---
_id: '9677'
abstract:
- lang: eng
  text: Progress in the atomic-scale modeling of matter over the past decade has been
    tremendous. This progress has been brought about by improvements in methods for
    evaluating interatomic forces that work by either solving the electronic structure
    problem explicitly, or by computing accurate approximations of the solution and
    by the development of techniques that use the Born–Oppenheimer (BO) forces to
    move the atoms on the BO potential energy surface. As a consequence of these developments
    it is now possible to identify stable or metastable states, to sample configurations
    consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics
    of reactions and phase transitions. All too often, however, progress is slowed
    down by the bottleneck associated with implementing new optimization algorithms
    and/or sampling techniques into the many existing electronic-structure and empirical-potential
    codes. To address this problem, we are thus releasing a new version of the i-PI
    software. This piece of software is an easily extensible framework for implementing
    advanced atomistic simulation techniques using interatomic potentials and forces
    calculated by an external driver code. While the original version of the code
    (Ceriotti et al., 2014) was developed with a focus on path integral molecular
    dynamics techniques, this second release of i-PI not only includes several new
    advanced path integral methods, but also offers other classes of algorithms. In
    other words, i-PI is moving towards becoming a universal force engine that is
    both modular and tightly coupled to the driver codes that evaluate the potential
    energy surface and its derivatives.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Venkat
  full_name: Kapil, Venkat
  last_name: Kapil
- first_name: Mariana
  full_name: Rossi, Mariana
  last_name: Rossi
- first_name: Ondrej
  full_name: Marsalek, Ondrej
  last_name: Marsalek
- first_name: Riccardo
  full_name: Petraglia, Riccardo
  last_name: Petraglia
- first_name: Yair
  full_name: Litman, Yair
  last_name: Litman
- first_name: Thomas
  full_name: Spura, Thomas
  last_name: Spura
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Alice
  full_name: Cuzzocrea, Alice
  last_name: Cuzzocrea
- first_name: Robert H.
  full_name: Meißner, Robert H.
  last_name: Meißner
- first_name: David M.
  full_name: Wilkins, David M.
  last_name: Wilkins
- first_name: Benjamin A.
  full_name: Helfrecht, Benjamin A.
  last_name: Helfrecht
- first_name: Przemysław
  full_name: Juda, Przemysław
  last_name: Juda
- first_name: Sébastien P.
  full_name: Bienvenue, Sébastien P.
  last_name: Bienvenue
- first_name: Wei
  full_name: Fang, Wei
  last_name: Fang
- first_name: Jan
  full_name: Kessler, Jan
  last_name: Kessler
- first_name: Igor
  full_name: Poltavsky, Igor
  last_name: Poltavsky
- first_name: Steven
  full_name: Vandenbrande, Steven
  last_name: Vandenbrande
- first_name: Jelle
  full_name: Wieme, Jelle
  last_name: Wieme
- first_name: Clemence
  full_name: Corminboeuf, Clemence
  last_name: Corminboeuf
- first_name: Thomas D.
  full_name: Kühne, Thomas D.
  last_name: Kühne
- first_name: David E.
  full_name: Manolopoulos, David E.
  last_name: Manolopoulos
- first_name: Thomas E.
  full_name: Markland, Thomas E.
  last_name: Markland
- first_name: Jeremy O.
  full_name: Richardson, Jeremy O.
  last_name: Richardson
- first_name: Alexandre
  full_name: Tkatchenko, Alexandre
  last_name: Tkatchenko
- first_name: Gareth A.
  full_name: Tribello, Gareth A.
  last_name: Tribello
- first_name: Veronique
  full_name: Van Speybroeck, Veronique
  last_name: Van Speybroeck
- first_name: Michele
  full_name: Ceriotti, Michele
  last_name: Ceriotti
citation:
  ama: 'Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for
    advanced molecular simulations. <i>Computer Physics Communications</i>. 2019;236:214-223.
    doi:<a href="https://doi.org/10.1016/j.cpc.2018.09.020">10.1016/j.cpc.2018.09.020</a>'
  apa: 'Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T.,
    … Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular
    simulations. <i>Computer Physics Communications</i>. Elsevier. <a href="https://doi.org/10.1016/j.cpc.2018.09.020">https://doi.org/10.1016/j.cpc.2018.09.020</a>'
  chicago: 'Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair
    Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine
    for Advanced Molecular Simulations.” <i>Computer Physics Communications</i>. Elsevier,
    2019. <a href="https://doi.org/10.1016/j.cpc.2018.09.020">https://doi.org/10.1016/j.cpc.2018.09.020</a>.'
  ieee: 'V. Kapil <i>et al.</i>, “i-PI 2.0: A universal force engine for advanced
    molecular simulations,” <i>Computer Physics Communications</i>, vol. 236. Elsevier,
    pp. 214–223, 2019.'
  ista: 'Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea
    A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler
    J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos
    DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti
    M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations.
    Computer Physics Communications. 236, 214–223.'
  mla: 'Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular
    Simulations.” <i>Computer Physics Communications</i>, vol. 236, Elsevier, 2019,
    pp. 214–23, doi:<a href="https://doi.org/10.1016/j.cpc.2018.09.020">10.1016/j.cpc.2018.09.020</a>.'
  short: V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng,
    A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue,
    W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf,
    T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko,
    G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications
    236 (2019) 214–223.
date_created: 2021-07-16T08:53:01Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2021-08-09T12:37:16Z
day: '01'
doi: 10.1016/j.cpc.2018.09.020
extern: '1'
external_id:
  arxiv:
  - '1808.03824'
intvolume: '       236'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1808.03824
month: '03'
oa: 1
oa_version: Preprint
page: 214-223
publication: Computer Physics Communications
publication_identifier:
  issn:
  - 0010-4655
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'i-PI 2.0: A universal force engine for advanced molecular simulations'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 236
year: '2019'
...
---
_id: '9680'
abstract:
- lang: eng
  text: Atomistic modeling of phase transitions, chemical reactions, or other rare
    events that involve overcoming high free energy barriers usually entails prohibitively
    long simulation times. Introducing a bias potential as a function of an appropriately
    chosen set of collective variables can significantly accelerate the exploration
    of phase space, albeit at the price of distorting the distribution of microstates.
    Efficient reweighting to recover the unbiased distribution can be nontrivial when
    employing adaptive sampling techniques such as metadynamics, variationally enhanced
    sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium
    manner under a time-dependent bias. We introduce an iterative unbiasing scheme
    that makes efficient use of all the trajectory data and that does not require
    the distribution to be evaluated on a grid. The method can thus be used even when
    the bias has a high dimensionality. We benchmark this approach against some of
    the existing schemes on model systems with different complexity and dimensionality.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: F.
  full_name: Giberti, F.
  last_name: Giberti
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: G. A.
  full_name: Tribello, G. A.
  last_name: Tribello
- first_name: M.
  full_name: Ceriotti, M.
  last_name: Ceriotti
citation:
  ama: Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium
    sampling. <i>Journal of Chemical Theory and Computation</i>. 2019;16(1):100-107.
    doi:<a href="https://doi.org/10.1021/acs.jctc.9b00907">10.1021/acs.jctc.9b00907</a>
  apa: Giberti, F., Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2019). Iterative
    unbiasing of quasi-equilibrium sampling. <i>Journal of Chemical Theory and Computation</i>.
    American Chemical Society. <a href="https://doi.org/10.1021/acs.jctc.9b00907">https://doi.org/10.1021/acs.jctc.9b00907</a>
  chicago: Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative
    Unbiasing of Quasi-Equilibrium Sampling.” <i>Journal of Chemical Theory and Computation</i>.
    American Chemical Society, 2019. <a href="https://doi.org/10.1021/acs.jctc.9b00907">https://doi.org/10.1021/acs.jctc.9b00907</a>.
  ieee: F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing
    of quasi-equilibrium sampling,” <i>Journal of Chemical Theory and Computation</i>,
    vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019.
  ista: Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of
    quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1),
    100–107.
  mla: Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” <i>Journal
    of Chemical Theory and Computation</i>, vol. 16, no. 1, American Chemical Society,
    2019, pp. 100–07, doi:<a href="https://doi.org/10.1021/acs.jctc.9b00907">10.1021/acs.jctc.9b00907</a>.
  short: F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory
    and Computation 16 (2019) 100–107.
date_created: 2021-07-19T06:56:45Z
date_published: 2019-01-14T00:00:00Z
date_updated: 2021-08-09T12:37:37Z
day: '14'
doi: 10.1021/acs.jctc.9b00907
extern: '1'
external_id:
  arxiv:
  - '1911.01140'
  pmid:
  - '31743021'
intvolume: '        16'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1911.01140
month: '01'
oa: 1
oa_version: Preprint
page: 100-107
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
  eissn:
  - 1549-9626
  issn:
  - 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Iterative unbiasing of quasi-equilibrium sampling
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 16
year: '2019'
...
---
_id: '9689'
abstract:
- lang: eng
  text: A central goal of computational physics and chemistry is to predict material
    properties by using first-principles methods based on the fundamental laws of
    quantum mechanics. However, the high computational costs of these methods typically
    prevent rigorous predictions of macroscopic quantities at finite temperatures,
    such as heat capacity, density, and chemical potential. Here, we enable such predictions
    by marrying advanced free-energy methods with data-driven machine-learning interatomic
    potentials. We show that, for the ubiquitous and technologically essential system
    of water, a first-principles thermodynamic description not only leads to excellent
    agreement with experiments, but also reveals the crucial role of nuclear quantum
    fluctuations in modulating the thermodynamic stabilities of different phases of
    water.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
  full_name: Cheng, Bingqing
  id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
  last_name: Cheng
  orcid: 0000-0002-3584-9632
- first_name: Edgar A.
  full_name: Engel, Edgar A.
  last_name: Engel
- first_name: Jörg
  full_name: Behler, Jörg
  last_name: Behler
- first_name: Christoph
  full_name: Dellago, Christoph
  last_name: Dellago
- first_name: Michele
  full_name: Ceriotti, Michele
  last_name: Ceriotti
citation:
  ama: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics
    of liquid and solid water. <i>Proceedings of the National Academy of Sciences</i>.
    2019;116(4):1110-1115. doi:<a href="https://doi.org/10.1073/pnas.1815117116">10.1073/pnas.1815117116</a>
  apa: Cheng, B., Engel, E. A., Behler, J., Dellago, C., &#38; Ceriotti, M. (2019).
    Ab initio thermodynamics of liquid and solid water. <i>Proceedings of the National
    Academy of Sciences</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.1815117116">https://doi.org/10.1073/pnas.1815117116</a>
  chicago: Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele
    Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” <i>Proceedings
    of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a
    href="https://doi.org/10.1073/pnas.1815117116">https://doi.org/10.1073/pnas.1815117116</a>.
  ieee: B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio
    thermodynamics of liquid and solid water,” <i>Proceedings of the National Academy
    of Sciences</i>, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115,
    2019.
  ista: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics
    of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4),
    1110–1115.
  mla: Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.”
    <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 4, National
    Academy of Sciences, 2019, pp. 1110–15, doi:<a href="https://doi.org/10.1073/pnas.1815117116">10.1073/pnas.1815117116</a>.
  short: B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of
    the National Academy of Sciences 116 (2019) 1110–1115.
date_created: 2021-07-19T10:17:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-02-23T14:05:08Z
day: '22'
doi: 10.1073/pnas.1815117116
extern: '1'
external_id:
  arxiv:
  - '1811.08630'
  pmid:
  - '30610171'
intvolume: '       116'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1073/pnas.1815117116
month: '01'
oa: 1
oa_version: Published Version
page: 1110-1115
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ab initio thermodynamics of liquid and solid water
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 116
year: '2019'
...
---
_id: '10065'
abstract:
- lang: eng
  text: We study double quantum dots in a Ge/SiGe heterostructure and test their maturity
    towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability,
    from two single quantum dots to a double quantum dot. We measure Pauli spin blockade
    and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for
    sensing charge transitions in the double quantum dot at interest. In conclusion,
    Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We thank Matthias Brauns for helpful discussions and careful proofreading
  of the manuscript. This project has received funding from the European Union’s Horizon
  2020 research and innovation program under the Marie Sklodowska-Curie grant agreement
  No 844511 and from the FWF project P30207. The research was supported by the Scientific
  Service Units of IST Austria through resources provided by the MIBA machine shop
  and the nanofabrication\r\nfacility."
article_number: '1910.05841'
article_processing_charge: No
arxiv: 1
author:
- first_name: Andrea C
  full_name: Hofmann, Andrea C
  id: 340F461A-F248-11E8-B48F-1D18A9856A87
  last_name: Hofmann
- first_name: Daniel
  full_name: Jirovec, Daniel
  id: 4C473F58-F248-11E8-B48F-1D18A9856A87
  last_name: Jirovec
  orcid: 0000-0002-7197-4801
- first_name: Maxim
  full_name: Borovkov, Maxim
  last_name: Borovkov
- first_name: Ivan
  full_name: Prieto Gonzalez, Ivan
  id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
  last_name: Prieto Gonzalez
  orcid: 0000-0002-7370-5357
- first_name: Andrea
  full_name: Ballabio, Andrea
  last_name: Ballabio
- first_name: Jacopo
  full_name: Frigerio, Jacopo
  last_name: Frigerio
- first_name: Daniel
  full_name: Chrastina, Daniel
  last_name: Chrastina
- first_name: Giovanni
  full_name: Isella, Giovanni
  last_name: Isella
- first_name: Georgios
  full_name: Katsaros, Georgios
  id: 38DB5788-F248-11E8-B48F-1D18A9856A87
  last_name: Katsaros
  orcid: 0000-0001-8342-202X
citation:
  ama: Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe
    quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.1910.05841">10.48550/arXiv.1910.05841</a>
  apa: Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A.,
    Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum
    dots as hosts for singlet-triplet qubits. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.1910.05841">https://doi.org/10.48550/arXiv.1910.05841</a>
  chicago: Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez,
    Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios
    Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet
    Qubits.” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.1910.05841">https://doi.org/10.48550/arXiv.1910.05841</a>.
  ieee: A. C. Hofmann <i>et al.</i>, “Assessing the potential of Ge/SiGe quantum dots
    as hosts for singlet-triplet qubits,” <i>arXiv</i>. .
  ista: Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio
    J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum
    dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.
  mla: Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots
    as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, 1910.05841, doi:<a href="https://doi.org/10.48550/arXiv.1910.05841">10.48550/arXiv.1910.05841</a>.
  short: A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J.
    Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).
date_created: 2021-10-01T12:14:51Z
date_published: 2019-10-13T00:00:00Z
date_updated: 2024-03-25T23:30:14Z
day: '13'
department:
- _id: GeKa
doi: 10.48550/arXiv.1910.05841
ec_funded: 1
external_id:
  arxiv:
  - '1910.05841'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1910.05841
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '844511'
  name: Majorana bound states in Ge/SiGe heterostructures
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P30207
  name: Hole spin orbit qubits in Ge quantum wells
publication: arXiv
publication_status: submitted
related_material:
  record:
  - id: '10058'
    relation: dissertation_contains
    status: public
status: public
title: Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet
  qubits
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '10190'
abstract:
- lang: eng
  text: 'The verification of concurrent programs remains an open challenge, as thread
    interaction has to be accounted for, which leads to state-space explosion. Stateless
    model checking battles this problem by exploring traces rather than states of
    the program. As there are exponentially many traces, dynamic partial-order reduction
    (DPOR) techniques are used to partition the trace space into equivalence classes,
    and explore a few representatives from each class. The standard equivalence that
    underlies most DPOR techniques is the happens-before equivalence, however recent
    works have spawned a vivid interest towards coarser equivalences. The efficiency
    of such approaches is a product of two parameters: (i) the size of the partitioning
    induced by the equivalence, and (ii) the time spent by the exploration algorithm
    in each class of the partitioning. In this work, we present a new equivalence,
    called value-happens-before and show that it has two appealing features. First,
    value-happens-before is always at least as coarse as the happens-before equivalence,
    and can be even exponentially coarser. Second, the value-happens-before partitioning
    is efficiently explorable when the number of threads is bounded. We present an
    algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning
    using polynomial time per class. Finally, we perform an experimental evaluation
    of VCDPOR on various benchmarks, and compare it against other state-of-the-art
    approaches. Our results show that value-happens-before typically induces a significant
    reduction in the size of the underlying partitioning, which leads to a considerable
    reduction in the running time for exploring the whole partitioning.'
acknowledgement: "The authors would also like to thank anonymous referees for their
  valuable comments and helpful suggestions. This work is supported by the Austrian
  Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE),
  by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian
  Science Fund (FWF) Schrodinger grant J-4220.\r\n"
article_number: '124'
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: Andreas
  full_name: Pavlogiannis, Andreas
  id: 49704004-F248-11E8-B48F-1D18A9856A87
  last_name: Pavlogiannis
  orcid: 0000-0002-8943-0722
- first_name: Viktor
  full_name: Toman, Viktor
  id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
  last_name: Toman
  orcid: 0000-0001-9036-063X
citation:
  ama: 'Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order
    reduction. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented
    Programming, Systems, Languages, and Applications</i>. Vol 3. ACM; 2019. doi:<a
    href="https://doi.org/10.1145/3360550">10.1145/3360550</a>'
  apa: 'Chatterjee, K., Pavlogiannis, A., &#38; Toman, V. (2019). Value-centric dynamic
    partial order reduction. In <i>Proceedings of the 34th ACM International Conference
    on Object-Oriented Programming, Systems, Languages, and Applications</i> (Vol.
    3). Athens, Greece: ACM. <a href="https://doi.org/10.1145/3360550">https://doi.org/10.1145/3360550</a>'
  chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric
    Dynamic Partial Order Reduction.” In <i>Proceedings of the 34th ACM International
    Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>,
    Vol. 3. ACM, 2019. <a href="https://doi.org/10.1145/3360550">https://doi.org/10.1145/3360550</a>.
  ieee: K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial
    order reduction,” in <i>Proceedings of the 34th ACM International Conference on
    Object-Oriented Programming, Systems, Languages, and Applications</i>, Athens,
    Greece, 2019, vol. 3.
  ista: 'Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial
    order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented
    Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming,
    Systems, Languages and Applications vol. 3, 124.'
  mla: Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.”
    <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming,
    Systems, Languages, and Applications</i>, vol. 3, 124, ACM, 2019, doi:<a href="https://doi.org/10.1145/3360550">10.1145/3360550</a>.
  short: K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM
    International Conference on Object-Oriented Programming, Systems, Languages, and
    Applications, ACM, 2019.
conference:
  end_date: 2019-10-25
  location: Athens, Greece
  name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications'
  start_date: 2019-10-23
date_created: 2021-10-27T14:57:06Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2025-07-14T09:10:15Z
day: '10'
ddc:
- '000'
department:
- _id: GradSch
- _id: KrCh
doi: 10.1145/3360550
external_id:
  arxiv:
  - '1909.00989'
file:
- access_level: open_access
  checksum: 2149979c46964c4d117af06ccb6c0834
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-11-12T11:41:56Z
  date_updated: 2021-11-12T11:41:56Z
  file_id: '10278'
  file_name: 2019_ACM_Chatterjee.pdf
  file_size: 570829
  relation: main_file
  success: 1
file_date_updated: 2021-11-12T11:41:56Z
has_accepted_license: '1'
intvolume: '         3'
keyword:
- safety
- risk
- reliability and quality
- software
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://dl.acm.org/doi/10.1145/3360550
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
  grant_number: ICT15-003
  name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11407
  name: Game Theory
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11402-N23
  name: Moderne Concurrency Paradigms
publication: Proceedings of the 34th ACM International Conference on Object-Oriented
  Programming, Systems, Languages, and Applications
publication_identifier:
  eissn:
  - 2475-1421
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
  record:
  - id: '10199'
    relation: dissertation_contains
    status: public
status: public
title: Value-centric dynamic partial order reduction
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: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2019'
...
---
_id: '10354'
abstract:
- lang: eng
  text: "Background\r\nESCRT-III is a membrane remodelling filament with the unique
    ability to cut membranes from the inside of the membrane neck. It is essential
    for the final stage of cell division, the formation of vesicles, the release of
    viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III
    filaments do not consume energy themselves, but work in conjunction with another
    ATP-consuming complex. Despite rapid progress in describing the cell biology of
    ESCRT-III, we lack an understanding of the physical mechanisms behind its force
    production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained
    model that captures all the experimentally reported cases of ESCRT-III driven
    membrane sculpting, including the formation of downward and upward cones and tubules.
    This model suggests that a change in the geometry of membrane bound ESCRT-III
    filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then
    show that such repetitive filament geometry transitions can induce the fission
    of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical
    mechanism that explains the full range of ESCRT-III-dependent membrane remodelling
    and scission events observed in cells. This mechanism for filament force production
    is distinct from the mechanisms described for other cytoskeletal elements discovered
    so far. The mechanistic principles revealed here suggest new ways of manipulating
    ESCRT-III-driven processes in cells and could be used to guide the engineering
    of synthetic membrane-sculpting systems."
acknowledgement: We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome
  Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful
  conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the
  membrane model implementation.
article_number: '82'
article_processing_charge: No
article_type: original
author:
- first_name: Lena
  full_name: Harker-Kirschneck, Lena
  last_name: Harker-Kirschneck
- first_name: Buzz
  full_name: Baum, Buzz
  last_name: Baum
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
citation:
  ama: Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry
    drive membrane remodelling and fission in silico. <i>BMC Biology</i>. 2019;17(1).
    doi:<a href="https://doi.org/10.1186/s12915-019-0700-2">10.1186/s12915-019-0700-2</a>
  apa: Harker-Kirschneck, L., Baum, B., &#38; Šarić, A. (2019). Changes in ESCRT-III
    filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>.
    Springer Nature. <a href="https://doi.org/10.1186/s12915-019-0700-2">https://doi.org/10.1186/s12915-019-0700-2</a>
  chicago: Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III
    Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>.
    Springer Nature, 2019. <a href="https://doi.org/10.1186/s12915-019-0700-2">https://doi.org/10.1186/s12915-019-0700-2</a>.
  ieee: L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament
    geometry drive membrane remodelling and fission in silico,” <i>BMC Biology</i>,
    vol. 17, no. 1. Springer Nature, 2019.
  ista: Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament
    geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1),
    82.
  mla: Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive
    Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>, vol. 17, no.
    1, 82, Springer Nature, 2019, doi:<a href="https://doi.org/10.1186/s12915-019-0700-2">10.1186/s12915-019-0700-2</a>.
  short: L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).
date_created: 2021-11-26T11:25:03Z
date_published: 2019-10-22T00:00:00Z
date_updated: 2021-11-26T11:54:29Z
day: '22'
ddc:
- '570'
doi: 10.1186/s12915-019-0700-2
extern: '1'
external_id:
  pmid:
  - '31640700'
file:
- access_level: open_access
  checksum: 31d8bae55a376d30925f53f7e1a02396
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-11-26T11:37:54Z
  date_updated: 2021-11-26T11:37:54Z
  file_id: '10356'
  file_name: 2019_BMCBio_Harker_Kirschneck.pdf
  file_size: 1648926
  relation: main_file
  success: 1
file_date_updated: 2021-11-26T11:37:54Z
has_accepted_license: '1'
intvolume: '        17'
issue: '1'
keyword:
- cell biology
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.biorxiv.org/content/10.1101/559898
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: BMC Biology
publication_identifier:
  issn:
  - 1741-7007
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Changes in ESCRT-III filament geometry drive membrane remodelling and fission
  in silico
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 17
year: '2019'
...
---
_id: '10355'
abstract:
- lang: eng
  text: The molecular machinery of life is largely created via self-organisation of
    individual molecules into functional assemblies. Minimal coarse-grained models,
    in which a whole macromolecule is represented by a small number of particles,
    can be of great value in identifying the main driving forces behind self-organisation
    in cell biology. Such models can incorporate data from both molecular and continuum
    scales, and their results can be directly compared to experiments. Here we review
    the state of the art of models for studying the formation and biological function
    of macromolecular assemblies in living organisms. We outline the key ingredients
    of each model and their main findings. We illustrate the contribution of this
    class of simulations to identifying the physical mechanisms behind life and diseases,
    and discuss their future developments.
acknowledgement: We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy
  of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the
  Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically
  reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.
article_processing_charge: No
article_type: original
author:
- first_name: Anne E
  full_name: Hafner, Anne E
  last_name: Hafner
- first_name: Johannes
  full_name: Krausser, Johannes
  last_name: Krausser
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
citation:
  ama: Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular
    self-organisation in biology. <i>Current Opinion in Structural Biology</i>. 2019;58:43-52.
    doi:<a href="https://doi.org/10.1016/j.sbi.2019.05.018">10.1016/j.sbi.2019.05.018</a>
  apa: Hafner, A. E., Krausser, J., &#38; Šarić, A. (2019). Minimal coarse-grained
    models for molecular self-organisation in biology. <i>Current Opinion in Structural
    Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.sbi.2019.05.018">https://doi.org/10.1016/j.sbi.2019.05.018</a>
  chicago: Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained
    Models for Molecular Self-Organisation in Biology.” <i>Current Opinion in Structural
    Biology</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.sbi.2019.05.018">https://doi.org/10.1016/j.sbi.2019.05.018</a>.
  ieee: A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for
    molecular self-organisation in biology,” <i>Current Opinion in Structural Biology</i>,
    vol. 58. Elsevier, pp. 43–52, 2019.
  ista: Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular
    self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.
  mla: Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation
    in Biology.” <i>Current Opinion in Structural Biology</i>, vol. 58, Elsevier,
    2019, pp. 43–52, doi:<a href="https://doi.org/10.1016/j.sbi.2019.05.018">10.1016/j.sbi.2019.05.018</a>.
  short: A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology
    58 (2019) 43–52.
date_created: 2021-11-26T11:33:21Z
date_published: 2019-06-18T00:00:00Z
date_updated: 2021-11-26T11:54:25Z
day: '18'
doi: 10.1016/j.sbi.2019.05.018
extern: '1'
external_id:
  pmid:
  - '31226513'
intvolume: '        58'
keyword:
- molecular biology
- structural biology
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1906.09349
month: '06'
oa: 1
oa_version: Preprint
page: 43-52
pmid: 1
publication: Current Opinion in Structural Biology
publication_identifier:
  issn:
  - 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Minimal coarse-grained models for molecular self-organisation in biology
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2019'
...
---
_id: '105'
abstract:
- lang: eng
  text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar
    hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease:
    615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2
    at 1p13.3. 4. OMIM# of the Gene(s): 102771.'
acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing
  as part of health care”), a Coordination Action under FP7 (Grant Agreement Number
  261469) and the European Society of Human Genetics. We acknowledge the participation
  of the patients and their families in these studies, as well as the generous financial
  support of the Lefroy and Handbury families. APLM was supported by an Australian
  Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364).
  RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.'
article_processing_charge: No
article_type: original
author:
- first_name: Ashley
  full_name: Marsh, Ashley
  last_name: Marsh
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
- first_name: Paul
  full_name: Lockhart, Paul
  last_name: Lockhart
- first_name: Richard
  full_name: Leventer, Richard
  last_name: Leventer
citation:
  ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia
    type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. 2019;27:161-166.
    doi:<a href="https://doi.org/10.1038/s41431-018-0231-2">10.1038/s41431-018-0231-2</a>
  apa: Marsh, A., Novarino, G., Lockhart, P., &#38; Leventer, R. (2019). CUGC for
    pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal
    of Human Genetics</i>. Springer Nature. <a href="https://doi.org/10.1038/s41431-018-0231-2">https://doi.org/10.1038/s41431-018-0231-2</a>
  chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC
    for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European
    Journal of Human Genetics</i>. Springer Nature, 2019. <a href="https://doi.org/10.1038/s41431-018-0231-2">https://doi.org/10.1038/s41431-018-0231-2</a>.
  ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar
    hypoplasia type 9 and spastic paraplegia-63,” <i>European Journal of Human Genetics</i>,
    vol. 27. Springer Nature, pp. 161–166, 2019.
  ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar
    hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics.
    27, 161–166.
  mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic
    Paraplegia-63.” <i>European Journal of Human Genetics</i>, vol. 27, Springer Nature,
    2019, pp. 161–66, doi:<a href="https://doi.org/10.1038/s41431-018-0231-2">10.1038/s41431-018-0231-2</a>.
  short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human
    Genetics 27 (2019) 161–166.
date_created: 2018-12-11T11:44:39Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-08-24T14:28:24Z
day: '01'
department:
- _id: GaNo
doi: 10.1038/s41431-018-0231-2
external_id:
  isi:
  - '000454111500019'
  pmid:
  - '30089829'
intvolume: '        27'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1038/s41431-018-0231-2
month: '01'
oa: 1
oa_version: Published Version
page: 161-166
pmid: 1
publication: European Journal of Human Genetics
publication_status: published
publisher: Springer Nature
publist_id: '7949'
quality_controlled: '1'
scopus_import: '1'
status: public
title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 27
year: '2019'
...
---
_id: '10619'
abstract:
- lang: eng
  text: The quantum anomalous Hall (QAH) effect combines topology and magnetism to
    produce precisely quantized Hall resistance at zero magnetic field. We report
    the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal
    boron nitride. The effect is driven by intrinsic strong interactions, which polarize
    the electrons into a single spin- and valley-resolved moiré miniband with Chern
    number C = 1. In contrast to magnetically doped systems, the measured transport
    energy gap is larger than the Curie temperature for magnetic ordering, and quantization
    to within 0.1% of the von Klitzing constant persists to temperatures of several
    kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably
    switch the magnetic order between states of opposite polarization, forming an
    electrically rewritable magnetic memory.
acknowledgement: The authors acknowledge discussions with A. Macdonald, Y. Saito,
  and M. Zaletel.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M.
  full_name: Serlin, M.
  last_name: Serlin
- first_name: C. L.
  full_name: Tschirhart, C. L.
  last_name: Tschirhart
- first_name: Hryhoriy
  full_name: Polshyn, Hryhoriy
  id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
  last_name: Polshyn
  orcid: 0000-0001-8223-8896
- first_name: Y.
  full_name: Zhang, Y.
  last_name: Zhang
- first_name: J.
  full_name: Zhu, J.
  last_name: Zhu
- first_name: K.
  full_name: Watanabe, K.
  last_name: Watanabe
- first_name: T.
  full_name: Taniguchi, T.
  last_name: Taniguchi
- first_name: L.
  full_name: Balents, L.
  last_name: Balents
- first_name: A. F.
  full_name: Young, A. F.
  last_name: Young
citation:
  ama: Serlin M, Tschirhart CL, Polshyn H, et al. Intrinsic quantized anomalous Hall
    effect in a moiré heterostructure. <i>Science</i>. 2019;367(6480):900-903. doi:<a
    href="https://doi.org/10.1126/science.aay5533">10.1126/science.aay5533</a>
  apa: Serlin, M., Tschirhart, C. L., Polshyn, H., Zhang, Y., Zhu, J., Watanabe, K.,
    … Young, A. F. (2019). Intrinsic quantized anomalous Hall effect in a moiré heterostructure.
    <i>Science</i>. American Association for the Advancement of Science. <a href="https://doi.org/10.1126/science.aay5533">https://doi.org/10.1126/science.aay5533</a>
  chicago: Serlin, M., C. L. Tschirhart, Hryhoriy Polshyn, Y. Zhang, J. Zhu, K. Watanabe,
    T. Taniguchi, L. Balents, and A. F. Young. “Intrinsic Quantized Anomalous Hall
    Effect in a Moiré Heterostructure.” <i>Science</i>. American Association for the
    Advancement of Science, 2019. <a href="https://doi.org/10.1126/science.aay5533">https://doi.org/10.1126/science.aay5533</a>.
  ieee: M. Serlin <i>et al.</i>, “Intrinsic quantized anomalous Hall effect in a moiré
    heterostructure,” <i>Science</i>, vol. 367, no. 6480. American Association for
    the Advancement of Science, pp. 900–903, 2019.
  ista: Serlin M, Tschirhart CL, Polshyn H, Zhang Y, Zhu J, Watanabe K, Taniguchi
    T, Balents L, Young AF. 2019. Intrinsic quantized anomalous Hall effect in a moiré
    heterostructure. Science. 367(6480), 900–903.
  mla: Serlin, M., et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.”
    <i>Science</i>, vol. 367, no. 6480, American Association for the Advancement of
    Science, 2019, pp. 900–03, doi:<a href="https://doi.org/10.1126/science.aay5533">10.1126/science.aay5533</a>.
  short: M. Serlin, C.L. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T.
    Taniguchi, L. Balents, A.F. Young, Science 367 (2019) 900–903.
date_created: 2022-01-13T14:21:32Z
date_published: 2019-12-19T00:00:00Z
date_updated: 2023-02-21T16:00:09Z
day: '19'
doi: 10.1126/science.aay5533
extern: '1'
external_id:
  arxiv:
  - '1907.00261'
  pmid:
  - '31857492'
intvolume: '       367'
issue: '6480'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1907.00261
month: '12'
oa: 1
oa_version: Preprint
page: 900-903
pmid: 1
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
  issn:
  - 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
  record:
  - id: '10697'
    relation: other
    status: public
  - id: '10698'
    relation: other
    status: public
  - id: '10699'
    relation: other
    status: public
scopus_import: '1'
status: public
title: Intrinsic quantized anomalous Hall effect in a moiré heterostructure
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 367
year: '2019'
...
---
_id: '10620'
abstract:
- lang: eng
  text: Partially filled Landau levels host competing electronic orders. For example,
    electron solids may prevail close to integer filling of the Landau levels before
    giving way to fractional quantum Hall liquids at higher carrier density1,2. Here,
    we report the observation of an electron solid with non-collinear spin texture
    in monolayer graphene, consistent with solidification of skyrmions3—topological
    spin textures characterized by quantized electrical charge4,5. We probe the spin
    texture of the solids using a modified Corbino geometry that allows ferromagnetic
    magnons to be launched and detected6,7. We find that magnon transport is highly
    efficient when one Landau level is filled (ν=1), consistent with quantum Hall
    ferromagnetic spin polarization. However, even minimal doping immediately quenches
    the magnon signal while leaving the vanishing low-temperature charge conductivity
    unchanged. Our results can be understood by the formation of a solid of charged
    skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay.
    Data near fractional fillings show evidence of several fractional skyrmion solids,
    suggesting that graphene hosts a highly tunable landscape of coupled spin and
    charge orders.
acknowledgement: We acknowledge discussions with B. Halperin, C. Huang, A. Macdonald
  and M. Zalatel. Experimental work at UCSB was supported by the Army Research Office
  under awards nos. MURI W911NF-16-1-0361 and W911NF-16-1-0482. K.W. and T.T. acknowledge
  support from the Elemental Strategy Initiative conducted by MEXT (Japan) and CREST
  (JPMJCR15F3), JST. A.F.Y. acknowledges the support of the David and Lucile Packard
  Foundation and and Alfred. P. Sloan Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: H.
  full_name: Zhou, H.
  last_name: Zhou
- first_name: Hryhoriy
  full_name: Polshyn, Hryhoriy
  id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
  last_name: Polshyn
  orcid: 0000-0001-8223-8896
- first_name: T.
  full_name: Taniguchi, T.
  last_name: Taniguchi
- first_name: K.
  full_name: Watanabe, K.
  last_name: Watanabe
- first_name: A. F.
  full_name: Young, A. F.
  last_name: Young
citation:
  ama: Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. Solids of quantum Hall
    skyrmions in graphene. <i>Nature Physics</i>. 2019;16(2):154-158. doi:<a href="https://doi.org/10.1038/s41567-019-0729-8">10.1038/s41567-019-0729-8</a>
  apa: Zhou, H., Polshyn, H., Taniguchi, T., Watanabe, K., &#38; Young, A. F. (2019).
    Solids of quantum Hall skyrmions in graphene. <i>Nature Physics</i>. Springer
    Nature. <a href="https://doi.org/10.1038/s41567-019-0729-8">https://doi.org/10.1038/s41567-019-0729-8</a>
  chicago: Zhou, H., Hryhoriy Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young.
    “Solids of Quantum Hall Skyrmions in Graphene.” <i>Nature Physics</i>. Springer
    Nature, 2019. <a href="https://doi.org/10.1038/s41567-019-0729-8">https://doi.org/10.1038/s41567-019-0729-8</a>.
  ieee: H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young, “Solids of
    quantum Hall skyrmions in graphene,” <i>Nature Physics</i>, vol. 16, no. 2. Springer
    Nature, pp. 154–158, 2019.
  ista: Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. 2019. Solids of quantum
    Hall skyrmions in graphene. Nature Physics. 16(2), 154–158.
  mla: Zhou, H., et al. “Solids of Quantum Hall Skyrmions in Graphene.” <i>Nature
    Physics</i>, vol. 16, no. 2, Springer Nature, 2019, pp. 154–58, doi:<a href="https://doi.org/10.1038/s41567-019-0729-8">10.1038/s41567-019-0729-8</a>.
  short: H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, A.F. Young, Nature Physics
    16 (2019) 154–158.
date_created: 2022-01-13T14:45:16Z
date_published: 2019-12-16T00:00:00Z
date_updated: 2022-01-13T15:34:44Z
day: '16'
doi: 10.1038/s41567-019-0729-8
extern: '1'
intvolume: '        16'
issue: '2'
keyword:
- General Physics and Astronomy
language:
- iso: eng
month: '12'
oa_version: None
page: 154-158
publication: Nature Physics
publication_identifier:
  eissn:
  - 1745-2481
  issn:
  - 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solids of quantum Hall skyrmions in graphene
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 16
year: '2019'
...
---
_id: '10621'
abstract:
- lang: eng
  text: Twisted bilayer graphene has recently emerged as a platform for hosting correlated
    phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure
    of twisted bilayer graphene features isolated bands with a flat dispersion1,2.
    Recent experiments have observed a variety of low-temperature phases that appear
    to be driven by electron interactions, including insulating states, superconductivity
    and magnetism3,4,5,6. Here we report electrical transport measurements up to room
    temperature for twist angles varying between 0.75° and 2°. We find that the resistivity,
    ρ, scales linearly with temperature, T, over a wide range of T before falling
    again owing to interband activation. The T-linear response is much larger than
    observed in monolayer graphene for all measured devices, and in particular increases
    by more than three orders of magnitude in the range where the flat band exists.
    Our results point to the dominant role of electron–phonon scattering in twisted
    bilayer graphene, with possible implications for the origin of the observed superconductivity.
acknowledgement: The authors thank S. Das Sarma and F. Wu for sharing their unpublished
  theoretical results, and acknowledge further discussions with L. Balents and T.
  Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under
  award W911NF-17-1-0323. Sample device design and fabrication was partially supported
  by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the
  support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support
  from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST
  (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara,
  supported by the National Science Foundation under grant number NSF PHY-1748958.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Hryhoriy
  full_name: Polshyn, Hryhoriy
  id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
  last_name: Polshyn
  orcid: 0000-0001-8223-8896
- first_name: Matthew
  full_name: Yankowitz, Matthew
  last_name: Yankowitz
- first_name: Shaowen
  full_name: Chen, Shaowen
  last_name: Chen
- first_name: Yuxuan
  full_name: Zhang, Yuxuan
  last_name: Zhang
- first_name: K.
  full_name: Watanabe, K.
  last_name: Watanabe
- first_name: T.
  full_name: Taniguchi, T.
  last_name: Taniguchi
- first_name: Cory R.
  full_name: Dean, Cory R.
  last_name: Dean
- first_name: Andrea F.
  full_name: Young, Andrea F.
  last_name: Young
citation:
  ama: Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity
    in twisted bilayer graphene. <i>Nature Physics</i>. 2019;15(10):1011-1016. doi:<a
    href="https://doi.org/10.1038/s41567-019-0596-3">10.1038/s41567-019-0596-3</a>
  apa: Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T.,
    … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer
    graphene. <i>Nature Physics</i>. Springer Nature. <a href="https://doi.org/10.1038/s41567-019-0596-3">https://doi.org/10.1038/s41567-019-0596-3</a>
  chicago: Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe,
    T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature
    Resistivity in Twisted Bilayer Graphene.” <i>Nature Physics</i>. Springer Nature,
    2019. <a href="https://doi.org/10.1038/s41567-019-0596-3">https://doi.org/10.1038/s41567-019-0596-3</a>.
  ieee: H. Polshyn <i>et al.</i>, “Large linear-in-temperature resistivity in twisted
    bilayer graphene,” <i>Nature Physics</i>, vol. 15, no. 10. Springer Nature, pp.
    1011–1016, 2019.
  ista: Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR,
    Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene.
    Nature Physics. 15(10), 1011–1016.
  mla: Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted
    Bilayer Graphene.” <i>Nature Physics</i>, vol. 15, no. 10, Springer Nature, 2019,
    pp. 1011–16, doi:<a href="https://doi.org/10.1038/s41567-019-0596-3">10.1038/s41567-019-0596-3</a>.
  short: H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R.
    Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016.
date_created: 2022-01-13T15:00:58Z
date_published: 2019-08-05T00:00:00Z
date_updated: 2022-01-20T09:33:38Z
day: '05'
doi: 10.1038/s41567-019-0596-3
extern: '1'
external_id:
  arxiv:
  - '1902.00763'
intvolume: '        15'
issue: '10'
keyword:
- general physics and astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1902.00763
month: '08'
oa: 1
oa_version: Preprint
page: 1011-1016
publication: Nature Physics
publication_identifier:
  eissn:
  - 1745-2481
  issn:
  - 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Large linear-in-temperature resistivity in twisted bilayer graphene
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 15
year: '2019'
...
---
_id: '10622'
abstract:
- lang: eng
  text: We demonstrate a method for manipulating small ensembles of vortices in multiply
    connected superconducting structures. A micron-size magnetic particle attached
    to the tip of a silicon cantilever is used to locally apply magnetic flux through
    the superconducting structure. By scanning the tip over the surface of the device
    and by utilizing the dynamical coupling between the vortices and the cantilever,
    a high-resolution spatial map of the different vortex configurations is obtained.
    Moving the tip to a particular location in the map stabilizes a distinct multivortex
    configuration. Thus, the scanning of the tip over a particular trajectory in space
    permits nontrivial operations to be performed, such as braiding of individual
    vortices within a larger vortex ensemble—a key capability required by many proposals
    for topological quantum computing.
acknowledgement: We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin
  for useful discussions. This work was supported by the DOE Basic Energy Sciences
  under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials
  Research Laboratory Central Facilities at the University of Illinois.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Hryhoriy
  full_name: Polshyn, Hryhoriy
  id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
  last_name: Polshyn
  orcid: 0000-0001-8223-8896
- first_name: Tyler
  full_name: Naibert, Tyler
  last_name: Naibert
- first_name: Raffi
  full_name: Budakian, Raffi
  last_name: Budakian
citation:
  ama: Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting
    structures. <i>Nano Letters</i>. 2019;19(8):5476-5482. doi:<a href="https://doi.org/10.1021/acs.nanolett.9b01983">10.1021/acs.nanolett.9b01983</a>
  apa: Polshyn, H., Naibert, T., &#38; Budakian, R. (2019). Manipulating multivortex
    states in superconducting structures. <i>Nano Letters</i>. American Chemical Society.
    <a href="https://doi.org/10.1021/acs.nanolett.9b01983">https://doi.org/10.1021/acs.nanolett.9b01983</a>
  chicago: Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex
    States in Superconducting Structures.” <i>Nano Letters</i>. American Chemical
    Society, 2019. <a href="https://doi.org/10.1021/acs.nanolett.9b01983">https://doi.org/10.1021/acs.nanolett.9b01983</a>.
  ieee: H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states
    in superconducting structures,” <i>Nano Letters</i>, vol. 19, no. 8. American
    Chemical Society, pp. 5476–5482, 2019.
  ista: Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in
    superconducting structures. Nano Letters. 19(8), 5476–5482.
  mla: Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting
    Structures.” <i>Nano Letters</i>, vol. 19, no. 8, American Chemical Society, 2019,
    pp. 5476–82, doi:<a href="https://doi.org/10.1021/acs.nanolett.9b01983">10.1021/acs.nanolett.9b01983</a>.
  short: H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482.
date_created: 2022-01-13T15:11:14Z
date_published: 2019-06-27T00:00:00Z
date_updated: 2022-01-13T15:41:24Z
day: '27'
doi: 10.1021/acs.nanolett.9b01983
extern: '1'
external_id:
  arxiv:
  - '1905.06303'
  pmid:
  - '31246034'
intvolume: '        19'
issue: '8'
keyword:
- mechanical engineering
- condensed matter physics
- general materials science
- general chemistry
- bioengineering
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1905.06303
month: '06'
oa: 1
oa_version: Preprint
page: 5476-5482
pmid: 1
publication: Nano Letters
publication_identifier:
  eissn:
  - 1530-6992
  issn:
  - 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Manipulating multivortex states in superconducting structures
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 19
year: '2019'
...
---
_id: '10625'
abstract:
- lang: eng
  text: The discovery of superconductivity and exotic insulating phases in twisted
    bilayer graphene has established this material as a model system of strongly correlated
    electrons. To achieve superconductivity, the two layers of graphene need to be
    at a very precise angle with respect to each other. Yankowitz et al. now show
    that another experimental knob, hydrostatic pressure, can be used to tune the
    phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying
    pressure increased the coupling between the layers, which shifted the superconducting
    transition to higher angles and somewhat higher temperatures.
acknowledgement: We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar,
  A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino,
  and P. Moon for helpful discussions.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew
  full_name: Yankowitz, Matthew
  last_name: Yankowitz
- first_name: Shaowen
  full_name: Chen, Shaowen
  last_name: Chen
- first_name: Hryhoriy
  full_name: Polshyn, Hryhoriy
  id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
  last_name: Polshyn
  orcid: 0000-0001-8223-8896
- first_name: Yuxuan
  full_name: Zhang, Yuxuan
  last_name: Zhang
- first_name: K.
  full_name: Watanabe, K.
  last_name: Watanabe
- first_name: T.
  full_name: Taniguchi, T.
  last_name: Taniguchi
- first_name: David
  full_name: Graf, David
  last_name: Graf
- first_name: Andrea F.
  full_name: Young, Andrea F.
  last_name: Young
- first_name: Cory R.
  full_name: Dean, Cory R.
  last_name: Dean
citation:
  ama: Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted
    bilayer graphene. <i>Science</i>. 2019;363(6431):1059-1064. doi:<a href="https://doi.org/10.1126/science.aav1910">10.1126/science.aav1910</a>
  apa: Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T.,
    … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. <i>Science</i>.
    American Association for the Advancement of Science (AAAS). <a href="https://doi.org/10.1126/science.aav1910">https://doi.org/10.1126/science.aav1910</a>
  chicago: Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe,
    T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity
    in Twisted Bilayer Graphene.” <i>Science</i>. American Association for the Advancement
    of Science (AAAS), 2019. <a href="https://doi.org/10.1126/science.aav1910">https://doi.org/10.1126/science.aav1910</a>.
  ieee: M. Yankowitz <i>et al.</i>, “Tuning superconductivity in twisted bilayer graphene,”
    <i>Science</i>, vol. 363, no. 6431. American Association for the Advancement of
    Science (AAAS), pp. 1059–1064, 2019.
  ista: Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D,
    Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene.
    Science. 363(6431), 1059–1064.
  mla: Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.”
    <i>Science</i>, vol. 363, no. 6431, American Association for the Advancement of
    Science (AAAS), 2019, pp. 1059–64, doi:<a href="https://doi.org/10.1126/science.aav1910">10.1126/science.aav1910</a>.
  short: M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D.
    Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064.
date_created: 2022-01-14T12:14:58Z
date_published: 2019-01-24T00:00:00Z
date_updated: 2022-01-14T13:48:32Z
day: '24'
doi: 10.1126/science.aav1910
extern: '1'
external_id:
  arxiv:
  - '1808.07865'
  pmid:
  - '30679385 '
intvolume: '       363'
issue: '6431'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1808.07865
month: '01'
oa: 1
oa_version: Preprint
page: 1059-1064
pmid: 1
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
  issn:
  - 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science (AAAS)
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tuning superconductivity in twisted bilayer graphene
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 363
year: '2019'
...
---
_id: '11826'
abstract:
- lang: eng
  text: "The diameter, radius and eccentricities are natural graph parameters. While
    these problems have been studied extensively, there are no known dynamic algorithms
    for them beyond the ones that follow from trivial recomputation after each update
    or from solving dynamic All-Pairs Shortest Paths (APSP), which is very computationally
    intensive. This is the situation for dynamic approximation algorithms as well,
    and even if only edge insertions or edge deletions need to be supported.\r\nThis
    paper provides a comprehensive study of the dynamic approximation of Diameter,
    Radius and Eccentricities, providing both conditional lower bounds, and new algorithms
    whose bounds are optimal under popular hypotheses in fine-grained complexity.
    Some of the highlights include:\r\n- Under popular hardness hypotheses, there
    can be no significantly better fully dynamic approximation algorithms than recomputing
    the answer after each update, or maintaining full APSP.\r\n- Nearly optimal partially
    dynamic (incremental/decremental) algorithms can be achieved via efficient reductions
    to (incremental/decremental) maintenance of Single-Source Shortest Paths. For
    instance, a nearly (3/2+epsilon)-approximation to Diameter in directed or undirected
    n-vertex, m-edge graphs can be maintained decrementally in total time m^{1+o(1)}sqrt{n}/epsilon^2.
    This nearly matches the static 3/2-approximation algorithm for the problem that
    is known to be conditionally optimal."
alternative_title:
- LIPIcs
article_number: '13'
article_processing_charge: No
arxiv: 1
author:
- first_name: Bertie
  full_name: Ancona, Bertie
  last_name: Ancona
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Liam
  full_name: Roditty, Liam
  last_name: Roditty
- first_name: Virginia Vassilevska
  full_name: Williams, Virginia Vassilevska
  last_name: Williams
- first_name: Nicole
  full_name: Wein, Nicole
  last_name: Wein
citation:
  ama: 'Ancona B, Henzinger MH, Roditty L, Williams VV, Wein N. Algorithms and hardness
    for diameter in dynamic graphs. In: <i>46th International Colloquium on Automata,
    Languages, and Programming</i>. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für
    Informatik; 2019. doi:<a href="https://doi.org/10.4230/LIPICS.ICALP.2019.13">10.4230/LIPICS.ICALP.2019.13</a>'
  apa: 'Ancona, B., Henzinger, M. H., Roditty, L., Williams, V. V., &#38; Wein, N.
    (2019). Algorithms and hardness for diameter in dynamic graphs. In <i>46th International
    Colloquium on Automata, Languages, and Programming</i> (Vol. 132). Patras, Greece:
    Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href="https://doi.org/10.4230/LIPICS.ICALP.2019.13">https://doi.org/10.4230/LIPICS.ICALP.2019.13</a>'
  chicago: Ancona, Bertie, Monika H Henzinger, Liam Roditty, Virginia Vassilevska
    Williams, and Nicole Wein. “Algorithms and Hardness for Diameter in Dynamic Graphs.”
    In <i>46th International Colloquium on Automata, Languages, and Programming</i>,
    Vol. 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href="https://doi.org/10.4230/LIPICS.ICALP.2019.13">https://doi.org/10.4230/LIPICS.ICALP.2019.13</a>.
  ieee: B. Ancona, M. H. Henzinger, L. Roditty, V. V. Williams, and N. Wein, “Algorithms
    and hardness for diameter in dynamic graphs,” in <i>46th International Colloquium
    on Automata, Languages, and Programming</i>, Patras, Greece, 2019, vol. 132.
  ista: 'Ancona B, Henzinger MH, Roditty L, Williams VV, Wein N. 2019. Algorithms
    and hardness for diameter in dynamic graphs. 46th International Colloquium on
    Automata, Languages, and Programming. ICALP: International Colloquium on Automata,
    Languages, and Programming, LIPIcs, vol. 132, 13.'
  mla: Ancona, Bertie, et al. “Algorithms and Hardness for Diameter in Dynamic Graphs.”
    <i>46th International Colloquium on Automata, Languages, and Programming</i>,
    vol. 132, 13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a
    href="https://doi.org/10.4230/LIPICS.ICALP.2019.13">10.4230/LIPICS.ICALP.2019.13</a>.
  short: B. Ancona, M.H. Henzinger, L. Roditty, V.V. Williams, N. Wein, in:, 46th
    International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl
    - Leibniz-Zentrum für Informatik, 2019.
conference:
  end_date: 2019-07-12
  location: Patras, Greece
  name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
  start_date: 2019-07-09
date_created: 2022-08-12T08:14:51Z
date_published: 2019-07-04T00:00:00Z
date_updated: 2023-02-16T10:48:24Z
day: '04'
doi: 10.4230/LIPICS.ICALP.2019.13
extern: '1'
external_id:
  arxiv:
  - '811.12527'
intvolume: '       132'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.4230/LIPIcs.ICALP.2019.13
month: '07'
oa: 1
oa_version: Published Version
publication: 46th International Colloquium on Automata, Languages, and Programming
publication_identifier:
  isbn:
  - 978-3-95977-109-2
  issn:
  - 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithms and hardness for diameter in dynamic graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2019'
...
---
_id: '11847'
abstract:
- lang: eng
  text: This paper serves as a user guide to the Vienna graph clustering framework.
    We review our general memetic algorithm, VieClus, to tackle the graph clustering
    problem. A key component of our contribution are natural recombine operators that
    employ ensemble clusterings as well as multi-level techniques. Lastly, we combine
    these techniques with a scalable communication protocol, producing a system that
    is able to compute high-quality solutions in a short amount of time. After giving
    a description of the algorithms employed, we establish the connection of the graph
    clustering problem to protein–protein interaction networks and moreover give a
    description on how the software can be used, what file formats are expected, and
    how this can be used to find functional groups in protein–protein interaction
    networks.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Sonja
  full_name: Biedermann, Sonja
  last_name: Biedermann
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Christian
  full_name: Schulz, Christian
  last_name: Schulz
- first_name: Bernhard
  full_name: Schuster, Bernhard
  last_name: Schuster
citation:
  ama: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. Vienna Graph Clustering.
    In: Canzar S, Rojas Ringeling F, eds. <i>Protein-Protein Interaction Networks</i>.
    Vol 2074. MIMB. Springer Nature; 2019:215–231. doi:<a href="https://doi.org/10.1007/978-1-4939-9873-9_16">10.1007/978-1-4939-9873-9_16</a>'
  apa: Biedermann, S., Henzinger, M. H., Schulz, C., &#38; Schuster, B. (2019). Vienna
    Graph Clustering. In S. Canzar &#38; F. Rojas Ringeling (Eds.), <i>Protein-Protein
    Interaction Networks</i> (Vol. 2074, pp. 215–231). Springer Nature. <a href="https://doi.org/10.1007/978-1-4939-9873-9_16">https://doi.org/10.1007/978-1-4939-9873-9_16</a>
  chicago: Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster.
    “Vienna Graph Clustering.” In <i>Protein-Protein Interaction Networks</i>, edited
    by Stefan Canzar and Francisca Rojas Ringeling, 2074:215–231. MIMB. Springer Nature,
    2019. <a href="https://doi.org/10.1007/978-1-4939-9873-9_16">https://doi.org/10.1007/978-1-4939-9873-9_16</a>.
  ieee: S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Vienna Graph
    Clustering,” in <i>Protein-Protein Interaction Networks</i>, vol. 2074, S. Canzar
    and F. Rojas Ringeling, Eds. Springer Nature, 2019, pp. 215–231.
  ista: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. 2019.Vienna Graph Clustering.
    In: Protein-Protein Interaction Networks. Methods in Molecular Biology, vol. 2074,
    215–231.'
  mla: Biedermann, Sonja, et al. “Vienna Graph Clustering.” <i>Protein-Protein Interaction
    Networks</i>, edited by Stefan Canzar and Francisca Rojas Ringeling, vol. 2074,
    Springer Nature, 2019, pp. 215–231, doi:<a href="https://doi.org/10.1007/978-1-4939-9873-9_16">10.1007/978-1-4939-9873-9_16</a>.
  short: S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, S. Canzar, F.
    Rojas Ringeling (Eds.), Protein-Protein Interaction Networks, Springer Nature,
    2019, pp. 215–231.
date_created: 2022-08-16T06:54:48Z
date_published: 2019-10-04T00:00:00Z
date_updated: 2023-02-17T09:34:26Z
day: '04'
doi: 10.1007/978-1-4939-9873-9_16
editor:
- first_name: Stefan
  full_name: Canzar, Stefan
  last_name: Canzar
- first_name: Francisca
  full_name: Rojas Ringeling, Francisca
  last_name: Rojas Ringeling
extern: '1'
external_id:
  pmid:
  - '31583641'
intvolume: '      2074'
language:
- iso: eng
month: '10'
oa_version: None
page: 215–231
pmid: 1
publication: Protein-Protein Interaction Networks
publication_identifier:
  eisbn:
  - '9781493998739'
  eissn:
  - 1940-6029
  isbn:
  - '9781493998722'
  issn:
  - 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Vienna Graph Clustering
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2074
year: '2019'
...
---
_id: '11850'
abstract:
- lang: eng
  text: 'Modern networked systems are increasingly reconfigurable, enabling demand-aware
    infrastructures whose resources can be adjusted according to the workload they
    currently serve. Such dynamic adjustments can be exploited to improve network
    utilization and hence performance, by moving frequently interacting communication
    partners closer, e.g., collocating them in the same server or datacenter. However,
    dynamically changing the embedding of workloads is algorithmically challenging:
    communication patterns are often not known ahead of time, but must be learned.
    During the learning process, overheads related to unnecessary moves (i.e., re-embeddings)
    should be minimized. This paper studies a fundamental model which captures the
    tradeoff between the benefits and costs of dynamically collocating communication
    partners on l servers, in an online manner. Our main contribution is a distributed
    online algorithm which is asymptotically almost optimal, i.e., almost matches
    the lower bound (also derived in this paper) on the competitive ratio of any (distributed
    or centralized) online algorithm.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Stefan
  full_name: Neumann, Stefan
  last_name: Neumann
- first_name: Stefan
  full_name: Schmid, Stefan
  last_name: Schmid
citation:
  ama: 'Henzinger MH, Neumann S, Schmid S. Efficient distributed workload (re-)embedding.
    In: <i>SIGMETRICS’19: International Conference on Measurement and Modeling of
    Computer Systems</i>. Association for Computing Machinery; 2019:43–44. doi:<a
    href="https://doi.org/10.1145/3309697.3331503">10.1145/3309697.3331503</a>'
  apa: 'Henzinger, M. H., Neumann, S., &#38; Schmid, S. (2019). Efficient distributed
    workload (re-)embedding. In <i>SIGMETRICS’19: International Conference on Measurement
    and Modeling of Computer Systems</i> (pp. 43–44). Phoenix, AZ, United States:
    Association for Computing Machinery. <a href="https://doi.org/10.1145/3309697.3331503">https://doi.org/10.1145/3309697.3331503</a>'
  chicago: 'Henzinger, Monika H, Stefan Neumann, and Stefan Schmid. “Efficient Distributed
    Workload (Re-)Embedding.” In <i>SIGMETRICS’19: International Conference on Measurement
    and Modeling of Computer Systems</i>, 43–44. Association for Computing Machinery,
    2019. <a href="https://doi.org/10.1145/3309697.3331503">https://doi.org/10.1145/3309697.3331503</a>.'
  ieee: 'M. H. Henzinger, S. Neumann, and S. Schmid, “Efficient distributed workload
    (re-)embedding,” in <i>SIGMETRICS’19: International Conference on Measurement
    and Modeling of Computer Systems</i>, Phoenix, AZ, United States, 2019, pp. 43–44.'
  ista: 'Henzinger MH, Neumann S, Schmid S. 2019. Efficient distributed workload (re-)embedding.
    SIGMETRICS’19: International Conference on Measurement and Modeling of Computer
    Systems. SIGMETRICS: International Conference on Measurement and Modeling of Computer
    Systems, 43–44.'
  mla: 'Henzinger, Monika H., et al. “Efficient Distributed Workload (Re-)Embedding.”
    <i>SIGMETRICS’19: International Conference on Measurement and Modeling of Computer
    Systems</i>, Association for Computing Machinery, 2019, pp. 43–44, doi:<a href="https://doi.org/10.1145/3309697.3331503">10.1145/3309697.3331503</a>.'
  short: 'M.H. Henzinger, S. Neumann, S. Schmid, in:, SIGMETRICS’19: International
    Conference on Measurement and Modeling of Computer Systems, Association for Computing
    Machinery, 2019, pp. 43–44.'
conference:
  end_date: 2019-06-28
  location: Phoenix, AZ, United States
  name: 'SIGMETRICS: International Conference on Measurement and Modeling of Computer
    Systems'
  start_date: 2019-06-24
date_created: 2022-08-16T07:14:57Z
date_published: 2019-06-20T00:00:00Z
date_updated: 2023-02-17T09:41:45Z
day: '20'
doi: 10.1145/3309697.3331503
extern: '1'
external_id:
  arxiv:
  - '1904.05474'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1904.05474
month: '06'
oa: 1
oa_version: Preprint
page: 43–44
publication: 'SIGMETRICS''19: International Conference on Measurement and Modeling
  of Computer Systems'
publication_identifier:
  isbn:
  - 978-1-4503-6678-6
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient distributed workload (re-)embedding
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '11851'
abstract:
- lang: eng
  text: The minimum cut problem for an undirected edge-weighted graph asks us to divide
    its set of nodes into two blocks while minimizing the weighted sum of the cut
    edges. In this paper, we engineer the fastest known exact algorithm for the problem.
    State-of-the-art algorithms like the algorithm of Padberg and Rinaldi or the algorithm
    of Nagamochi, Ono and Ibaraki identify edges that can be contracted to reduce
    the graph size such that at least one minimum cut is maintained in the contracted
    graph. Our algorithm achieves improvements in running time over these algorithms
    by a multitude of techniques. First, we use a recently developed fast and parallel
    inexact minimum cut algorithm to obtain a better bound for the problem. Afterwards,
    we use reductions that depend on this bound to reduce the size of the graph much
    faster than previously possible. We use improved data structures to further lower
    the running time of our algorithm. Additionally, we parallelize the contraction
    routines of Nagamochi et al. . Overall, we arrive at a system that significantly
    outperforms the fastest state-of-the-art solvers for the exact minimum cut problem.
article_number: '8820968'
article_processing_charge: No
arxiv: 1
author:
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Alexander
  full_name: Noe, Alexander
  last_name: Noe
- first_name: Christian
  full_name: Schulz, Christian
  last_name: Schulz
citation:
  ama: 'Henzinger MH, Noe A, Schulz C. Shared-memory exact minimum cuts. In: <i>33rd
    International Parallel and Distributed Processing Symposium</i>. Institute of
    Electrical and Electronics Engineers; 2019. doi:<a href="https://doi.org/10.1109/ipdps.2019.00013">10.1109/ipdps.2019.00013</a>'
  apa: 'Henzinger, M. H., Noe, A., &#38; Schulz, C. (2019). Shared-memory exact minimum
    cuts. In <i>33rd International Parallel and Distributed Processing Symposium</i>.
    Rio de Janeiro, Brazil: Institute of Electrical and Electronics Engineers. <a
    href="https://doi.org/10.1109/ipdps.2019.00013">https://doi.org/10.1109/ipdps.2019.00013</a>'
  chicago: Henzinger, Monika H, Alexander Noe, and Christian Schulz. “Shared-Memory
    Exact Minimum Cuts.” In <i>33rd International Parallel and Distributed Processing
    Symposium</i>. Institute of Electrical and Electronics Engineers, 2019. <a href="https://doi.org/10.1109/ipdps.2019.00013">https://doi.org/10.1109/ipdps.2019.00013</a>.
  ieee: M. H. Henzinger, A. Noe, and C. Schulz, “Shared-memory exact minimum cuts,”
    in <i>33rd International Parallel and Distributed Processing Symposium</i>, Rio
    de Janeiro, Brazil, 2019.
  ista: 'Henzinger MH, Noe A, Schulz C. 2019. Shared-memory exact minimum cuts. 33rd
    International Parallel and Distributed Processing Symposium. IPDPS: International
    Parallel and Distributed Processing Symposium, 8820968.'
  mla: Henzinger, Monika H., et al. “Shared-Memory Exact Minimum Cuts.” <i>33rd International
    Parallel and Distributed Processing Symposium</i>, 8820968, Institute of Electrical
    and Electronics Engineers, 2019, doi:<a href="https://doi.org/10.1109/ipdps.2019.00013">10.1109/ipdps.2019.00013</a>.
  short: M.H. Henzinger, A. Noe, C. Schulz, in:, 33rd International Parallel and Distributed
    Processing Symposium, Institute of Electrical and Electronics Engineers, 2019.
conference:
  end_date: 2019-05-24
  location: Rio de Janeiro, Brazil
  name: 'IPDPS: International Parallel and Distributed Processing Symposium'
  start_date: 2019-05-20
date_created: 2022-08-16T07:25:23Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-02-21T16:30:34Z
day: '01'
doi: 10.1109/ipdps.2019.00013
extern: '1'
external_id:
  arxiv:
  - '1808.05458'
language:
- iso: eng
main_file_link:
- url: https://arxiv.org/abs/1808.05458
month: '05'
oa_version: Preprint
publication: 33rd International Parallel and Distributed Processing Symposium
publication_identifier:
  eisbn:
  - 978-1-7281-1246-6
  eissn:
  - 1530-2075
  isbn:
  - 978-1-7281-1247-3
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
related_material:
  record:
  - id: '11851'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: Shared-memory exact minimum cuts
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '11853'
abstract:
- lang: eng
  text: We present a deterministic dynamic algorithm for maintaining a (1+ε)f-approximate
    minimum cost set cover with O(f log(Cn)/ε^2) amortized update time, when the input
    set system is undergoing element insertions and deletions. Here, n denotes the
    number of elements, each element appears in at most f sets, and the cost of each
    set lies in the range [1/C, 1]. Our result, together with that of Gupta~et~al.~[STOC'17],
    implies that there is a deterministic algorithm for this problem with O(f log(Cn))
    amortized update time and O(min(log n, f)) -approximation ratio, which nearly
    matches the polynomial-time hardness of approximation for minimum set cover in
    the static setting. Our update time is only O(log (Cn)) away from a trivial lower
    bound. Prior to our work, the previous best approximation ratio guaranteed by
    deterministic algorithms was O(f^2), which was due to Bhattacharya~et~al.~[ICALP`15].
    In contrast, the only result that guaranteed O(f) -approximation was obtained
    very recently by Abboud~et~al.~[STOC`19], who designed a dynamic algorithm with
    (1+ε)f-approximation ratio and O(f^2 log n/ε) amortized update time. Besides the
    extra O(f) factor in the update time compared to our and Gupta~et~al.'s results,
    the Abboud~et~al.~algorithm is randomized, and works only when the adversary is
    oblivious and the sets are unweighted (each set has the same cost). We achieve
    our result via the primal-dual approach, by maintaining a fractional packing solution
    as a dual certificate. This approach was pursued previously by Bhattacharya~et~al.~and
    Gupta~et~al., but not in the recent paper by Abboud~et~al. Unlike previous primal-dual
    algorithms that try to satisfy some local constraints for individual sets at all
    time, our algorithm basically waits until the dual solution changes significantly
    globally, and fixes the solution only where the fix is needed.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sayan
  full_name: Bhattacharya, Sayan
  last_name: Bhattacharya
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Danupon
  full_name: Nanongkai, Danupon
  last_name: Nanongkai
citation:
  ama: 'Bhattacharya S, Henzinger MH, Nanongkai D. A new deterministic algorithm for
    dynamic set cover. In: <i>60th Annual Symposium on Foundations of Computer Science</i>.
    Institute of Electrical and Electronics Engineers; 2019:406-423. doi:<a href="https://doi.org/10.1109/focs.2019.00033">10.1109/focs.2019.00033</a>'
  apa: 'Bhattacharya, S., Henzinger, M. H., &#38; Nanongkai, D. (2019). A new deterministic
    algorithm for dynamic set cover. In <i>60th Annual Symposium on Foundations of
    Computer Science</i> (pp. 406–423). Baltimore, MD, United States: Institute of
    Electrical and Electronics Engineers. <a href="https://doi.org/10.1109/focs.2019.00033">https://doi.org/10.1109/focs.2019.00033</a>'
  chicago: Bhattacharya, Sayan, Monika H Henzinger, and Danupon Nanongkai. “A New
    Deterministic Algorithm for Dynamic Set Cover.” In <i>60th Annual Symposium on
    Foundations of Computer Science</i>, 406–23. Institute of Electrical and Electronics
    Engineers, 2019. <a href="https://doi.org/10.1109/focs.2019.00033">https://doi.org/10.1109/focs.2019.00033</a>.
  ieee: S. Bhattacharya, M. H. Henzinger, and D. Nanongkai, “A new deterministic algorithm
    for dynamic set cover,” in <i>60th Annual Symposium on Foundations of Computer
    Science</i>, Baltimore, MD, United States, 2019, pp. 406–423.
  ista: 'Bhattacharya S, Henzinger MH, Nanongkai D. 2019. A new deterministic algorithm
    for dynamic set cover. 60th Annual Symposium on Foundations of Computer Science.
    FOCS: Annual Symposium on Foundations of Computer Science, 406–423.'
  mla: Bhattacharya, Sayan, et al. “A New Deterministic Algorithm for Dynamic Set
    Cover.” <i>60th Annual Symposium on Foundations of Computer Science</i>, Institute
    of Electrical and Electronics Engineers, 2019, pp. 406–23, doi:<a href="https://doi.org/10.1109/focs.2019.00033">10.1109/focs.2019.00033</a>.
  short: S. Bhattacharya, M.H. Henzinger, D. Nanongkai, in:, 60th Annual Symposium
    on Foundations of Computer Science, Institute of Electrical and Electronics Engineers,
    2019, pp. 406–423.
conference:
  end_date: 2019-11-12
  location: Baltimore, MD, United States
  name: 'FOCS: Annual Symposium on Foundations of Computer Science'
  start_date: 2019-11-09
date_created: 2022-08-16T08:00:00Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-02-17T09:50:37Z
day: '01'
doi: 10.1109/focs.2019.00033
extern: '1'
external_id:
  arxiv:
  - '1909.11600'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1909.11600
month: '11'
oa: 1
oa_version: Preprint
page: 406-423
publication: 60th Annual Symposium on Foundations of Computer Science
publication_identifier:
  eisbn:
  - 978-1-7281-4952-3
  isbn:
  - 978-1-7281-4953-0
  issn:
  - 2575-8454
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new deterministic algorithm for dynamic set cover
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '11865'
abstract:
- lang: eng
  text: We present the first sublinear-time algorithm that can compute the edge connectivity
    λ of a network exactly on distributed message-passing networks (the CONGEST model),
    as long as the network contains no multi-edge. We present the first sublinear-time
    algorithm for a distributed message-passing network sto compute its edge connectivity
    λ exactly in the CONGEST model, as long as there are no parallel edges. Our algorithm
    takes Õ(n1−1/353D1/353+n1−1/706) time to compute λ and a cut of cardinality λ
    with high probability, where n and D are the number of nodes and the diameter
    of the network, respectively, and Õ hides polylogarithmic factors. This running
    time is sublinear in n (i.e. Õ(n1−є)) whenever D is. Previous sublinear-time distributed
    algorithms can solve this problem either (i) exactly only when λ=O(n1/8−є) [Thurimella
    PODC’95; Pritchard, Thurimella, ACM Trans. Algorithms’11; Nanongkai, Su, DISC’14]
    or (ii) approximately [Ghaffari, Kuhn, DISC’13; Nanongkai, Su, DISC’14]. To achieve
    this we develop and combine several new techniques. First, we design the first
    distributed algorithm that can compute a k-edge connectivity certificate for any
    k=O(n1−є) in time Õ(√nk+D). The previous sublinear-time algorithm can do so only
    when k=o(√n) [Thurimella PODC’95]. In fact, our algorithm can be turned into the
    first parallel algorithm with polylogarithmic depth and near-linear work. Previous
    near-linear work algorithms are essentially sequential and previous polylogarithmic-depth
    algorithms require Ω(mk) work in the worst case (e.g. [Karger, Motwani, STOC’93]).
    Second, we show that by combining the recent distributed expander decomposition
    technique of [Chang, Pettie, Zhang, SODA’19] with techniques from the sequential
    deterministic edge connectivity algorithm of [Kawarabayashi, Thorup, STOC’15],
    we can decompose the network into a sublinear number of clusters with small average
    diameter and without any mincut separating a cluster (except the “trivial” ones).
    This leads to a simplification of the Kawarabayashi-Thorup framework (except that
    we are randomized while they are deterministic). This might make this framework
    more useful in other models of computation. Finally, by extending the tree packing
    technique from [Karger STOC’96], we can find the minimum cut in time proportional
    to the number of components. As a byproduct of this technique, we obtain an Õ(n)-time
    algorithm for computing exact minimum cut for weighted graphs.
article_processing_charge: No
arxiv: 1
author:
- first_name: Mohit
  full_name: Daga, Mohit
  last_name: Daga
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Danupon
  full_name: Nanongkai, Danupon
  last_name: Nanongkai
- first_name: Thatchaphol
  full_name: Saranurak, Thatchaphol
  last_name: Saranurak
citation:
  ama: 'Daga M, Henzinger MH, Nanongkai D, Saranurak T. Distributed edge connectivity
    in sublinear time. In: <i>Proceedings of the 51st Annual ACM SIGACT Symposium
    on Theory of Computing</i>. Association for Computing Machinery; 2019:343–354.
    doi:<a href="https://doi.org/10.1145/3313276.3316346">10.1145/3313276.3316346</a>'
  apa: 'Daga, M., Henzinger, M. H., Nanongkai, D., &#38; Saranurak, T. (2019). Distributed
    edge connectivity in sublinear time. In <i>Proceedings of the 51st Annual ACM
    SIGACT Symposium on Theory of Computing</i> (pp. 343–354). Phoenix, AZ, United
    States: Association for Computing Machinery. <a href="https://doi.org/10.1145/3313276.3316346">https://doi.org/10.1145/3313276.3316346</a>'
  chicago: Daga, Mohit, Monika H Henzinger, Danupon Nanongkai, and Thatchaphol Saranurak.
    “Distributed Edge Connectivity in Sublinear Time.” In <i>Proceedings of the 51st
    Annual ACM SIGACT Symposium on Theory of Computing</i>, 343–354. Association for
    Computing Machinery, 2019. <a href="https://doi.org/10.1145/3313276.3316346">https://doi.org/10.1145/3313276.3316346</a>.
  ieee: M. Daga, M. H. Henzinger, D. Nanongkai, and T. Saranurak, “Distributed edge
    connectivity in sublinear time,” in <i>Proceedings of the 51st Annual ACM SIGACT
    Symposium on Theory of Computing</i>, Phoenix, AZ, United States, 2019, pp. 343–354.
  ista: 'Daga M, Henzinger MH, Nanongkai D, Saranurak T. 2019. Distributed edge connectivity
    in sublinear time. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
    of Computing. STOC: Symposium on Theory of Computing, 343–354.'
  mla: Daga, Mohit, et al. “Distributed Edge Connectivity in Sublinear Time.” <i>Proceedings
    of the 51st Annual ACM SIGACT Symposium on Theory of Computing</i>, Association
    for Computing Machinery, 2019, pp. 343–354, doi:<a href="https://doi.org/10.1145/3313276.3316346">10.1145/3313276.3316346</a>.
  short: M. Daga, M.H. Henzinger, D. Nanongkai, T. Saranurak, in:, Proceedings of
    the 51st Annual ACM SIGACT Symposium on Theory of Computing, Association for Computing
    Machinery, 2019, pp. 343–354.
conference:
  end_date: 2019-06-26
  location: Phoenix, AZ, United States
  name: 'STOC: Symposium on Theory of Computing'
  start_date: 2019-06-23
date_created: 2022-08-16T09:11:17Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-02-17T10:26:25Z
day: '01'
doi: 10.1145/3313276.3316346
extern: '1'
external_id:
  arxiv:
  - '1904.04341'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1904.04341
month: '06'
oa: 1
oa_version: Preprint
page: 343–354
publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
  isbn:
  - 978-1-4503-6705-9
  issn:
  - 0737-8017
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distributed edge connectivity in sublinear time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '11871'
abstract:
- lang: eng
  text: "Many dynamic graph algorithms have an amortized update time, rather than
    a stronger worst-case guarantee. But amortized data structures are not suitable
    for real-time systems, where each individual operation has to be executed quickly.
    For this reason, there exist many recent randomized results that aim to provide
    a guarantee stronger than amortized expected. The strongest possible guarantee
    for a randomized algorithm is that it is always correct (Las Vegas), and has high-probability
    worst-case update time, which gives a bound on the time for each individual operation
    that holds with high probability.\r\n\r\nIn this paper we present the first polylogarithmic
    high-probability worst-case time bounds for the dynamic spanner and the dynamic
    maximal matching problem.\r\n\r\n1.\t\r\nFor dynamic spanner, the only known o(n)
    worst-case bounds were O(n3/4) high-probability worst-case update time for maintaining
    a 3-spanner, and O(n5/9) for maintaining a 5-spanner. We give a O(1)k log3(n)
    high-probability worst-case time bound for maintaining a (2k – 1)-spanner, which
    yields the first worst-case polylog update time for all constant k. (All the results
    above maintain the optimal tradeoff of stretch 2k – 1 and Õ(n1+1/k) edges.)\r\n\r\n2.\t\r\nFor
    dynamic maximal matching, or dynamic 2-approximate maximum matching, no algorithm
    with o(n) worst-case time bound was known and we present an algorithm with O(log5
    (n)) high-probability worst-case time; similar worst-case bounds existed only
    for maintaining a matching that was (2 + ∊)-approximate, and hence not maximal.\r\n\r\nOur
    results are achieved using a new approach for converting amortized guarantees
    to worst-case ones for randomized data structures by going through a third type
    of guarantee, which is a middle ground between the two above: an algorithm is
    said to have worst-case expected update time α if for every update σ, the expected
    time to process σ is at most α. Although stronger than amortized expected, the
    worst-case expected guarantee does not resolve the fundamental problem of amortization:
    a worst-case expected update time of O(1) still allows for the possibility that
    every 1/f(n) updates requires Θ(f(n)) time to process, for arbitrarily high f(n).
    In this paper we present a black-box reduction that converts any data structure
    with worst-case expected update time into one with a high-probability worst-case
    update time: the query time remains the same, while the update time increases
    by a factor of O(log2(n)).\r\n\r\nThus we achieve our results in two steps: (1)
    First we show how to convert existing dynamic graph algorithms with amortized
    expected polylogarithmic running times into algorithms with worst-case expected
    polylogarithmic running times. (2) Then we use our black-box reduction to achieve
    the polylogarithmic high-probability worst-case time bound. All our algorithms
    are Las-Vegas-type algorithms."
article_processing_charge: No
arxiv: 1
author:
- first_name: Aaron
  full_name: Bernstein, Aaron
  last_name: Bernstein
- first_name: Sebastian
  full_name: Forster, Sebastian
  last_name: Forster
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  ama: 'Bernstein A, Forster S, Henzinger MH. A deamortization approach for dynamic
    spanner and dynamic maximal matching. In: <i>30th Annual ACM-SIAM Symposium on
    Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2019:1899-1918.
    doi:<a href="https://doi.org/10.1137/1.9781611975482.115">10.1137/1.9781611975482.115</a>'
  apa: 'Bernstein, A., Forster, S., &#38; Henzinger, M. H. (2019). A deamortization
    approach for dynamic spanner and dynamic maximal matching. In <i>30th Annual ACM-SIAM
    Symposium on Discrete Algorithms</i> (pp. 1899–1918). San Diego, CA, United States:
    Society for Industrial and Applied Mathematics. <a href="https://doi.org/10.1137/1.9781611975482.115">https://doi.org/10.1137/1.9781611975482.115</a>'
  chicago: Bernstein, Aaron, Sebastian Forster, and Monika H Henzinger. “A Deamortization
    Approach for Dynamic Spanner and Dynamic Maximal Matching.” In <i>30th Annual
    ACM-SIAM Symposium on Discrete Algorithms</i>, 1899–1918. Society for Industrial
    and Applied Mathematics, 2019. <a href="https://doi.org/10.1137/1.9781611975482.115">https://doi.org/10.1137/1.9781611975482.115</a>.
  ieee: A. Bernstein, S. Forster, and M. H. Henzinger, “A deamortization approach
    for dynamic spanner and dynamic maximal matching,” in <i>30th Annual ACM-SIAM
    Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2019, pp.
    1899–1918.
  ista: 'Bernstein A, Forster S, Henzinger MH. 2019. A deamortization approach for
    dynamic spanner and dynamic maximal matching. 30th Annual ACM-SIAM Symposium on
    Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1899–1918.'
  mla: Bernstein, Aaron, et al. “A Deamortization Approach for Dynamic Spanner and
    Dynamic Maximal Matching.” <i>30th Annual ACM-SIAM Symposium on Discrete Algorithms</i>,
    Society for Industrial and Applied Mathematics, 2019, pp. 1899–918, doi:<a href="https://doi.org/10.1137/1.9781611975482.115">10.1137/1.9781611975482.115</a>.
  short: A. Bernstein, S. Forster, M.H. Henzinger, in:, 30th Annual ACM-SIAM Symposium
    on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2019,
    pp. 1899–1918.
conference:
  end_date: 2019-01-09
  location: San Diego, CA, United States
  name: 'SODA: Symposium on Discrete Algorithms'
  start_date: 2019-01-06
date_created: 2022-08-16T09:50:33Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2023-02-21T16:31:21Z
day: '01'
doi: 10.1137/1.9781611975482.115
extern: '1'
external_id:
  arxiv:
  - '1810.10932'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1810.10932
month: '01'
oa: 1
oa_version: Preprint
page: 1899-1918
publication: 30th Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
  eisbn:
  - 978-1-61197-548-2
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
  record:
  - id: '11871'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: A deamortization approach for dynamic spanner and dynamic maximal matching
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
