---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '22538'
abstract:
- lang: eng
  text: 'Numerous studies have explored the role of vegetation in controlling and
    mediating hydrological states and fluxes at the level of individual processes,
    which has led to improvements in our understanding of plot-scale dynamics. Relatively
    less effort has been directed toward spatially-explicit studies of vegetation-hydrology
    interactions at larger scales of a landscape. Only few continuous, process-oriented
    ecohydrological models had been proposed with structures of varying complexity.
    This study contributes to their further evolution and presents a novel ecohydrological
    model, Tethys-Chloris. The model synthesizes the state-of-the-art knowledge on
    individual processes and coupling mechanisms drawn from the disciplines of hydrology,
    plant physiology, and ecology. Specifically, the model reproduces all essential
    components of the hydrological cycle: it resolves the mass and energy budgets
    in the atmospheric surface layer at the hourly scale, while representing up to
    two layers of vegetation; it includes a module of snowpack evolution; it describes
    the saturated and unsaturated soil water dynamics, processes of runoff generation
    and flow routing. The component of vegetation dynamics parameterizes life cycle
    processes of different plant functional types, including photosynthesis, phenology,
    carbon allocation, and tissue turnover. This study presents a confirmation of
    the long-term, plot-scale model performance by simulating two types of ecosystems
    corresponding to different climate conditions. A consistent and highly satisfactory
    model skill in reproducing the energy and water budgets as well as physiological
    cycles of plants with minimum calibration overhead is demonstrated. Furthermore,
    these applications demonstrate that the model permits the identification of data
    types and observation frequencies crucial for appropriate evaluation of modeled
    dynamics. More importantly, through a synthesis of a wide array of process representations,
    the model ensures that climate, soil, vegetation, and topography collectively
    identify essential modes controlling ecohydrological systems, i.e., that satisfactory
    performance is a result of appropriate mimicking of internal processes.'
article_number: 2011MS000086
article_processing_charge: No
article_type: original
author:
- first_name: Simone
  full_name: Fatichi, Simone
  id: cf8e546b-a9b0-11f0-a43b-aa89ed1b56d6
  last_name: Fatichi
- first_name: V. Y.
  full_name: Ivanov, V. Y.
  last_name: Ivanov
- first_name: E.
  full_name: Caporali, E.
  last_name: Caporali
citation:
  ama: 'Fatichi S, Ivanov VY, Caporali E. A mechanistic ecohydrological model to investigate
    complex interactions in cold and warm water‐controlled environments: 1. Theoretical
    framework and plot‐scale analysis. <i>Journal of Advances in Modeling Earth Systems</i>.
    2012;4(2). doi:<a href="https://doi.org/10.1029/2011ms000086">10.1029/2011ms000086</a>'
  apa: 'Fatichi, S., Ivanov, V. Y., &#38; Caporali, E. (2012). A mechanistic ecohydrological
    model to investigate complex interactions in cold and warm water‐controlled environments:
    1. Theoretical framework and plot‐scale analysis. <i>Journal of Advances in Modeling
    Earth Systems</i>. American Geophysical Union. <a href="https://doi.org/10.1029/2011ms000086">https://doi.org/10.1029/2011ms000086</a>'
  chicago: 'Fatichi, Simone, V. Y. Ivanov, and E. Caporali. “A Mechanistic Ecohydrological
    Model to Investigate Complex Interactions in Cold and Warm Water‐controlled Environments:
    1. Theoretical Framework and Plot‐scale Analysis.” <i>Journal of Advances in Modeling
    Earth Systems</i>. American Geophysical Union, 2012. <a href="https://doi.org/10.1029/2011ms000086">https://doi.org/10.1029/2011ms000086</a>.'
  ieee: 'S. Fatichi, V. Y. Ivanov, and E. Caporali, “A mechanistic ecohydrological
    model to investigate complex interactions in cold and warm water‐controlled environments:
    1. Theoretical framework and plot‐scale analysis,” <i>Journal of Advances in Modeling
    Earth Systems</i>, vol. 4, no. 2. American Geophysical Union, 2012.'
  ista: 'Fatichi S, Ivanov VY, Caporali E. 2012. A mechanistic ecohydrological model
    to investigate complex interactions in cold and warm water‐controlled environments:
    1. Theoretical framework and plot‐scale analysis. Journal of Advances in Modeling
    Earth Systems. 4(2), 2011MS000086.'
  mla: 'Fatichi, Simone, et al. “A Mechanistic Ecohydrological Model to Investigate
    Complex Interactions in Cold and Warm Water‐controlled Environments: 1. Theoretical
    Framework and Plot‐scale Analysis.” <i>Journal of Advances in Modeling Earth Systems</i>,
    vol. 4, no. 2, 2011MS000086, American Geophysical Union, 2012, doi:<a href="https://doi.org/10.1029/2011ms000086">10.1029/2011ms000086</a>.'
  short: S. Fatichi, V.Y. Ivanov, E. Caporali, Journal of Advances in Modeling Earth
    Systems 4 (2012).
das_tickbox: '1'
date_created: 2026-07-27T12:30:24Z
date_published: 2012-05-30T00:00:00Z
date_updated: 2026-08-12T12:02:45Z
day: '30'
doi: 10.1029/2011ms000086
extern: '1'
fulldoi: https://doi.org/10.1029/2011ms000086
intvolume: '         4'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1029/2011MS000086
month: '05'
oa: 1
oa_version: Published Version
publication: Journal of Advances in Modeling Earth Systems
publication_identifier:
  eissn:
  - 1942-2466
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A mechanistic ecohydrological model to investigate complex interactions in
  cold and warm water‐controlled environments: 1. Theoretical framework and plot‐scale
  analysis'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2012'
...
---
_id: '2965'
abstract:
- lang: eng
  text: Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern
    und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open
    Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).
article_processing_charge: No
author:
- first_name: Patrick
  full_name: Danowski, Patrick
  id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
  last_name: Danowski
  orcid: 0000-0002-6026-4409
citation:
  ama: 'Danowski P. Kontext Open Access: Creative Commons. <i>Mitteilungen der Vereinigung
    Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2012;65(2):200-212.'
  apa: 'Danowski, P. (2012). Kontext Open Access: Creative Commons. <i>Mitteilungen
    der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung
    Österreichischer Bibliothekarinnen und Bibliothekare.'
  chicago: 'Danowski, Patrick. “Kontext Open Access: Creative Commons.” <i>Mitteilungen
    der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung
    Österreichischer Bibliothekarinnen und Bibliothekare, 2012.'
  ieee: 'P. Danowski, “Kontext Open Access: Creative Commons,” <i>Mitteilungen der
    Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 65,
    no. 2. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 200–212,
    2012.'
  ista: 'Danowski P. 2012. Kontext Open Access: Creative Commons. Mitteilungen der
    Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 65(2), 200–212.'
  mla: 'Danowski, Patrick. “Kontext Open Access: Creative Commons.” <i>Mitteilungen
    der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol.
    65, no. 2, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2012,
    pp. 200–12.'
  short: P. Danowski, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen
    und Bibliothekare 65 (2012) 200–212.
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:00:35Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2026-08-12T14:15:14Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
file:
- access_level: open_access
  checksum: 162eea47d9d840c26b496ba6ae4d1c09
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:08:42Z
  date_updated: 2020-07-14T12:45:57Z
  file_id: '4703'
  file_name: IST-2012-95-v1+1_sp-beitrag_danowski_kontext_open_access_creative_commons.pdf
  file_size: 503345
  relation: main_file
file_date_updated: 2020-07-14T12:45:57Z
has_accepted_license: '1'
intvolume: '        65'
issue: '2'
language:
- iso: ger
main_file_link:
- open_access: '1'
  url: ' http://hdl.handle.net/10760/17625'
month: '09'
oa: 1
oa_version: Published Version
page: 200 - 212
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publist_id: '3754'
pubrep_id: '95'
scopus_import: '1'
status: public
title: 'Kontext Open Access: Creative Commons'
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: 65
year: '2012'
...
---
_id: '3262'
abstract:
- lang: eng
  text: Living cells must control the reading out or &quot;expression&quot; of information
    encoded in their genomes, and this regulation often is mediated by transcription
    factors--proteins that bind to DNA and either enhance or repress the expression
    of nearby genes. But the expression of transcription factor proteins is itself
    regulated, and many transcription factors regulate their own expression in addition
    to responding to other input signals. Here we analyze the simplest of such self-regulatory
    circuits, asking how parameters can be chosen to optimize information transmission
    from inputs to outputs in the steady state. Some nonzero level of self-regulation
    is almost always optimal, with self-activation dominant when transcription factor
    concentrations are low and self-repression dominant when concentrations are high.
    In steady state the optimal self-activation is never strong enough to induce bistability,
    although there is a limit in which the optimal parameters are very close to the
    critical point.
acknowledgement: "We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan
  for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants
  No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W.
  M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant
  No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania."
article_number: '041903'
article_processing_charge: No
arxiv: 1
author:
- first_name: Gasper
  full_name: Tkacik, Gasper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
- first_name: Aleksandra
  full_name: Walczak, Aleksandra
  last_name: Walczak
- first_name: William
  full_name: Bialek, William
  last_name: Bialek
citation:
  ama: Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic
    networks. III. A self-interacting gene. <i>Physical Review E</i>. 2012;85(4).
    doi:<a href="https://doi.org/10.1103/PhysRevE.85.041903">10.1103/PhysRevE.85.041903</a>
  apa: Tkačik, G., Walczak, A., &#38; Bialek, W. (2012). Optimizing information flow
    in small genetic networks. III. A self-interacting gene. <i>Physical Review E</i>.
    American Physical Society. <a href="https://doi.org/10.1103/PhysRevE.85.041903">https://doi.org/10.1103/PhysRevE.85.041903</a>
  chicago: Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information
    Flow in Small Genetic Networks. III. A Self-Interacting Gene.” <i>Physical Review
    E</i>. American Physical Society, 2012. <a href="https://doi.org/10.1103/PhysRevE.85.041903">https://doi.org/10.1103/PhysRevE.85.041903</a>.
  ieee: G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small
    genetic networks. III. A self-interacting gene,” <i>Physical Review E</i>, vol.
    85, no. 4. American Physical Society, 2012.
  ista: Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small
    genetic networks. III. A self-interacting gene. Physical Review E. 85(4), 041903.
  mla: Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks.
    III. A Self-Interacting Gene.” <i>Physical Review E</i>, vol. 85, no. 4, 041903,
    American Physical Society, 2012, doi:<a href="https://doi.org/10.1103/PhysRevE.85.041903">10.1103/PhysRevE.85.041903</a>.
  short: G. Tkačik, A. Walczak, W. Bialek, Physical Review E 85 (2012).
corr_author: '1'
das_tickbox: '1'
date_created: 2018-12-11T12:02:20Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2026-08-12T14:29:02Z
day: '01'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.85.041903
external_id:
  arxiv:
  - '1112.5026'
  isi:
  - '000302410200006'
fulldoi: https://doi.org/10.1103/PhysRevE.85.041903
intvolume: '        85'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1112.5026
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
publist_id: '3386'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimizing information flow in small genetic networks. III. A self-interacting
  gene
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2012'
...
---
_id: '2936'
abstract:
- lang: eng
  text: The notion of delays arises naturally in many computational models, such as,
    in the design of circuits, control systems, and dataflow languages. In this work,
    we introduce automata with delay blocks (ADBs), extending finite state automata
    with variable time delay blocks, for deferring individual transition output symbols,
    in a discrete-time setting. We show that the ADB languages strictly subsume the
    regular languages, and are incomparable in expressive power to the context-free
    languages. We show that ADBs are closed under union, concatenation and Kleene
    star, and under intersection with regular languages, but not closed under complementation
    and intersection with other ADB languages. We show that the emptiness and the
    membership problems are decidable in polynomial time for ADBs, whereas the universality
    problem is undecidable. Finally we consider the linear-time model checking problem,
    i.e., whether the language of an ADB is contained in a regular language, and show
    that the model checking problem is PSPACE-complete. Copyright 2012 ACM.
acknowledgement: 'This work has been financially supported in part by the European
  Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract
  # 270180 (NOPTILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008
  (Modeling and control of Networked vehicle systems in persistent autonomous operations);
  by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic
  Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start
  grant (279307: Graph Games); Microsoft faculty fellows award; ERC Advanced grant
  QUAREM; and FWF Grant No S11403-N23 (RiSE).'
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: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Vinayak
  full_name: Prabhu, Vinayak
  last_name: Prabhu
citation:
  ama: 'Chatterjee K, Henzinger TA, Prabhu V. Finite automata with time delay blocks.
    In: <i>Proceedings of the 10th ACM International Conference on Embedded Software</i>.
    ACM; 2012:43-52. doi:<a href="https://doi.org/10.1145/2380356.2380370">10.1145/2380356.2380370</a>'
  apa: 'Chatterjee, K., Henzinger, T. A., &#38; Prabhu, V. (2012). Finite automata
    with time delay blocks. In <i>Proceedings of the 10th ACM international conference
    on Embedded software</i> (pp. 43–52). Tampere, Finland: ACM. <a href="https://doi.org/10.1145/2380356.2380370">https://doi.org/10.1145/2380356.2380370</a>'
  chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Finite
    Automata with Time Delay Blocks.” In <i>Proceedings of the 10th ACM International
    Conference on Embedded Software</i>, 43–52. ACM, 2012. <a href="https://doi.org/10.1145/2380356.2380370">https://doi.org/10.1145/2380356.2380370</a>.
  ieee: K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Finite automata with time
    delay blocks,” in <i>Proceedings of the 10th ACM international conference on Embedded
    software</i>, Tampere, Finland, 2012, pp. 43–52.
  ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2012. Finite automata with time delay
    blocks. Proceedings of the 10th ACM international conference on Embedded software.
    EMSOFT: Embedded Software , 43–52.'
  mla: Chatterjee, Krishnendu, et al. “Finite Automata with Time Delay Blocks.” <i>Proceedings
    of the 10th ACM International Conference on Embedded Software</i>, ACM, 2012,
    pp. 43–52, doi:<a href="https://doi.org/10.1145/2380356.2380370">10.1145/2380356.2380370</a>.
  short: K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Proceedings of the 10th ACM
    International Conference on Embedded Software, ACM, 2012, pp. 43–52.
conference:
  end_date: 2012-10-12
  location: Tampere, Finland
  name: 'EMSOFT: Embedded Software '
  start_date: 2012-10-07
date_created: 2018-12-11T12:00:26Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2026-08-12T14:34:15Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/2380356.2380370
ec_funded: 1
external_id:
  arxiv:
  - '1207.7019'
fulldoi: https://doi.org/10.1145/2380356.2380370
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/1207.7019
month: '10'
oa: 1
oa_version: Preprint
page: 43 - 52
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P 23499-N23
  name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
- _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: Proceedings of the 10th ACM international conference on Embedded software
publication_status: published
publisher: ACM
publist_id: '3799'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Finite automata with time delay blocks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...