---
_id: '1496'
abstract:
- lang: eng
  text: The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is
    theoretically investigated within a fully relativistic framework and a second-order
    perturbation theory. We focus our analysis on how electron correlation, as well
    as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For
    this purpose, we include the electronic correlation via an effective local potential
    and within a single configuration-state model. Due to its experimental interest,
    evaluations of decay rates are performed for berylliumlike xenon and uranium.
    We find that the negative-energy contribution can be neglected at the present
    level of accuracy in the evaluation of the decay rate. On the other hand, if contributions
    of electronic correlation are not carefully taken into account, it may change
    the lifetime of the metastable state by up to 20%. By performing a full-relativistic
    jj-coupling calculation, we found a decrease of the decay rate by two orders of
    magnitude compared to non-relativistic LS-coupling calculations, for the selected
    heavy ions.
acknowledgement: 'This  research  was  supported  in  part  by  FCT, Portugal, through
  Project No. PTDC/FIS/117606/2010, financed by the European Community  Fund  FEDER  through  the  COMPETE. '
article_number: '032502'
article_processing_charge: No
arxiv: 1
author:
- first_name: Pedro
  full_name: Amaro, Pedro
  last_name: Amaro
- first_name: Filippo
  full_name: Fratini, Filippo
  last_name: Fratini
- first_name: Laleh
  full_name: Safari, Laleh
  id: 3C325E5E-F248-11E8-B48F-1D18A9856A87
  last_name: Safari
- first_name: Jorge
  full_name: Machado, Jorge
  last_name: Machado
- first_name: Mauro
  full_name: Guerra, Mauro
  last_name: Guerra
- first_name: Paul
  full_name: Indelicato, Paul
  last_name: Indelicato
- first_name: José
  full_name: Santos, José
  last_name: Santos
citation:
  ama: Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon
    decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
    model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;93(3).
    doi:<a href="https://doi.org/10.1103/PhysRevA.93.032502">10.1103/PhysRevA.93.032502</a>
  apa: Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P.,
    &#38; Santos, J. (2016). Relativistic evaluation of the two-photon decay of the
    metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
    model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American
    Physical Society. <a href="https://doi.org/10.1103/PhysRevA.93.032502">https://doi.org/10.1103/PhysRevA.93.032502</a>
  chicago: Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra,
    Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay
    of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential
    Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American
    Physical Society, 2016. <a href="https://doi.org/10.1103/PhysRevA.93.032502">https://doi.org/10.1103/PhysRevA.93.032502</a>.
  ieee: P. Amaro <i>et al.</i>, “Relativistic evaluation of the two-photon decay of
    the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential
    model,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol.
    93, no. 3. American Physical Society, 2016.
  ista: Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J.
    2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0
    state in berylliumlike ions with an effective-potential model. Physical Review
    A - Atomic, Molecular, and Optical Physics. 93(3), 032502.
  mla: Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the
    Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential
    Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol.
    93, no. 3, 032502, American Physical Society, 2016, doi:<a href="https://doi.org/10.1103/PhysRevA.93.032502">10.1103/PhysRevA.93.032502</a>.
  short: P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J.
    Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).
date_created: 2018-12-11T11:52:21Z
date_published: 2016-03-07T00:00:00Z
date_updated: 2025-09-18T11:10:38Z
day: '07'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.93.032502
ec_funded: 1
external_id:
  arxiv:
  - '1508.06169'
  isi:
  - '000371724100008'
intvolume: '        93'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1508.06169
month: '03'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5683'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0
  state in berylliumlike ions with an effective-potential model
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 93
year: '2016'
...
---
_id: '1518'
abstract:
- lang: eng
  text: The inference of demographic history from genome data is hindered by a lack
    of efficient computational approaches. In particular, it has proved difficult
    to exploit the information contained in the distribution of genealogies across
    the genome. We have previously shown that the generating function (GF) of genealogies
    can be used to analytically compute likelihoods of demographic models from configurations
    of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has
    a simple, recursive form, the size of such likelihood calculations explodes quickly
    with the number of individuals and applications of this framework have so far
    been mainly limited to small samples (pairs and triplets) for which the GF can
    be written by hand. Here we investigate several strategies for exploiting the
    inherent symmetries of the coalescent. In particular, we show that the GF of genealogies
    can be decomposed into a set of equivalence classes that allows likelihood calculations
    from nontrivial samples. Using this strategy, we automated blockwise likelihood
    calculations for a general set of demographic scenarios in Mathematica. These
    histories may involve population size changes, continuous migration, discrete
    divergence, and admixture between multiple populations. To give a concrete example,
    we calculate the likelihood for a model of isolation with migration (IM), assuming
    two diploid samples without phase and outgroup information. We demonstrate the
    new inference scheme with an analysis of two individual butterfly genomes from
    the sister species Heliconius melpomene rosina and H. cydno.
acknowledgement: "We thank Lynsey Bunnefeld for discussions throughout the project
  and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on
  an earlier version of this manuscript. This work was supported by funding from the\r\nUnited
  Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant
  from the European\r\nResearch Council (250152) (to N.H.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Konrad
  full_name: Lohse, Konrad
  last_name: Lohse
- first_name: Martin
  full_name: Chmelik, Martin
  id: 3624234E-F248-11E8-B48F-1D18A9856A87
  last_name: Chmelik
- first_name: Simon
  full_name: Martin, Simon
  last_name: Martin
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
citation:
  ama: Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating
    blockwise likelihoods under the coalescent. <i>Genetics</i>. 2016;202(2):775-786.
    doi:<a href="https://doi.org/10.1534/genetics.115.183814">10.1534/genetics.115.183814</a>
  apa: Lohse, K., Chmelik, M., Martin, S., &#38; Barton, N. H. (2016). Efficient strategies
    for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. Genetics
    Society of America. <a href="https://doi.org/10.1534/genetics.115.183814">https://doi.org/10.1534/genetics.115.183814</a>
  chicago: Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient
    Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>.
    Genetics Society of America, 2016. <a href="https://doi.org/10.1534/genetics.115.183814">https://doi.org/10.1534/genetics.115.183814</a>.
  ieee: K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for
    calculating blockwise likelihoods under the coalescent,” <i>Genetics</i>, vol.
    202, no. 2. Genetics Society of America, pp. 775–786, 2016.
  ista: Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating
    blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.
  mla: Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods
    under the Coalescent.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America,
    2016, pp. 775–86, doi:<a href="https://doi.org/10.1534/genetics.115.183814">10.1534/genetics.115.183814</a>.
  short: K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.
date_created: 2018-12-11T11:52:29Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2025-09-18T11:09:34Z
day: '01'
ddc:
- '570'
department:
- _id: KrCh
- _id: NiBa
doi: 10.1534/genetics.115.183814
ec_funded: 1
external_id:
  isi:
  - '000371304600032'
  pmid:
  - '26715666'
file:
- access_level: open_access
  checksum: 41c9b5d72e7fe4624dd22dfe622337d5
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:16:51Z
  date_updated: 2020-07-14T12:45:00Z
  file_id: '5241'
  file_name: IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf
  file_size: 957466
  relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: '       202'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Preprint
page: 775 - 786
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '250152'
  name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5658'
pubrep_id: '561'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient strategies for calculating blockwise likelihoods under the coalescent
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 202
year: '2016'
...
---
_id: '1521'
abstract:
- lang: eng
  text: Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular
    energy production, coupling electron transfer between NADH and quinone to proton
    translocation. It is the largest protein assembly of respiratory chains and one
    of the most elaborate redox membrane proteins known. Bacterial enzyme is about
    half the size of mitochondrial and thus provides its important &quot;minimal&quot;
    model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative
    diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer
    occurs, and a membrane arm, where proton translocation takes place. We have solved
    the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus,
    the membrane domain from Escherichia coli and recently of the intact, entire complex
    I from T. thermophilus (536. kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane
    helices). The 95. Å long electron transfer pathway through the enzyme proceeds
    from the primary electron acceptor flavin mononucleotide through seven conserved
    Fe-S clusters to the unusual elongated quinone-binding site at the interface with
    the membrane domain. Four putative proton translocation channels are found in
    the membrane domain, all linked by the central flexible axis containing charged
    residues. The redox energy of electron transfer is coupled to proton translocation
    by the as yet undefined mechanism proposed to involve long-range conformational
    changes. This article is part of a Special Issue entitled Respiratory complex
    I, edited by Volker Zickermann and Ulrich Brandt.
acknowledgement: funded by the Medical Research Council (Grant number MC_U105674180)
article_processing_charge: No
author:
- first_name: John
  full_name: Berrisford, John
  last_name: Berrisford
- first_name: Rozbeh
  full_name: Baradaran, Rozbeh
  last_name: Baradaran
- first_name: Leonid A
  full_name: Sazanov, Leonid A
  id: 338D39FE-F248-11E8-B48F-1D18A9856A87
  last_name: Sazanov
  orcid: 0000-0002-0977-7989
citation:
  ama: Berrisford J, Baradaran R, Sazanov LA. Structure of bacterial respiratory complex
    I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2016;1857(7):892-901.
    doi:<a href="https://doi.org/10.1016/j.bbabio.2016.01.012">10.1016/j.bbabio.2016.01.012</a>
  apa: Berrisford, J., Baradaran, R., &#38; Sazanov, L. A. (2016). Structure of bacterial
    respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.bbabio.2016.01.012">https://doi.org/10.1016/j.bbabio.2016.01.012</a>
  chicago: Berrisford, John, Rozbeh Baradaran, and Leonid A Sazanov. “Structure of
    Bacterial Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>.
    Elsevier, 2016. <a href="https://doi.org/10.1016/j.bbabio.2016.01.012">https://doi.org/10.1016/j.bbabio.2016.01.012</a>.
  ieee: J. Berrisford, R. Baradaran, and L. A. Sazanov, “Structure of bacterial respiratory
    complex I,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no.
    7. Elsevier, pp. 892–901, 2016.
  ista: Berrisford J, Baradaran R, Sazanov LA. 2016. Structure of bacterial respiratory
    complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(7), 892–901.
  mla: Berrisford, John, et al. “Structure of Bacterial Respiratory Complex I.” <i>Biochimica
    et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 7, Elsevier, 2016, pp.
    892–901, doi:<a href="https://doi.org/10.1016/j.bbabio.2016.01.012">10.1016/j.bbabio.2016.01.012</a>.
  short: J. Berrisford, R. Baradaran, L.A. Sazanov, Biochimica et Biophysica Acta
    - Bioenergetics 1857 (2016) 892–901.
corr_author: '1'
date_created: 2018-12-11T11:52:30Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2025-09-18T11:08:50Z
day: '01'
department:
- _id: LeSa
doi: 10.1016/j.bbabio.2016.01.012
external_id:
  isi:
  - '000377727500005'
intvolume: '      1857'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 892 - 901
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_status: published
publisher: Elsevier
publist_id: '5654'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of bacterial respiratory complex I
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 1857
year: '2016'
...
---
_id: '1522'
abstract:
- lang: eng
  text: 'We classify smooth Brunnian (i.e., unknotted on both components) embeddings
    (S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to
    an explicitly constructed embedding fk,m,n for some integers k, m, n such that
    m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if
    k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification
    of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2
    × S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show
    that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such
    that the componentwise embedded connected sum f # g is isotopic to f # g′ but
    g is not isotopic to g′.'
acknowledgement: "I thank A. Skopenkov for telling me about the problem and for his
  useful remarks.  I also thank A. Sossinsky,\r\nA. Zhubr, M. Skopenkov, P. Akhmetiev,
  and an anonymous referee for their feedback.  Author was partially\r\nsupported
  by Dobrushin fellowship, 2013, and by RFBR grant 15-01-06302."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Serhii
  full_name: Avvakumov, Serhii
  id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
  last_name: Avvakumov
citation:
  ama: Avvakumov S. The classification of certain linked 3-manifolds in 6-space. <i>Moscow
    Mathematical Journal</i>. 2016;16(1):1-25. doi:<a href="https://doi.org/10.17323/1609-4514-2016-16-1-1-25">10.17323/1609-4514-2016-16-1-1-25</a>
  apa: Avvakumov, S. (2016). The classification of certain linked 3-manifolds in 6-space.
    <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href="https://doi.org/10.17323/1609-4514-2016-16-1-1-25">https://doi.org/10.17323/1609-4514-2016-16-1-1-25</a>
  chicago: Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in
    6-Space.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow,
    2016. <a href="https://doi.org/10.17323/1609-4514-2016-16-1-1-25">https://doi.org/10.17323/1609-4514-2016-16-1-1-25</a>.
  ieee: S. Avvakumov, “The classification of certain linked 3-manifolds in 6-space,”
    <i>Moscow Mathematical Journal</i>, vol. 16, no. 1. Independent University of
    Moscow, pp. 1–25, 2016.
  ista: Avvakumov S. 2016. The classification of certain linked 3-manifolds in 6-space.
    Moscow Mathematical Journal. 16(1), 1–25.
  mla: Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.”
    <i>Moscow Mathematical Journal</i>, vol. 16, no. 1, Independent University of
    Moscow, 2016, pp. 1–25, doi:<a href="https://doi.org/10.17323/1609-4514-2016-16-1-1-25">10.17323/1609-4514-2016-16-1-1-25</a>.
  short: S. Avvakumov, Moscow Mathematical Journal 16 (2016) 1–25.
corr_author: '1'
date_created: 2018-12-11T11:52:30Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2024-10-09T20:56:44Z
day: '01'
department:
- _id: UlWa
doi: 10.17323/1609-4514-2016-16-1-1-25
external_id:
  arxiv:
  - '1408.3918'
intvolume: '        16'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1408.3918
month: '01'
oa: 1
oa_version: Preprint
page: 1 - 25
publication: Moscow Mathematical Journal
publication_identifier:
  eissn:
  - 1609-4514
publication_status: published
publisher: Independent University of Moscow
publist_id: '5652'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The classification of certain linked 3-manifolds in 6-space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2016'
...
---
_id: '1523'
abstract:
- lang: eng
  text: For random graphs, the containment problem considers the probability that
    a binomial random graph G(n, p) contains a given graph as a substructure. When
    asking for the graph as a topological minor, i.e., for a copy of a subdivision
    of the given graph, it is well known that the (sharp) threshold is at p = 1/n.
    We consider a natural analogue of this question for higher-dimensional random
    complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k =
    2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold
    for containing a subdivision of any fixed complete 2-complex. For higher dimensions
    k &gt; 2, we get that p = O(n−1/k) is an upper bound for the threshold probability
    of containing a subdivision of a fixed k-dimensional complex.
acknowledgement: This research was supported by the Swiss National Science Foundation
  (SNF Projects 200021-125309 and 200020-138230
article_processing_charge: No
arxiv: 1
author:
- first_name: Anna
  full_name: Gundert, Anna
  last_name: Gundert
- first_name: Uli
  full_name: Wagner, Uli
  id: 36690CA2-F248-11E8-B48F-1D18A9856A87
  last_name: Wagner
  orcid: 0000-0002-1494-0568
citation:
  ama: Gundert A, Wagner U. On topological minors in random simplicial complexes.
    <i>Proceedings of the American Mathematical Society</i>. 2016;144(4):1815-1828.
    doi:<a href="https://doi.org/10.1090/proc/12824">10.1090/proc/12824</a>
  apa: Gundert, A., &#38; Wagner, U. (2016). On topological minors in random simplicial
    complexes. <i>Proceedings of the American Mathematical Society</i>. American Mathematical
    Society. <a href="https://doi.org/10.1090/proc/12824">https://doi.org/10.1090/proc/12824</a>
  chicago: Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial
    Complexes.” <i>Proceedings of the American Mathematical Society</i>. American
    Mathematical Society, 2016. <a href="https://doi.org/10.1090/proc/12824">https://doi.org/10.1090/proc/12824</a>.
  ieee: A. Gundert and U. Wagner, “On topological minors in random simplicial complexes,”
    <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American
    Mathematical Society, pp. 1815–1828, 2016.
  ista: Gundert A, Wagner U. 2016. On topological minors in random simplicial complexes.
    Proceedings of the American Mathematical Society. 144(4), 1815–1828.
  mla: Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial
    Complexes.” <i>Proceedings of the American Mathematical Society</i>, vol. 144,
    no. 4, American Mathematical Society, 2016, pp. 1815–28, doi:<a href="https://doi.org/10.1090/proc/12824">10.1090/proc/12824</a>.
  short: A. Gundert, U. Wagner, Proceedings of the American Mathematical Society 144
    (2016) 1815–1828.
corr_author: '1'
date_created: 2018-12-11T11:52:30Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2025-09-18T11:07:39Z
day: '01'
department:
- _id: UlWa
doi: 10.1090/proc/12824
external_id:
  arxiv:
  - '1404.2106'
  isi:
  - '000369298400040'
intvolume: '       144'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1404.2106
month: '04'
oa: 1
oa_version: Preprint
page: 1815 - 1828
publication: Proceedings of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '5650'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On topological minors in random simplicial complexes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 144
year: '2016'
...
---
_id: '1524'
abstract:
- lang: eng
  text: "When designing genetic circuits, the typical primitives used in major existing
    modelling formalisms are gene interaction graphs, where edges between genes denote
    either an activation or inhibition relation. However, when designing experiments,
    it is important to be precise about the low-level mechanistic details as to how
    each such relation is implemented. The rule-based modelling language Kappa allows
    to unambiguously specify mechanistic details such as DNA binding sites, dimerisation
    of transcription factors, or co-operative interactions. Such a detailed description
    comes with complexity and computationally costly executions. We propose a general
    method for automatically transforming a rule-based program, by eliminating intermediate
    species and adjusting the rate constants accordingly. To the best of our knowledge,
    we show the first automated reduction of rule-based models based on equilibrium
    approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which
    was designed for reducing reaction-based programs; our version of the algorithm
    scans the rule-based Kappa model in search for those interaction patterns known
    to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional
    checks are then performed in order to verify if the reduction is meaningful in
    the context of the full model. The reduced model is efficiently obtained by static
    inspection over the rule-set. The tool is tested on a detailed rule-based model
    of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has
    11 rules and 5 agents, and provides a dramatic reduction in simulation time of
    several orders of magnitude."
acknowledgement: This research was supported by the People Programme (Marie Curie
  Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under
  REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship,
  the grant number P2EZP2_148797.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Andreea
  full_name: Beica, Andreea
  last_name: Beica
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Tatjana
  full_name: Petrov, Tatjana
  id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
  last_name: Petrov
  orcid: 0000-0002-9041-0905
citation:
  ama: 'Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static
    inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:<a href="https://doi.org/10.1007/978-3-319-26916-0_10">10.1007/978-3-319-26916-0_10</a>'
  apa: 'Beica, A., Guet, C. C., &#38; Petrov, T. (2016). Efficient reduction of kappa
    models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented
    at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. <a href="https://doi.org/10.1007/978-3-319-26916-0_10">https://doi.org/10.1007/978-3-319-26916-0_10</a>'
  chicago: Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction
    of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer,
    2016. <a href="https://doi.org/10.1007/978-3-319-26916-0_10">https://doi.org/10.1007/978-3-319-26916-0_10</a>.
  ieee: 'A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models
    by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology,
    Madrid, Spain, 2016, vol. 9271, pp. 173–191.'
  ista: 'Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by
    static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271,
    173–191.'
  mla: Beica, Andreea, et al. <i>Efficient Reduction of Kappa Models by Static Inspection
    of the Rule-Set</i>. Vol. 9271, Springer, 2016, pp. 173–91, doi:<a href="https://doi.org/10.1007/978-3-319-26916-0_10">10.1007/978-3-319-26916-0_10</a>.
  short: A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.
conference:
  end_date: 2015-09-05
  location: Madrid, Spain
  name: 'HSB: Hybrid Systems Biology'
  start_date: 2015-09-04
corr_author: '1'
date_created: 2018-12-11T11:52:31Z
date_published: 2016-01-10T00:00:00Z
date_updated: 2025-06-04T12:06:27Z
day: '10'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-319-26916-0_10
ec_funded: 1
external_id:
  arxiv:
  - '1501.00440'
intvolume: '      9271'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1501.00440
month: '01'
oa: 1
oa_version: Preprint
page: 173 - 191
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '5649'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient reduction of kappa models by static inspection of the rule-set
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9271
year: '2016'
...
---
_id: '15242'
abstract:
- lang: eng
  text: The recent discovery of gravitational radiation from merging black holes poses
    a challenge of how to organize the electromagnetic follow-up of gravitational-wave
    events as well as observed bursts of neutrinos. We propose a technique to select
    the galaxies that are most likely to host the event given some assumptions of
    whether the particular event is associated with recent star formation, low-metallicity
    stars or simply proportional to the total stellar mass in the galaxy. We combine
    data from the 2-MASS Photometric Redshift Galaxy Catalogue with results from galaxy
    formation simulations to develop observing strategies that potentially reduce
    the area of sky to search by up to a factor of 2 relative to an unweighted search
    of galaxies, and a factor of 20 to a search over the entire LIGO localization
    region.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Elisa
  full_name: Antolini, Elisa
  last_name: Antolini
- first_name: Ilaria
  full_name: Caiazzo, Ilaria
  id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
  last_name: Caiazzo
  orcid: 0000-0002-4770-5388
- first_name: Romeel
  full_name: Davé, Romeel
  last_name: Davé
- first_name: Jeremy S.
  full_name: Heyl, Jeremy S.
  last_name: Heyl
citation:
  ama: Antolini E, Caiazzo I, Davé R, Heyl JS. Using galaxy formation simulations
    to optimize LIGO follow-up observations. <i>Monthly Notices of the Royal Astronomical
    Society</i>. 2016;466(2):2212-2216. doi:<a href="https://doi.org/10.1093/mnras/stw3292">10.1093/mnras/stw3292</a>
  apa: Antolini, E., Caiazzo, I., Davé, R., &#38; Heyl, J. S. (2016). Using galaxy
    formation simulations to optimize LIGO follow-up observations. <i>Monthly Notices
    of the Royal Astronomical Society</i>. Oxford University Press. <a href="https://doi.org/10.1093/mnras/stw3292">https://doi.org/10.1093/mnras/stw3292</a>
  chicago: Antolini, Elisa, Ilaria Caiazzo, Romeel Davé, and Jeremy S. Heyl. “Using
    Galaxy Formation Simulations to Optimize LIGO Follow-up Observations.” <i>Monthly
    Notices of the Royal Astronomical Society</i>. Oxford University Press, 2016.
    <a href="https://doi.org/10.1093/mnras/stw3292">https://doi.org/10.1093/mnras/stw3292</a>.
  ieee: E. Antolini, I. Caiazzo, R. Davé, and J. S. Heyl, “Using galaxy formation
    simulations to optimize LIGO follow-up observations,” <i>Monthly Notices of the
    Royal Astronomical Society</i>, vol. 466, no. 2. Oxford University Press, pp.
    2212–2216, 2016.
  ista: Antolini E, Caiazzo I, Davé R, Heyl JS. 2016. Using galaxy formation simulations
    to optimize LIGO follow-up observations. Monthly Notices of the Royal Astronomical
    Society. 466(2), 2212–2216.
  mla: Antolini, Elisa, et al. “Using Galaxy Formation Simulations to Optimize LIGO
    Follow-up Observations.” <i>Monthly Notices of the Royal Astronomical Society</i>,
    vol. 466, no. 2, Oxford University Press, 2016, pp. 2212–16, doi:<a href="https://doi.org/10.1093/mnras/stw3292">10.1093/mnras/stw3292</a>.
  short: E. Antolini, I. Caiazzo, R. Davé, J.S. Heyl, Monthly Notices of the Royal
    Astronomical Society 466 (2016) 2212–2216.
date_created: 2024-03-26T10:41:04Z
date_published: 2016-12-17T00:00:00Z
date_updated: 2024-04-08T07:05:23Z
day: '17'
doi: 10.1093/mnras/stw3292
extern: '1'
external_id:
  arxiv:
  - '1612.04412'
intvolume: '       466'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.1612.04412
month: '12'
oa: 1
oa_version: Preprint
page: 2212-2216
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
  eissn:
  - 1365-2966
  issn:
  - 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using galaxy formation simulations to optimize LIGO follow-up observations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 466
year: '2016'
...
---
_id: '15244'
abstract:
- lang: eng
  text: XIPE, the X-ray Imaging Polarimetry Explorer, is a mission dedicated to X-ray
    Astronomy. At the time of writing XIPE is in a competitive phase A as fourth medium
    size mission of ESA (M4). It promises to reopen the polarimetry window in high
    energy Astrophysics after more than 4 decades thanks to a detector that efficiently
    exploits the photoelectric effect and to X-ray optics with large effective area.
    XIPE uniqueness is time-spectrally-spatially- resolved X-ray polarimetry as a
    breakthrough in high energy astrophysics and fundamental physics. Indeed the payload
    consists of three Gas Pixel Detectors at the focus of three X-ray optics with
    a total effective area larger than one XMM mirror but with a low weight. The payload
    is compatible with the fairing of the Vega launcher. XIPE is designed as an observatory
    for X-ray astronomers with 75 % of the time dedicated to a Guest Observer competitive
    program and it is organized as a consortium across Europe with main contributions
    from Italy, Germany, Spain, United Kingdom, Poland, Sweden.
article_number: '990515'
article_processing_charge: No
arxiv: 1
author:
- first_name: Paolo
  full_name: Soffitta, Paolo
  last_name: Soffitta
- first_name: Ronaldo
  full_name: Bellazzini, Ronaldo
  last_name: Bellazzini
- first_name: Enrico
  full_name: Bozzo, Enrico
  last_name: Bozzo
- first_name: Vadim
  full_name: Burwitz, Vadim
  last_name: Burwitz
- first_name: Alberto
  full_name: Castro Tirado, Alberto
  last_name: Castro Tirado
- first_name: Enrico
  full_name: Costa, Enrico
  last_name: Costa
- first_name: Thierry
  full_name: Courvoisier, Thierry
  last_name: Courvoisier
- first_name: Hua
  full_name: Feng, Hua
  last_name: Feng
- first_name: Szymon
  full_name: Gburek, Szymon
  last_name: Gburek
- first_name: Rene'
  full_name: Goosmann, Rene'
  last_name: Goosmann
- first_name: Vladimir
  full_name: Karas, Vladimir
  last_name: Karas
- first_name: Giorgio
  full_name: Matt, Giorgio
  last_name: Matt
- first_name: Fabio
  full_name: Muleri, Fabio
  last_name: Muleri
- first_name: Kirpal
  full_name: Nandra, Kirpal
  last_name: Nandra
- first_name: Mark
  full_name: Pearce, Mark
  last_name: Pearce
- first_name: Juri
  full_name: Poutanen, Juri
  last_name: Poutanen
- first_name: Victor
  full_name: Reglero, Victor
  last_name: Reglero
- first_name: Maria Dolores
  full_name: Graziati, Maria Dolores
  last_name: Graziati
- first_name: Andrea
  full_name: Santangelo, Andrea
  last_name: Santangelo
- first_name: Gianpiero
  full_name: Tagliaferri, Gianpiero
  last_name: Tagliaferri
- first_name: Christopher
  full_name: Tenzer, Christopher
  last_name: Tenzer
- first_name: Jacco
  full_name: Vink, Jacco
  last_name: Vink
- first_name: Martin
  full_name: Weisskopf, Martin
  last_name: Weisskopf
- first_name: Silvia
  full_name: Zane, Silvia
  last_name: Zane
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conference:
  end_date: 2016-07-01
  location: Edinburgh, UK
  name: Astronomical Telescopes + Instrumentation
  start_date: 2016-06-26
date_created: 2024-03-26T10:41:49Z
date_published: 2016-10-11T00:00:00Z
date_updated: 2024-04-08T07:06:39Z
day: '11'
doi: 10.1117/12.2233046
extern: '1'
external_id:
  arxiv:
  - '1309.6995'
intvolume: '      9905'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.1309.6995
month: '10'
oa: 1
oa_version: Preprint
publication: 'Space Telescopes and Instrumentation 2016: Ultraviolet to Gamma Ray'
publication_identifier:
  issn:
  - 0168-9002
publication_status: published
publisher: SPIE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'XIPE: The x-ray imaging polarimetry explorer'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9905
year: '2016'
...
---
_id: '15245'
abstract:
- lang: eng
  text: 'eXTP is a science mission designed to study the state of matter under extreme
    conditions of density, gravity and magnetism. Primary goals are the determination
    of the equation of state of matter at supra-nuclear density, the measurement of
    QED effects in highly magnetized star, and the study of accretion in the strong-field
    regime of gravity. Primary targets include isolated and binary neutron stars,
    strong magnetic field systems like magnetars, and stellar-mass and supermassive
    black holes. The mission carries a unique and unprecedented suite of state-of-the-art
    scientific instruments enabling for the first time ever the simultaneous spectral-timing-polarimetry
    studies of cosmic sources in the energy range from 0.5-30 keV (and beyond). Key
    elements of the payload are: the Spectroscopic Focusing Array (SFA) - a set of
    11 X-ray optics for a total effective area of ∼0.9 m2 and 0.6 m2 at 2 keV and
    6 keV respectively, equipped with Silicon Drift Detectors offering <180 eV spectral
    resolution; the Large Area Detector (LAD) - a deployable set of 640 Silicon Drift
    Detectors, for a total effective area of ∼3.4 m2, between 6 and 10 keV, and spectral
    resolution better than 250 eV; the Polarimetry Focusing Array (PFA) - a set of
    2 X-ray telescope, for a total effective area of 250 cm2 at 2 keV, equipped with
    imaging gas pixel photoelectric polarimeters; the Wide Field Monitor (WFM) - a
    set of 3 coded mask wide field units, equipped with position-sensitive Silicon
    Drift Detectors, each covering a 90 degrees x 90 degrees field of view. The eXTP
    international consortium includes major institutions of the Chinese Academy of
    Sciences and Universities in China, as well as major institutions in several European
    countries and the United States. The predecessor of eXTP, the XTP mission concept,
    has been selected and funded as one of the so-called background missions in the
    Strategic Priority Space Science Program of the Chinese Academy of Sciences since
    2011. The strong European participation has significantly enhanced the scientific
    capabilities of eXTP. The planned launch date of the mission is earlier than 2025.'
article_number: '99051Q '
article_processing_charge: No
arxiv: 1
author:
- first_name: S. N.
  full_name: Zhang, S. N.
  last_name: Zhang
- first_name: M.
  full_name: Feroci, M.
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  full_name: Santangelo, A.
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citation:
  ama: 'Zhang SN, Feroci M, Santangelo A, et al. eXTP: Enhanced X-ray timing and polarization
    mission. In: <i>Proceedings of the SPIE</i>. Vol 9905. SPIE; 2016. doi:<a href="https://doi.org/10.1117/12.2232034">10.1117/12.2232034</a>'
  apa: 'Zhang, S. N., Feroci, M., Santangelo, A., Dong, Y. W., Feng, H., Lu, F. J.,
    … Zhou, X. L. (2016). eXTP: Enhanced X-ray timing and polarization mission. In
    <i>Proceedings of the SPIE</i> (Vol. 9905). SPIE. <a href="https://doi.org/10.1117/12.2232034">https://doi.org/10.1117/12.2232034</a>'
  chicago: 'Zhang, S. N., M. Feroci, A. Santangelo, Y. W. Dong, H. Feng, F. J. Lu,
    K. Nandra, et al. “EXTP: Enhanced X-Ray Timing and Polarization Mission.” In <i>Proceedings
    of the SPIE</i>, Vol. 9905. SPIE, 2016. <a href="https://doi.org/10.1117/12.2232034">https://doi.org/10.1117/12.2232034</a>.'
  ieee: 'S. N. Zhang <i>et al.</i>, “eXTP: Enhanced X-ray timing and polarization
    mission,” in <i>Proceedings of the SPIE</i>, 2016, vol. 9905.'
  ista: 'Zhang SN et al. 2016. eXTP: Enhanced X-ray timing and polarization mission.
    Proceedings of the SPIE. vol. 9905, 99051Q.'
  mla: 'Zhang, S. N., et al. “EXTP: Enhanced X-Ray Timing and Polarization Mission.”
    <i>Proceedings of the SPIE</i>, vol. 9905, 99051Q, SPIE, 2016, doi:<a href="https://doi.org/10.1117/12.2232034">10.1117/12.2232034</a>.'
  short: S.N. Zhang, M. Feroci, A. Santangelo, Y.W. Dong, H. Feng, F.J. Lu, K. Nandra,
    Z.S. Wang, S. Zhang, E. Bozzo, S. Brandt, A. De Rosa, L.J. Gou, M. Hernanz, M.
    van der Klis, X.D. Li, Y. Liu, P. Orleanski, G. Pareschi, M. Pohl, J. Poutanen,
    J.L. Qu, S. Schanne, L. Stella, P. Uttley, A. Watts, R.X. Xu, W.F. Yu, J.J.M.
    in ’t Zand, S. Zane, L. Alvarez, L. Amati, L. Baldini, C. Bambi, S. Basso, S.
    Bhattacharyya, R. Bellazzini, T. Belloni, P. Bellutti, S. Bianchi, A. Brez, M.
    Bursa, V. Burwitz, C. Budtz-Jørgensen, I. Caiazzo, R. Campana, X.L. Cao, P. Casella,
    C.Y. Chen, L. Chen, T. Chen, Y. Chen, Y. Chen, Y.P. Chen, M. Civitani, F. Coti
    Zelati, W. Cui, W.W. Cui, Z.G. Dai, E. Del Monte, D. de Martino, S. Di Cosimo,
    S. Diebold, M. Dovciak, I. Donnarumma, V. Doroshenko, P. Esposito, Y. Evangelista,
    Y. Favre, P. Friedrich, F. Fuschino, J.L. Galvez, Z.L. Gao, M.Y. Ge, O. Gevin,
    D. Goetz, D.W. Han, J. Heyl, J. Horak, W. Hu, F. Huang, Q.S. Huang, R. Hudec,
    D. Huppenkothen, G.L. Israel, A. Ingram, V. Karas, D. Karelin, P.A. Jenke, L.
    Ji, S. Korpela, D. Kunneriath, C. Labanti, G. Li, X. Li, Z.S. Li, E.W. Liang,
    O. Limousin, L. Lin, Z.X. Ling, H.B. Liu, H.W. Liu, Z. Liu, B. Lu, N. Lund, D.
    Lai, B. Luo, T. Luo, B. Ma, S. Mahmoodifar, M. Marisaldi, A. Martindale, N. Meidinger,
    Y.P. Men, M. Michalska, R. Mignani, M. Minuti, S. Motta, F. Muleri, J. Neilsen,
    M. Orlandini, A.T. Pan, A. Patruno, E. Perinati, A. Picciotto, C. Piemonte, M.
    Pinchera, A. Rachevski, M. Rapisarda, N. Rea, E.M.R. Rossi, A. Rubini, G. Sala,
    X.W. Shu, C. Sgro, Z.X. Shen, P. Soffitta, L.M. Song, G. Spandre, G. Stratta,
    T.E. Strohmayer, L. Sun, J. Svoboda, G. Tagliaferri, C. Tenzer, T. Hong, R. Taverna,
    G. Torok, R. Turolla, S. Vacchi, J. Wang, D. Walton, K. Wang, J.F. Wang, R.J.
    Wang, Y.F. Wang, S.S. Weng, J. Wilms, B. Winter, X. Wu, X.F. Wu, S.L. Xiong, Y.P.
    Xu, Y.Q. Xue, Z. Yan, S. Yang, X. Yang, Y.J. Yang, F. Yuan, W.M. Yuan, Y.F. Yuan,
    G. Zampa, N. Zampa, A. Zdziarski, C. Zhang, C.L. Zhang, L. Zhang, X. Zhang, Z.
    Zhang, W.D. Zhang, S.J. Zheng, P. Zhou, X.L. Zhou, in:, Proceedings of the SPIE,
    SPIE, 2016.
date_created: 2024-03-26T10:42:21Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2024-03-27T08:23:11Z
day: '01'
doi: 10.1117/12.2232034
extern: '1'
external_id:
  arxiv:
  - '1607.08823'
intvolume: '      9905'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.1607.08823
month: '07'
oa: 1
oa_version: Preprint
publication: Proceedings of the SPIE
publication_identifier:
  issn:
  - 0277-786X
publication_status: published
publisher: SPIE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'eXTP: Enhanced X-ray timing and polarization mission'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9905
year: '2016'
...
---
_id: '1526'
abstract:
- lang: eng
  text: 'We present the first study of robustness of systems that are both timed as
    well as reactive (I/O). We study the behavior of such timed I/O systems in the
    presence of uncertain inputs and formalize their robustness using the analytic
    notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if
    the perturbation in its output is at most K times the perturbation in its input.
    We quantify input and output perturbation using similarity functions over timed
    words such as the timed version of the Manhattan distance and the Skorokhod distance.
    We consider two models of timed I/O systems — timed transducers and asynchronous
    sequential circuits. We show that K-robustness of timed transducers can be decided
    in polynomial space under certain conditions. For asynchronous sequential circuits,
    we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete
    letter-to-letter transducers and show PSpace-completeness of the problem.'
acknowledgement: This research was supported in part by the European Research Council
  (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants
  S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science
  Centre (NCN), Poland under grant 2014/15/D/ST6/04543.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Jan
  full_name: Otop, Jan
  id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
  last_name: Otop
- first_name: Roopsha
  full_name: Samanta, Roopsha
  id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87
  last_name: Samanta
citation:
  ama: 'Henzinger TA, Otop J, Samanta R. Lipschitz robustness of timed I/O systems.
    In: Vol 9583. Springer; 2016:250-267. doi:<a href="https://doi.org/10.1007/978-3-662-49122-5_12">10.1007/978-3-662-49122-5_12</a>'
  apa: 'Henzinger, T. A., Otop, J., &#38; Samanta, R. (2016). Lipschitz robustness
    of timed I/O systems (Vol. 9583, pp. 250–267). Presented at the VMCAI: Verification,
    Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer.
    <a href="https://doi.org/10.1007/978-3-662-49122-5_12">https://doi.org/10.1007/978-3-662-49122-5_12</a>'
  chicago: Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness
    of Timed I/O Systems,” 9583:250–67. Springer, 2016. <a href="https://doi.org/10.1007/978-3-662-49122-5_12">https://doi.org/10.1007/978-3-662-49122-5_12</a>.
  ieee: 'T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of timed
    I/O systems,” presented at the VMCAI: Verification, Model Checking and Abstract
    Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 250–267.'
  ista: 'Henzinger TA, Otop J, Samanta R. 2016. Lipschitz robustness of timed I/O
    systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS,
    vol. 9583, 250–267.'
  mla: Henzinger, Thomas A., et al. <i>Lipschitz Robustness of Timed I/O Systems</i>.
    Vol. 9583, Springer, 2016, pp. 250–67, doi:<a href="https://doi.org/10.1007/978-3-662-49122-5_12">10.1007/978-3-662-49122-5_12</a>.
  short: T.A. Henzinger, J. Otop, R. Samanta, in:, Springer, 2016, pp. 250–267.
conference:
  end_date: 2016-01-19
  location: St. Petersburg, FL, USA
  name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
  start_date: 2016-01-17
corr_author: '1'
date_created: 2018-12-11T11:52:32Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-09-18T11:06:25Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-662-49122-5_12
ec_funded: 1
external_id:
  arxiv:
  - '1506.01233'
  isi:
  - '000375148800012'
intvolume: '      9583'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1506.01233
month: '01'
oa: 1
oa_version: Preprint
page: 250 - 267
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: Formal methods for the design and analysis of complex systems
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5647'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lipschitz robustness of timed I/O systems
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9583
year: '2016'
...
---
_id: '1529'
abstract:
- lang: eng
  text: 'We consider partially observable Markov decision processes (POMDPs) with
    a set of target states and an integer cost associated with every transition. The
    optimization objective we study asks to minimize the expected total cost of reaching
    a state in the target set, while ensuring that the target set is reached almost
    surely (with probability 1). We show that for integer costs approximating the
    optimal cost is undecidable. For positive costs, our results are as follows: (i)
    we establish matching lower and upper bounds for the optimal cost, both double
    exponential in the POMDP state space size; (ii) we show that the problem of approximating
    the optimal cost is decidable and present approximation algorithms developing
    on the existing algorithms for POMDPs with finite-horizon objectives. While the
    worst-case running time of our algorithm is double exponential, we also present
    efficient stopping criteria for the algorithm and show experimentally that it
    performs well in many examples of interest.'
acknowledgement: 'We thank Blai Bonet for helping us with RTDP-Bel. The research was
  partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant
  No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty
  fellows award.'
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: Martin
  full_name: Chmelik, Martin
  id: 3624234E-F248-11E8-B48F-1D18A9856A87
  last_name: Chmelik
- first_name: Raghav
  full_name: Gupta, Raghav
  last_name: Gupta
- first_name: Ayush
  full_name: Kanodia, Ayush
  last_name: Kanodia
citation:
  ama: Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability
    in POMDPs. <i>Artificial Intelligence</i>. 2016;234:26-48. doi:<a href="https://doi.org/10.1016/j.artint.2016.01.007">10.1016/j.artint.2016.01.007</a>
  apa: Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2016). Optimal cost
    almost-sure reachability in POMDPs. <i>Artificial Intelligence</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.artint.2016.01.007">https://doi.org/10.1016/j.artint.2016.01.007</a>
  chicago: Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia.
    “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Artificial Intelligence</i>.
    Elsevier, 2016. <a href="https://doi.org/10.1016/j.artint.2016.01.007">https://doi.org/10.1016/j.artint.2016.01.007</a>.
  ieee: K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure
    reachability in POMDPs,” <i>Artificial Intelligence</i>, vol. 234. Elsevier, pp.
    26–48, 2016.
  ista: Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure
    reachability in POMDPs. Artificial Intelligence. 234, 26–48.
  mla: Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.”
    <i>Artificial Intelligence</i>, vol. 234, Elsevier, 2016, pp. 26–48, doi:<a href="https://doi.org/10.1016/j.artint.2016.01.007">10.1016/j.artint.2016.01.007</a>.
  short: K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence
    234 (2016) 26–48.
corr_author: '1'
date_created: 2018-12-11T11:52:33Z
date_published: 2016-05-01T00:00:00Z
date_updated: 2025-09-18T11:05:09Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.artint.2016.01.007
ec_funded: 1
external_id:
  arxiv:
  - '1411.3880'
  isi:
  - '000372683700002'
intvolume: '       234'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1411.3880
month: '05'
oa: 1
oa_version: Preprint
page: 26 - 48
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P 23499-N23
  name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
publication: Artificial Intelligence
publication_status: published
publisher: Elsevier
publist_id: '5642'
quality_controlled: '1'
related_material:
  record:
  - id: '5425'
    relation: earlier_version
    status: public
  - id: '1820'
    relation: earlier_version
    status: public
scopus_import: '1'
status: public
title: Optimal cost almost-sure reachability in POMDPs
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 234
year: '2016'
...
---
_id: '1545'
abstract:
- lang: eng
  text: We provide general conditions for which bosonic quadratic Hamiltonians on
    Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover
    the case when quantum systems have infinite degrees of freedom and the associated
    one-body kinetic and paring operators are unbounded. Our sufficient conditions
    are optimal in the sense that they become necessary when the relevant one-body
    operators commute.
acknowledgement: We thank Jan Dereziński for several inspiring discussions and useful
  remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger
  Institute for the hospitality during the thematic programme “Quantum many-body systems,
  random matrices, and disorder”. We gratefully acknowledge the financial supports
  by the European Union's Seventh Framework Programme under the ERC Advanced Grant
  ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as
  well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185
  and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).
article_processing_charge: No
arxiv: 1
author:
- first_name: Phan
  full_name: Nam, Phan
  id: 404092F4-F248-11E8-B48F-1D18A9856A87
  last_name: Nam
- first_name: Marcin M
  full_name: Napiórkowski, Marcin M
  id: 4197AD04-F248-11E8-B48F-1D18A9856A87
  last_name: Napiórkowski
- first_name: Jan
  full_name: Solovej, Jan
  last_name: Solovej
citation:
  ama: Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians
    by Bogoliubov transformations. <i>Journal of Functional Analysis</i>. 2016;270(11):4340-4368.
    doi:<a href="https://doi.org/10.1016/j.jfa.2015.12.007">10.1016/j.jfa.2015.12.007</a>
  apa: Nam, P., Napiórkowski, M. M., &#38; Solovej, J. (2016). Diagonalization of
    bosonic quadratic Hamiltonians by Bogoliubov transformations. <i>Journal of Functional
    Analysis</i>. Academic Press. <a href="https://doi.org/10.1016/j.jfa.2015.12.007">https://doi.org/10.1016/j.jfa.2015.12.007</a>
  chicago: Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of
    Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” <i>Journal of Functional
    Analysis</i>. Academic Press, 2016. <a href="https://doi.org/10.1016/j.jfa.2015.12.007">https://doi.org/10.1016/j.jfa.2015.12.007</a>.
  ieee: P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic
    Hamiltonians by Bogoliubov transformations,” <i>Journal of Functional Analysis</i>,
    vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016.
  ista: Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic
    Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11),
    4340–4368.
  mla: Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov
    Transformations.” <i>Journal of Functional Analysis</i>, vol. 270, no. 11, Academic
    Press, 2016, pp. 4340–68, doi:<a href="https://doi.org/10.1016/j.jfa.2015.12.007">10.1016/j.jfa.2015.12.007</a>.
  short: P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270
    (2016) 4340–4368.
corr_author: '1'
date_created: 2018-12-11T11:52:38Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2025-09-18T11:04:09Z
day: '01'
department:
- _id: RoSe
doi: 10.1016/j.jfa.2015.12.007
ec_funded: 1
external_id:
  arxiv:
  - '1508.07321'
  isi:
  - '000375241700011'
intvolume: '       270'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1508.07321
month: '06'
oa: 1
oa_version: Submitted Version
page: 4340 - 4368
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: 25C878CE-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P27533_N27
  name: Structure of the Excitation Spectrum for Many-Body Quantum Systems
publication: Journal of Functional Analysis
publication_status: published
publisher: Academic Press
publist_id: '5626'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 270
year: '2016'
...
---
_id: '1059'
abstract:
- lang: eng
  text: A range of bright and photostable rhodamines and carbopyronines with absorption
    maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling
    of cytoskeletal filaments using HaloTag technology followed by staining with 1
    μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters,
    fluorogenic behavior, and structure-property relationships of the new dyes are
    discussed. Light microscopy with stimulated emission depletion (STED) provided
    one- and two-color images of living cells with an optical resolution of 40-60
    nm.
acknowledgement: We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka,
  Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC,
  Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC),
  Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare
  Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS
  spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring
  fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to
  a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium
  für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für
  Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds
  from the People Programme (Marie Curie Actions) of the European Union's Seventh
  Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283).
article_processing_charge: No
author:
- first_name: Alexey
  full_name: Butkevich, Alexey
  last_name: Butkevich
- first_name: Gyuzel
  full_name: Mitronova, Gyuzel
  last_name: Mitronova
- first_name: Sven
  full_name: Sidenstein, Sven
  last_name: Sidenstein
- first_name: Jessica
  full_name: Klocke, Jessica
  last_name: Klocke
- first_name: Dirk
  full_name: Kamin, Dirk
  last_name: Kamin
- first_name: Dirk
  full_name: Meineke, Dirk
  last_name: Meineke
- first_name: Elisa
  full_name: D'Este, Elisa
  last_name: D'Este
- first_name: Philip
  full_name: Kraemer, Philip
  last_name: Kraemer
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Vladimir
  full_name: Belov, Vladimir
  last_name: Belov
- first_name: Stefan
  full_name: Hell, Stefan
  last_name: Hell
citation:
  ama: Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic
    carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte
    Chemie - International Edition</i>. 2016;55(10):3290-3294. doi:<a href="https://doi.org/10.1002/anie.201511018">10.1002/anie.201511018</a>
  apa: Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke,
    D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for
    super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International
    Edition</i>. Wiley-Blackwell. <a href="https://doi.org/10.1002/anie.201511018">https://doi.org/10.1002/anie.201511018</a>
  chicago: Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk
    Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic
    Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte
    Chemie - International Edition</i>. Wiley-Blackwell, 2016. <a href="https://doi.org/10.1002/anie.201511018">https://doi.org/10.1002/anie.201511018</a>.
  ieee: A. Butkevich <i>et al.</i>, “Fluorescent rhodamines and fluorogenic carbopyronines
    for super-resolution STED microscopy in living cells,” <i>Angewandte Chemie -
    International Edition</i>, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.
  ista: Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este
    E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic
    carbopyronines for super-resolution STED microscopy in living cells. Angewandte
    Chemie - International Edition. 55(10), 3290–3294.
  mla: Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines
    for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie -
    International Edition</i>, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94,
    doi:<a href="https://doi.org/10.1002/anie.201511018">10.1002/anie.201511018</a>.
  short: A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke,
    E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International
    Edition 55 (2016) 3290–3294.
date_created: 2018-12-11T11:49:55Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:47:59Z
day: '01'
doi: 10.1002/anie.201511018
extern: '1'
intvolume: '        55'
issue: '10'
language:
- iso: eng
month: '03'
oa_version: None
page: 3290 - 3294
publication: Angewandte Chemie - International Edition
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6330'
status: public
title: Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution
  STED microscopy in living cells
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1060'
abstract:
- lang: eng
  text: Superresolution fluorescence microscopy of multiple fluorophores still requires
    development. Here we present simultaneous three-colour stimulated emission depletion
    (STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam
    between two or more power levels (&quot;multilevelSTEDv) optimizes resolution
    and contrast in all colour channels, which are intrinsically co-aligned and well
    separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal
    organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified
    periodic actin/betaII spectrin lattices along dendrites and spines; however, at
    presynaptic and postsynaptic sites, these patterns were found to be absent. Both
    our multicolour scheme and the 620 nm STED line should be attractive for routine
    STED microscopy applications.
acknowledgement: We acknowledge the assistance of I. Herfort with neuron preparation,
  and of J. Bienert and K. Müller with analyses of the dye 540R derivatives. We thank
  T. Gilat and E. Rothermel for sample preparation as well as J. Keller, F. Winter
  (all MPI-BPC) and C.A. Wurm (Abberior Instruments) for helpful discussion, and S.J.
  Sahl (MPI-BPC) for a critical reading of the manuscript.
article_processing_charge: No
author:
- first_name: Sven
  full_name: Sidenstein, Sven
  last_name: Sidenstein
- first_name: Elisa
  full_name: D'Este, Elisa
  last_name: D'Este
- first_name: Marvin
  full_name: Böhm, Marvin
  last_name: Böhm
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Vladimir
  full_name: Belov, Vladimir
  last_name: Belov
- first_name: Stefan
  full_name: Hell, Stefan
  last_name: Hell
citation:
  ama: Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. Multicolour multilevel
    STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>.
    2016;6:1-8. doi:<a href="https://doi.org/10.1038/srep26725">10.1038/srep26725</a>
  apa: Sidenstein, S., D’Este, E., Böhm, M., Danzl, J. G., Belov, V., &#38; Hell,
    S. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organization
    at synapses. <i>Scientific Reports</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/srep26725">https://doi.org/10.1038/srep26725</a>
  chicago: Sidenstein, Sven, Elisa D’Este, Marvin Böhm, Johann G Danzl, Vladimir Belov,
    and Stefan Hell. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization
    at Synapses.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href="https://doi.org/10.1038/srep26725">https://doi.org/10.1038/srep26725</a>.
  ieee: S. Sidenstein, E. D’Este, M. Böhm, J. G. Danzl, V. Belov, and S. Hell, “Multicolour
    multilevel STED nanoscopy of actin/spectrin organization at synapses,” <i>Scientific
    Reports</i>, vol. 6. Nature Publishing Group, pp. 1–8, 2016.
  ista: Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. 2016. Multicolour
    multilevel STED nanoscopy of actin/spectrin organization at synapses. Scientific
    Reports. 6, 1–8.
  mla: Sidenstein, Sven, et al. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin
    Organization at Synapses.” <i>Scientific Reports</i>, vol. 6, Nature Publishing
    Group, 2016, pp. 1–8, doi:<a href="https://doi.org/10.1038/srep26725">10.1038/srep26725</a>.
  short: S. Sidenstein, E. D’Este, M. Böhm, J.G. Danzl, V. Belov, S. Hell, Scientific
    Reports 6 (2016) 1–8.
date_created: 2018-12-11T11:49:56Z
date_published: 2016-05-25T00:00:00Z
date_updated: 2021-01-12T06:47:59Z
day: '25'
doi: 10.1038/srep26725
extern: '1'
intvolume: '         6'
language:
- iso: eng
month: '05'
oa_version: None
page: 1 - 8
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6329'
status: public
title: Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1068'
abstract:
- lang: eng
  text: 'Games on graphs provide the appropriate framework to study several central
    problems in computer science, such as verification and synthesis of reactive systems.
    One of the most basic objectives for games on graphs is the liveness (or Büchi)
    objective that given a target set of vertices requires that some vertex in the
    target set is visited infinitely often. We study generalized Büchi objectives
    (i.e., conjunction of liveness objectives), and implications between two generalized
    Büchi objectives (known as GR(1) objectives), that arise in numerous applications
    in computer-aided verification. We present improved algorithms and conditional
    super-linear lower bounds based on widely believed assumptions about the complexity
    of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider
    graph games with n vertices, m edges, and generalized Büchi objectives with k
    conjunctions. First, we present an algorithm with running time O(k*n^2), improving
    the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm
    is optimal for dense graphs under (A1). Second, we show that the basic algorithm
    for the problem is optimal for sparse graphs when the target sets have constant
    size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions
    in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1
    k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time
    algorithm for m &gt; n^{1.5}. '
acknowledgement: K. C., M. H., and W. D. are partially supported by the Vienna Science
  and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported
  by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC
  Start grant (279307
alternative_title:
- LIPIcs
article_number: '25'
article_processing_charge: No
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Wolfgang
  full_name: Dvorák, Wolfgang
  last_name: Dvorák
- 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: Veronika
  full_name: Loitzenbauer, Veronika
  last_name: Loitzenbauer
citation:
  ama: 'Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. Conditionally optimal
    algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum
    für Informatik; 2016. doi:<a href="https://doi.org/10.4230/LIPIcs.MFCS.2016.25">10.4230/LIPIcs.MFCS.2016.25</a>'
  apa: 'Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016).
    Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented
    at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland: Schloss
    Dagstuhl - Leibniz-Zentrum für Informatik. <a href="https://doi.org/10.4230/LIPIcs.MFCS.2016.25">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>'
  chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Veronika
    Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,”
    Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href="https://doi.org/10.4230/LIPIcs.MFCS.2016.25">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>.
  ieee: 'K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Conditionally
    optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical
    Foundations of Computer Science, Krakow, Poland, 2016, vol. 58.'
  ista: 'Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. 2016. Conditionally
    optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations
    of Computer Science, LIPIcs, vol. 58, 25.'
  mla: Chatterjee, Krishnendu, et al. <i>Conditionally Optimal Algorithms for Generalized
    Büchi Games</i>. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
    2016, doi:<a href="https://doi.org/10.4230/LIPIcs.MFCS.2016.25">10.4230/LIPIcs.MFCS.2016.25</a>.
  short: K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl
    - Leibniz-Zentrum für Informatik, 2016.
conference:
  end_date: 2016-08-26
  location: Krakow, Poland
  name: 'MFCS: Mathematical Foundations of Computer Science'
  start_date: 2016-08-22
date_created: 2018-12-11T11:49:58Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-07-10T11:49:55Z
day: '01'
ddc:
- '000'
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.MFCS.2016.25
ec_funded: 1
file:
- access_level: open_access
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:16:02Z
  date_updated: 2018-12-12T10:16:02Z
  file_id: '5187'
  file_name: IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf
  file_size: 632786
  relation: main_file
file_date_updated: 2018-12-12T10:16:02Z
has_accepted_license: '1'
intvolume: '        58'
language:
- iso: eng
month: '08'
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: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6317'
pubrep_id: '779'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Conditionally optimal algorithms for generalized Büchi Games
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
  name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
  short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2016'
...
---
_id: '1069'
abstract:
- lang: eng
  text: "The Continuous Skolem Problem asks whether a real-valued function satisfying
    a linear differen-\r\ntial equation has a zero in a given interval of real numbers.
    This is a fundamental reachability\r\nproblem for continuous linear dynamical
    systems, such as linear hybrid automata and continuous-\r\ntime Markov chains.
    Decidability of the problem is currently open – indeed decidability is open\r\neven
    for the sub-problem in which a zero is sought in a bounded interval. In this paper
    we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture,
    a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse
    the unbounded problem in terms of the\r\nfrequencies of the differential equation,
    that is, the imaginary parts of the characteristic roots.\r\nWe show that the
    unbounded problem can be reduced to the bounded problem if there is at most\r\none
    rationally linearly independent frequency, or if there are two rationally linearly
    independent\r\nfrequencies and all characteristic roots are simple. We complete
    the picture by showing that de-\r\ncidability of the unbounded problem in the
    case of two (or more) rationally linearly independent\r\nfrequencies would entail
    a major new effectiveness result in Diophantine approximation, namely\r\ncomputability
    of the Diophantine-approximation types of all real algebraic numbers."
acknowledgement: 'Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN
  Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:  Graph Games), and ERC
  Advanced Grant (267989: QUAREM).'
alternative_title:
- LIPIcs
article_number: '100'
article_processing_charge: No
author:
- first_name: Ventsislav K
  full_name: Chonev, Ventsislav K
  id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
  last_name: Chonev
- first_name: Joël
  full_name: Ouaknine, Joël
  last_name: Ouaknine
- first_name: James
  full_name: Worrell, James
  last_name: Worrell
citation:
  ama: 'Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear
    dynamical systems. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
    2016. doi:<a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.100">10.4230/LIPIcs.ICALP.2016.100</a>'
  apa: 'Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the skolem problem
    for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata,
    Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für
    Informatik. <a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.100">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>'
  chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem
    Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl -
    Leibniz-Zentrum für Informatik, 2016. <a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.100">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.
  ieee: 'V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous
    linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming,
    Rome, Italy, 2016, vol. 55.'
  ista: 'Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous
    linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs,
    vol. 55, 100.'
  mla: Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear
    Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
    2016, doi:<a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.100">10.4230/LIPIcs.ICALP.2016.100</a>.
  short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum
    für Informatik, 2016.
conference:
  end_date: 2016-07-15
  location: Rome, Italy
  name: 'ICALP: Automata, Languages and Programming'
  start_date: 2016-07-12
date_created: 2018-12-11T11:49:59Z
date_published: 2016-08-01T00:00:00Z
date_updated: 2025-06-03T11:32:08Z
day: '01'
ddc:
- '004'
- '006'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ICALP.2016.100
ec_funded: 1
file:
- access_level: open_access
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:16:26Z
  date_updated: 2018-12-12T10:16:26Z
  file_id: '5213'
  file_name: IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf
  file_size: 521415
  relation: main_file
file_date_updated: 2018-12-12T10:16:26Z
has_accepted_license: '1'
intvolume: '        55'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6314'
pubrep_id: '778'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the skolem problem for continuous linear dynamical systems
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '1070'
abstract:
- lang: eng
  text: 'We present a logic that extends CTL (Computation Tree Logic) with operators
    that express synchronization properties. A property is synchronized in a system
    if it holds in all paths of a certain length. The new logic is obtained by using
    the same path quantifiers and temporal operators as in CTL, but allowing a different
    order of the quantifiers. This small syntactic variation induces a logic that
    can express non-regular properties for which known extensions of MSO with equality
    of path length are undecidable. We show that our variant of CTL is decidable and
    that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We
    analogously consider quantifier exchange in extensions of CTL, and we present
    operators defined using basic operators of CTL* that express the occurrence of
    infinitely many synchronization points. We show that the model-checking problem
    remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide
    if the Next operator is allowed in the logics, thus the classical bisimulation
    quotient can be used for state-space reduction before model checking. '
acknowledgement: "This research was partially supported by Austrian Science Fund (FWF)
  NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna
  Science and Technology Fund (WWTF) through project ICT15-003, and European project
  Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for
  their insightful\r\ncomments and suggestions.\r\n"
alternative_title:
- LIPIcs
article_number: '98'
article_processing_charge: No
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Laurent
  full_name: Doyen, Laurent
  last_name: Doyen
citation:
  ama: 'Chatterjee K, Doyen L. Computation tree logic for synchronization properties.
    In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.98">10.4230/LIPIcs.ICALP.2016.98</a>'
  apa: 'Chatterjee, K., &#38; Doyen, L. (2016). Computation tree logic for synchronization
    properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming,
    Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.98">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>'
  chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for
    Synchronization Properties,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
    2016. <a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.98">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>.
  ieee: 'K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,”
    presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016,
    vol. 55.'
  ista: 'Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties.
    ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.'
  mla: Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization
    Properties</i>. Vol. 55, 98, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
    2016, doi:<a href="https://doi.org/10.4230/LIPIcs.ICALP.2016.98">10.4230/LIPIcs.ICALP.2016.98</a>.
  short: K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
    2016.
conference:
  end_date: 2016-07-15
  location: Rome, Italy
  name: 'ICALP: Automata, Languages and Programming'
  start_date: 2016-07-12
date_created: 2018-12-11T11:49:59Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2025-06-03T11:18:54Z
day: '01'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.4230/LIPIcs.ICALP.2016.98
ec_funded: 1
file:
- access_level: open_access
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:08:52Z
  date_updated: 2018-12-12T10:08:52Z
  file_id: '4714'
  file_name: IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf
  file_size: 546133
  relation: main_file
file_date_updated: 2018-12-12T10:08:52Z
has_accepted_license: '1'
intvolume: '        55'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S 11407_N23
  name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '279307'
  name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
  grant_number: ICT15-003
  name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6313'
pubrep_id: '812'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computation tree logic for synchronization properties
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2016'
...
---
_id: '10746'
abstract:
- lang: eng
  text: Vortex states in superconducting (SC) structures, their dynamics and ways
    to manipulate them are topics of great interest. We report a new method of magnetic
    force microscopy (MFM) that allows the study of vortex states in mesoscopic SC
    samples. For the case of a SC ring, which is biased to a half-integer flux quantum,
    the flux modulation through the ring caused by the motion of the magnetic tip
    drives the ring between two consecutive fluxoid states. The corresponding current
    switching in the ring produces strong position-dependent forces on the cantilever.
    In the regime where the frequency of the thermally activated jumps between fluxoid
    states is close to the frequency of the cantilever, large changes in the cantilever
    frequency and dissipation are observed. This effect may be understood as a stochastic
    resonance (SR) process. These changes in the cantilever’s mechanical properties
    are used to “image” the barrier energies between fluxoid states. Additionally,
    SR imaging of the barrier energies are used to study the effect of the locally
    applied magnetic field from the MFM tip on the barrier heights. We report the
    results of measurements for Al rings. Further, the same imaging technique can
    be applied to more sophisticated SC structures such as arrays of Josephson junctions.
alternative_title:
- Bulletin of the American Physical Society
article_number: E25.00007
article_processing_charge: No
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: Victor
  full_name: Chua, Victor
  last_name: Chua
- first_name: Raffi
  full_name: Budakian, Raffi
  last_name: Budakian
citation:
  ama: 'Polshyn H, Naibert T, Chua V, Budakian R. Study of vortex states and dynamics
    in mesoscopic superconducting samples with MFM. In: <i>APS March Meeting 2016</i>.
    Vol 61. American Physical Society; 2016.'
  apa: 'Polshyn, H., Naibert, T., Chua, V., &#38; Budakian, R. (2016). Study of vortex
    states and dynamics in mesoscopic superconducting samples with MFM. In <i>APS
    March Meeting 2016</i> (Vol. 61). Baltimore, MD, United States: American Physical
    Society.'
  chicago: Polshyn, Hryhoriy, Tyler Naibert, Victor Chua, and Raffi Budakian. “Study
    of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.”
    In <i>APS March Meeting 2016</i>, Vol. 61. American Physical Society, 2016.
  ieee: H. Polshyn, T. Naibert, V. Chua, and R. Budakian, “Study of vortex states
    and dynamics in mesoscopic superconducting samples with MFM,” in <i>APS March
    Meeting 2016</i>, Baltimore, MD, United States, 2016, vol. 61, no. 2.
  ista: 'Polshyn H, Naibert T, Chua V, Budakian R. 2016. Study of vortex states and
    dynamics in mesoscopic superconducting samples with MFM. APS March Meeting 2016.
    APS: American Physical Society, Bulletin of the American Physical Society, vol.
    61, E25.00007.'
  mla: Polshyn, Hryhoriy, et al. “Study of Vortex States and Dynamics in Mesoscopic
    Superconducting Samples with MFM.” <i>APS March Meeting 2016</i>, vol. 61, no.
    2, E25.00007, American Physical Society, 2016.
  short: H. Polshyn, T. Naibert, V. Chua, R. Budakian, in:, APS March Meeting 2016,
    American Physical Society, 2016.
conference:
  end_date: 2016-03-18
  location: Baltimore, MD, United States
  name: 'APS: American Physical Society'
  start_date: 2016-03-14
date_created: 2022-02-08T09:55:09Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-02-08T10:44:06Z
day: '01'
extern: '1'
intvolume: '        61'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://meetings.aps.org/Meeting/MAR16/Session/E25.7
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2016
publication_identifier:
  issn:
  - 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Study of vortex states and dynamics in mesoscopic superconducting samples with
  MFM
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 61
year: '2016'
...
---
_id: '10747'
abstract:
- lang: eng
  text: Vortex interactions are key to explaining the behavior of many two dimensional
    superconducting systems. We report on the development of a technique to locally
    probe vortex interactions in a 2D array of Josephson junctions. Scanning a magnetic
    tip attached to an ultra-soft cantilever over the array produces changes in the
    frequency of the cantilever along certain lines, forming geometric patterns in
    the scans. Different tip-surface separations and external magnetic fields produce
    a number of different patterns. These patterns correspond to tip locations in
    which two configurations of vortices in the lattice have degenerate energies.
    By imaging the locations of these degeneracies, information on the local vortex
    interactions may be obtained.
alternative_title:
- Bulletin of the American Physical Society
article_number: H25.00006
article_processing_charge: No
author:
- first_name: Tyler
  full_name: Naibert, Tyler
  last_name: Naibert
- first_name: Hryhoriy
  full_name: Polshyn, Hryhoriy
  id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48
  last_name: Polshyn
  orcid: 0000-0001-8223-8896
- first_name: Brian
  full_name: Wolin, Brian
  last_name: Wolin
- first_name: Malcolm
  full_name: Durkin, Malcolm
  last_name: Durkin
- first_name: Rita
  full_name: Garrido Menacho, Rita
  last_name: Garrido Menacho
- first_name: Ian Mondragon
  full_name: Shem, Ian Mondragon
  last_name: Shem
- first_name: Victor
  full_name: Chua, Victor
  last_name: Chua
- first_name: Taylor
  full_name: Hughes, Taylor
  last_name: Hughes
- first_name: Nadya
  full_name: Mason, Nadya
  last_name: Mason
- first_name: Raffi
  full_name: Budakian, Raffi
  last_name: Budakian
citation:
  ama: 'Naibert T, Polshyn H, Wolin B, et al. Stochastic resonance magnetic force
    microscopy imaging of Josephson arrays. In: <i>APS March Meeting 2016</i>. Vol
    61. American Physical Society; 2016.'
  apa: 'Naibert, T., Polshyn, H., Wolin, B., Durkin, M., Garrido Menacho, R., Shem,
    I. M., … Budakian, R. (2016). Stochastic resonance magnetic force microscopy imaging
    of Josephson arrays. In <i>APS March Meeting 2016</i> (Vol. 61). Baltimore, MD,
    United States: American Physical Society.'
  chicago: Naibert, Tyler, Hryhoriy Polshyn, Brian Wolin, Malcolm Durkin, Rita Garrido
    Menacho, Ian Mondragon Shem, Victor Chua, Taylor Hughes, Nadya Mason, and Raffi
    Budakian. “Stochastic Resonance Magnetic Force Microscopy Imaging of Josephson
    Arrays.” In <i>APS March Meeting 2016</i>, Vol. 61. American Physical Society,
    2016.
  ieee: T. Naibert <i>et al.</i>, “Stochastic resonance magnetic force microscopy
    imaging of Josephson arrays,” in <i>APS March Meeting 2016</i>, Baltimore, MD,
    United States, 2016, vol. 61, no. 2.
  ista: 'Naibert T, Polshyn H, Wolin B, Durkin M, Garrido Menacho R, Shem IM, Chua
    V, Hughes T, Mason N, Budakian R. 2016. Stochastic resonance magnetic force microscopy
    imaging of Josephson arrays. APS March Meeting 2016. APS: American Physical Society,
    Bulletin of the American Physical Society, vol. 61, H25.00006.'
  mla: Naibert, Tyler, et al. “Stochastic Resonance Magnetic Force Microscopy Imaging
    of Josephson Arrays.” <i>APS March Meeting 2016</i>, vol. 61, no. 2, H25.00006,
    American Physical Society, 2016.
  short: T. Naibert, H. Polshyn, B. Wolin, M. Durkin, R. Garrido Menacho, I.M. Shem,
    V. Chua, T. Hughes, N. Mason, R. Budakian, in:, APS March Meeting 2016, American
    Physical Society, 2016.
conference:
  end_date: 2016-03-18
  location: Baltimore, MD, United States
  name: 'APS: American Physical Society'
  start_date: 2016-03-14
date_created: 2022-02-08T10:10:39Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2022-02-08T10:43:33Z
day: '01'
extern: '1'
intvolume: '        61'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://meetings.aps.org/Meeting/MAR16/Session/H25.6
month: '03'
oa: 1
oa_version: Published Version
publication: APS March Meeting 2016
publication_identifier:
  issn:
  - 0003-0503
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Stochastic resonance magnetic force microscopy imaging of Josephson arrays
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 61
year: '2016'
...
---
_id: '1081'
abstract:
- lang: eng
  text: The asymmetric localization of proteins in the plasma membrane domains of
    eukaryotic cells is a fundamental manifestation of cell polarity that is central
    to multicellular organization and developmental patterning. In plants, the mechanisms
    underlying the polar localization of cargo proteins are still largely unknown
    and appear to be fundamentally distinct from those operating in mammals. Here,
    we present a systematic, quantitative comparative analysis of the polar delivery
    and subcellular localization of proteins that characterize distinct polar plasma
    membrane domains in plant cells. The combination of microscopic analyses and computational
    modeling revealed a mechanistic framework common to diverse polar cargos and underlying
    the establishment and maintenance of apical, basal, and lateral polar domains
    in plant cells. This mechanism depends on the polar secretion, constitutive endocytic
    recycling, and restricted lateral diffusion of cargos within the plasma membrane.
    Moreover, our observations suggest that polar cargo distribution involves the
    individual protein potential to form clusters within the plasma membrane and interact
    with the extracellular matrix. Our observations provide insights into the shared
    cellular mechanisms of polar cargo delivery and polarity maintenance in plant
    cells.
acknowledgement: "We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor
  sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing
  the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP);
  Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute
  of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research
  Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety
  for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the
  Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN."
article_number: '16018'
article_processing_charge: No
author:
- first_name: Łukasz
  full_name: Łangowski, Łukasz
  last_name: Łangowski
- first_name: Krzysztof T
  full_name: Wabnik, Krzysztof T
  id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
  last_name: Wabnik
  orcid: 0000-0001-7263-0560
- first_name: Hongjiang
  full_name: Li, Hongjiang
  id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
  last_name: Li
  orcid: 0000-0001-5039-9660
- first_name: Steffen
  full_name: Vanneste, Steffen
  last_name: Vanneste
- first_name: Satoshi
  full_name: Naramoto, Satoshi
  last_name: Naramoto
- first_name: Hirokazu
  full_name: Tanaka, Hirokazu
  last_name: Tanaka
- first_name: Jirí
  full_name: Friml, Jirí
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
citation:
  ama: Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery
    and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>.
    2016;2. doi:<a href="https://doi.org/10.1038/celldisc.2016.18">10.1038/celldisc.2016.18</a>
  apa: Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H.,
    &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance
    at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing
    Group. <a href="https://doi.org/10.1038/celldisc.2016.18">https://doi.org/10.1038/celldisc.2016.18</a>
  chicago: Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste,
    Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo
    Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.”
    <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href="https://doi.org/10.1038/celldisc.2016.18">https://doi.org/10.1038/celldisc.2016.18</a>.
  ieee: Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity
    maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>,
    vol. 2. Nature Publishing Group, 2016.
  ista: Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016.
    Cellular mechanisms for cargo delivery and polarity maintenance at different polar
    domains in plant cells. Cell Discovery. 2, 16018.
  mla: Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity
    Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>,
    vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href="https://doi.org/10.1038/celldisc.2016.18">10.1038/celldisc.2016.18</a>.
  short: Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J.
    Friml, Cell Discovery 2 (2016).
date_created: 2018-12-11T11:50:02Z
date_published: 2016-07-19T00:00:00Z
date_updated: 2025-09-22T14:19:46Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1038/celldisc.2016.18
ec_funded: 1
external_id:
  isi:
  - '000414797400001'
file:
- access_level: open_access
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:13:33Z
  date_updated: 2018-12-12T10:13:33Z
  file_id: '5017'
  file_name: IST-2017-757-v1+1_celldisc201618.pdf
  file_size: 5261671
  relation: main_file
file_date_updated: 2018-12-12T10:13:33Z
has_accepted_license: '1'
intvolume: '         2'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '282300'
  name: Polarity and subcellular dynamics in plants
publication: Cell Discovery
publication_status: published
publisher: Nature Publishing Group
publist_id: '6299'
pubrep_id: '757'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cellular mechanisms for cargo delivery and polarity maintenance at different
  polar domains in plant cells
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2
year: '2016'
...