chicago: Medina Ramos, Raimel A, Romain Vasseur, and Maksym Serbyn. “Entanglement
    Transitions from Restricted Boltzmann Machines.” <i>Physical Review B</i>. American
    Physical Society, 2021. <a href="https://doi.org/10.1103/physrevb.104.104205">https://doi.org/10.1103/physrevb.104.104205</a>.
  ieee: R. A. Medina Ramos, R. Vasseur, and M. Serbyn, “Entanglement transitions from
    restricted Boltzmann machines,” <i>Physical Review B</i>, vol. 104, no. 10. American
    Physical Society, 2021.
  ista: Medina Ramos RA, Vasseur R, Serbyn M. 2021. Entanglement transitions from
    restricted Boltzmann machines. Physical Review B. 104(10), 104205.
  mla: Medina Ramos, Raimel A., et al. “Entanglement Transitions from Restricted Boltzmann
    Machines.” <i>Physical Review B</i>, vol. 104, no. 10, 104205, American Physical
    Society, 2021, doi:<a href="https://doi.org/10.1103/physrevb.104.104205">10.1103/physrevb.104.104205</a>.
  short: R.A. Medina Ramos, R. Vasseur, M. Serbyn, Physical Review B 104 (2021).
corr_author: '1'
date_created: 2021-10-02T09:03:42Z
date_published: 2021-09-30T00:00:00Z
date_updated: 2026-10-02T11:36:06Z
day: '30'
department:
- _id: MaSe
doi: 10.1103/physrevb.104.104205
ec_funded: 1
external_id:
  arxiv:
  - '2107.05735'
  isi:
  - '000704414400002'
fulldoi: https://doi.org/10.1103/physrevb.104.104205
intvolume: '       104'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2107.05735
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
  call_identifier: H2020
  grant_number: '850899'
  name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review B
publication_identifier:
  eissn:
  - 2469-9969
  issn:
  - 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
  record:
  - id: '17208'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Entanglement transitions from restricted Boltzmann machines
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '10545'
abstract:
- lang: eng
  text: Classical models with complex energy landscapes represent a perspective avenue
    for the near-term application of quantum simulators. Until now, many theoretical
    works studied the performance of quantum algorithms for models with a unique ground
    state. However, when the classical problem is in a so-called clustering phase,
    the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT
    model defined on simple hypergraphs. The degeneracy of classical ground state
    manifold translates into the emergence of an extensive number of Z2 symmetries,
    which remain intact even in the presence of a quantum transverse magnetic field.
    We establish a general duality approach that restricts the quantum problem to
    a given sector of conserved Z2 charges and use it to study how the outcome of
    the quantum adiabatic algorithm depends on the hypergraph geometry. We show that
    the tree hypergraph which corresponds to a classically solvable instance of the
    3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters
    a second-order phase transition with a gap vanishing as a power-law in the problem
    size. The duality developed in this work provides a practical tool for studies
    of quantum models with classically degenerate energy manifold and reveals potential
    connections between glasses and gauge theories.
acknowledgement: We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y.
  Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback
  on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo,
  and C. Laumann. We acknowledge support from the European Research Council (ERC)
  under the European Union's Horizon 2020 Research and Innovation Programme Grant
  Agreement No. 850899.
article_number: '062423'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Raimel A
  full_name: Medina Ramos, Raimel A
  id: CE680B90-D85A-11E9-B684-C920E6697425
  last_name: Medina Ramos
  orcid: 0000-0002-5383-2869
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
citation:
  ama: Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable
    exclusive-or satisfiability problem (3-XORSAT). <i>Physical Review A</i>. 2021;104(6).
    doi:<a href="https://doi.org/10.1103/physreva.104.062423">10.1103/physreva.104.062423</a>
  apa: Medina Ramos, R. A., &#38; Serbyn, M. (2021). Duality approach to quantum annealing
    of the 3-variable exclusive-or satisfiability problem (3-XORSAT). <i>Physical
    Review A</i>. American Physical Society. <a href="https://doi.org/10.1103/physreva.104.062423">https://doi.org/10.1103/physreva.104.062423</a>
  chicago: Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum
    Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” <i>Physical
    Review A</i>. American Physical Society, 2021. <a href="https://doi.org/10.1103/physreva.104.062423">https://doi.org/10.1103/physreva.104.062423</a>.
  ieee: R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of
    the 3-variable exclusive-or satisfiability problem (3-XORSAT),” <i>Physical Review
    A</i>, vol. 104, no. 6. American Physical Society, 2021.
  ista: Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of
    the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review
    A. 104(6), 062423.
  mla: Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing
    of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” <i>Physical
    Review A</i>, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:<a
    href="https://doi.org/10.1103/physreva.104.062423">10.1103/physreva.104.062423</a>.
  short: R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).
date_created: 2021-12-14T20:46:07Z
date_published: 2021-12-14T00:00:00Z
date_updated: 2026-10-02T11:36:06Z
day: '14'
department:
- _id: MaSe
doi: 10.1103/physreva.104.062423
ec_funded: 1
external_id:
  arxiv:
  - '2106.06344'
  isi:
  - '000753659200004'
fulldoi: https://doi.org/10.1103/physreva.104.062423
intvolume: '       104'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2106.06344
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
  call_identifier: H2020
  grant_number: '850899'
  name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Physical Review A
publication_identifier:
  eissn:
  - 2469-9934
  issn:
  - 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
  record:
  - id: '17208'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability
  problem (3-XORSAT)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 104
year: '2021'
...
---
_id: '7553'
abstract:
- lang: eng
  text: Normative theories and statistical inference provide complementary approaches
    for the study of biological systems. A normative theory postulates that organisms
    have adapted to efficiently solve essential tasks, and proceeds to mathematically
    work out testable consequences of such optimality; parameters that maximize the
    hypothesized organismal function can be derived ab initio, without reference to
    experimental data. In contrast, statistical inference focuses on efficient utilization
    of data to learn model parameters, without reference to any a priori notion of
    biological function, utility, or fitness. Traditionally, these two approaches
    were developed independently and applied separately. Here we unify them in a coherent
    Bayesian framework that embeds a normative theory into a family of maximum-entropy
    “optimization priors.” This family defines a smooth interpolation between a data-rich
    inference regime (characteristic of “bottom-up” statistical models), and a data-limited
    ab inito prediction regime (characteristic of “top-down” normative theory). We
    demonstrate the applicability of our framework using data from the visual cortex,
    and argue that the flexibility it affords is essential to address a number of
    fundamental challenges relating to inference and prediction in complex, high-dimensional
    biological problems.
acknowledgement: The authors thank Dario Ringach for providing the V1 receptive fields
  and Olivier Marre for providing the retinal receptive fields. W.M. was funded by
  the European Union’s Horizon 2020 research and innovation programme under the Marie
  Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers
  Science grant no. HFSP RGP0032/2018.
article_processing_charge: No
author:
- first_name: Wiktor F
  full_name: Mlynarski, Wiktor F
  id: 358A453A-F248-11E8-B48F-1D18A9856A87
  last_name: Mlynarski
- first_name: Michal
  full_name: Hledik, Michal
  id: 4171253A-F248-11E8-B48F-1D18A9856A87
  last_name: Hledik
- first_name: Thomas R
  full_name: Sokolowski, Thomas R
  id: 3E999752-F248-11E8-B48F-1D18A9856A87
  last_name: Sokolowski
  orcid: 0000-0002-1287-3779
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
citation:
  ama: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality
    of neural systems. <i>Neuron</i>. 2021;109(7):1227-1241.e5. doi:<a href="https://doi.org/10.1016/j.neuron.2021.01.020">10.1016/j.neuron.2021.01.020</a>
  apa: Mlynarski, W. F., Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2021). Statistical
    analysis and optimality of neural systems. <i>Neuron</i>. Cell Press. <a href="https://doi.org/10.1016/j.neuron.2021.01.020">https://doi.org/10.1016/j.neuron.2021.01.020</a>
  chicago: Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik.
    “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>. Cell Press,
    2021. <a href="https://doi.org/10.1016/j.neuron.2021.01.020">https://doi.org/10.1016/j.neuron.2021.01.020</a>.
  ieee: W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical
    analysis and optimality of neural systems,” <i>Neuron</i>, vol. 109, no. 7. Cell
    Press, p. 1227–1241.e5, 2021.
  ista: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis
    and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.
  mla: Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural
    Systems.” <i>Neuron</i>, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:<a
    href="https://doi.org/10.1016/j.neuron.2021.01.020">10.1016/j.neuron.2021.01.020</a>.
  short: W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021)
    1227–1241.e5.
corr_author: '1'
date_created: 2020-02-28T11:00:12Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2026-10-02T11:40:30Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.neuron.2021.01.020
ec_funded: 1
external_id:
  isi:
  - '000637809600006'
  pmid:
  - '33592180'
fulldoi: https://doi.org/10.1016/j.neuron.2021.01.020
intvolume: '       109'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/848374
month: '04'
oa: 1
oa_version: Preprint
page: 1227-1241.e5
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Neuron
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/can-evolution-be-predicted/
  record:
  - id: '15020'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Statistical analysis and optimality of neural systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2021'
...
---
OA_type: free access
_id: '9298'
abstract:
- lang: eng
  text: 'In 2008, we published the first set of guidelines for standardizing research
    in autophagy. Since then, this topic has received increasing attention, and many
    scientists have entered the field. Our knowledge base and relevant new technologies
    have also been expanding. Thus, it is important to formulate on a regular basis
    updated guidelines for monitoring autophagy in different organisms. Despite numerous
    reviews, there continues to be confusion regarding acceptable methods to evaluate
    autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines
    for investigators to select and interpret methods to examine autophagy and related
    processes, and for reviewers to provide realistic and reasonable critiques of
    reports that are focused on these processes. These guidelines are not meant to
    be a dogmatic set of rules, because the appropriateness of any assay largely depends
    on the question being asked and the system being used. Moreover, no individual
    assay is perfect for every situation, calling for the use of multiple techniques
    to properly monitor autophagy in each experimental setting. Finally, several core
    components of the autophagy machinery have been implicated in distinct autophagic
    processes (canonical and noncanonical autophagy), implying that genetic approaches
    to block autophagy should rely on targeting two or more autophagy-related genes
    that ideally participate in distinct steps of the pathway. Along similar lines,
    because multiple proteins involved in autophagy also regulate other cellular pathways
    including apoptosis, not all of them can be used as a specific marker for bona
    fide autophagic responses. Here, we critically discuss current methods of assessing
    autophagy and the information they can, or cannot, provide. Our ultimate goal
    is to encourage intellectual and technical innovation in the field. '
acknowledgement: This work was supported by the National Institute of General Medical
  Sciences [GM131919]. Due to space and other limitations, it is not possible to include
  all other sources of financial support.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel J.
  full_name: Klionsky, Daniel J.
  last_name: Klionsky
- first_name: Amal Kamal
  full_name: Abdel-Aziz, Amal Kamal
  last_name: Abdel-Aziz
- first_name: Sara
  full_name: Abdelfatah, Sara
  last_name: Abdelfatah
- first_name: Mahmoud
  full_name: Abdellatif, Mahmoud
  last_name: Abdellatif
- first_name: Asghar
  full_name: Abdoli, Asghar
  last_name: Abdoli
- first_name: Steffen
  full_name: Abel, Steffen
  last_name: Abel
- first_name: Hagai
  full_name: Abeliovich, Hagai
  last_name: Abeliovich
- first_name: Marie H.
  full_name: Abildgaard, Marie H.
  last_name: Abildgaard
- first_name: Yakubu Princely
  full_name: Abudu, Yakubu Princely
  last_name: Abudu
- first_name: Abraham
  full_name: Acevedo-Arozena, Abraham
  last_name: Acevedo-Arozena
- first_name: Iannis E.
  full_name: Adamopoulos, Iannis E.
  last_name: Adamopoulos
- first_name: Khosrow
  full_name: Adeli, Khosrow
  last_name: Adeli
- first_name: Timon E.
  full_name: Adolph, Timon E.
  last_name: Adolph
- first_name: Annagrazia
  full_name: Adornetto, Annagrazia
  last_name: Adornetto
- first_name: Elma
  full_name: Aflaki, Elma
  last_name: Aflaki
- first_name: Galila
  full_name: Agam, Galila
  last_name: Agam
- first_name: Anupam
  full_name: Agarwal, Anupam
  last_name: Agarwal
- first_name: Bharat B.
  full_name: Aggarwal, Bharat B.
  last_name: Aggarwal
- first_name: Maria
  full_name: Agnello, Maria
  last_name: Agnello
- first_name: Patrizia
  full_name: Agostinis, Patrizia
  last_name: Agostinis
- first_name: Javed N.
  full_name: Agrewala, Javed N.
  last_name: Agrewala
- first_name: Alexander
  full_name: Agrotis, Alexander
  last_name: Agrotis
- first_name: Patricia V.
  full_name: Aguilar, Patricia V.
  last_name: Aguilar
- first_name: S. Tariq
  full_name: Ahmad, S. Tariq
  last_name: Ahmad
- first_name: Zubair M.
  full_name: Ahmed, Zubair M.
  last_name: Ahmed
- first_name: Ulises
  full_name: Ahumada-Castro, Ulises
  last_name: Ahumada-Castro
- first_name: Sonja
  full_name: Aits, Sonja
  last_name: Aits
- first_name: Shu
  full_name: Aizawa, Shu
  last_name: Aizawa
- first_name: Yunus
  full_name: Akkoc, Yunus
  last_name: Akkoc
- first_name: Tonia
  full_name: Akoumianaki, Tonia
  last_name: Akoumianaki
- first_name: Hafize Aysin
  full_name: Akpinar, Hafize Aysin
  last_name: Akpinar
- first_name: Ahmed M.
  full_name: Al-Abd, Ahmed M.
  last_name: Al-Abd
- first_name: Lina
  full_name: Al-Akra, Lina
  last_name: Al-Akra
- first_name: Abeer
  full_name: Al-Gharaibeh, Abeer
  last_name: Al-Gharaibeh
- first_name: Moulay A.
  full_name: Alaoui-Jamali, Moulay A.
  last_name: Alaoui-Jamali
- first_name: Simon
  full_name: Alberti, Simon
  last_name: Alberti
- first_name: Elísabet
  full_name: Alcocer-Gómez, Elísabet
  last_name: Alcocer-Gómez
- first_name: Cristiano
  full_name: Alessandri, Cristiano
  last_name: Alessandri
- first_name: Muhammad
  full_name: Ali, Muhammad
  last_name: Ali
- first_name: M. Abdul
  full_name: Alim Al-Bari, M. Abdul
  last_name: Alim Al-Bari
- first_name: Saeb
  full_name: Aliwaini, Saeb
  last_name: Aliwaini
- first_name: Javad
  full_name: Alizadeh, Javad
  last_name: Alizadeh
- first_name: Eugènia
  full_name: Almacellas, Eugènia
  last_name: Almacellas
- first_name: Alexandru
  full_name: Almasan, Alexandru
  last_name: Almasan
- first_name: Alicia
  full_name: Alonso, Alicia
  last_name: Alonso
- first_name: Guillermo D.
  full_name: Alonso, Guillermo D.
  last_name: Alonso
- first_name: Nihal
  full_name: Altan-Bonnet, Nihal
  last_name: Altan-Bonnet
- first_name: Dario C.
  full_name: Altieri, Dario C.
  last_name: Altieri
- first_name: Élida M.C.
  full_name: Álvarez, Élida M.C.
  last_name: Álvarez
- first_name: Sara
  full_name: Alves, Sara
  last_name: Alves
- first_name: Cristine
  full_name: Alves Da Costa, Cristine
  last_name: Alves Da Costa
- first_name: Mazen M.
  full_name: Alzaharna, Mazen M.
  last_name: Alzaharna
- first_name: Marialaura
  full_name: Amadio, Marialaura
  last_name: Amadio
- first_name: Consuelo
  full_name: Amantini, Consuelo
  last_name: Amantini
- first_name: Cristina
  full_name: Amaral, Cristina
  last_name: Amaral
- first_name: Susanna
  full_name: Ambrosio, Susanna
  last_name: Ambrosio
- first_name: Amal O.
  full_name: Amer, Amal O.
  last_name: Amer
- first_name: Veena
  full_name: Ammanathan, Veena
  last_name: Ammanathan
- first_name: Zhenyi
  full_name: An, Zhenyi
  last_name: An
- first_name: Stig U.
  full_name: Andersen, Stig U.
  last_name: Andersen
- first_name: Shaida A.
  full_name: Andrabi, Shaida A.
  last_name: Andrabi
- first_name: Magaiver
  full_name: Andrade-Silva, Magaiver
  last_name: Andrade-Silva
- first_name: Allen M.
  full_name: Andres, Allen M.
  last_name: Andres
- first_name: Sabrina
  full_name: Angelini, Sabrina
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date_created: 2021-03-28T22:01:44Z
date_published: 2021-02-08T00:00:00Z
date_updated: 2026-10-05T13:54:55Z
day: '08'
ddc:
- '580'
- '570'
department:
- _id: JiFr
doi: 10.1080/15548627.2020.1797280
external_id:
  isi:
  - '000636121800001'
  pmid:
  - '33634751'
fulldoi: https://doi.org/10.1080/15548627.2020.1797280
intvolume: '        17'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1080/15548627.2020.1797280
month: '02'
oa: 1
oa_version: Published Version
page: 1-382
pmid: 1
publication: Autophagy
publication_identifier:
  eissn:
  - 1554-8635
  issn:
  - 1554-8627
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guidelines for the use and interpretation of assays for monitoring autophagy
  (4th edition)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 17
year: '2021'
...
---
_id: '12909'
article_processing_charge: No
author:
- first_name: Alois
  full_name: Schlögl, Alois
  id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
  last_name: Schlögl
  orcid: 0000-0002-5621-8100
- first_name: Stefano
  full_name: Elefante, Stefano
  id: 490F40CE-F248-11E8-B48F-1D18A9856A87
  last_name: Elefante
- first_name: Andrei
  full_name: Hornoiu, Andrei
  id: 77129392-B450-11EA-8745-D4653DDC885E
  last_name: Hornoiu
- first_name: Stephan
  full_name: Stadlbauer, Stephan
  id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
  last_name: Stadlbauer
citation:
  ama: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous
    HPC cluster. In: <i>ASHPC21 – Austrian-Slovenian HPC Meeting 2021</i>. University
    of Ljubljana; 2021:5. doi:<a href="https://doi.org/10.3359/2021hpc">10.3359/2021hpc</a>'
  apa: 'Schlögl, A., Elefante, S., Hornoiu, A., &#38; Stadlbauer, S. (2021). Managing
    software on a heterogenous HPC cluster. In <i>ASHPC21 – Austrian-Slovenian HPC
    Meeting 2021</i> (p. 5). Virtual: University of Ljubljana. <a href="https://doi.org/10.3359/2021hpc">https://doi.org/10.3359/2021hpc</a>'
  chicago: Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer.
    “Managing Software on a Heterogenous HPC Cluster.” In <i>ASHPC21 – Austrian-Slovenian
    HPC Meeting 2021</i>, 5. University of Ljubljana, 2021. <a href="https://doi.org/10.3359/2021hpc">https://doi.org/10.3359/2021hpc</a>.
  ieee: A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software
    on a heterogenous HPC cluster,” in <i>ASHPC21 – Austrian-Slovenian HPC Meeting
    2021</i>, Virtual, 2021, p. 5.
  ista: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on
    a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC:
    Austrian-Slovenian HPC Meeting, 5.'
  mla: Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” <i>ASHPC21
    – Austrian-Slovenian HPC Meeting 2021</i>, University of Ljubljana, 2021, p. 5,
    doi:<a href="https://doi.org/10.3359/2021hpc">10.3359/2021hpc</a>.
  short: A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian
    HPC Meeting 2021, University of Ljubljana, 2021, p. 5.
conference:
  end_date: 2021-06-02
  location: Virtual
  name: 'ASHPC: Austrian-Slovenian HPC Meeting'
  start_date: 2021-05-31
corr_author: '1'
date_created: 2023-05-05T13:17:36Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2026-10-14T09:47:31Z
day: '02'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.3359/2021hpc
file:
- access_level: open_access
  checksum: ba73f85858fb9d5737ebc7724646dd45
  content_type: application/pdf
  creator: dernst
  date_created: 2023-05-16T07:36:34Z
  date_updated: 2023-05-16T07:36:34Z
  file_id: '12971'
  file_name: 2021_ASHPC_Schloegl.pdf
  file_size: 422761
  relation: main_file
  success: 1
file_date_updated: 2023-05-16T07:36:34Z
fulldoi: https://doi.org/10.3359/2021hpc
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf
month: '06'
oa: 1
oa_version: Published Version
page: '5'
publication: ASHPC21 – Austrian-Slovenian HPC Meeting 2021
publication_identifier:
  isbn:
  - 978-961-6980-77-7
  - 978-961-6133-48-7
publication_status: published
publisher: University of Ljubljana
status: public
title: Managing software on a heterogenous HPC cluster
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10004'
abstract:
- lang: eng
  text: 'Markov chains are the de facto finite-state model for stochastic dynamical
    systems, and Markov decision processes (MDPs) extend Markov chains by incorporating
    non-deterministic behaviors. Given an MDP and rewards on states, a classical optimization
    criterion is the maximal expected total reward where the MDP stops after T steps,
    which can be computed by a simple dynamic programming algorithm. We consider a
    natural generalization of the problem where the stopping times can be chosen according
    to a probability distribution, such that the expected stopping time is T, to optimize
    the expected total reward. Quite surprisingly we establish inter-reducibility
    of the expected stopping-time problem for Markov chains with the Positivity problem
    (which is related to the well-known Skolem problem), for which establishing either
    decidability or undecidability would be a major breakthrough. Given the hardness
    of the exact problem, we consider the approximate version of the problem: we show
    that it can be solved in exponential time for Markov chains and in exponential
    space for MDPs.'
acknowledgement: We are grateful to the anonymous reviewers of LICS 2021 and of a
  previous version of this paper for insightful comments that helped improving the
  presentation. This research was partially supported by the grant ERC CoG 863818
  (ForM-SMArt).
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Laurent
  full_name: Doyen, Laurent
  last_name: Doyen
citation:
  ama: 'Chatterjee K, Doyen L. Stochastic processes with expected stopping time. In:
    <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>.
    IEEE; 2021:1-13. doi:<a href="https://doi.org/10.1109/LICS52264.2021.9470595">10.1109/LICS52264.2021.9470595</a>'
  apa: 'Chatterjee, K., &#38; Doyen, L. (2021). Stochastic processes with expected
    stopping time. In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
    in Computer Science</i> (pp. 1–13). Rome, Italy: IEEE. <a href="https://doi.org/10.1109/LICS52264.2021.9470595">https://doi.org/10.1109/LICS52264.2021.9470595</a>'
  chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
    Stopping Time.” In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
    in Computer Science</i>, 1–13. IEEE, 2021. <a href="https://doi.org/10.1109/LICS52264.2021.9470595">https://doi.org/10.1109/LICS52264.2021.9470595</a>.
  ieee: K. Chatterjee and L. Doyen, “Stochastic processes with expected stopping time,”
    in <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>,
    Rome, Italy, 2021, pp. 1–13.
  ista: 'Chatterjee K, Doyen L. 2021. Stochastic processes with expected stopping
    time. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science.
    LICS: Logic in Computer Science, 1–13.'
  mla: Chatterjee, Krishnendu, and Laurent Doyen. “Stochastic Processes with Expected
    Stopping Time.” <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic
    in Computer Science</i>, IEEE, 2021, pp. 1–13, doi:<a href="https://doi.org/10.1109/LICS52264.2021.9470595">10.1109/LICS52264.2021.9470595</a>.
  short: K. Chatterjee, L. Doyen, in:, Proceedings of the 36th Annual ACM/IEEE Symposium
    on Logic in Computer Science, IEEE, 2021, pp. 1–13.
conference:
  end_date: 2021-07-02
  location: Rome, Italy
  name: 'LICS: Logic in Computer Science'
  start_date: 2021-06-29
date_created: 2021-09-12T22:01:25Z
date_published: 2021-07-07T00:00:00Z
date_updated: 2026-10-16T07:57:38Z
day: '07'
department:
- _id: KrCh
doi: 10.1109/LICS52264.2021.9470595
ec_funded: 1
external_id:
  arxiv:
  - '2104.07278'
  isi:
  - '000947350400036'
fulldoi: https://doi.org/10.1109/LICS52264.2021.9470595
isi: 1
keyword:
- Computer science
- Heuristic algorithms
- Memory management
- Automata
- Markov processes
- Probability distribution
- Complexity theory
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2104.07278
month: '07'
oa: 1
oa_version: Preprint
page: 1-13
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '863818'
  name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer
  Science
publication_identifier:
  eisbn:
  - 978-1-6654-4895-6
  isbn:
  - 978-1-6654-4896-3
  issn:
  - 1043-6871
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
  record:
  - id: '18630'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: Stochastic processes with expected stopping time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10408'
abstract:
- lang: eng
  text: 'Key trees are often the best solution in terms of transmission cost and storage
    requirements for managing keys in a setting where a group needs to share a secret
    key, while being able to efficiently rotate the key material of users (in order
    to recover from a potential compromise, or to add or remove users). Applications
    include multicast encryption protocols like LKH (Logical Key Hierarchies) or group
    messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced)
    binary tree, where each node is identified with a key: leaf nodes hold users’
    secret keys while the root is the shared group key. For a group of size N, each
    user just holds   log(N)  keys (the keys on the path from its leaf to the root)
    and its entire key material can be rotated by broadcasting   2log(N)  ciphertexts
    (encrypting each fresh key on the path under the keys of its parents). In this
    work we consider the natural setting where we have many groups with partially
    overlapping sets of users, and ask if we can find solutions where the cost of
    rotating a key is better than in the trivial one where we have a separate key
    tree for each group. We show that in an asymptotic setting (where the number m
    of groups is fixed while the number N of users grows) there exist more general
    key graphs whose cost converges to the cost of a single group, thus saving a factor
    linear in the number of groups over the trivial solution. As our asymptotic “solution”
    converges very slowly and performs poorly on concrete examples, we propose an
    algorithm that uses a natural heuristic to compute a key graph for any given group
    structure. Our algorithm combines two greedy algorithms, and is thus very efficient:
    it first converts the group structure into a “lattice graph”, which is then turned
    into a key graph by repeatedly applying the algorithm for constructing a Huffman
    code. To better understand how far our proposal is from an optimal solution, we
    prove lower bounds on the update cost of continuous group-key agreement and multicast
    encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom
    generators, and secret sharing as building blocks.'
acknowledgement: B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the
  European Research Council (ERC) under the European Union’s Horizon 2020 research
  and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by
  ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the
  ERC under the European Union’s Horizon 2020 research and innovation programme (682815
  - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020
  research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
  No. 665385; Michael Walter conducted part of this work at IST Austria, funded by
  the ERC under the European Union’s Horizon 2020 research and innovation programme
  (682815 - TOCNeT).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Joel F
  full_name: Alwen, Joel F
  id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
  last_name: Alwen
- first_name: Benedikt
  full_name: Auerbach, Benedikt
  id: D33D2B18-E445-11E9-ABB7-15F4E5697425
  last_name: Auerbach
  orcid: 0000-0002-7553-6606
- first_name: Mirza Ahad
  full_name: Baig, Mirza Ahad
  id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425
  last_name: Baig
- first_name: Miguel
  full_name: Cueto Noval, Miguel
  id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
  last_name: Cueto Noval
  orcid: 0000-0002-2505-4246
- first_name: Karen
  full_name: Klein, Karen
  id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
  last_name: Klein
- first_name: Guillermo
  full_name: Pascual Perez, Guillermo
  id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
  last_name: Pascual Perez
  orcid: 0000-0001-8630-415X
- first_name: Krzysztof Z
  full_name: Pietrzak, Krzysztof Z
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
- first_name: Michael
  full_name: Walter, Michael
  id: 488F98B0-F248-11E8-B48F-1D18A9856A87
  last_name: Walter
  orcid: 0000-0003-3186-2482
citation:
  ama: 'Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management
    for overlapping groups. In: <i>19th International Conference</i>. Vol 13044. Springer
    Nature; 2021:222-253. doi:<a href="https://doi.org/10.1007/978-3-030-90456-2_8">10.1007/978-3-030-90456-2_8</a>'
  apa: 'Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual
    Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for
    overlapping groups. In <i>19th International Conference</i> (Vol. 13044, pp. 222–253).
    Raleigh, NC, United States: Springer Nature. <a href="https://doi.org/10.1007/978-3-030-90456-2_8">https://doi.org/10.1007/978-3-030-90456-2_8</a>'
  chicago: 'Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval,
    Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter.
    “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In <i>19th
    International Conference</i>, 13044:222–53. Springer Nature, 2021. <a href="https://doi.org/10.1007/978-3-030-90456-2_8">https://doi.org/10.1007/978-3-030-90456-2_8</a>.'
  ieee: 'J. F. Alwen <i>et al.</i>, “Grafting key trees: Efficient key management
    for overlapping groups,” in <i>19th International Conference</i>, Raleigh, NC,
    United States, 2021, vol. 13044, pp. 222–253.'
  ista: 'Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak
    KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping
    groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol.
    13044, 222–253.'
  mla: 'Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping
    Groups.” <i>19th International Conference</i>, vol. 13044, Springer Nature, 2021,
    pp. 222–53, doi:<a href="https://doi.org/10.1007/978-3-030-90456-2_8">10.1007/978-3-030-90456-2_8</a>.'
  short: J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual
    Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer
    Nature, 2021, pp. 222–253.
conference:
  end_date: 2021-11-11
  location: Raleigh, NC, United States
  name: 'TCC: Theory of Cryptography'
  start_date: 2021-11-08
date_created: 2021-12-05T23:01:42Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2026-10-16T08:11:07Z
day: '04'
department:
- _id: KrPi
doi: 10.1007/978-3-030-90456-2_8
ec_funded: 1
external_id:
  isi:
  - '000728363700008'
fulldoi: https://doi.org/10.1007/978-3-030-90456-2_8
intvolume: '     13044'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2021/1158
month: '11'
oa: 1
oa_version: Preprint
page: 222-253
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '682815'
  name: Teaching Old Crypto New Tricks
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication: 19th International Conference
publication_identifier:
  eisbn:
  - 978-3-030-90456-2
  eissn:
  - 1611-3349
  isbn:
  - 9-783-0309-0455-5
  issn:
  - 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '18088'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: 'Grafting key trees: Efficient key management for overlapping groups'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13044
year: '2021'
...
---
_id: '10049'
abstract:
- lang: eng
  text: While messaging systems with strong security guarantees are widely used in
    practice, designing a protocol that scales efficiently to large groups and enjoys
    similar security guarantees remains largely open. The two existing proposals to
    date are ART (Cohn-Gordon et al., CCS18) and TreeKEM (IETF, The Messaging Layer
    Security Protocol, draft). TreeKEM is the currently considered candidate by the
    IETF MLS working group, but dynamic group operations (i.e. adding and removing
    users) can cause efficiency issues. In this paper we formalize and analyze a variant
    of TreeKEM which we term Tainted TreeKEM (TTKEM for short). The basic idea underlying
    TTKEM was suggested by Millican (MLS mailing list, February 2018). This version
    is more efficient than TreeKEM for some natural distributions of group operations,
    we quantify this through simulations.Our second contribution is two security proofs
    for TTKEM which establish post compromise and forward secrecy even against adaptive
    attackers. The security loss (to the underlying PKE) in the Random Oracle Model
    is a polynomial factor, and a quasipolynomial one in the Standard Model. Our proofs
    can be adapted to TreeKEM as well. Before our work no security proof for any TreeKEM-like
    protocol establishing tight security against an adversary who can adaptively choose
    the sequence of operations was known. We also are the first to prove (or even
    formalize) active security where the server can arbitrarily deviate from the protocol
    specification. Proving fully active security – where also the users can arbitrarily
    deviate – remains open.
acknowledgement: The first three authors contributed equally to this work. Funded
  by the European Research Council (ERC) under the European Union’s Horizon2020 research
  and innovation programme (682815-TOCNeT). Funded by the European Union’s Horizon
  2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
  No.665385.
article_processing_charge: No
author:
- first_name: Karen
  full_name: Klein, Karen
  id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
  last_name: Klein
- first_name: Guillermo
  full_name: Pascual Perez, Guillermo
  id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87
  last_name: Pascual Perez
  orcid: 0000-0001-8630-415X
- first_name: Michael
  full_name: Walter, Michael
  id: 488F98B0-F248-11E8-B48F-1D18A9856A87
  last_name: Walter
  orcid: 0000-0003-3186-2482
- first_name: Chethan
  full_name: Kamath Hosdurg, Chethan
  id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
  last_name: Kamath Hosdurg
  orcid: 0009-0006-6812-7317
- first_name: Margarita
  full_name: Capretto, Margarita
  last_name: Capretto
- first_name: Miguel
  full_name: Cueto Noval, Miguel
  id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc
  last_name: Cueto Noval
  orcid: 0000-0002-2505-4246
- first_name: Ilia
  full_name: Markov, Ilia
  id: D0CF4148-C985-11E9-8066-0BDEE5697425
  last_name: Markov
- first_name: Michelle X
  full_name: Yeo, Michelle X
  id: 2D82B818-F248-11E8-B48F-1D18A9856A87
  last_name: Yeo
  orcid: 0009-0001-3676-4809
- first_name: Joel F
  full_name: Alwen, Joel F
  id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87
  last_name: Alwen
- first_name: Krzysztof Z
  full_name: Pietrzak, Krzysztof Z
  id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
  last_name: Pietrzak
  orcid: 0000-0002-9139-1654
citation:
  ama: 'Klein K, Pascual Perez G, Walter M, et al. Keep the dirt: tainted TreeKEM,
    adaptively and actively secure continuous group key agreement. In: <i>2021 IEEE
    Symposium on Security and Privacy </i>. IEEE; 2021:268-284. doi:<a href="https://doi.org/10.1109/sp40001.2021.00035">10.1109/sp40001.2021.00035</a>'
  apa: 'Klein, K., Pascual Perez, G., Walter, M., Kamath Hosdurg, C., Capretto, M.,
    Cueto Noval, M., … Pietrzak, K. Z. (2021). Keep the dirt: tainted TreeKEM, adaptively
    and actively secure continuous group key agreement. In <i>2021 IEEE Symposium
    on Security and Privacy </i> (pp. 268–284). San Francisco, CA, United States:
    IEEE. <a href="https://doi.org/10.1109/sp40001.2021.00035">https://doi.org/10.1109/sp40001.2021.00035</a>'
  chicago: 'Klein, Karen, Guillermo Pascual Perez, Michael Walter, Chethan Kamath
    Hosdurg, Margarita Capretto, Miguel Cueto Noval, Ilia Markov, Michelle X Yeo,
    Joel F Alwen, and Krzysztof Z Pietrzak. “Keep the Dirt: Tainted TreeKEM, Adaptively
    and Actively Secure Continuous Group Key Agreement.” In <i>2021 IEEE Symposium
    on Security and Privacy </i>, 268–84. IEEE, 2021. <a href="https://doi.org/10.1109/sp40001.2021.00035">https://doi.org/10.1109/sp40001.2021.00035</a>.'
  ieee: 'K. Klein <i>et al.</i>, “Keep the dirt: tainted TreeKEM, adaptively and actively
    secure continuous group key agreement,” in <i>2021 IEEE Symposium on Security
    and Privacy </i>, San Francisco, CA, United States, 2021, pp. 268–284.'
  ista: 'Klein K, Pascual Perez G, Walter M, Kamath Hosdurg C, Capretto M, Cueto Noval
    M, Markov I, Yeo MX, Alwen JF, Pietrzak KZ. 2021. Keep the dirt: tainted TreeKEM,
    adaptively and actively secure continuous group key agreement. 2021 IEEE Symposium
    on Security and Privacy . SP: Symposium on Security and Privacy, 268–284.'
  mla: 'Klein, Karen, et al. “Keep the Dirt: Tainted TreeKEM, Adaptively and Actively
    Secure Continuous Group Key Agreement.” <i>2021 IEEE Symposium on Security and
    Privacy </i>, IEEE, 2021, pp. 268–84, doi:<a href="https://doi.org/10.1109/sp40001.2021.00035">10.1109/sp40001.2021.00035</a>.'
  short: K. Klein, G. Pascual Perez, M. Walter, C. Kamath Hosdurg, M. Capretto, M.
    Cueto Noval, I. Markov, M.X. Yeo, J.F. Alwen, K.Z. Pietrzak, in:, 2021 IEEE Symposium
    on Security and Privacy , IEEE, 2021, pp. 268–284.
conference:
  end_date: 2021-05-27
  location: San Francisco, CA, United States
  name: 'SP: Symposium on Security and Privacy'
  start_date: 2021-05-24
corr_author: '1'
date_created: 2021-09-27T13:46:27Z
date_published: 2021-08-26T00:00:00Z
date_updated: 2026-10-16T08:11:07Z
day: '26'
department:
- _id: KrPi
- _id: DaAl
doi: 10.1109/sp40001.2021.00035
ec_funded: 1
external_id:
  isi:
  - '001316065000016'
fulldoi: https://doi.org/10.1109/sp40001.2021.00035
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprint.iacr.org/2019/1489
month: '08'
oa: 1
oa_version: Preprint
page: 268-284
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '682815'
  name: Teaching Old Crypto New Tricks
publication: '2021 IEEE Symposium on Security and Privacy '
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
  record:
  - id: '10035'
    relation: dissertation_contains
    status: public
  - id: '18088'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: 'Keep the dirt: tainted TreeKEM, adaptively and actively secure continuous
  group key agreement'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2021'
...
---
_id: '8602'
abstract:
- lang: eng
  text: Collective cell migration offers a rich field of study for non-equilibrium
    physics and cellular biology, revealing phenomena such as glassy dynamics, pattern
    formation and active turbulence. However, how mechanical and chemical signalling
    are integrated at the cellular level to give rise to such collective behaviours
    remains unclear. We address this by focusing on the highly conserved phenomenon
    of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK)
    activation, which appear both in vitro and in vivo during collective cell migration
    and wound healing. First, we propose a biophysical theory, backed by mechanical
    and optogenetic perturbation experiments, showing that patterns can be quantitatively
    explained by a mechanochemical coupling between active cellular tensions and the
    mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism
    can robustly induce long-ranged order and migration in a desired orientation,
    and we determine the theoretically optimal wavelength and period for inducing
    maximal migration towards free edges, which fits well with experimentally observed
    dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal
    instabilities and the design principles of robust and efficient long-ranged migration.
acknowledgement: We would like to thank G. Tkacik and all of the members of the Hannezo
  and Hirashima groups for useful discussions, X. Trepat for help on traction force
  microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants
  from the Austrian Science Fund (FWF) (P 31639) and the European Research Council
  (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project
  has received funding from the European Union’s Horizon 2020 research and innovation
  programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.),
  from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto
  University (to E.H. and T.H.).
article_processing_charge: No
article_type: original
author:
- first_name: Daniel R
  full_name: Boocock, Daniel R
  id: 453AF628-F248-11E8-B48F-1D18A9856A87
  last_name: Boocock
  orcid: 0000-0002-1585-2631
- first_name: Naoya
  full_name: Hino, Naoya
  last_name: Hino
- first_name: Natalia
  full_name: Ruzickova, Natalia
  id: D2761128-D73D-11E9-A1BF-BA0DE6697425
  last_name: Ruzickova
- first_name: Tsuyoshi
  full_name: Hirashima, Tsuyoshi
  last_name: Hirashima
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
citation:
  ama: Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical
    patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274.
    doi:<a href="https://doi.org/10.1038/s41567-020-01037-7">10.1038/s41567-020-01037-7</a>
  apa: Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B.
    (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers.
    <i>Nature Physics</i>. Springer Nature. <a href="https://doi.org/10.1038/s41567-020-01037-7">https://doi.org/10.1038/s41567-020-01037-7</a>
  chicago: Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and
    Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration
    in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href="https://doi.org/10.1038/s41567-020-01037-7">https://doi.org/10.1038/s41567-020-01037-7</a>.
  ieee: D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory
    of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature
    Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.
  ista: Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of
    mechanochemical patterning and optimal migration in cell monolayers. Nature Physics.
    17, 267–274.
  mla: Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal
    Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature,
    2021, pp. 267–74, doi:<a href="https://doi.org/10.1038/s41567-020-01037-7">10.1038/s41567-020-01037-7</a>.
  short: D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics
    17 (2021) 267–274.
corr_author: '1'
date_created: 2020-10-04T22:01:37Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2026-11-12T23:30:06Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-020-01037-7
ec_funded: 1
external_id:
  isi:
  - '000573519500002'
fulldoi: https://doi.org/10.1038/s41567-020-01037-7
intvolume: '        17'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2020.05.15.096479
month: '02'
oa: 1
oa_version: Preprint
page: 267-274
project:
- _id: 268294B6-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P31639
  name: Active mechano-chemical description of the cell cytoskeleton
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '851288'
  name: Design Principles of Branching Morphogenesis
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication: Nature Physics
publication_identifier:
  eissn:
  - 1745-2481
  issn:
  - 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/wound-healing-waves/
  record:
  - id: '12964'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Theory of mechanochemical patterning and optimal migration in cell monolayers
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '9817'
abstract:
- lang: eng
  text: Elastic bending of initially flat slender elements allows the realization
    and economic fabrication of intriguing curved shapes. In this work, we derive
    an intuitive but rigorous geometric characterization of the design space of plane
    elastic rods with variable stiffness. It enables designers to determine which
    shapes are physically viable with active bending by visual inspection alone. Building
    on these insights, we propose a method for efficiently designing the geometry
    of a flat elastic rod that realizes a target equilibrium curve, which only requires
    solving a linear program. We implement this method in an interactive computational
    design tool that gives feedback about the feasibility of a design, and computes
    the geometry of the structural elements necessary to realize it within an instant.
    The tool also offers an iterative optimization routine that improves the fabricability
    of a model while modifying it as little as possible. In addition, we use our geometric
    characterization to derive an algorithm for analyzing and recovering the stability
    of elastic curves that would otherwise snap out of their unstable equilibrium
    shapes by buckling. We show the efficacy of our approach by designing and manufacturing
    several physical models that are assembled from flat elements.
acknowledgement: "We thank the anonymous reviewers for their generous feedback, and
  Michal Piovarči for his help in producing the supplemental video. This project has
  received funding from the European Research Council (ERC) under the European Union’s
  Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n"
article_number: '126'
article_processing_charge: No
article_type: original
author:
- first_name: Christian
  full_name: Hafner, Christian
  id: 400429CC-F248-11E8-B48F-1D18A9856A87
  last_name: Hafner
- first_name: Bernd
  full_name: Bickel, Bernd
  id: 49876194-F248-11E8-B48F-1D18A9856A87
  last_name: Bickel
  orcid: 0000-0001-6511-9385
citation:
  ama: Hafner C, Bickel B. The design space of plane elastic curves. <i>ACM Transactions
    on Graphics</i>. 2021;40(4). doi:<a href="https://doi.org/10.1145/3450626.3459800">10.1145/3450626.3459800</a>
  apa: 'Hafner, C., &#38; Bickel, B. (2021). The design space of plane elastic curves.
    <i>ACM Transactions on Graphics</i>. Virtual: Association for Computing Machinery.
    <a href="https://doi.org/10.1145/3450626.3459800">https://doi.org/10.1145/3450626.3459800</a>'
  chicago: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic
    Curves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery,
    2021. <a href="https://doi.org/10.1145/3450626.3459800">https://doi.org/10.1145/3450626.3459800</a>.
  ieee: C. Hafner and B. Bickel, “The design space of plane elastic curves,” <i>ACM
    Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery,
    2021.
  ista: Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions
    on Graphics. 40(4), 126.
  mla: Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.”
    <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 126, Association for Computing
    Machinery, 2021, doi:<a href="https://doi.org/10.1145/3450626.3459800">10.1145/3450626.3459800</a>.
  short: C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).
conference:
  end_date: 2021-08-13
  location: Virtual
  name: 'SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques'
  start_date: 2021-08-09
date_created: 2021-08-08T22:01:26Z
date_published: 2021-07-19T00:00:00Z
date_updated: 2026-11-12T23:30:07Z
day: '19'
ddc:
- '516'
department:
- _id: BeBi
doi: 10.1145/3450626.3459800
ec_funded: 1
external_id:
  isi:
  - '000674930900091'
file:
- access_level: open_access
  checksum: 7e5d08ce46b0451b3102eacd3d00f85f
  content_type: application/pdf
  creator: chafner
  date_created: 2021-10-18T10:42:15Z
  date_updated: 2021-10-18T10:42:15Z
  file_id: '10150'
  file_name: elastic-curves-paper.pdf
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  relation: main_file
  success: 1
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  checksum: 0088643478be7c01a703b5b10767348f
  content_type: application/pdf
  creator: chafner
  date_created: 2021-10-18T10:42:22Z
  date_updated: 2021-10-18T10:42:22Z
  file_id: '10151'
  file_name: elastic-curves-supp.pdf
  file_size: 547156
  relation: supplementary_material
file_date_updated: 2021-10-18T10:42:22Z
fulldoi: https://doi.org/10.1145/3450626.3459800
has_accepted_license: '1'
intvolume: '        40'
isi: 1
issue: '4'
keyword:
- Computing methodologies
- shape modeling
- modeling and simulation
- theory of computation
- computational geometry
- mathematics of computing
- mathematical optimization
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715767'
  name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
    Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
  eissn:
  - 1557-7368
  issn:
  - 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Website
    relation: press_release
    url: https://ist.ac.at/en/news/designing-with-elastic-structures/
  record:
  - id: '12897'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: The design space of plane elastic curves
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 40
year: '2021'
...
---
_id: '8966'
abstract:
- lang: eng
  text: During development, a single cell is transformed into a highly complex organism
    through progressive cell division, specification and rearrangement. An important
    prerequisite for the emergence of patterns within the developing organism is to
    establish asymmetries at various scales, ranging from individual cells to the
    entire embryo, eventually giving rise to the different body structures. This becomes
    especially apparent during gastrulation, when the earliest major lineage restriction
    events lead to the formation of the different germ layers. Traditionally, the
    unfolding of the developmental program from symmetry breaking to germ layer formation
    has been studied by dissecting the contributions of different signaling pathways
    and cellular rearrangements in the in vivo context of intact embryos. Recent efforts,
    using the intrinsic capacity of embryonic stem cells to self-assemble and generate
    embryo-like structures de novo, have opened new avenues for understanding the
    many ways by which an embryo can be built and the influence of extrinsic factors
    therein. Here, we discuss and compare divergent and conserved strategies leading
    to germ layer formation in embryos as compared to in vitro systems, their upstream
    molecular cascades and the role of extrinsic factors in this process.
acknowledgement: We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and
  Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is
  supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient
  of a DOC Fellowship of the Austrian Academy of Science.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexandra
  full_name: Schauer, Alexandra
  id: 30A536BA-F248-11E8-B48F-1D18A9856A87
  last_name: Schauer
  orcid: 0000-0001-7659-9142
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
citation:
  ama: Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>.
    2021;474:71-81. doi:<a href="https://doi.org/10.1016/j.ydbio.2020.12.014">10.1016/j.ydbio.2020.12.014</a>
  apa: Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation.
    <i>Developmental Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.ydbio.2020.12.014">https://doi.org/10.1016/j.ydbio.2020.12.014</a>
  chicago: Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.”
    <i>Developmental Biology</i>. Elsevier, 2021. <a href="https://doi.org/10.1016/j.ydbio.2020.12.014">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.
  ieee: A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental
    Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021.
  ista: Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental
    Biology. 474, 71–81.
  mla: Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.”
    <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href="https://doi.org/10.1016/j.ydbio.2020.12.014">10.1016/j.ydbio.2020.12.014</a>.
  short: A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81.
date_created: 2020-12-22T09:53:34Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2026-11-12T23:30:10Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.ydbio.2020.12.014
ec_funded: 1
external_id:
  isi:
  - '000639461800008'
  pmid:
  - '33352181'
file:
- access_level: open_access
  checksum: fa2a5731fd16ab171b029f32f031c440
  content_type: application/pdf
  creator: kschuh
  date_created: 2021-08-11T10:28:06Z
  date_updated: 2021-08-11T10:28:06Z
  file_id: '9880'
  file_name: 2021_DevBiology_Schauer.pdf
  file_size: 1440321
  relation: main_file
  success: 1
file_date_updated: 2021-08-11T10:28:06Z
fulldoi: https://doi.org/10.1016/j.ydbio.2020.12.014
has_accepted_license: '1'
intvolume: '       474'
isi: 1
keyword:
- Developmental Biology
- Cell Biology
- Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 71-81
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742573'
  name: Interaction and feedback between cell mechanics and fate specification in
    vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
  grant_number: '25239'
  name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication: Developmental Biology
publication_identifier:
  issn:
  - 0012-1606
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '12891'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Reassembling gastrulation
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 474
year: '2021'
...
---
_id: '9438'
abstract:
- lang: eng
  text: Rigorous investigation of synaptic transmission requires analysis of unitary
    synaptic events by simultaneous recording from presynaptic terminals and postsynaptic
    target neurons. However, this has been achieved at only a limited number of model
    synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical
    presynaptic terminals have been largely inaccessible to direct presynaptic recording,
    due to their small size. Here, we describe a protocol for improved subcellular
    patch-clamp recording in rat and mouse brain slices, with the synapse in a largely
    intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc
    morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals
    are stimulated minimally invasively in the bouton-attached configuration, in which
    the cytoplasmic content remains unperturbed, or in the whole-bouton configuration,
    in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic
    recordings can be integrated with biocytin labeling and morphological analysis,
    allowing correlative investigation of synapse structure and function. Paired recordings
    can be obtained from mossy fiber terminals in slices from both rats and mice,
    implying applicability to genetically modified synapses. Paired recordings can
    also be performed together with axon tract stimulation or optogenetic activation,
    allowing comparison of unitary and compound synaptic events in the same target
    cell. Finally, paired recordings can be combined with spontaneous event analysis,
    permitting collection of miniature events generated at a single identified synapse.
    In conclusion, the subcellular patch-clamp techniques detailed here should facilitate
    analysis of biophysics, plasticity and circuit function of cortical synapses in
    the mammalian central nervous system.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This project received funding from the European Research Council
  (ERC) under the European Union’s Horizon 2020 research and innovation programme
  (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
  Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful
  to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction,
  E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST
  Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: David H
  full_name: Vandael, David H
  id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
  last_name: Vandael
  orcid: 0000-0001-7577-1676
- first_name: Yuji
  full_name: Okamoto, Yuji
  id: 3337E116-F248-11E8-B48F-1D18A9856A87
  last_name: Okamoto
  orcid: 0000-0003-0408-6094
- first_name: Carolina
  full_name: Borges Merjane, Carolina
  id: 4305C450-F248-11E8-B48F-1D18A9856A87
  last_name: Borges Merjane
  orcid: 0000-0003-0005-401X
- first_name: Victor M
  full_name: Vargas Barroso, Victor M
  id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
  last_name: Vargas Barroso
- first_name: Benjamin
  full_name: Suter, Benjamin
  id: 4952F31E-F248-11E8-B48F-1D18A9856A87
  last_name: Suter
  orcid: 0000-0002-9885-6936
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
citation:
  ama: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
    PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous
    pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>.
    2021;16(6):2947–2967. doi:<a href="https://doi.org/10.1038/s41596-021-00526-0">10.1038/s41596-021-00526-0</a>
  apa: Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter,
    B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton
    stimulation and simultaneous pre- and postsynaptic recording at cortical synapses.
    <i>Nature Protocols</i>. Springer Nature. <a href="https://doi.org/10.1038/s41596-021-00526-0">https://doi.org/10.1038/s41596-021-00526-0</a>
  chicago: Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas
    Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques
    for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording
    at Cortical Synapses.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href="https://doi.org/10.1038/s41596-021-00526-0">https://doi.org/10.1038/s41596-021-00526-0</a>.
  ieee: D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter,
    and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation
    and simultaneous pre- and postsynaptic recording at cortical synapses,” <i>Nature
    Protocols</i>, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.
  ista: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
    PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and
    simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols.
    16(6), 2947–2967.
  mla: Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton
    Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.”
    <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967,
    doi:<a href="https://doi.org/10.1038/s41596-021-00526-0">10.1038/s41596-021-00526-0</a>.
  short: D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter,
    P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.
corr_author: '1'
date_created: 2021-05-30T22:01:24Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-04-22T22:30:43Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1038/s41596-021-00526-0
ec_funded: 1
external_id:
  isi:
  - '000650528700003'
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  - '33990799'
file:
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isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 2947–2967
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '692692'
  name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z00312
  name: Synaptic communication in neuronal microcircuits
- _id: 2696E7FE-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: V00739
  name: Structural plasticity at mossy fiber-CA3 synapses
publication: Nature Protocols
publication_identifier:
  eissn:
  - 1750-2799
  issn:
  - 1754-2189
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous
  pre- and postsynaptic recording at cortical synapses
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2021'
...
---
OA_place: publisher
OA_type: hybrid
_id: '7883'
abstract:
- lang: eng
  text: All vertebrates have a spinal cord with dimensions and shape specific to their
    species. Yet how species‐specific organ size and shape are achieved is a fundamental
    unresolved question in biology. The formation and sculpting of organs begins during
    embryonic development. As it develops, the spinal cord extends in anterior–posterior
    direction in synchrony with the overall growth of the body. The dorsoventral (DV)
    and apicobasal lengths of the spinal cord neuroepithelium also change, while at
    the same time a characteristic pattern of neural progenitor subtypes along the
    DV axis is established and elaborated. At the basis of these changes in tissue
    size and shape are biophysical determinants, such as the change in cell number,
    cell size and shape, and anisotropic tissue growth. These processes are controlled
    by global tissue‐scale regulators, such as morphogen signaling gradients as well
    as mechanical forces. Current challenges in the field are to uncover how these
    tissue‐scale regulatory mechanisms are translated to the cellular and molecular
    level, and how regulation of distinct cellular processes gives rise to an overall
    defined size. Addressing these questions will help not only to achieve a better
    understanding of how size is controlled, but also of how tissue size is coordinated
    with the specification of pattern.
acknowledgement: 'Austrian Academy of Sciences, Grant/Award Number: DOC fellowship
  for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem
  Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037'
article_number: e383
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Katarzyna
  full_name: Kuzmicz-Kowalska, Katarzyna
  id: 4CED352A-F248-11E8-B48F-1D18A9856A87
  last_name: Kuzmicz-Kowalska
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
citation:
  ama: 'Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate
    spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>.
    2021. doi:<a href="https://doi.org/10.1002/wdev.383">10.1002/wdev.383</a>'
  apa: 'Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale
    in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental
    Biology</i>. Wiley. <a href="https://doi.org/10.1002/wdev.383">https://doi.org/10.1002/wdev.383</a>'
  chicago: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and
    Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews:
    Developmental Biology</i>. Wiley, 2021. <a href="https://doi.org/10.1002/wdev.383">https://doi.org/10.1002/wdev.383</a>.'
  ieee: 'K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate
    spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>.
    Wiley, 2021.'
  ista: 'Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate
    spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology.,
    e383.'
  mla: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale
    in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental
    Biology</i>, e383, Wiley, 2021, doi:<a href="https://doi.org/10.1002/wdev.383">10.1002/wdev.383</a>.'
  short: 'K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental
    Biology (2021).'
corr_author: '1'
date_created: 2020-05-24T22:01:00Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2026-11-12T23:30:17Z
day: '15'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1002/wdev.383
ec_funded: 1
external_id:
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  - '000531419400001'
  pmid:
  - '32391980'
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file_date_updated: 2020-11-24T13:11:39Z
fulldoi: https://doi.org/10.1002/wdev.383
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
  call_identifier: H2020
  grant_number: '680037'
  name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 267AF0E4-B435-11E9-9278-68D0E5697425
  name: The role of morphogens in the regulation of neural tube growth
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
  grant_number: F7802
  name: Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen
    control of growth and pattern in the spinal cord
publication: 'Wiley Interdisciplinary Reviews: Developmental Biology'
publication_identifier:
  eissn:
  - 1759-7692
  issn:
  - 1759-7684
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
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scopus_import: '1'
status: public
title: Regulation of size and scale in vertebrate spinal cord development
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
year: '2021'
...
---
_id: '9349'
abstract:
- lang: eng
  text: 'The way in which interactions between mechanics and biochemistry lead to
    the emergence of complex cell and tissue organization is an old question that
    has recently attracted renewed interest from biologists, physicists, mathematicians
    and computer scientists. Rapid advances in optical physics, microscopy and computational
    image analysis have greatly enhanced our ability to observe and quantify spatiotemporal
    patterns of signalling, force generation, deformation, and flow in living cells
    and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation
    are allowing us to perturb the underlying machinery that generates these patterns
    in increasingly sophisticated ways. Rapid advances in theory and computing have
    made it possible to construct predictive models that describe how cell and tissue
    organization and dynamics emerge from the local coupling of biochemistry and mechanics.
    Together, these advances have opened up a wealth of new opportunities to explore
    how mechanochemical patterning shapes organismal development. In this roadmap,
    we present a series of forward-looking case studies on mechanochemical patterning
    in development, written by scientists working at the interface between the physical
    and biological sciences, and covering a wide range of spatial and temporal scales,
    organisms, and modes of development. Together, these contributions highlight the
    many ways in which the dynamic coupling of mechanics and biochemistry shapes biological
    dynamics: from mechanoenzymes that sense force to tune their activity and motor
    output, to collectives of cells in tissues that flow and redistribute biochemical
    signals during development.'
acknowledgement: The AK group is supported by IST Austria and by the ERC under European
  Union Horizon 2020 research and innovation programme Grant 680037. Apologies to
  those whose work could not be mentioned due to limited space. We thank all my lab
  members, both past and present, for stimulating discussion. This work was funded
  by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis
  Corson for continuous discussion and collaboration contributing to these views and
  for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's
  Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
  Grant Agreement No. 665807. Research in JG's laboratory is funded by the European
  Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC
  Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour
  la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We
  thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi
  for help with figure 5. This project has received funding from the European Union's
  Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG
  Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as
  Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for
  fruitful discussions on these topics—and apologize for not being able to cite many
  very relevant publications due to the strict 10-reference limit. EH acknowledges
  the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council
  under the European Union's Horizon 2020 Research and Innovation Programme Grant
  Agreements (851288). The authors acknowledge the inspiring scientists whose work
  could not be cited in this perspective due to space constraints; the members of
  the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation,
  the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health,
  and the Centre for Cellular Construction, an NSF Science and Technology Centre.
  The Minc laboratory is currently funded by the CNRS and the European Research Council
  (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut
  Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National
  de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the
  ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche
  via the Fondation pour la Recherche Médicale, the European Research Council Starting
  Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator
  programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas
  (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005)
  grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02).
  We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and
  my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported
  by NIH-R01GM122936. The authors acknowledge the support by a grant from the European
  Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements
  d'Avenir' French Government programme managed by the French National Research Agency
  (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX,
  and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).
article_number: '041501'
article_processing_charge: No
article_type: original
author:
- first_name: Pierre François
  full_name: Lenne, Pierre François
  last_name: Lenne
- first_name: Edwin
  full_name: Munro, Edwin
  last_name: Munro
- first_name: Idse
  full_name: Heemskerk, Idse
  last_name: Heemskerk
- first_name: Aryeh
  full_name: Warmflash, Aryeh
  last_name: Warmflash
- first_name: Laura
  full_name: Bocanegra, Laura
  id: 4896F754-F248-11E8-B48F-1D18A9856A87
  last_name: Bocanegra
- first_name: Kasumi
  full_name: Kishi, Kasumi
  id: 3065DFC4-F248-11E8-B48F-1D18A9856A87
  last_name: Kishi
  orcid: 0000-0001-6060-4795
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
- first_name: Yuchen
  full_name: Long, Yuchen
  last_name: Long
- first_name: Antoine
  full_name: Fruleux, Antoine
  last_name: Fruleux
- first_name: Arezki
  full_name: Boudaoud, Arezki
  last_name: Boudaoud
- first_name: Timothy E.
  full_name: Saunders, Timothy E.
  last_name: Saunders
- first_name: Paolo
  full_name: Caldarelli, Paolo
  last_name: Caldarelli
- first_name: Arthur
  full_name: Michaut, Arthur
  last_name: Michaut
- first_name: Jerome
  full_name: Gros, Jerome
  last_name: Gros
- first_name: Yonit
  full_name: Maroudas-Sacks, Yonit
  last_name: Maroudas-Sacks
- first_name: Kinneret
  full_name: Keren, Kinneret
  last_name: Keren
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
- first_name: Zev J.
  full_name: Gartner, Zev J.
  last_name: Gartner
- first_name: Benjamin
  full_name: Stormo, Benjamin
  last_name: Stormo
- first_name: Amy
  full_name: Gladfelter, Amy
  last_name: Gladfelter
- first_name: Alan
  full_name: Rodrigues, Alan
  last_name: Rodrigues
- first_name: Amy
  full_name: Shyer, Amy
  last_name: Shyer
- first_name: Nicolas
  full_name: Minc, Nicolas
  last_name: Minc
- first_name: Jean Léon
  full_name: Maître, Jean Léon
  last_name: Maître
- first_name: Stefano
  full_name: Di Talia, Stefano
  last_name: Di Talia
- first_name: Bassma
  full_name: Khamaisi, Bassma
  last_name: Khamaisi
- first_name: David
  full_name: Sprinzak, David
  last_name: Sprinzak
- first_name: Sham
  full_name: Tlili, Sham
  last_name: Tlili
citation:
  ama: Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling
    of biochemical and mechanical signals during development. <i>Physical biology</i>.
    2021;18(4). doi:<a href="https://doi.org/10.1088/1478-3975/abd0db">10.1088/1478-3975/abd0db</a>
  apa: Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi,
    K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and
    mechanical signals during development. <i>Physical Biology</i>. IOP Publishing.
    <a href="https://doi.org/10.1088/1478-3975/abd0db">https://doi.org/10.1088/1478-3975/abd0db</a>
  chicago: Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura
    Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling
    of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>.
    IOP Publishing, 2021. <a href="https://doi.org/10.1088/1478-3975/abd0db">https://doi.org/10.1088/1478-3975/abd0db</a>.
  ieee: P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical
    and mechanical signals during development,” <i>Physical biology</i>, vol. 18,
    no. 4. IOP Publishing, 2021.
  ista: Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva
    A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J,
    Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues
    A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021.
    Roadmap for the multiscale coupling of biochemical and mechanical signals during
    development. Physical biology. 18(4), 041501.
  mla: Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical
    and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18,
    no. 4, 041501, IOP Publishing, 2021, doi:<a href="https://doi.org/10.1088/1478-3975/abd0db">10.1088/1478-3975/abd0db</a>.
  short: P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi,
    A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A.
    Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B.
    Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia,
    B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).
date_created: 2021-04-25T22:01:29Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2026-11-12T23:30:19Z
day: '14'
ddc:
- '570'
department:
- _id: AnKi
- _id: EdHa
doi: 10.1088/1478-3975/abd0db
ec_funded: 1
external_id:
  isi:
  - '000640396400001'
  pmid:
  - '33276350'
file:
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intvolume: '        18'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
  call_identifier: H2020
  grant_number: '680037'
  name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 268294B6-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P31639
  name: Active mechano-chemical description of the cell cytoskeleton
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '851288'
  name: Design Principles of Branching Morphogenesis
publication: Physical biology
publication_identifier:
  eissn:
  - 1478-3975
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
  record:
  - id: '13081'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Roadmap for the multiscale coupling of biochemical and mechanical signals during
  development
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2021'
...
---
_id: '9250'
abstract:
- lang: eng
  text: Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry
    occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides
    and parasitic reactions that are caused by the highly reactive singlet oxygen
    (1O2). Redox mediators are recognized to be key for improving rechargeability.
    However, it is unclear how they affect 1O2 formation, which hinders strategies
    for their improvement. Here we clarify the mechanism of mediated peroxide and
    superoxide oxidation and thus explain how redox mediators either enhance or suppress
    1O2 formation. We show that charging commences with peroxide oxidation to a superoxide
    intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution
    from superoxide oxidation, while disproportionation always generates some 1O2.
    We find that 1O2 suppression requires oxidation to be faster than the generation
    of 1O2 from disproportionation. Oxidation rates decrease with growing driving
    force following Marcus inverted-region behaviour, establishing a region of maximum
    rate.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: S.A.F. is indebted to the European Research Council (ERC) under the
  European Union’s Horizon 2020 research and innovation programme (grant agreement
  No. 636069) as well as IST Austria. O.F thanks the French National Research Agency
  (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany)
  for the pressure test cell. We thank R. Saf for help with the mass spectrometry,
  J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier
  and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.
article_processing_charge: No
article_type: original
author:
- first_name: Yann K.
  full_name: Petit, Yann K.
  last_name: Petit
- first_name: Eléonore
  full_name: Mourad, Eléonore
  last_name: Mourad
- first_name: Christian
  full_name: Prehal, Christian
  last_name: Prehal
- first_name: Christian
  full_name: Leypold, Christian
  last_name: Leypold
- first_name: Andreas
  full_name: Windischbacher, Andreas
  last_name: Windischbacher
- first_name: Daniel
  full_name: Mijailovic, Daniel
  last_name: Mijailovic
- first_name: Christian
  full_name: Slugovc, Christian
  last_name: Slugovc
- first_name: Sergey M.
  full_name: Borisov, Sergey M.
  last_name: Borisov
- first_name: Egbert
  full_name: Zojer, Egbert
  last_name: Zojer
- first_name: Sergio
  full_name: Brutti, Sergio
  last_name: Brutti
- first_name: Olivier
  full_name: Fontaine, Olivier
  last_name: Fontaine
- first_name: Stefan Alexander
  full_name: Freunberger, Stefan Alexander
  id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
  last_name: Freunberger
  orcid: 0000-0003-2902-5319
citation:
  ama: Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide
    oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>.
    2021;13(5):465-471. doi:<a href="https://doi.org/10.1038/s41557-021-00643-z">10.1038/s41557-021-00643-z</a>
  apa: Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic,
    D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation
    and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer
    Nature. <a href="https://doi.org/10.1038/s41557-021-00643-z">https://doi.org/10.1038/s41557-021-00643-z</a>
  chicago: Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas
    Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated
    Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature
    Chemistry</i>. Springer Nature, 2021. <a href="https://doi.org/10.1038/s41557-021-00643-z">https://doi.org/10.1038/s41557-021-00643-z</a>.
  ieee: Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation
    and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13,
    no. 5. Springer Nature, pp. 465–471, 2021.
  ista: Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc
    C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism
    of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation.
    Nature Chemistry. 13(5), 465–471.
  mla: Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and
    Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no.
    5, Springer Nature, 2021, pp. 465–71, doi:<a href="https://doi.org/10.1038/s41557-021-00643-z">10.1038/s41557-021-00643-z</a>.
  short: Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic,
    C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger,
    Nature Chemistry 13 (2021) 465–471.
corr_author: '1'
date_created: 2021-03-16T11:12:20Z
date_published: 2021-03-15T00:00:00Z
date_updated: 2024-10-09T21:00:28Z
day: '15'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1038/s41557-021-00643-z
external_id:
  isi:
  - '000629296400001'
  pmid:
  - '33723377'
file:
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  file_size: 1811448
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file_date_updated: 2021-09-16T22:30:03Z
fulldoi: https://doi.org/10.1038/s41557-021-00643-z
has_accepted_license: '1'
intvolume: '        13'
isi: 1
issue: '5'
keyword:
- General Chemistry
- General Chemical Engineering
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 465-471
pmid: 1
publication: Nature Chemistry
publication_identifier:
  eissn:
  - 1755-4349
  issn:
  - 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism of mediated alkali peroxide oxidation and triplet versus singlet
  oxygen formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2021'
...
---
_id: '9428'
abstract:
- lang: eng
  text: Thermalization is the inevitable fate of many complex quantum systems, whose
    dynamics allow them to fully explore the vast configuration space regardless of
    the initial state---the behaviour known as quantum ergodicity. In a quest for
    experimental realizations of coherent long-time dynamics, efforts have focused
    on ergodicity-breaking mechanisms, such as integrability and localization. The
    recent discovery of persistent revivals in quantum simulators based on Rydberg
    atoms have pointed to the existence of a new type of behaviour where the system
    rapidly relaxes for most initial conditions, while certain initial states give
    rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body
    scarring’by analogy with a related form of weak ergodicity breaking that occurs
    for a single particle inside a stadium billiard potential. In this Review, we
    provide a pedagogical introduction to quantum many-body scars and highlight the
    emerging connections with the semiclassical quantization of many-body systems.
    We discuss the relation between scars and more general routes towards weak violations
    of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight
    possible applications of scars in quantum technology.
acknowledgement: We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W.
  Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular
  A. Michailidis and C. Turner, without whom this work would not have been possible.
  We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran,
  P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research
  Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
  (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science
  Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation
  programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme
  Trust Research Leadership Award RL-2019-015.
article_processing_charge: No
article_type: review
arxiv: 1
author:
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
- first_name: Dmitry A.
  full_name: Abanin, Dmitry A.
  last_name: Abanin
- first_name: Zlatko
  full_name: Papić, Zlatko
  last_name: Papić
citation:
  ama: Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of
    ergodicity. <i>Nature Physics</i>. 2021;17(6):675–685. doi:<a href="https://doi.org/10.1038/s41567-021-01230-2">10.1038/s41567-021-01230-2</a>
  apa: Serbyn, M., Abanin, D. A., &#38; Papić, Z. (2021). Quantum many-body scars
    and weak breaking of ergodicity. <i>Nature Physics</i>. Nature Research. <a href="https://doi.org/10.1038/s41567-021-01230-2">https://doi.org/10.1038/s41567-021-01230-2</a>
  chicago: Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body
    Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>. Nature Research,
    2021. <a href="https://doi.org/10.1038/s41567-021-01230-2">https://doi.org/10.1038/s41567-021-01230-2</a>.
  ieee: M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking
    of ergodicity,” <i>Nature Physics</i>, vol. 17, no. 6. Nature Research, pp. 675–685,
    2021.
  ista: Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking
    of ergodicity. Nature Physics. 17(6), 675–685.
  mla: Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.”
    <i>Nature Physics</i>, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:<a
    href="https://doi.org/10.1038/s41567-021-01230-2">10.1038/s41567-021-01230-2</a>.
  short: M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.
date_created: 2021-05-28T09:03:50Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2025-04-14T07:52:09Z
day: '01'
ddc:
- '539'
department:
- _id: MaSe
doi: 10.1038/s41567-021-01230-2
ec_funded: 1
external_id:
  arxiv:
  - '2011.09486'
  isi:
  - '000655563800002'
file:
- access_level: open_access
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  date_created: 2021-09-20T09:27:43Z
  date_updated: 2021-12-02T23:30:03Z
  embargo: 2021-12-01
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  file_name: RevisedQMBSreview.pdf
  file_size: 10028836
  relation: main_file
file_date_updated: 2021-12-02T23:30:03Z
fulldoi: https://doi.org/10.1038/s41567-021-01230-2
has_accepted_license: '1'
intvolume: '        17'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Preprint
page: 675–685
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
  call_identifier: H2020
  grant_number: '850899'
  name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Nature Physics
publication_identifier:
  eissn:
  - 1745-2481
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum many-body scars and weak breaking of ergodicity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
OA_place: publisher
_id: '9397'
abstract:
- lang: eng
  text: Accumulation of interstitial fluid (IF) between embryonic cells is a common
    phenomenon in vertebrate embryogenesis. Unlike other model systems, where these
    accumulations coalesce into a large central cavity – the blastocoel, in zebrafish,
    IF is more uniformly distributed between the deep cells (DC) before the onset
    of gastrulation. This is likely due to the presence of a large extraembryonic
    structure – the yolk cell (YC) at the position where the blastocoel typically
    forms in other model organisms. IF has long been speculated to play a role in
    tissue morphogenesis during embryogenesis, but direct evidence supporting such
    function is still sparse. Here we show that the relocalization of IF to the interface
    between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion
    formation and migration along this interface, a key process in embryonic axis
    formation. We further demonstrate that axial ME cell migration and IF relocalization
    engage in a positive feedback loop, where axial ME migration triggers IF accumulation
    ahead of the advancing axial ME tissue by mechanically compressing the overlying
    epiblast cell layer. Upon compression, locally induced flow relocalizes the IF
    through the porous epiblast tissue resulting in an IF accumulation ahead of the
    leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation
    and migration of the leading axial ME cells, thereby facilitating axial ME extension.
    Our findings reveal a central role of dynamic IF relocalization in orchestrating
    germ layer morphogenesis during gastrulation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karla
  full_name: Huljev, Karla
  id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
  last_name: Huljev
citation:
  ama: Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is
    required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a
    href="https://doi.org/10.15479/at:ista:9397">10.15479/at:ista:9397</a>
  apa: Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial
    fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>.
    Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:9397">https://doi.org/10.15479/at:ista:9397</a>
  chicago: Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial
    Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.”
    Institute of Science and Technology Austria, 2021. <a href="https://doi.org/10.15479/at:ista:9397">https://doi.org/10.15479/at:ista:9397</a>.
  ieee: K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid
    is required for axial mesendoderm migration in zebrafish gastrulation,” Institute
    of Science and Technology Austria, 2021.
  ista: Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial
    fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute
    of Science and Technology Austria.
  mla: Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial
    Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>.
    Institute of Science and Technology Austria, 2021, doi:<a href="https://doi.org/10.15479/at:ista:9397">10.15479/at:ista:9397</a>.
  short: K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid
    Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute
    of Science and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-05-17T12:31:30Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2026-04-08T07:12:51Z
day: '18'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: CaHe
- _id: GradSch
doi: 10.15479/at:ista:9397
file:
- access_level: closed
  checksum: 7f98532f5324a0b2f3fa8de2967baa19
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: khuljev
  date_created: 2021-05-17T12:29:12Z
  date_updated: 2022-05-21T22:30:04Z
  embargo_to: open_access
  file_id: '9398'
  file_name: KHuljev_Thesis_corrections.docx
  file_size: 47799741
  relation: source_file
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  creator: khuljev
  date_created: 2021-05-18T14:50:28Z
  date_updated: 2022-05-21T22:30:04Z
  embargo: 2022-05-20
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  file_size: 16542131
  relation: main_file
file_date_updated: 2022-05-21T22:30:04Z
fulldoi: https://doi.org/10.15479/at:ista:9397
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '101'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
title: Coordinated spatiotemporal reorganization of interstitial fluid is required
  for axial mesendoderm migration in zebrafish gastrulation
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
OA_place: publisher
_id: '9992'
abstract:
- lang: eng
  text: "Blood – this is what animals use to heal wounds fast and efficient. Plants
    do not have blood circulation and their cells cannot move. However, plants have
    evolved remarkable capacities to regenerate tissues and organs preventing further
    damage. In my PhD research, I studied the wound healing in the Arabidopsis root.
    I used a UV laser to ablate single cells in the root tip and observed the consequent
    wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane
    switch and subsequently adopted the cell type of the killed cell to replace it.
    We termed this form of wound healing “restorative divisions”. This initial observation
    triggered the questions of my PhD studies: How and why do cells orient their division
    planes, how do they feel the wound and why does this happen only in inner adjacent
    cells.\r\nFor answering these questions, I used a quite simple experimental setup:
    5 day - old seedlings were stained with propidium iodide to visualize cell walls
    and dead cells; ablation was carried out using a special laser cutter and a confocal
    microscope. Adaptation of the novel vertical microscope system made it possible
    to observe wounds in real time. This revealed that restorative divisions occur
    at increased frequency compared to normal divisions. Additionally,\r\nthe major
    plant hormone auxin accumulates in wound adjacent cells and drives the expression
    of the wound-stress responsive transcription factor ERF115. Using this as a marker
    gene for wound responses, we found that an important part of wound signalling
    is the sensing of the collapse of the ablated cell. The collapse causes a radical
    pressure drop, which results in strong tissue deformations. These deformations
    manifest in an invasion of the now free spot specifically by the inner adjacent
    cells within seconds, probably because of higher pressure of the inner tissues.
    Long-term imaging revealed that those deformed cells continuously expand towards
    the wound hole and that this is crucial for the restorative division. These wound-expanding
    cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the
    division. Experiments inhibiting cell expansion suggest that it is the biphasic
    stretching that induces those MT arrays. Adapting the micromanipulator aspiration
    system from animal scientists at our institute confirmed the hypothesis that stretching
    influences microtubule stability. In conclusion, this shows that microtubules
    react to tissue deformation\r\nand this facilitates the observed division plane
    switch. This puts mechanical cues and tensions at the most prominent position
    for explaining the growth and wound healing properties of plants. Hence, it shines
    light onto the importance of understanding mechanical signal transduction. "
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lukas
  full_name: Hörmayer, Lukas
  id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
  last_name: Hörmayer
  orcid: 0000-0001-8295-2926
citation:
  ama: Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href="https://doi.org/10.15479/at:ista:9992">10.15479/at:ista:9992</a>
  apa: Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>.
    Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:9992">https://doi.org/10.15479/at:ista:9992</a>
  chicago: Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute
    of Science and Technology Austria, 2021. <a href="https://doi.org/10.15479/at:ista:9992">https://doi.org/10.15479/at:ista:9992</a>.
  ieee: L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of
    Science and Technology Austria, 2021.
  ista: Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute
    of Science and Technology Austria.
  mla: Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute
    of Science and Technology Austria, 2021, doi:<a href="https://doi.org/10.15479/at:ista:9992">10.15479/at:ista:9992</a>.
  short: L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of
    Science and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-09-09T07:37:20Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2026-04-08T07:11:47Z
day: '13'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JiFr
doi: 10.15479/at:ista:9992
ec_funded: 1
file:
- access_level: closed
  checksum: c763064adaa720e16066c1a4f9682bbb
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: lhoermaye
  date_created: 2021-09-09T07:29:48Z
  date_updated: 2021-09-15T22:30:26Z
  embargo_to: open_access
  file_id: '9993'
  file_name: Thesis_vupload.docx
  file_size: 25179004
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  date_created: 2021-09-09T14:25:08Z
  date_updated: 2021-09-15T22:30:26Z
  embargo: 2021-09-09
  file_id: '9996'
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file_date_updated: 2021-09-15T22:30:26Z
fulldoi: https://doi.org/10.15479/at:ista:9992
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '168'
project:
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P29988
  name: RNA-directed DNA methylation in plant development
- _id: 261099A6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742985'
  name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '6943'
    relation: part_of_dissertation
    status: public
  - id: '8002'
    relation: part_of_dissertation
    status: public
  - id: '6351'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
title: Wound healing in the Arabidopsis root meristem
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2021'
...
---
OA_place: publisher
_id: '9728'
abstract:
- lang: eng
  text: "Most real-world flows are multiphase, yet we know little about them compared
    to their single-phase counterparts. Multiphase flows are more difficult to investigate
    as their dynamics occur in large parameter space and involve complex phenomena
    such as preferential concentration, turbulence modulation, non-Newtonian rheology,
    etc. Over the last few decades, experiments in particle-laden flows have taken
    a back seat in favour of ever-improving computational resources. However, computers
    are still not powerful enough to simulate a real-world fluid with millions of
    finite-size particles. Experiments are essential not only because they offer a
    reliable way to investigate real-world multiphase flows but also because they
    serve to validate numerical studies and steer the research in a relevant direction.
    In this work, we have experimentally investigated particle-laden flows in pipes,
    and in particular, examined the effect of particles on the laminar-turbulent transition
    and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows,
    an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic)
    transition that occurs via localised turbulent structures called puffs is affected
    by the addition of particles. In this study, in addition to this known transition,
    we found a super-critical transition to a globally fluctuating state with increasing
    particle concentration. At the same time, the Newtonian-type transition via puffs
    is delayed to larger Reynolds numbers. At an even higher concentration, only the
    globally fluctuating state is found. The dynamics of particle-laden flows are
    hence determined by two competing instabilities that give rise to three flow regimes:
    Newtonian-type turbulence at low, a particle-induced globally fluctuating state
    at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect
    of particles on turbulent drag is ambiguous, with studies reporting drag reduction,
    no net change, and even drag increase. The ambiguity arises because, in addition
    to particle concentration, particle shape, size, and density also affect the net
    drag. Even similar particles might affect the flow dissimilarly in different Reynolds
    number and concentration ranges. In the present study, we explored a wide range
    of both Reynolds number and concentration, using spherical as well as cylindrical
    particles. We found that the spherical particles do not reduce drag while the
    cylindrical particles are drag-reducing within a specific Reynolds number interval.
    The interval strongly depends on the particle concentration and the relative size
    of the pipe and particles. Within this interval, the magnitude of drag reduction
    reaches a maximum. These drag reduction maxima appear to fall onto a distinct
    power-law curve irrespective of the pipe diameter and particle concentration,
    and this curve can be considered as the maximum drag reduction asymptote for a
    given fibre shape. Such an asymptote is well known for polymeric flows but had
    not been identified for particle-laden flows prior to this work."
acknowledged_ssus:
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Nishchal
  full_name: Agrawal, Nishchal
  id: 469E6004-F248-11E8-B48F-1D18A9856A87
  last_name: Agrawal
citation:
  ama: Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe
    flows. 2021. doi:<a href="https://doi.org/10.15479/at:ista:9728">10.15479/at:ista:9728</a>
  apa: Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden
    pipe flows</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:9728">https://doi.org/10.15479/at:ista:9728</a>
  chicago: Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden
    Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href="https://doi.org/10.15479/at:ista:9728">https://doi.org/10.15479/at:ista:9728</a>.
  ieee: N. Agrawal, “Transition to turbulence and drag reduction in particle-laden
    pipe flows,” Institute of Science and Technology Austria, 2021.
  ista: Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden
    pipe flows. Institute of Science and Technology Austria.
  mla: Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden
    Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href="https://doi.org/10.15479/at:ista:9728">10.15479/at:ista:9728</a>.
  short: N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden
    Pipe Flows, Institute of Science and Technology Austria, 2021.
corr_author: '1'
date_created: 2021-07-27T13:40:30Z
date_published: 2021-07-29T00:00:00Z
date_updated: 2026-04-16T08:43:20Z
day: '29'
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degree_awarded: PhD
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doi: 10.15479/at:ista:9728
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fulldoi: https://doi.org/10.15479/at:ista:9728
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keyword:
- Drag Reduction
- Transition to Turbulence
- Multiphase Flows
- particle Laden Flows
- Complex Flows
- Experiments
- Fluid Dynamics
language:
- iso: eng
month: '07'
oa: 1
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page: '118'
publication_identifier:
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  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
supervisor:
- first_name: Björn
  full_name: Hof, Björn
  id: 3A374330-F248-11E8-B48F-1D18A9856A87
  last_name: Hof
  orcid: 0000-0003-2057-2754
title: Transition to turbulence and drag reduction in particle-laden pipe flows
tmp:
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  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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...
---
_id: '10077'
abstract:
- lang: eng
  text: Although much is known about how single neurons in the hippocampus represent
    an animal’s position, how cell-cell interactions contribute to spatial coding
    remains poorly understood. Using a novel statistical estimator and theoretical
    modeling, both developed in the framework of maximum entropy models, we reveal
    highly structured cell-to-cell interactions whose statistics depend on familiar
    vs. novel environment. In both conditions the circuit interactions optimize the
    encoding of spatial information, but for regimes that differ in the signal-to-noise
    ratio of their spatial inputs. Moreover, the topology of the interactions facilitates
    linear decodability, making the information easy to read out by downstream circuits.
    These findings suggest that the efficient coding hypothesis is not applicable
    only to individual neuron properties in the sensory periphery, but also to neural
    interactions in the central brain.
acknowledgement: We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for
  the acquisition of the data. We thank Federico Stella for comments on an earlier
  version of the manuscript. MN was supported by European Union Horizon 2020 grant
  665385, JC was supported by European Research Council consolidator grant 281511,
  GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported
  by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01,
  by the National Science Foundation under NSF Award No. 1922658 and a Google faculty
  award.
article_processing_charge: No
author:
- first_name: Michele
  full_name: Nardin, Michele
  id: 30BD0376-F248-11E8-B48F-1D18A9856A87
  last_name: Nardin
  orcid: 0000-0001-8849-6570
- first_name: Jozsef L
  full_name: Csicsvari, Jozsef L
  id: 3FA14672-F248-11E8-B48F-1D18A9856A87
  last_name: Csicsvari
  orcid: 0000-0002-5193-4036
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
- first_name: Cristina
  full_name: Savin, Cristina
  id: 3933349E-F248-11E8-B48F-1D18A9856A87
  last_name: Savin
citation:
  ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
    interactions optimizes spatial coding across experience. <i>bioRxiv</i>. doi:<a
    href="https://doi.org/10.1101/2021.09.28.460602">10.1101/2021.09.28.460602</a>
  apa: Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (n.d.). The structure
    of hippocampal CA1 interactions optimizes spatial coding across experience. <i>bioRxiv</i>.
    <a href="https://doi.org/10.1101/2021.09.28.460602">https://doi.org/10.1101/2021.09.28.460602</a>
  chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
    “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
    Experience.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.1101/2021.09.28.460602">https://doi.org/10.1101/2021.09.28.460602</a>.
  ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
    CA1 interactions optimizes spatial coding across experience,” <i>bioRxiv</i>.
    .
  ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
    interactions optimizes spatial coding across experience. bioRxiv, <a href="https://doi.org/10.1101/2021.09.28.460602">10.1101/2021.09.28.460602</a>.
  mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
    Spatial Coding across Experience.” <i>BioRxiv</i>, doi:<a href="https://doi.org/10.1101/2021.09.28.460602">10.1101/2021.09.28.460602</a>.
  short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
das_tickbox: '1'
date_created: 2021-10-04T06:23:34Z
date_published: 2021-09-29T00:00:00Z
date_updated: 2026-11-12T23:30:26Z
day: '29'
department:
- _id: GradSch
- _id: JoCs
- _id: GaTk
doi: 10.1101/2021.09.28.460602
ec_funded: 1
fulldoi: https://doi.org/10.1101/2021.09.28.460602
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.biorxiv.org/content/10.1101/2021.09.28.460602
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 257A4776-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '281511'
  name: Memory-related information processing in neuronal circuits of the hippocampus
    and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
  grant_number: P34015
  name: Efficient coding with biophysical realism
publication: bioRxiv
publication_status: draft
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title: The structure of hippocampal CA1 interactions optimizes spatial coding across
  experience
tmp:
  image: /images/cc_by_nc_nd.png
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...
