---
_id: '3329'
abstract:
- lang: eng
  text: 'We consider the offset-deconstruction problem: Given a polygonal shape Q
    with n vertices, can it be expressed, up to a tolerance µ in Hausdorff distance,
    as the Minkowski sum of another polygonal shape P with a disk of fixed radius?
    If it does, we also seek a preferably simple-looking solution shape P; then, P''s
    offset constitutes an accurate, vertex-reduced, and smoothened approximation of
    Q. We give an O(n log n)-time exact decision algorithm that handles any polygonal
    shape, assuming the real-RAM model of computation. An alternative algorithm, based
    purely on rational arithmetic, answers the same deconstruction problem, up to
    an uncertainty parameter, and its running time depends on the parameter δ (in
    addition to the other input parameters: n, δ and the radius of the disk). If the
    input shape is found to be approximable, the rational-arithmetic algorithm also
    computes an approximate solution shape for the problem. For convex shapes, the
    complexity of the exact decision algorithm drops to O(n), which is also the time
    required to compute a solution shape P with at most one more vertex than a vertex-minimal
    one. Our study is motivated by applications from two different domains. However,
    since the offset operation has numerous uses, we anticipate that the reverse question
    that we study here will be still more broadly applicable. We present results obtained
    with our implementation of the rational-arithmetic algorithm.'
author:
- first_name: Eric
  full_name: Berberich, Eric
  last_name: Berberich
- first_name: Dan
  full_name: Halperin, Dan
  last_name: Halperin
- first_name: Michael
  full_name: Kerber, Michael
  id: 36E4574A-F248-11E8-B48F-1D18A9856A87
  last_name: Kerber
  orcid: 0000-0002-8030-9299
- first_name: Roza
  full_name: Pogalnikova, Roza
  last_name: Pogalnikova
citation:
  ama: 'Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate
    offsets. In: <i>Proceedings of the Twenty-Seventh Annual Symposium on Computational
    Geometry</i>. ACM; 2011:187-196. doi:<a href="https://doi.org/10.1145/1998196.1998225">10.1145/1998196.1998225</a>'
  apa: 'Berberich, E., Halperin, D., Kerber, M., &#38; Pogalnikova, R. (2011). Deconstructing
    approximate offsets. In <i>Proceedings of the twenty-seventh annual symposium
    on Computational geometry</i> (pp. 187–196). Paris, France: ACM. <a href="https://doi.org/10.1145/1998196.1998225">https://doi.org/10.1145/1998196.1998225</a>'
  chicago: Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing
    Approximate Offsets.” In <i>Proceedings of the Twenty-Seventh Annual Symposium
    on Computational Geometry</i>, 187–96. ACM, 2011. <a href="https://doi.org/10.1145/1998196.1998225">https://doi.org/10.1145/1998196.1998225</a>.
  ieee: E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing
    approximate offsets,” in <i>Proceedings of the twenty-seventh annual symposium
    on Computational geometry</i>, Paris, France, 2011, pp. 187–196.
  ista: 'Berberich E, Halperin D, Kerber M, Pogalnikova R. 2011. Deconstructing approximate
    offsets. Proceedings of the twenty-seventh annual symposium on Computational geometry.
    SCG: Symposium on Computational Geometry, 187–196.'
  mla: Berberich, Eric, et al. “Deconstructing Approximate Offsets.” <i>Proceedings
    of the Twenty-Seventh Annual Symposium on Computational Geometry</i>, ACM, 2011,
    pp. 187–96, doi:<a href="https://doi.org/10.1145/1998196.1998225">10.1145/1998196.1998225</a>.
  short: E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, in:, Proceedings of
    the Twenty-Seventh Annual Symposium on Computational Geometry, ACM, 2011, pp.
    187–196.
conference:
  end_date: 2011-06-15
  location: Paris, France
  name: 'SCG: Symposium on Computational Geometry'
  start_date: 2011-06-13
date_created: 2018-12-11T12:02:42Z
date_published: 2011-06-13T00:00:00Z
date_updated: 2023-02-23T11:12:57Z
day: '13'
department:
- _id: HeEd
doi: 10.1145/1998196.1998225
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1109.2158
month: '06'
oa: 1
oa_version: Preprint
page: 187 - 196
publication: Proceedings of the twenty-seventh annual symposium on Computational geometry
publication_status: published
publisher: ACM
publist_id: '3306'
quality_controlled: '1'
related_material:
  record:
  - id: '3115'
    relation: later_version
    status: public
scopus_import: 1
status: public
title: Deconstructing approximate offsets
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3330'
abstract:
- lang: eng
  text: We consider the problem of approximating all real roots of a square-free polynomial
    f. Given isolating intervals, our algorithm refines each of them to a width at
    most 2-L, that is, each of the roots is approximated to L bits after the binary
    point. Our method provides a certified answer for arbitrary real polynomials,
    only requiring finite approximations of the polynomial coefficient and choosing
    a suitable working precision adaptively. In this way, we get a correct algorithm
    that is simple to implement and practically efficient. Our algorithm uses the
    quadratic interval refinement method; we adapt that method to be able to cope
    with inaccuracies when evaluating f, without sacrificing its quadratic convergence
    behavior. We prove a bound on the bit complexity of our algorithm in terms of
    degree, coefficient size and discriminant. Our bound improves previous work on
    integer polynomials by a factor of deg f and essentially matches best known theoretical
    bounds on root approximation which are obtained by very sophisticated algorithms.
article_processing_charge: No
arxiv: 1
author:
- first_name: Michael
  full_name: Kerber, Michael
  id: 36E4574A-F248-11E8-B48F-1D18A9856A87
  last_name: Kerber
  orcid: 0000-0002-8030-9299
- first_name: Michael
  full_name: Sagraloff, Michael
  last_name: Sagraloff
citation:
  ama: 'Kerber M, Sagraloff M. Root refinement for real polynomials. In: Springer;
    2011:209-216. doi:<a href="https://doi.org/10.1145/1993886.1993920">10.1145/1993886.1993920</a>'
  apa: 'Kerber, M., &#38; Sagraloff, M. (2011). Root refinement for real polynomials
    (pp. 209–216). Presented at the ISSAC: International Symposium on Symbolic and
    Algebraic Computation, California, USA: Springer. <a href="https://doi.org/10.1145/1993886.1993920">https://doi.org/10.1145/1993886.1993920</a>'
  chicago: Kerber, Michael, and Michael Sagraloff. “Root Refinement for Real Polynomials,”
    209–16. Springer, 2011. <a href="https://doi.org/10.1145/1993886.1993920">https://doi.org/10.1145/1993886.1993920</a>.
  ieee: 'M. Kerber and M. Sagraloff, “Root refinement for real polynomials,” presented
    at the ISSAC: International Symposium on Symbolic and Algebraic Computation, California,
    USA, 2011, pp. 209–216.'
  ista: 'Kerber M, Sagraloff M. 2011. Root refinement for real polynomials. ISSAC:
    International Symposium on Symbolic and Algebraic Computation, 209–216.'
  mla: Kerber, Michael, and Michael Sagraloff. <i>Root Refinement for Real Polynomials</i>.
    Springer, 2011, pp. 209–16, doi:<a href="https://doi.org/10.1145/1993886.1993920">10.1145/1993886.1993920</a>.
  short: M. Kerber, M. Sagraloff, in:, Springer, 2011, pp. 209–216.
conference:
  end_date: 2011-06-11
  location: California, USA
  name: 'ISSAC: International Symposium on Symbolic and Algebraic Computation'
  start_date: 2011-06-08
date_created: 2018-12-11T12:02:43Z
date_published: 2011-06-08T00:00:00Z
date_updated: 2021-01-12T07:42:42Z
day: '08'
department:
- _id: HeEd
doi: 10.1145/1993886.1993920
external_id:
  arxiv:
  - '1104.1362'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1104.1362
month: '06'
oa: 1
oa_version: Preprint
page: 209 - 216
publication_status: published
publisher: Springer
publist_id: '3304'
quality_controlled: '1'
scopus_import: 1
status: public
title: Root refinement for real polynomials
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3332'
abstract:
- lang: eng
  text: Given an algebraic hypersurface O in ℝd, how many simplices are necessary
    for a simplicial complex isotopic to O? We address this problem and the variant
    where all vertices of the complex must lie on O. We give asymptotically tight
    worst-case bounds for algebraic plane curves. Our results gradually improve known
    bounds in higher dimensions; however, the question for tight bounds remains unsolved
    for d ≥ 3.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
  full_name: Kerber, Michael
  id: 36E4574A-F248-11E8-B48F-1D18A9856A87
  last_name: Kerber
  orcid: 0000-0002-8030-9299
- first_name: Michael
  full_name: Sagraloff, Michael
  last_name: Sagraloff
citation:
  ama: Kerber M, Sagraloff M. A note on the complexity of real algebraic hypersurfaces.
    <i>Graphs and Combinatorics</i>. 2011;27(3):419-430. doi:<a href="https://doi.org/10.1007/s00373-011-1020-7">10.1007/s00373-011-1020-7</a>
  apa: Kerber, M., &#38; Sagraloff, M. (2011). A note on the complexity of real algebraic
    hypersurfaces. <i>Graphs and Combinatorics</i>. Springer. <a href="https://doi.org/10.1007/s00373-011-1020-7">https://doi.org/10.1007/s00373-011-1020-7</a>
  chicago: Kerber, Michael, and Michael Sagraloff. “A Note on the Complexity of Real
    Algebraic Hypersurfaces.” <i>Graphs and Combinatorics</i>. Springer, 2011. <a
    href="https://doi.org/10.1007/s00373-011-1020-7">https://doi.org/10.1007/s00373-011-1020-7</a>.
  ieee: M. Kerber and M. Sagraloff, “A note on the complexity of real algebraic hypersurfaces,”
    <i>Graphs and Combinatorics</i>, vol. 27, no. 3. Springer, pp. 419–430, 2011.
  ista: Kerber M, Sagraloff M. 2011. A note on the complexity of real algebraic hypersurfaces.
    Graphs and Combinatorics. 27(3), 419–430.
  mla: Kerber, Michael, and Michael Sagraloff. “A Note on the Complexity of Real Algebraic
    Hypersurfaces.” <i>Graphs and Combinatorics</i>, vol. 27, no. 3, Springer, 2011,
    pp. 419–30, doi:<a href="https://doi.org/10.1007/s00373-011-1020-7">10.1007/s00373-011-1020-7</a>.
  short: M. Kerber, M. Sagraloff, Graphs and Combinatorics 27 (2011) 419–430.
date_created: 2018-12-11T12:02:43Z
date_published: 2011-03-17T00:00:00Z
date_updated: 2021-01-12T07:42:43Z
day: '17'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1007/s00373-011-1020-7
file:
- access_level: open_access
  checksum: a63a1e3e885dcc68f1e3dea68dfbe213
  content_type: application/pdf
  creator: dernst
  date_created: 2020-05-19T16:11:36Z
  date_updated: 2020-07-14T12:46:08Z
  file_id: '7869'
  file_name: 2011_GraphsCombi_Kerber.pdf
  file_size: 143976
  relation: main_file
file_date_updated: 2020-07-14T12:46:08Z
has_accepted_license: '1'
intvolume: '        27'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 419 - 430
publication: Graphs and Combinatorics
publication_status: published
publisher: Springer
publist_id: '3301'
quality_controlled: '1'
scopus_import: 1
status: public
title: A note on the complexity of real algebraic hypersurfaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2011'
...
---
_id: '3335'
abstract:
- lang: eng
  text: We study the topology of the Megaparsec Cosmic Web in terms of the scale-dependent
    Betti numbers, which formalize the topological information content of the cosmic
    mass distribution. While the Betti numbers do not fully quantify topology, they
    extend the information beyond conventional cosmological studies of topology in
    terms of genus and Euler characteristic. The richer information content of Betti
    numbers goes along the availability of fast algorithms to compute them. For continuous
    density fields, we determine the scale-dependence of Betti numbers by invoking
    the cosmologically familiar filtration of sublevel or superlevel sets defined
    by density thresholds. For the discrete galaxy distribution, however, the analysis
    is based on the alpha shapes of the particles. These simplicial complexes constitute
    an ordered sequence of nested subsets of the Delaunay tessellation, a filtration
    defined by the scale parameter, α. As they are homotopy equivalent to the sublevel
    sets of the distance field, they are an excellent tool for assessing the topological
    structure of a discrete point distribution. In order to develop an intuitive understanding
    for the behavior of Betti numbers as a function of α, and their relation to the
    morphological patterns in the Cosmic Web, we first study them within the context
    of simple heuristic Voronoi clustering models. These can be tuned to consist of
    specific morphological elements of the Cosmic Web, i.e. clusters, filaments, or
    sheets. To elucidate the relative prominence of the various Betti numbers in different
    stages of morphological evolution, we introduce the concept of alpha tracks. Subsequently,
    we address the topology of structures emerging in the standard LCDM scenario and
    in cosmological scenarios with alternative dark energy content. The evolution
    of the Betti numbers is shown to reflect the hierarchical evolution of the Cosmic
    Web. We also demonstrate that the scale-dependence of the Betti numbers yields
    a promising measure of cosmological parameters, with a potential to help in determining
    the nature of dark energy and to probe primordial non-Gaussianities. We also discuss
    the expected Betti numbers as a function of the density threshold for superlevel
    sets of a Gaussian random field. Finally, we introduce the concept of persistent
    homology. It measures scale levels of the mass distribution and allows us to separate
    small from large scale features. Within the context of the hierarchical cosmic
    structure formation, persistence provides a natural formalism for a multiscale
    topology study of the Cosmic Web.
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Rien
  full_name: Van De Weygaert, Rien
  last_name: Van De Weygaert
- first_name: Gert
  full_name: Vegter, Gert
  last_name: Vegter
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Bernard
  full_name: Jones, Bernard
  last_name: Jones
- first_name: Pratyush
  full_name: Pranav, Pratyush
  last_name: Pranav
- first_name: Changbom
  full_name: Park, Changbom
  last_name: Park
- first_name: Wojciech
  full_name: Hellwing, Wojciech
  last_name: Hellwing
- first_name: Bob
  full_name: Eldering, Bob
  last_name: Eldering
- first_name: Nico
  full_name: Kruithof, Nico
  last_name: Kruithof
- first_name: Patrick
  full_name: Bos, Patrick
  last_name: Bos
- first_name: Johan
  full_name: Hidding, Johan
  last_name: Hidding
- first_name: Job
  full_name: Feldbrugge, Job
  last_name: Feldbrugge
- first_name: Eline
  full_name: Ten Have, Eline
  last_name: Ten Have
- first_name: Matti
  full_name: Van Engelen, Matti
  last_name: Van Engelen
- first_name: Manuel
  full_name: Caroli, Manuel
  last_name: Caroli
- first_name: Monique
  full_name: Teillaud, Monique
  last_name: Teillaud
citation:
  ama: 'Van De Weygaert R, Vegter G, Edelsbrunner H, et al. Alpha, Betti and the Megaparsec
    Universe: On the topology of the Cosmic Web. In: Gavrilova M, Tan K, Mostafavi
    M, eds. <i>Transactions on Computational Science XIV</i>. Vol 6970. Special Issue
    on Voronoi Diagrams and Delaunay Triangulation. Springer; 2011:60-101. doi:<a
    href="https://doi.org/10.1007/978-3-642-25249-5_3">10.1007/978-3-642-25249-5_3</a>'
  apa: 'Van De Weygaert, R., Vegter, G., Edelsbrunner, H., Jones, B., Pranav, P.,
    Park, C., … Teillaud, M. (2011). Alpha, Betti and the Megaparsec Universe: On
    the topology of the Cosmic Web. In M. Gavrilova, K. Tan, &#38; M. Mostafavi (Eds.),
    <i>Transactions on Computational Science XIV</i> (Vol. 6970, pp. 60–101). Springer.
    <a href="https://doi.org/10.1007/978-3-642-25249-5_3">https://doi.org/10.1007/978-3-642-25249-5_3</a>'
  chicago: 'Van De Weygaert, Rien, Gert Vegter, Herbert Edelsbrunner, Bernard Jones,
    Pratyush Pranav, Changbom Park, Wojciech Hellwing, et al. “Alpha, Betti and the
    Megaparsec Universe: On the Topology of the Cosmic Web.” In <i>Transactions on
    Computational Science XIV</i>, edited by Marina Gavrilova, Kenneth Tan, and Mir
    Mostafavi, 6970:60–101. Special Issue on Voronoi Diagrams and Delaunay Triangulation.
    Springer, 2011. <a href="https://doi.org/10.1007/978-3-642-25249-5_3">https://doi.org/10.1007/978-3-642-25249-5_3</a>.'
  ieee: 'R. Van De Weygaert <i>et al.</i>, “Alpha, Betti and the Megaparsec Universe:
    On the topology of the Cosmic Web,” in <i>Transactions on Computational Science
    XIV</i>, vol. 6970, M. Gavrilova, K. Tan, and M. Mostafavi, Eds. Springer, 2011,
    pp. 60–101.'
  ista: 'Van De Weygaert R, Vegter G, Edelsbrunner H, Jones B, Pranav P, Park C, Hellwing
    W, Eldering B, Kruithof N, Bos P, Hidding J, Feldbrugge J, Ten Have E, Van Engelen
    M, Caroli M, Teillaud M. 2011.Alpha, Betti and the Megaparsec Universe: On the
    topology of the Cosmic Web. In: Transactions on Computational Science XIV. LNCS,
    vol. 6970, 60–101.'
  mla: 'Van De Weygaert, Rien, et al. “Alpha, Betti and the Megaparsec Universe: On
    the Topology of the Cosmic Web.” <i>Transactions on Computational Science XIV</i>,
    edited by Marina Gavrilova et al., vol. 6970, Springer, 2011, pp. 60–101, doi:<a
    href="https://doi.org/10.1007/978-3-642-25249-5_3">10.1007/978-3-642-25249-5_3</a>.'
  short: R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park,
    W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten
    Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi
    (Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101.
date_created: 2018-12-11T12:02:44Z
date_published: 2011-11-09T00:00:00Z
date_updated: 2021-01-12T07:42:44Z
day: '09'
department:
- _id: HeEd
doi: 10.1007/978-3-642-25249-5_3
editor:
- first_name: Marina
  full_name: Gavrilova, Marina
  last_name: Gavrilova
- first_name: Kenneth
  full_name: Tan, Kenneth
  last_name: Tan
- first_name: Mir
  full_name: Mostafavi, Mir
  last_name: Mostafavi
external_id:
  arxiv:
  - '1306.3640'
intvolume: '      6970'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1306.3640
month: '11'
oa: 1
oa_version: Preprint
page: 60 - 101
publication: Transactions on Computational Science XIV
publication_status: published
publisher: Springer
publist_id: '3295'
quality_controlled: '1'
scopus_import: 1
series_title: Special Issue on Voronoi Diagrams and Delaunay Triangulation
status: public
title: 'Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web'
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6970
year: '2011'
...
---
_id: '3338'
abstract:
- lang: eng
  text: 'We consider 2-player games played on a finite state space for an infinite
    number of rounds. The games are concurrent: in each round, the two players (player
    1 and player 2) choose their moves inde- pendently and simultaneously; the current
    state and the two moves determine the successor state. We study concurrent games
    with ω-regular winning conditions specified as parity objectives. We consider
    the qualitative analysis problems: the computation of the almost-sure and limit-sure
    winning set of states, where player 1 can ensure to win with probability 1 and
    with probability arbitrarily close to 1, respec- tively. In general the almost-sure
    and limit-sure winning strategies require both infinite-memory as well as infinite-precision
    (to describe probabilities). We study the bounded-rationality problem for qualitative
    analysis of concurrent parity games, where the strategy set for player 1 is restricted
    to bounded-resource strategies. In terms of precision, strategies can be deterministic,
    uniform, finite-precision or infinite- precision; and in terms of memory, strategies
    can be memoryless, finite-memory or infinite-memory. We present a precise and
    complete characterization of the qualitative winning sets for all combinations
    of classes of strategies. In particular, we show that uniform memoryless strategies
    are as powerful as finite-precision infinite-memory strategies, and infinite-precision
    memoryless strategies are as power- ful as infinite-precision finite-memory strategies.
    We show that the winning sets can be computed in O(n2d+3) time, where n is the
    size of the game structure and 2d is the number of priorities (or colors), and
    our algorithms are symbolic. The membership problem of whether a state belongs
    to a winning set can be decided in NP ∩ coNP. While this complexity is the same
    as for the simpler class of turn-based parity games, where in each state only
    one of the two players has a choice of moves, our algorithms, that are obtained
    by characterization of the winning sets as μ-calculus formulas, are considerably
    more involved than those for turn-based games.'
arxiv: 1
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
citation:
  ama: Chatterjee K. Bounded rationality in concurrent parity games. <i>arXiv</i>.
    2011:1-51.
  apa: Chatterjee, K. (2011). Bounded rationality in concurrent parity games. <i>arXiv</i>.
    ArXiv.
  chicago: Chatterjee, Krishnendu. “Bounded Rationality in Concurrent Parity Games.”
    <i>ArXiv</i>. ArXiv, 2011.
  ieee: K. Chatterjee, “Bounded rationality in concurrent parity games,” <i>arXiv</i>.
    ArXiv, pp. 1–51, 2011.
  ista: Chatterjee K. 2011. Bounded rationality in concurrent parity games. arXiv,
    1–51, .
  mla: Chatterjee, Krishnendu. “Bounded Rationality in Concurrent Parity Games.” <i>ArXiv</i>,
    ArXiv, 2011, pp. 1–51.
  short: K. Chatterjee, ArXiv (2011) 1–51.
date_created: 2018-12-11T12:02:45Z
date_published: 2011-07-11T00:00:00Z
date_updated: 2023-02-23T12:23:40Z
day: '11'
department:
- _id: KrCh
external_id:
  arxiv:
  - '1107.2146'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1107.2146
month: '07'
oa: 1
oa_version: Preprint
page: 1 - 51
publication: arXiv
publication_status: published
publisher: ArXiv
publist_id: '3287'
related_material:
  record:
  - id: '5380'
    relation: earlier_version
    status: public
status: public
title: Bounded rationality in concurrent parity games
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3339'
abstract:
- lang: eng
  text: 'Turn-based stochastic games and its important subclass Markov decision processes
    (MDPs) provide models for systems with both probabilistic and nondeterministic
    behaviors. We consider turn-based stochastic games with two classical quantitative
    objectives: discounted-sum and long-run average objectives. The game models and
    the quantitative objectives are widely used in probabilistic verification, planning,
    optimal inventory control, network protocol and performance analysis. Games and
    MDPs that model realistic systems often have very large state spaces, and probabilistic
    abstraction techniques are necessary to handle the state-space explosion. The
    commonly used full-abstraction techniques do not yield space-savings for systems
    that have many states with similar value, but does not necessarily have similar
    transition structure. A semi-abstraction technique, namely Magnifying-lens abstractions
    (MLA), that clusters states based on value only, disregarding differences in their
    transition relation was proposed for qualitative objectives (reachability and
    safety objectives). In this paper we extend the MLA technique to solve stochastic
    games with discounted-sum and long-run average objectives. We present the MLA
    technique based abstraction-refinement algorithm for stochastic games and MDPs
    with discounted-sum objectives. For long-run average objectives, our solution
    works for all MDPs and a sub-class of stochastic games where every state has the
    same value. '
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: Luca
  full_name: De Alfaro, Luca
  last_name: De Alfaro
- first_name: Roy
  full_name: Pritam, Roy
  last_name: Pritam
citation:
  ama: Chatterjee K, De Alfaro L, Pritam R. Magnifying lens abstraction for stochastic
    games with discounted and long-run average objectives. <i>arXiv</i>. 2011.
  apa: Chatterjee, K., De Alfaro, L., &#38; Pritam, R. (2011). Magnifying lens abstraction
    for stochastic games with discounted and long-run average objectives. <i>arXiv</i>.
    ArXiv.
  chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Roy Pritam. “Magnifying Lens
    Abstraction for Stochastic Games with Discounted and Long-Run Average Objectives.”
    <i>ArXiv</i>. ArXiv, 2011.
  ieee: K. Chatterjee, L. De Alfaro, and R. Pritam, “Magnifying lens abstraction for
    stochastic games with discounted and long-run average objectives,” <i>arXiv</i>.
    ArXiv, 2011.
  ista: Chatterjee K, De Alfaro L, Pritam R. 2011. Magnifying lens abstraction for
    stochastic games with discounted and long-run average objectives. arXiv, .
  mla: Chatterjee, Krishnendu, et al. “Magnifying Lens Abstraction for Stochastic
    Games with Discounted and Long-Run Average Objectives.” <i>ArXiv</i>, ArXiv, 2011.
  short: K. Chatterjee, L. De Alfaro, R. Pritam, ArXiv (2011).
date_created: 2018-12-11T12:02:46Z
date_published: 2011-07-11T00:00:00Z
date_updated: 2021-01-12T07:42:46Z
day: '11'
department:
- _id: KrCh
external_id:
  arxiv:
  - '1107.2132'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1107.2132
month: '07'
oa: 1
oa_version: Preprint
page: '17'
publication: arXiv
publication_status: published
publisher: ArXiv
publist_id: '3286'
status: public
title: Magnifying lens abstraction for stochastic games with discounted and long-run
  average objectives
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3342'
abstract:
- lang: eng
  text: 'We consider Markov decision processes (MDPs) with ω-regular specifications
    given as parity objectives. We consider the problem of computing the set of almost-sure
    winning states from where the objective can be ensured with probability 1. The
    algorithms for the computation of the almost-sure winning set for parity objectives
    iteratively use the solutions for the almost-sure winning set for Büchi objectives
    (a special case of parity objectives). Our contributions are as follows: First,
    we present the first subquadratic symbolic algorithm to compute the almost-sure
    winning set for MDPs with Büchi objectives; our algorithm takes O(nm)  symbolic
    steps as compared to the previous known algorithm that takes O(n 2) symbolic steps,
    where n is the number of states and m is the number of edges of the MDP. In practice
    MDPs often have constant out-degree, and then our symbolic algorithm takes O(nn)  symbolic
    steps, as compared to the previous known O(n 2) symbolic steps algorithm. Second,
    we present a new algorithm, namely win-lose algorithm, with the following two
    properties: (a) the algorithm iteratively computes subsets of the almost-sure
    winning set and its complement, as compared to all previous algorithms that discover
    the almost-sure winning set upon termination; and (b) requires O(nK)  symbolic
    steps, where K is the maximal number of edges of strongly connected components
    (scc’s) of the MDP. The win-lose algorithm requires symbolic computation of scc’s.
    Third, we improve the algorithm for symbolic scc computation; the previous known
    algorithm takes linear symbolic steps, and our new algorithm improves the constants
    associated with the linear number of steps. In the worst case the previous known
    algorithm takes 5·n symbolic steps, whereas our new algorithm takes 4 ·n symbolic
    steps.'
alternative_title:
- LNCS
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: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Manas
  full_name: Joglekar, Manas
  last_name: Joglekar
- first_name: Shah
  full_name: Nisarg, Shah
  last_name: Nisarg
citation:
  ama: 'Chatterjee K, Henzinger MH, Joglekar M, Nisarg S. Symbolic algorithms for
    qualitative analysis of Markov decision processes with Büchi objectives. In: Gopalakrishnan
    G, Qadeer S, eds. Vol 6806. Springer; 2011:260-276. doi:<a href="https://doi.org/10.1007/978-3-642-22110-1_21">10.1007/978-3-642-22110-1_21</a>'
  apa: 'Chatterjee, K., Henzinger, M. H., Joglekar, M., &#38; Nisarg, S. (2011). Symbolic
    algorithms for qualitative analysis of Markov decision processes with Büchi objectives.
    In G. Gopalakrishnan &#38; S. Qadeer (Eds.) (Vol. 6806, pp. 260–276). Presented
    at the CAV: Computer Aided Verification, Snowbird, USA: Springer. <a href="https://doi.org/10.1007/978-3-642-22110-1_21">https://doi.org/10.1007/978-3-642-22110-1_21</a>'
  chicago: Chatterjee, Krishnendu, Monika H Henzinger, Manas Joglekar, and Shah Nisarg.
    “Symbolic Algorithms for Qualitative Analysis of Markov Decision Processes with
    Büchi Objectives.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:260–76.
    Springer, 2011. <a href="https://doi.org/10.1007/978-3-642-22110-1_21">https://doi.org/10.1007/978-3-642-22110-1_21</a>.
  ieee: 'K. Chatterjee, M. H. Henzinger, M. Joglekar, and S. Nisarg, “Symbolic algorithms
    for qualitative analysis of Markov decision processes with Büchi objectives,”
    presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806,
    pp. 260–276.'
  ista: 'Chatterjee K, Henzinger MH, Joglekar M, Nisarg S. 2011. Symbolic algorithms
    for qualitative analysis of Markov decision processes with Büchi objectives. CAV:
    Computer Aided Verification, LNCS, vol. 6806, 260–276.'
  mla: Chatterjee, Krishnendu, et al. <i>Symbolic Algorithms for Qualitative Analysis
    of Markov Decision Processes with Büchi Objectives</i>. Edited by Ganesh Gopalakrishnan
    and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 260–76, doi:<a href="https://doi.org/10.1007/978-3-642-22110-1_21">10.1007/978-3-642-22110-1_21</a>.
  short: K. Chatterjee, M.H. Henzinger, M. Joglekar, S. Nisarg, in:, G. Gopalakrishnan,
    S. Qadeer (Eds.), Springer, 2011, pp. 260–276.
conference:
  end_date: 2011-07-20
  location: Snowbird, USA
  name: 'CAV: Computer Aided Verification'
  start_date: 2011-07-14
date_created: 2018-12-11T12:02:47Z
date_published: 2011-08-11T00:00:00Z
date_updated: 2023-02-23T11:00:13Z
day: '11'
department:
- _id: KrCh
doi: 10.1007/978-3-642-22110-1_21
editor:
- first_name: Ganesh
  full_name: Gopalakrishnan, Ganesh
  last_name: Gopalakrishnan
- first_name: Shaz
  full_name: Qadeer, Shaz
  last_name: Qadeer
external_id:
  arxiv:
  - '1104.3348'
intvolume: '      6806'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1104.3348
month: '08'
oa: 1
oa_version: Preprint
page: 260 - 276
project:
- _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: '3282'
quality_controlled: '1'
related_material:
  record:
  - id: '2831'
    relation: later_version
    status: public
status: public
title: Symbolic algorithms for qualitative analysis of Markov decision processes with
  Büchi objectives
type: conference
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 6806
year: '2011'
...
---
_id: '3343'
abstract:
- lang: eng
  text: 'We present faster and dynamic algorithms for the following problems arising
    in probabilistic verification: Computation of the maximal end-component (mec)
    decomposition of Markov decision processes (MDPs), and of the almost sure winning
    set for reachability and parity objectives in MDPs. We achieve the following running
    time for static algorithms in MDPs with graphs of n vertices and m edges: (1)
    O(m · min{ √m, n2/3 }) for the mec decomposition, improving the longstanding O(m·n)
    bound; (2) O(m·n2/3) for reachability objectives, improving the previous O(m ·
    √m) bound for m &gt; n4/3; and (3) O(m · min{ √m, n2/3 } · log(d)) for parity
    objectives with d priorities, improving the previous O(m · √m · d) bound. We also
    give incremental and decremental algorithms in linear time for mec decomposition
    and reachability objectives and O(m · log d) time for parity ob jectives.'
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: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
citation:
  ama: 'Chatterjee K, Henzinger MH. Faster and dynamic algorithms for maximal end-component
    decomposition and related graph problems in probabilistic verification. In: SIAM;
    2011:1318-1336. doi:<a href="https://doi.org/10.1137/1.9781611973082.101">10.1137/1.9781611973082.101</a>'
  apa: 'Chatterjee, K., &#38; Henzinger, M. H. (2011). Faster and dynamic algorithms
    for maximal end-component decomposition and related graph problems in probabilistic
    verification (pp. 1318–1336). Presented at the SODA: Symposium on Discrete Algorithms,
    San Francisco, SA, United States: SIAM. <a href="https://doi.org/10.1137/1.9781611973082.101">https://doi.org/10.1137/1.9781611973082.101</a>'
  chicago: Chatterjee, Krishnendu, and Monika H Henzinger. “Faster and Dynamic Algorithms
    for Maximal End-Component Decomposition and Related Graph Problems in Probabilistic
    Verification,” 1318–36. SIAM, 2011. <a href="https://doi.org/10.1137/1.9781611973082.101">https://doi.org/10.1137/1.9781611973082.101</a>.
  ieee: 'K. Chatterjee and M. H. Henzinger, “Faster and dynamic algorithms for maximal
    end-component decomposition and related graph problems in probabilistic verification,”
    presented at the SODA: Symposium on Discrete Algorithms, San Francisco, SA, United
    States, 2011, pp. 1318–1336.'
  ista: 'Chatterjee K, Henzinger MH. 2011. Faster and dynamic algorithms for maximal
    end-component decomposition and related graph problems in probabilistic verification.
    SODA: Symposium on Discrete Algorithms, 1318–1336.'
  mla: Chatterjee, Krishnendu, and Monika H. Henzinger. <i>Faster and Dynamic Algorithms
    for Maximal End-Component Decomposition and Related Graph Problems in Probabilistic
    Verification</i>. SIAM, 2011, pp. 1318–36, doi:<a href="https://doi.org/10.1137/1.9781611973082.101">10.1137/1.9781611973082.101</a>.
  short: K. Chatterjee, M.H. Henzinger, in:, SIAM, 2011, pp. 1318–1336.
conference:
  end_date: 2011-01-25
  location: San Francisco, SA, United States
  name: 'SODA: Symposium on Discrete Algorithms'
  start_date: 2011-01-23
date_created: 2018-12-11T12:02:47Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2023-02-14T10:36:10Z
day: '01'
department:
- _id: KrCh
doi: 10.1137/1.9781611973082.101
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://eprints.cs.univie.ac.at/21/
month: '01'
oa: 1
oa_version: Submitted Version
page: 1318 - 1336
publication_status: published
publisher: SIAM
publist_id: '3278'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster and dynamic algorithms for maximal end-component decomposition and related
  graph problems in probabilistic verification
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '11094'
abstract:
- lang: eng
  text: Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear
    envelope (NE) reformation and into an intact NE as cells progress through interphase.
    Although recent studies have shown that NPC formation occurs by two different
    molecular mechanisms at two distinct cell cycle stages, little is known about
    the molecular players that mediate the fusion of the outer and inner nuclear membranes
    to form pores. In this paper, we provide evidence that the transmembrane nucleoporin
    (Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly
    sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear
    membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the
    INM and ONM. Additionally, Sun1, an INM protein that is known to interact with
    the cytoskeleton, was specifically required for interphase assembly and localized
    with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact
    transiently to promote early steps of interphase NPC assembly.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
  full_name: Talamas, Jessica A.
  last_name: Talamas
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Talamas JA, Hetzer M. POM121 and Sun1 play a role in early steps of interphase
    NPC assembly. <i>Journal of Cell Biology</i>. 2011;194(1):27-37. doi:<a href="https://doi.org/10.1083/jcb.201012154">10.1083/jcb.201012154</a>
  apa: Talamas, J. A., &#38; Hetzer, M. (2011). POM121 and Sun1 play a role in early
    steps of interphase NPC assembly. <i>Journal of Cell Biology</i>. Rockefeller
    University Press. <a href="https://doi.org/10.1083/jcb.201012154">https://doi.org/10.1083/jcb.201012154</a>
  chicago: Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in
    Early Steps of Interphase NPC Assembly.” <i>Journal of Cell Biology</i>. Rockefeller
    University Press, 2011. <a href="https://doi.org/10.1083/jcb.201012154">https://doi.org/10.1083/jcb.201012154</a>.
  ieee: J. A. Talamas and M. Hetzer, “POM121 and Sun1 play a role in early steps of
    interphase NPC assembly,” <i>Journal of Cell Biology</i>, vol. 194, no. 1. Rockefeller
    University Press, pp. 27–37, 2011.
  ista: Talamas JA, Hetzer M. 2011. POM121 and Sun1 play a role in early steps of
    interphase NPC assembly. Journal of Cell Biology. 194(1), 27–37.
  mla: Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early
    Steps of Interphase NPC Assembly.” <i>Journal of Cell Biology</i>, vol. 194, no.
    1, Rockefeller University Press, 2011, pp. 27–37, doi:<a href="https://doi.org/10.1083/jcb.201012154">10.1083/jcb.201012154</a>.
  short: J.A. Talamas, M. Hetzer, Journal of Cell Biology 194 (2011) 27–37.
date_created: 2022-04-07T07:52:18Z
date_published: 2011-07-04T00:00:00Z
date_updated: 2022-07-18T08:53:46Z
day: '04'
doi: 10.1083/jcb.201012154
extern: '1'
external_id:
  pmid:
  - '21727197'
intvolume: '       194'
issue: '1'
keyword:
- Cell Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1083/jcb.201012154
month: '07'
oa: 1
oa_version: Published Version
page: 27-37
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
  eissn:
  - 1540-8140
  issn:
  - 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: POM121 and Sun1 play a role in early steps of interphase NPC assembly
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 194
year: '2011'
...
---
_id: '112'
abstract:
- lang: eng
  text: Particle beams are important tools for probing atomic and molecular interactions.
    Here we demonstrate that particle beams also offer a unique opportunity to investigate
    interactions in macroscopic systems, such as granular media. Motivated by recent
    experiments on streams of grains that exhibit liquid-like breakup into droplets,
    we use molecular dynamics simulations to investigate the evolution of a dense
    stream of macroscopic spheres accelerating out of an opening at the bottom of
    a reservoir. We show how nanoscale details associated with energy dissipation
    during collisions modify the stream\'s macroscopic behavior. We find that inelastic
    collisions collimate the stream, while the presence of short-range attractive
    interactions drives structure formation. Parameterizing the collision dynamics
    by the coefficient of restitution (i.e., the ratio of relative velocities before
    and after impact) and the strength of the cohesive interaction, we map out a spectrum
    of behaviors that ranges from gaslike jets in which all grains drift apart to
    liquid-like streams that break into large droplets containing hundreds of grains.
    We also find a new, intermediate regime in which small aggregates form by capture
    from the gas phase, similar to what can be observed in molecular beams. Our results
    show that nearly all aspects of stream behavior are closely related to the velocity
    gradient associated with vertical free fall. Led by this observation, we propose
    a simple energy balance model to explain the droplet formation process. The qualitative
    as well as many quantitative features of the simulations and the model compare
    well with available experimental data and provide a first quantitative measure
    of the role of attractions in freely cooling granular streams.
acknowledgement: This work was supported by the NSF through CBET-0933242. We acknowledge
  use of shared facilities provided by the Keck Facility for Ultrafast Imaging at
  the University of Chicago and by the Chicago MRSEC through NSF DMR-0820054. Software
  support by Itasca Consulting Group, Inc., under the Itasca Educational Partnership
  is gratefully acknowledged. H.G. thanks the German-American Fulbright Commission
  for fellowship support during his stay at the University of Chicago.
article_number: '051302'
arxiv: 1
author:
- first_name: Scott R
  full_name: Waitukaitis, Scott R
  id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
  last_name: Waitukaitis
  orcid: 0000-0002-2299-3176
- first_name: Helge
  full_name: Grütjen, Helge
  last_name: Grütjen
- first_name: John
  full_name: Royer, John
  last_name: Royer
- first_name: Heinrich
  full_name: Jaeger, Heinrich
  last_name: Jaeger
citation:
  ama: Waitukaitis SR, Grütjen H, Royer J, Jaeger H. Droplet and cluster formation
    in freely falling granular streams. <i>Physical Review E</i>. 2011;83(5). doi:<a
    href="https://doi.org/10.1103/PhysRevE.83.051302">10.1103/PhysRevE.83.051302</a>
  apa: Waitukaitis, S. R., Grütjen, H., Royer, J., &#38; Jaeger, H. (2011). Droplet
    and cluster formation in freely falling granular streams. <i>Physical Review E</i>.
    American Physical Society. <a href="https://doi.org/10.1103/PhysRevE.83.051302">https://doi.org/10.1103/PhysRevE.83.051302</a>
  chicago: Waitukaitis, Scott R, Helge Grütjen, John Royer, and Heinrich Jaeger. “Droplet
    and Cluster Formation in Freely Falling Granular Streams.” <i>Physical Review
    E</i>. American Physical Society, 2011. <a href="https://doi.org/10.1103/PhysRevE.83.051302">https://doi.org/10.1103/PhysRevE.83.051302</a>.
  ieee: S. R. Waitukaitis, H. Grütjen, J. Royer, and H. Jaeger, “Droplet and cluster
    formation in freely falling granular streams,” <i>Physical Review E</i>, vol.
    83, no. 5. American Physical Society, 2011.
  ista: Waitukaitis SR, Grütjen H, Royer J, Jaeger H. 2011. Droplet and cluster formation
    in freely falling granular streams. Physical Review E. 83(5), 051302.
  mla: Waitukaitis, Scott R., et al. “Droplet and Cluster Formation in Freely Falling
    Granular Streams.” <i>Physical Review E</i>, vol. 83, no. 5, 051302, American
    Physical Society, 2011, doi:<a href="https://doi.org/10.1103/PhysRevE.83.051302">10.1103/PhysRevE.83.051302</a>.
  short: S.R. Waitukaitis, H. Grütjen, J. Royer, H. Jaeger, Physical Review E 83 (2011).
date_created: 2018-12-11T11:44:41Z
date_published: 2011-05-12T00:00:00Z
date_updated: 2021-01-12T06:48:25Z
day: '12'
doi: 10.1103/PhysRevE.83.051302
extern: '1'
external_id:
  arxiv:
  - '1006.1371'
intvolume: '        83'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1006.1371
month: '05'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
publist_id: '7942'
quality_controlled: '1'
status: public
title: Droplet and cluster formation in freely falling granular streams
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2011'
...
---
_id: '8025'
abstract:
- lang: eng
  text: Chandelier (axoaxonic) cells (ChCs) are a distinct group of GABAergic interneurons
    that innervate the axon initial segments of pyramidal cells. However, their circuit
    role and the function of their clearly defined anatomical specificity remain unclear.
    Recent work has demonstrated that chandelier cells can produce depolarizing GABAergic
    PSPs, occasionally driving postsynaptic targets to spike. On the other hand, other
    work suggests that ChCs are hyperpolarizing and may have an inhibitory role. These
    disparate functional effects may reflect heterogeneity among ChCs. Here, using
    brain slices from transgenic mouse strains, we first demonstrate that, across
    different neocortical areas and genetic backgrounds, upper Layer 2/3 ChCs belong
    to a single electrophysiologically and morphologically defined population, extensively
    sampling Layer 1 inputs with asymmetric dendrites. Consistent with being a single
    cell type, we find electrical coupling between ChCs. We then investigate the effect
    of chandelier cell activation on pyramidal neuron spiking in several conditions,
    ranging from the resting membrane potential to stimuli designed to approximate
    in vivo membrane potential dynamics. We find that under quiescent conditions,
    chandelier cells are capable of both promoting and inhibiting spike generation,
    depending on the postsynaptic membrane potential. However, during in vivo-like
    membrane potential fluctuations, the dominant postsynaptic effect was a strong
    inhibition. Thus, neocortical chandelier cells, even from within a homogeneous
    population, appear to play a dual role in the circuit, helping to activate quiescent
    pyramidal neurons, while at the same time inhibiting active ones.
article_processing_charge: No
article_type: original
author:
- first_name: A. R.
  full_name: Woodruff, A. R.
  last_name: Woodruff
- first_name: L. M.
  full_name: McGarry, L. M.
  last_name: McGarry
- first_name: Tim P
  full_name: Vogels, Tim P
  id: CB6FF8D2-008F-11EA-8E08-2637E6697425
  last_name: Vogels
  orcid: 0000-0003-3295-6181
- first_name: M.
  full_name: Inan, M.
  last_name: Inan
- first_name: S. A.
  full_name: Anderson, S. A.
  last_name: Anderson
- first_name: R.
  full_name: Yuste, R.
  last_name: Yuste
citation:
  ama: Woodruff AR, McGarry LM, Vogels TP, Inan M, Anderson SA, Yuste R. State-dependent
    function of neocortical chandelier cells. <i>Journal of Neuroscience</i>. 2011;31(49):17872-17886.
    doi:<a href="https://doi.org/10.1523/jneurosci.3894-11.2011">10.1523/jneurosci.3894-11.2011</a>
  apa: Woodruff, A. R., McGarry, L. M., Vogels, T. P., Inan, M., Anderson, S. A.,
    &#38; Yuste, R. (2011). State-dependent function of neocortical chandelier cells.
    <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href="https://doi.org/10.1523/jneurosci.3894-11.2011">https://doi.org/10.1523/jneurosci.3894-11.2011</a>
  chicago: Woodruff, A. R., L. M. McGarry, Tim P Vogels, M. Inan, S. A. Anderson,
    and R. Yuste. “State-Dependent Function of Neocortical Chandelier Cells.” <i>Journal
    of Neuroscience</i>. Society for Neuroscience, 2011. <a href="https://doi.org/10.1523/jneurosci.3894-11.2011">https://doi.org/10.1523/jneurosci.3894-11.2011</a>.
  ieee: A. R. Woodruff, L. M. McGarry, T. P. Vogels, M. Inan, S. A. Anderson, and
    R. Yuste, “State-dependent function of neocortical chandelier cells,” <i>Journal
    of Neuroscience</i>, vol. 31, no. 49. Society for Neuroscience, pp. 17872–17886,
    2011.
  ista: Woodruff AR, McGarry LM, Vogels TP, Inan M, Anderson SA, Yuste R. 2011. State-dependent
    function of neocortical chandelier cells. Journal of Neuroscience. 31(49), 17872–17886.
  mla: Woodruff, A. R., et al. “State-Dependent Function of Neocortical Chandelier
    Cells.” <i>Journal of Neuroscience</i>, vol. 31, no. 49, Society for Neuroscience,
    2011, pp. 17872–86, doi:<a href="https://doi.org/10.1523/jneurosci.3894-11.2011">10.1523/jneurosci.3894-11.2011</a>.
  short: A.R. Woodruff, L.M. McGarry, T.P. Vogels, M. Inan, S.A. Anderson, R. Yuste,
    Journal of Neuroscience 31 (2011) 17872–17886.
date_created: 2020-06-25T13:09:49Z
date_published: 2011-12-07T00:00:00Z
date_updated: 2021-01-12T08:16:36Z
day: '7'
doi: 10.1523/jneurosci.3894-11.2011
extern: '1'
external_id:
  pmid:
  - '22159102'
intvolume: '        31'
issue: '49'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071969/
month: '12'
oa: 1
oa_version: Published Version
page: 17872-17886
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
  issn:
  - 0270-6474
  - 1529-2401
publication_status: published
publisher: Society for Neuroscience
quality_controlled: '1'
status: public
title: State-dependent function of neocortical chandelier cells
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 31
year: '2011'
...
---
_id: '1754'
abstract:
- lang: eng
  text: 'We report on a technique enabling electrical control of the contact silicidation
    process in silicon nanowire devices. Undoped silicon nanowires were contacted
    by pairs of nickel electrodes and each contact was selectively silicided by means
    of the Joule effect. By a realtime monitoring of the nanowire electrical resistance
    during the contact silicidation process we were able to fabricate nickel-silicide/silicon/nickel-
    silicide devices with controlled silicon channel length down to 8 nm. '
acknowledgement: This work was supported by the Agence Nationale de la Recherche (ANR)
  through the ACCESS and COHESION projects and by the European Commission through
  the Chemtronics program MEST-CT-2005-020513
arxiv: 1
author:
- first_name: Massimo
  full_name: Mongillo, Massimo
  last_name: Mongillo
- first_name: Panayotis
  full_name: Spathis, Panayotis
  last_name: Spathis
- first_name: Georgios
  full_name: Katsaros, Georgios
  id: 38DB5788-F248-11E8-B48F-1D18A9856A87
  last_name: Katsaros
- first_name: Pascal
  full_name: Gentile, Pascal
  last_name: Gentile
- first_name: Marc
  full_name: Sanquer, Marc
  last_name: Sanquer
- first_name: Silvano
  full_name: De Franceschi, Silvano
  last_name: De Franceschi
citation:
  ama: Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S. Joule-assisted
    silicidation for short-channel silicon nanowire devices. <i>ACS Nano</i>. 2011;5(9):7117-7123.
    doi:<a href="https://doi.org/10.1021/nn202524j">10.1021/nn202524j</a>
  apa: Mongillo, M., Spathis, P., Katsaros, G., Gentile, P., Sanquer, M., &#38; De
    Franceschi, S. (2011). Joule-assisted silicidation for short-channel silicon nanowire
    devices. <i>ACS Nano</i>. American Chemical Society. <a href="https://doi.org/10.1021/nn202524j">https://doi.org/10.1021/nn202524j</a>
  chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Pascal Gentile,
    Marc Sanquer, and Silvano De Franceschi. “Joule-Assisted Silicidation for Short-Channel
    Silicon Nanowire Devices.” <i>ACS Nano</i>. American Chemical Society, 2011. <a
    href="https://doi.org/10.1021/nn202524j">https://doi.org/10.1021/nn202524j</a>.
  ieee: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, and S. De Franceschi,
    “Joule-assisted silicidation for short-channel silicon nanowire devices,” <i>ACS
    Nano</i>, vol. 5, no. 9. American Chemical Society, pp. 7117–7123, 2011.
  ista: Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S.
    2011. Joule-assisted silicidation for short-channel silicon nanowire devices.
    ACS Nano. 5(9), 7117–7123.
  mla: Mongillo, Massimo, et al. “Joule-Assisted Silicidation for Short-Channel Silicon
    Nanowire Devices.” <i>ACS Nano</i>, vol. 5, no. 9, American Chemical Society,
    2011, pp. 7117–23, doi:<a href="https://doi.org/10.1021/nn202524j">10.1021/nn202524j</a>.
  short: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, S. De Franceschi,
    ACS Nano 5 (2011) 7117–7123.
date_created: 2018-12-11T11:53:50Z
date_published: 2011-09-27T00:00:00Z
date_updated: 2021-01-12T06:52:59Z
day: '27'
doi: 10.1021/nn202524j
extern: '1'
external_id:
  arxiv:
  - '1110.5668'
intvolume: '         5'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1110.5668
month: '09'
oa: 1
oa_version: Preprint
page: 7117 - 7123
publication: ACS Nano
publication_status: published
publisher: American Chemical Society
publist_id: '5370'
quality_controlled: '1'
status: public
title: Joule-assisted silicidation for short-channel silicon nanowire devices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2011'
...
---
_id: '1755'
abstract:
- lang: eng
  text: Spin-selective tunneling of holes in SiGe nanocrystals contacted by normal-metal
    leads is reported. The spin selectivity arises from an interplay of the orbital
    effect of the magnetic field with the strong spin-orbit interaction present in
    the valence band of the semiconductor. We demonstrate both experimentally and
    theoretically that spin-selective tunneling in semiconductor nanostructures can
    be achieved without the use of ferromagnetic contacts. The reported effect, which
    relies on mixing the light and heavy holes, should be observable in a broad class
    of quantum-dot systems formed in semiconductors with a degenerate valence band.
acknowledgement: The work was supported by the Agence Nationale de la Recherche (through
  the ACCESS and COHESION projects), U.S. DOE Contract No. DE-FG02-08ER46482 (Yale),
  and the Nanosciences Foundation at Grenoble, France. G. K. acknowledges support
  from the Deutsche Forschungsgemeinschaft
author:
- first_name: Georgios
  full_name: Georgios Katsaros
  id: 38DB5788-F248-11E8-B48F-1D18A9856A87
  last_name: Katsaros
- first_name: Vitaly
  full_name: Golovach, Vitaly N
  last_name: Golovach
- first_name: Panayotis
  full_name: Spathis, Panayotis N
  last_name: Spathis
- first_name: Natalia
  full_name: Ares, Natalia
  last_name: Ares
- first_name: Mathieu
  full_name: Stoffel, Mathieu
  last_name: Stoffel
- first_name: Frank
  full_name: Fournel, Frank
  last_name: Fournel
- first_name: Oliver
  full_name: Schmidt, Oliver G
  last_name: Schmidt
- first_name: Leonid
  full_name: Glazman, Leonid I
  last_name: Glazman
- first_name: Silvano
  full_name: De Franceschi, Silvano
  last_name: De Franceschi
citation:
  ama: Katsaros G, Golovach V, Spathis P, et al. Observation of spin-selective tunneling
    in sige nanocrystals. <i>Physical Review Letters</i>. 2011;107(24). doi:<a href="https://doi.org/10.1103/PhysRevLett.107.246601">10.1103/PhysRevLett.107.246601</a>
  apa: Katsaros, G., Golovach, V., Spathis, P., Ares, N., Stoffel, M., Fournel, F.,
    … De Franceschi, S. (2011). Observation of spin-selective tunneling in sige nanocrystals.
    <i>Physical Review Letters</i>. American Physical Society. <a href="https://doi.org/10.1103/PhysRevLett.107.246601">https://doi.org/10.1103/PhysRevLett.107.246601</a>
  chicago: Katsaros, Georgios, Vitaly Golovach, Panayotis Spathis, Natalia Ares, Mathieu
    Stoffel, Frank Fournel, Oliver Schmidt, Leonid Glazman, and Silvano De Franceschi.
    “Observation of Spin-Selective Tunneling in Sige Nanocrystals.” <i>Physical Review
    Letters</i>. American Physical Society, 2011. <a href="https://doi.org/10.1103/PhysRevLett.107.246601">https://doi.org/10.1103/PhysRevLett.107.246601</a>.
  ieee: G. Katsaros <i>et al.</i>, “Observation of spin-selective tunneling in sige
    nanocrystals,” <i>Physical Review Letters</i>, vol. 107, no. 24. American Physical
    Society, 2011.
  ista: Katsaros G, Golovach V, Spathis P, Ares N, Stoffel M, Fournel F, Schmidt O,
    Glazman L, De Franceschi S. 2011. Observation of spin-selective tunneling in sige
    nanocrystals. Physical Review Letters. 107(24).
  mla: Katsaros, Georgios, et al. “Observation of Spin-Selective Tunneling in Sige
    Nanocrystals.” <i>Physical Review Letters</i>, vol. 107, no. 24, American Physical
    Society, 2011, doi:<a href="https://doi.org/10.1103/PhysRevLett.107.246601">10.1103/PhysRevLett.107.246601</a>.
  short: G. Katsaros, V. Golovach, P. Spathis, N. Ares, M. Stoffel, F. Fournel, O.
    Schmidt, L. Glazman, S. De Franceschi, Physical Review Letters 107 (2011).
date_created: 2018-12-11T11:53:50Z
date_published: 2011-12-07T00:00:00Z
date_updated: 2021-01-12T06:53:00Z
day: '07'
doi: 10.1103/PhysRevLett.107.246601
extern: 1
intvolume: '       107'
issue: '24'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1107.3919
month: '12'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5369'
quality_controlled: 0
status: public
title: Observation of spin-selective tunneling in sige nanocrystals
type: journal_article
volume: 107
year: '2011'
...
---
_id: '1777'
abstract:
- lang: eng
  text: A wide range of experiments studying microwave photons localized in superconducting
    cavities have made important contributions to our understanding of the quantum
    properties of radiation. Propagating microwave photons, however, have so far been
    studied much less intensely. Here we present measurements in which we reconstruct
    the quantum state of itinerant single photon Fock states and their superposition
    with the vacuum by analyzing moments of the measured amplitude distribution up
    to fourth order. Using linear amplifiers and quadrature amplitude detectors, we
    have developed efficient methods to separate the detected single photon signal
    from the noise added by the amplifier. From our measurement data we have also
    reconstructed the corresponding Wigner function.
acknowledgement: This work was supported by the European Research Council (ERC) through
  a Starting Grant and by ETHZ
article_processing_charge: No
author:
- first_name: Christopher
  full_name: Eichler, Christopher
  last_name: Eichler
- first_name: Deniz
  full_name: Bozyigit, Deniz
  last_name: Bozyigit
- first_name: C
  full_name: Lang, C
  last_name: Lang
- first_name: L.
  full_name: Steffen, L.
  last_name: Steffen
- first_name: Johannes M
  full_name: Fink, Johannes M
  id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
  last_name: Fink
  orcid: 0000-0001-8112-028X
- first_name: Andreas
  full_name: Wallraff, Andreas
  last_name: Wallraff
citation:
  ama: Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. Experimental
    state tomography of itinerant single microwave photons. <i>Physical Review Letters</i>.
    2011;106(22). doi:<a href="https://doi.org/10.1103/PhysRevLett.106.220503">10.1103/PhysRevLett.106.220503</a>
  apa: Eichler, C., Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., &#38; Wallraff,
    A. (2011). Experimental state tomography of itinerant single microwave photons.
    <i>Physical Review Letters</i>. American Physical Society. <a href="https://doi.org/10.1103/PhysRevLett.106.220503">https://doi.org/10.1103/PhysRevLett.106.220503</a>
  chicago: Eichler, Christopher, Deniz Bozyigit, C Lang, L. Steffen, Johannes M Fink,
    and Andreas Wallraff. “Experimental State Tomography of Itinerant Single Microwave
    Photons.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a
    href="https://doi.org/10.1103/PhysRevLett.106.220503">https://doi.org/10.1103/PhysRevLett.106.220503</a>.
  ieee: C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J. M. Fink, and A. Wallraff,
    “Experimental state tomography of itinerant single microwave photons,” <i>Physical
    Review Letters</i>, vol. 106, no. 22. American Physical Society, 2011.
  ista: Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. 2011. Experimental
    state tomography of itinerant single microwave photons. Physical Review Letters.
    106(22).
  mla: Eichler, Christopher, et al. “Experimental State Tomography of Itinerant Single
    Microwave Photons.” <i>Physical Review Letters</i>, vol. 106, no. 22, American
    Physical Society, 2011, doi:<a href="https://doi.org/10.1103/PhysRevLett.106.220503">10.1103/PhysRevLett.106.220503</a>.
  short: C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, A. Wallraff, Physical
    Review Letters 106 (2011).
date_created: 2018-12-11T11:53:57Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-11-16T07:57:13Z
day: '01'
doi: 10.1103/PhysRevLett.106.220503
extern: '1'
intvolume: '       106'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1011.6668
month: '06'
oa: 1
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5338'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1103/PhysRevLett.106.249901
status: public
title: Experimental state tomography of itinerant single microwave photons
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 106
year: '2011'
...
---
_id: '1778'
abstract:
- lang: eng
  text: Creating a train of single photons and monitoring its propagation and interaction
    is challenging in most physical systems, as photons generally interact very weakly
    with other systems. However, when confining microwave frequency photons in a transmission
    line resonator, effective photon-photon interactions can be mediated by qubits
    embedded in the resonator. Here, we observe the phenomenon of photon blockade
    through second-order correlation function measurements. The experiments clearly
    demonstrate antibunching in a continuously pumped source of single microwave photons
    measured by using microwave beam splitters, linear amplifiers, and quadrature
    amplitude detectors. We also investigate resonance fluorescence and Rayleigh scattering
    in Mollow-triplet-like spectra.
acknowledgement: This work was supported by the European Research Council (ERC) through
  a Starting Grant and by ETHZ. M. P. d. S. was supported by NSERC. A. B. was supported
  by NSERC, CIFAR, and the Alfred P. Sloan Foundation
author:
- first_name: C
  full_name: Lang, C
  last_name: Lang
- first_name: Deniz
  full_name: Bozyigit, Deniz
  last_name: Bozyigit
- first_name: Christopher
  full_name: Eichler, Christopher
  last_name: Eichler
- first_name: L.
  full_name: Steffen, L. Kraig
  last_name: Steffen
- first_name: Johannes M
  full_name: Johannes Fink
  id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
  last_name: Fink
  orcid: 0000-0001-8112-028X
- first_name: Abdufarrukh
  full_name: Abdumalikov, Abdufarrukh A
  last_name: Abdumalikov
- first_name: Matthias
  full_name: Baur, Matthias P
  last_name: Baur
- first_name: Stefan
  full_name: Filipp, Stefan
  last_name: Filipp
- first_name: Marcus
  full_name: Da Silva, Marcus P
  last_name: Da Silva
- first_name: Alexandre
  full_name: Blais, Alexandre
  last_name: Blais
- first_name: Andreas
  full_name: Wallraff, Andreas
  last_name: Wallraff
citation:
  ama: Lang C, Bozyigit D, Eichler C, et al. Observation of resonant photon blockade
    at microwave frequencies using correlation function measurements. <i>Physical
    Review Letters</i>. 2011;106(24). doi:<a href="https://doi.org/10.1103/PhysRevLett.106.243601">10.1103/PhysRevLett.106.243601</a>
  apa: Lang, C., Bozyigit, D., Eichler, C., Steffen, L., Fink, J. M., Abdumalikov,
    A., … Wallraff, A. (2011). Observation of resonant photon blockade at microwave
    frequencies using correlation function measurements. <i>Physical Review Letters</i>.
    American Physical Society. <a href="https://doi.org/10.1103/PhysRevLett.106.243601">https://doi.org/10.1103/PhysRevLett.106.243601</a>
  chicago: Lang, C, Deniz Bozyigit, Christopher Eichler, L. Steffen, Johannes M Fink,
    Abdufarrukh Abdumalikov, Matthias Baur, et al. “Observation of Resonant Photon
    Blockade at Microwave Frequencies Using Correlation Function Measurements.” <i>Physical
    Review Letters</i>. American Physical Society, 2011. <a href="https://doi.org/10.1103/PhysRevLett.106.243601">https://doi.org/10.1103/PhysRevLett.106.243601</a>.
  ieee: C. Lang <i>et al.</i>, “Observation of resonant photon blockade at microwave
    frequencies using correlation function measurements,” <i>Physical Review Letters</i>,
    vol. 106, no. 24. American Physical Society, 2011.
  ista: Lang C, Bozyigit D, Eichler C, Steffen L, Fink JM, Abdumalikov A, Baur M,
    Filipp S, Da Silva M, Blais A, Wallraff A. 2011. Observation of resonant photon
    blockade at microwave frequencies using correlation function measurements. Physical
    Review Letters. 106(24).
  mla: Lang, C., et al. “Observation of Resonant Photon Blockade at Microwave Frequencies
    Using Correlation Function Measurements.” <i>Physical Review Letters</i>, vol.
    106, no. 24, American Physical Society, 2011, doi:<a href="https://doi.org/10.1103/PhysRevLett.106.243601">10.1103/PhysRevLett.106.243601</a>.
  short: C. Lang, D. Bozyigit, C. Eichler, L. Steffen, J.M. Fink, A. Abdumalikov,
    M. Baur, S. Filipp, M. Da Silva, A. Blais, A. Wallraff, Physical Review Letters
    106 (2011).
date_created: 2018-12-11T11:53:57Z
date_published: 2011-06-15T00:00:00Z
date_updated: 2021-01-12T06:53:08Z
day: '15'
doi: 10.1103/PhysRevLett.106.243601
extern: 1
intvolume: '       106'
issue: '24'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1102.0461
month: '06'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5336'
quality_controlled: 0
status: public
title: Observation of resonant photon blockade at microwave frequencies using correlation
  function measurements
type: journal_article
volume: 106
year: '2011'
...
---
_id: '1815'
abstract:
- lang: eng
  text: Many membrane channels and receptors exhibit adaptive, or desensitized, response
    to a strong sustained input stimulus, often supported by protein activity-dependent
    inactivation. Adaptive response is thought to be related to various cellular functions
    such as homeostasis and enlargement of dynamic range by background compensation.
    Here we study the quantitative relation between adaptive response and background
    compensation within a modeling framework. We show that any particular type of
    adaptive response is neither sufficient nor necessary for adaptive enlargement
    of dynamic range. In particular a precise adaptive response, where system activity
    is maintained at a constant level at steady state, does not ensure a large dynamic
    range neither in input signal nor in system output. A general mechanism for input
    dynamic range enlargement can come about from the activity-dependent modulation
    of protein responsiveness by multiple biochemical modification, regardless of
    the type of adaptive response it induces. Therefore hierarchical biochemical processes
    such as methylation and phosphorylation are natural candidates to induce this
    property in signaling systems.
author:
- first_name: Tamar
  full_name: Tamar Friedlander
  id: 36A5845C-F248-11E8-B48F-1D18A9856A87
  last_name: Friedlander
- first_name: Naama
  full_name: Brenner, Naama
  last_name: Brenner
citation:
  ama: Friedlander T, Brenner N. Adaptive response and enlargement of dynamic range.
    <i>Mathematical Biosciences and Engineering</i>. 2011;8(2):515-526. doi:<a href="https://doi.org/10.3934/mbe.2011.8.515">10.3934/mbe.2011.8.515</a>
  apa: Friedlander, T., &#38; Brenner, N. (2011). Adaptive response and enlargement
    of dynamic range. <i>Mathematical Biosciences and Engineering</i>. Arizona State
    University. <a href="https://doi.org/10.3934/mbe.2011.8.515">https://doi.org/10.3934/mbe.2011.8.515</a>
  chicago: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement
    of Dynamic Range.” <i>Mathematical Biosciences and Engineering</i>. Arizona State
    University, 2011. <a href="https://doi.org/10.3934/mbe.2011.8.515">https://doi.org/10.3934/mbe.2011.8.515</a>.
  ieee: T. Friedlander and N. Brenner, “Adaptive response and enlargement of dynamic
    range,” <i>Mathematical Biosciences and Engineering</i>, vol. 8, no. 2. Arizona
    State University, pp. 515–526, 2011.
  ista: Friedlander T, Brenner N. 2011. Adaptive response and enlargement of dynamic
    range. Mathematical Biosciences and Engineering. 8(2), 515–526.
  mla: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of
    Dynamic Range.” <i>Mathematical Biosciences and Engineering</i>, vol. 8, no. 2,
    Arizona State University, 2011, pp. 515–26, doi:<a href="https://doi.org/10.3934/mbe.2011.8.515">10.3934/mbe.2011.8.515</a>.
  short: T. Friedlander, N. Brenner, Mathematical Biosciences and Engineering 8 (2011)
    515–526.
date_created: 2018-12-11T11:54:10Z
date_published: 2011-04-02T00:00:00Z
date_updated: 2021-01-12T06:53:23Z
day: '02'
doi: 10.3934/mbe.2011.8.515
extern: 1
intvolume: '         8'
issue: '2'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1003.2791
month: '04'
oa: 1
page: 515 - 526
publication: Mathematical Biosciences and Engineering
publication_status: published
publisher: Arizona State University
publist_id: '5291'
quality_controlled: 0
status: public
title: Adaptive response and enlargement of dynamic range
type: journal_article
volume: 8
year: '2011'
...
---
_id: '2072'
abstract:
- lang: eng
  text: Many species have morphologically and genetically differentiated sex chromosomes,
    such as the XY pair of mammals. Y chromosomes are often highly degenerated and
    carry few functional genes, so that XY males have only one copy of most Xlinked
    genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage
    compensation, such as the mammalian X-inactivation, often evolve to reestablish
    expression balance. A similar phenomenon is expected in femaleheterogametic species,
    where ZW females should suffer from imbalances due to W-chromosome degeneration.
    However, no global dosage compensation mechanisms have been detected in the two
    independent ZW systems that have been studied systematically (birds and silkworm),
    leading to the suggestion that lack of global dosage compensation may be a general
    feature of female-heterogametic species. However, analyses of other independently
    evolved ZW systems are required to test if this is the case. In this study, we
    use published genomic and expression data to test for the presence of global dosage
    compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis
    in humans. We find that Z-linked expression is reduced relative to autosomal expression
    in females but not males, consistent with incomplete or localized dosage compensation.
    This gives further support to the theory that female-heterogametic species may
    not require global mechanisms of dosage compensation.
author:
- first_name: Beatriz
  full_name: Vicoso, Beatriz
  id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
  last_name: Vicoso
  orcid: 0000-0002-4579-8306
- first_name: Doris
  full_name: Bachtrog, Doris
  last_name: Bachtrog
citation:
  ama: Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni,
    a female-heterogametic parasite. <i>Genome Biology and Evolution</i>. 2011;3(1):230-235.
    doi:<a href="https://doi.org/10.1093/gbe/evr010">10.1093/gbe/evr010</a>
  apa: Vicoso, B., &#38; Bachtrog, D. (2011). Lack of global dosage compensation in
    Schistosoma mansoni, a female-heterogametic parasite. <i>Genome Biology and Evolution</i>.
    Oxford University Press. <a href="https://doi.org/10.1093/gbe/evr010">https://doi.org/10.1093/gbe/evr010</a>
  chicago: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation
    in Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and
    Evolution</i>. Oxford University Press, 2011. <a href="https://doi.org/10.1093/gbe/evr010">https://doi.org/10.1093/gbe/evr010</a>.
  ieee: B. Vicoso and D. Bachtrog, “Lack of global dosage compensation in Schistosoma
    mansoni, a female-heterogametic parasite,” <i>Genome Biology and Evolution</i>,
    vol. 3, no. 1. Oxford University Press, pp. 230–235, 2011.
  ista: Vicoso B, Bachtrog D. 2011. Lack of global dosage compensation in Schistosoma
    mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 3(1),
    230–235.
  mla: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in
    Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and Evolution</i>,
    vol. 3, no. 1, Oxford University Press, 2011, pp. 230–35, doi:<a href="https://doi.org/10.1093/gbe/evr010">10.1093/gbe/evr010</a>.
  short: B. Vicoso, D. Bachtrog, Genome Biology and Evolution 3 (2011) 230–235.
date_created: 2018-12-11T11:55:33Z
date_published: 2011-02-11T00:00:00Z
date_updated: 2021-01-12T06:55:08Z
day: '11'
ddc:
- '570'
doi: 10.1093/gbe/evr010
extern: '1'
file:
- access_level: open_access
  checksum: 7855c134436e4f6a13d63b6606d7e8dd
  content_type: application/pdf
  creator: dernst
  date_created: 2019-05-10T07:41:28Z
  date_updated: 2020-07-14T12:45:27Z
  file_id: '6395'
  file_name: 2011_GBE_Vicoso.pdf
  file_size: 212547
  relation: main_file
file_date_updated: 2020-07-14T12:45:27Z
has_accepted_license: '1'
intvolume: '         3'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: 230 - 235
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '4966'
quality_controlled: '1'
status: public
title: Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic
  parasite
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2011'
...
---
_id: '2116'
abstract:
- lang: eng
  text: Let P be the Ornstein-Uhlenbeck semigroup associated with the stochastic Cauchy
    problem  dU(t)=AU(t)dt+dWH(t), where A is the generator of a C 0-semigroup S on
    a Banach space E, H is a Hilbert subspace of E, and W H is an H-cylindrical Brownian
    motion. Assuming that S restricts to a C 0-semigroup on H, we obtain L p -bounds
    for D H P(t). We show that if P is analytic, then the invariance assumption is
    fulfilled. As an application we determine the L p -domain of the generator of
    P explicitly in the case where S restricts to a C 0-semigroup on H which is similar
    to an analytic contraction semigroup. The results are applied to the 1D stochastic
    heat equation driven by additive space-time white noise.
acknowledgement: 'The authors are supported by VIDI subsidy 639.032.201 (JM) and VICI
  subsidy 639.033.604 (JvN) of the Netherlands Organisation for Scientific Research
  (NWO). '
author:
- first_name: Jan
  full_name: Jan Maas
  id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
  last_name: Maas
  orcid: 0000-0002-0845-1338
- first_name: Jan
  full_name: Van Neerven, Jan
  last_name: Van Neerven
citation:
  ama: 'Maas J, Van Neerven J. Gradient estimates and domain identification for analytic
    Ornstein-Uhlenbeck operators. In: <i>Parabolic Problems</i>. Vol 80. Birkhäuser;
    2011:463-477. doi:<a href="https://doi.org/10.1007/978-3-0348-0075-4_24">10.1007/978-3-0348-0075-4_24</a>'
  apa: Maas, J., &#38; Van Neerven, J. (2011). Gradient estimates and domain identification
    for analytic Ornstein-Uhlenbeck operators. In <i>Parabolic Problems</i> (Vol.
    80, pp. 463–477). Birkhäuser. <a href="https://doi.org/10.1007/978-3-0348-0075-4_24">https://doi.org/10.1007/978-3-0348-0075-4_24</a>
  chicago: Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification
    for Analytic Ornstein-Uhlenbeck Operators.” In <i>Parabolic Problems</i>, 80:463–77.
    Birkhäuser, 2011. <a href="https://doi.org/10.1007/978-3-0348-0075-4_24">https://doi.org/10.1007/978-3-0348-0075-4_24</a>.
  ieee: J. Maas and J. Van Neerven, “Gradient estimates and domain identification
    for analytic Ornstein-Uhlenbeck operators,” in <i>Parabolic Problems</i>, vol.
    80, Birkhäuser, 2011, pp. 463–477.
  ista: 'Maas J, Van Neerven J. 2011.Gradient estimates and domain identification
    for analytic Ornstein-Uhlenbeck operators. In: Parabolic Problems. vol. 80, 463–477.'
  mla: Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification
    for Analytic Ornstein-Uhlenbeck Operators.” <i>Parabolic Problems</i>, vol. 80,
    Birkhäuser, 2011, pp. 463–77, doi:<a href="https://doi.org/10.1007/978-3-0348-0075-4_24">10.1007/978-3-0348-0075-4_24</a>.
  short: J. Maas, J. Van Neerven, in:, Parabolic Problems, Birkhäuser, 2011, pp. 463–477.
date_created: 2018-12-11T11:55:48Z
date_published: 2011-06-10T00:00:00Z
date_updated: 2021-01-12T06:55:24Z
day: '10'
doi: 10.1007/978-3-0348-0075-4_24
extern: 1
intvolume: '        80'
main_file_link:
- open_access: '1'
  url: 'http://arxiv.org/abs/0911.4336 '
month: '06'
oa: 1
page: 463 - 477
publication: Parabolic Problems
publication_status: published
publisher: Birkhäuser
publist_id: '4918'
quality_controlled: 0
status: public
title: Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck
  operators
type: book_chapter
volume: 80
year: '2011'
...
---
_id: '2122'
abstract:
- lang: eng
  text: We study, in L1(R̃n; γ) with respect to the gaussian measure, non- tangential
    maximal functions and conical square functions associ- ated with the Ornstein-Uhlenbeck
    operator by developing a set of techniques which allow us, to some extent, to
    compensate for the non-doubling character of the gaussian measure. The main result
    asserts that conical square functions can be controlled in L1-norm by non-tangential
    maximal functions. Along the way we prove a change of aperture result for the
    latter. This complements recent results on gaussian Hardy spaces due to Mauceri
    and Meda.
acknowledgement: The first named author is supported by Rubicon subsidy 680-50-0901
  of the Netherlands Organisation for Scientific Research (NWO). The second named
  author is supported by VICI subsidy 639.033.604 of the Netherlands Organisation
  for Scientific Research (NWO
author:
- first_name: Jan
  full_name: Jan Maas
  id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
  last_name: Maas
  orcid: 0000-0002-0845-1338
- first_name: Jan
  full_name: van Neerven, Jan M
  last_name: Van Neerven
- first_name: Pierre
  full_name: Portal, Pierre
  last_name: Portal
citation:
  ama: Maas J, Van Neerven J, Portal P. Conical square functions and non-tangential
    maximal functions with respect to the Gaussian measure. <i>Publicacions Matemàtiques</i>.
    2011;55(2):313-341. doi:<a href="https://doi.org/10.5565/PUBLMAT_55211_03  ">10.5565/PUBLMAT_55211_03 
    </a>
  apa: Maas, J., Van Neerven, J., &#38; Portal, P. (2011). Conical square functions
    and non-tangential maximal functions with respect to the Gaussian measure. <i>Publicacions
    Matemàtiques</i>. Universitat Autònoma de Barcelona, Departament de Matemàtique.
    <a href="https://doi.org/10.5565/PUBLMAT_55211_03  ">https://doi.org/10.5565/PUBLMAT_55211_03 
    </a>
  chicago: Maas, Jan, Jan Van Neerven, and Pierre Portal. “Conical Square Functions
    and Non-Tangential Maximal Functions with Respect to the Gaussian Measure.” <i>Publicacions
    Matemàtiques</i>. Universitat Autònoma de Barcelona, Departament de Matemàtique,
    2011. <a href="https://doi.org/10.5565/PUBLMAT_55211_03  ">https://doi.org/10.5565/PUBLMAT_55211_03 
    </a>.
  ieee: J. Maas, J. Van Neerven, and P. Portal, “Conical square functions and non-tangential
    maximal functions with respect to the Gaussian measure,” <i>Publicacions Matemàtiques</i>,
    vol. 55, no. 2. Universitat Autònoma de Barcelona, Departament de Matemàtique,
    pp. 313–341, 2011.
  ista: Maas J, Van Neerven J, Portal P. 2011. Conical square functions and non-tangential
    maximal functions with respect to the Gaussian measure. Publicacions Matemàtiques.
    55(2), 313–341.
  mla: Maas, Jan, et al. “Conical Square Functions and Non-Tangential Maximal Functions
    with Respect to the Gaussian Measure.” <i>Publicacions Matemàtiques</i>, vol.
    55, no. 2, Universitat Autònoma de Barcelona, Departament de Matemàtique, 2011,
    pp. 313–41, doi:<a href="https://doi.org/10.5565/PUBLMAT_55211_03  ">10.5565/PUBLMAT_55211_03 
    </a>.
  short: J. Maas, J. Van Neerven, P. Portal, Publicacions Matemàtiques 55 (2011) 313–341.
date_created: 2018-12-11T11:55:50Z
date_published: 2011-07-01T00:00:00Z
date_updated: 2021-01-12T06:55:26Z
day: '01'
doi: "10.5565/PUBLMAT_55211_03\t "
extern: 1
intvolume: '        55'
issue: '2'
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1003.4092
month: '07'
oa: 1
page: 313 - 341
publication: Publicacions Matemàtiques
publication_status: published
publisher: Universitat Autònoma de Barcelona, Departament de Matemàtique
publist_id: '4910'
quality_controlled: 0
status: public
title: Conical square functions and non-tangential maximal functions with respect
  to the Gaussian measure
type: journal_article
volume: 55
year: '2011'
...
---
_id: '2123'
abstract:
- lang: eng
  text: We prove a Trotter product formula for gradient flows in metric spaces. This
    result is applied to establish convergence in the L 2-Wasserstein metric of the
    splitting method for some Fokker-Planck equations and porous medium type equations
    perturbed by a potential.
acknowledgement: The second named author is supported by Rubicon subsidy 680-50-0901
  of the Netherlands Organisation for Scientific Research (NWO).
article_processing_charge: No
author:
- first_name: Philippe
  full_name: Clément, Philippe
  last_name: Clément
- first_name: Jan
  full_name: Maas, Jan
  id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
  last_name: Maas
  orcid: 0000-0002-0845-1338
citation:
  ama: Clément P, Maas J. A Trotter product formula for gradient flows in metric spaces.
    <i>Journal of Evolution Equations</i>. 2011;11(2):405-427. doi:<a href="https://doi.org/10.1007/s00028-010-0096-5">10.1007/s00028-010-0096-5</a>
  apa: Clément, P., &#38; Maas, J. (2011). A Trotter product formula for gradient
    flows in metric spaces. <i>Journal of Evolution Equations</i>. Birkhäuser. <a
    href="https://doi.org/10.1007/s00028-010-0096-5">https://doi.org/10.1007/s00028-010-0096-5</a>
  chicago: Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient
    Flows in Metric Spaces.” <i>Journal of Evolution Equations</i>. Birkhäuser, 2011.
    <a href="https://doi.org/10.1007/s00028-010-0096-5">https://doi.org/10.1007/s00028-010-0096-5</a>.
  ieee: P. Clément and J. Maas, “A Trotter product formula for gradient flows in metric
    spaces,” <i>Journal of Evolution Equations</i>, vol. 11, no. 2. Birkhäuser, pp.
    405–427, 2011.
  ista: Clément P, Maas J. 2011. A Trotter product formula for gradient flows in metric
    spaces. Journal of Evolution Equations. 11(2), 405–427.
  mla: Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient Flows
    in Metric Spaces.” <i>Journal of Evolution Equations</i>, vol. 11, no. 2, Birkhäuser,
    2011, pp. 405–27, doi:<a href="https://doi.org/10.1007/s00028-010-0096-5">10.1007/s00028-010-0096-5</a>.
  short: P. Clément, J. Maas, Journal of Evolution Equations 11 (2011) 405–427.
date_created: 2018-12-11T11:55:51Z
date_published: 2011-01-21T00:00:00Z
date_updated: 2021-11-16T08:05:46Z
day: '21'
doi: 10.1007/s00028-010-0096-5
extern: '1'
intvolume: '        11'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1005.0998
month: '01'
oa: 1
oa_version: None
page: 405 - 427
publication: Journal of Evolution Equations
publication_status: published
publisher: Birkhäuser
publist_id: '4911'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1007/s00028-012-0173-z
status: public
title: A Trotter product formula for gradient flows in metric spaces
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11
year: '2011'
...
