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  • Dredging  (2)
  • *Motion  (1)
  • Organic Chemistry
  • 2015-2019  (3)
  • 1920-1924
  • 1
    Publication Date: 2016-04-30
    Description: Systems in thermodynamic equilibrium are not only characterized by time-independent macroscopic properties, but also satisfy the principle of detailed balance in the transitions between microscopic configurations. Living systems function out of equilibrium and are characterized by directed fluxes through chemical states, which violate detailed balance at the molecular scale. Here we introduce a method to probe for broken detailed balance and demonstrate how such nonequilibrium dynamics are manifest at the mesosopic scale. The periodic beating of an isolated flagellum from Chlamydomonas reinhardtii exhibits probability flux in the phase space of shapes. With a model, we show how the breaking of detailed balance can also be quantified in stationary, nonequilibrium stochastic systems in the absence of periodic motion. We further demonstrate such broken detailed balance in the nonperiodic fluctuations of primary cilia of epithelial cells. Our analysis provides a general tool to identify nonequilibrium dynamics in cells and tissues.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Battle, Christopher -- Broedersz, Chase P -- Fakhri, Nikta -- Geyer, Veikko F -- Howard, Jonathon -- Schmidt, Christoph F -- MacKintosh, Fred C -- P50GM068763/GM/NIGMS NIH HHS/ -- R13GM085967/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Apr 29;352(6285):604-7. doi: 10.1126/science.aac8167.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Drittes Physikalisches Institut, Georg-August-Universitat, 37077 Gottingen, Germany. The Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA. ; The Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA. Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universitat Munchen, Theresienstrasse 37, D-80333 Munchen, Germany. Lewis-Sigler Institute for Integrative Genomics and Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA. ; Drittes Physikalisches Institut, Georg-August-Universitat, 37077 Gottingen, Germany. The Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA. Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. ; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. ; Drittes Physikalisches Institut, Georg-August-Universitat, 37077 Gottingen, Germany. The Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA. fcmack@gmail.com christoph.schmidt@phys.uni-goettingen.de. ; The Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA. Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Netherlands. fcmack@gmail.com christoph.schmidt@phys.uni-goettingen.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27126047" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chlamydomonas reinhardtii/*physiology ; Cilia/physiology ; Dogs ; Epithelial Cells/physiology ; Flagella/*physiology ; Madin Darby Canine Kidney Cells ; Microscopy/methods ; Models, Biological ; *Motion ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2022-10-20
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Oceans 124 (2019): 196-211, doi:10.1029/2018JC014313.
    Description: Since the late nineteenth century, channel depths have more than doubled in parts of New York Harbor and the tidal Hudson River, wetlands have been reclaimed and navigational channels widened, and river flow has been regulated. To quantify the effects of these modifications, observations and numerical simulations using historical and modern bathymetry are used to analyze changes in the barotropic dynamics. Model results and water level records for Albany (1868 to present) and New York Harbor (1844 to present) recovered from archives show that the tidal amplitude has more than doubled near the head of tides, whereas increases in the lower estuary have been slight (〈10%). Channel deepening has reduced the effective drag in the upper tidal river, shifting the system from hyposynchronous (tide decaying landward) to hypersynchronous (tide amplifying). Similarly, modeling shows that coastal storm effects propagate farther landward, with a 20% increase in amplitude for a major event. In contrast, the decrease in friction with channel deepening has lowered the tidally averaged water level during discharge events, more than compensating for increased surge amplitude. Combined with river regulation that reduced peak discharges, the overall risk of extreme water levels in the upper tidal river decreased after channel construction, reducing the water level for the 10‐year recurrence interval event by almost 3 m. Mean water level decreased sharply with channel modifications around 1930, and subsequent decadal variability has depended both on river discharge and sea level rise. Channel construction has only slightly altered tidal and storm surge amplitudes in the lower estuary.
    Description: Funding for D. K. R., W. R. G., and C. K. S. was provided by NSF Coastal SEES awards OCE-1325136 and OCE-1325102. Funding for S.T. and H. Z. was provided by the U.S. Army Corps of Engineers (award W1927 N-14-2-0015), and NSF (Career Award 1455350). Data supporting this study are posted to Zenodo (https://doi.org/10.5281/zenodo.1298636).
    Description: 2019-06-11
    Keywords: Barotropic tides ; Flood frequency ; Storm surge ; Dredging ; Estuary ; Tidal river
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Publication Date: 2022-10-20
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Oceans 124(7), (2019): 4784-4802, doi: 10.1029/2019JC015006.
    Description: Modifications for navigation since the late 1800s have increased channel depth (H) in the lower Hudson River estuary by 10–30%, and at the mouth the depth has more than doubled. Observations along the lower estuary show that both salinity and stratification have increased over the past century. Model results comparing predredging bathymetry from the 1860s with modern conditions indicate an increase in the salinity intrusion of about 30%, which is roughly consistent with the H5/3 scaling expected from theory for salt flux dominated by steady exchange. While modifications including a recent deepening project have been concentrated near the mouth, the changes increase salinity and threaten drinking water supplies more than 100 km landward. The deepening has not changed the responses to river discharge (Qr) of the salinity intrusion (~Qr−1/3) or mean stratification (Qr2/3). Surprisingly, the increase in salinity intrusion with channel deepening results in almost no change in the estuarine circulation. This contrasts sharply with local scaling based on local dynamics of an H2 dependence, but it is consistent with a steady state salt balance that allows scaling of the estuarine circulation based on external forcing factors and is independent of depth. In contrast, the observed and modeled increases in stratification are opposite of expectations from the steady state balance, which could be due to reduction in mixing with loss of shallow subtidal regions. Overall, the mean shift in estuarine parameter space due to channel deepening has been modest compared with the monthly‐to‐seasonal variability due to tides and river discharge.
    Description: Funding was provided by NSF Coastal SEES (OCE 1325136). Data supporting this study are posted to Zenodo (https://doi.org/10.5281/zenodo.2551285) or are available by contacting the author.
    Description: 2019-12-07
    Keywords: Estuarine circulation ; Salinity intrusion ; Stratification ; Dredging ; Hudson River
    Repository Name: Woods Hole Open Access Server
    Type: Article
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