Advances in the visualization and analysis of boundary layer flow in swimming fish

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2005In biology, the importance of fluid drag, diffusion, and heat transfer both internally and externally, suggest the boundary layer as an important subject of investigation, however, the complexities of biological systems present significant and unique challenges to analysis by experimental fluid dynamics. In this investigation, a system for automatically profiling the boundary layer over free-swimming, deforming bodies was developed and the boundary layer over rigid and live mackerel, bluefish, scup and eel was profiled. The profiling system combined robotics, particle imaging velocimetry, a custom particle tracking code, and an automatic boundary layer analysis code. Over 100,000 image pairs of flow in the boundary layer were acquired in swimming fish alone, making spatial and temporal ensemble averaging possible. A flat plate boundary layer was profiled and compared to known laminar and turbulent boundary layer theory. In general, profiles resembled those of Blasius for sub-critical length Reynolds numbers, Reχ. Transition to a turbulent boundary layer was observed near the expected critical Reχ and subsequent profiles agreed well with the law of the wall. The flat plate analysis demonstrated that the particle tracking and boundary layer analysis algorithms were highly accurate. In rigid fish, separation of flow was clearly evident and the boundary layer transitioned to turbulent at lower Reχ than in swimming fish and the flat plate. Wall shear stress, τo forward of separation was slightly higher than flat plate values. Friction drag in rigid and swimming fish was determined by integrating τo over the surface of the fish. The analysis was facilitated by the definition of the relative local coefficient of friction. In general, there was no significant difference in friction drag between the rigid-body and swimming cases. In swimming, separation was, on average, delayed. Therefore, pressure drag was estimated on the basis of thickness ratio and used to calculate an upper-bound total drag on a swimming fish. Total drag was used to determine the required muscle power output during swimming and compare that with existing muscle power data. τo and boundary layer thickness oscillated with undulatory phase. The magnitude of oscillation appears to be linked to body wave amplitude.The author is grateful for the funding received from the Office of Naval Research, Grants N00014-99-1-1082 and N00014-96-1141, the MRI program of the National Science Foundation, Grant OCE-9724383, the National Science Foundation Graduate Research Traineeship in Coastal Oceanography, the WHOI Ocean Ventures Fund, the WHOI Academic Programs Office, and the MIT Department of Ocean Engineering

M/V WELLWOOD Coral Reef Restoration Monitoring Report, Monitoring Events 2004-2006. Florida Keys National Marine Sanctuary Monroe County, Florida

This document presents the results of the first two monitoring events to track the recovery of a repaired coral reef injured by the M/V Wellwood vessel grounding incident of August 4, 1984. This grounding occurred within the boundaries of what at the time was designated the Key Largo National Marine Sanctuary (NMS), now designated the Key Largo NMS Existing Management Area within the Florida Keys National Marine Sanctuary (FKNMS). Pursuant to the National Marine Sanctuaries Act (NMSA) 16 U.S.C. 1431 et seq., and the Florida Keys National Marine Sanctuary and Protection Act (FKNMSPA) of 1990, NOAA is the federal trustee for the natural and cultural resources of the FKNMS. Under Section 312 of the NMSA, NOAA has the authority to recover monetary damages for injury, destruction, or loss of Sanctuary resources, and to use the recovered monies to restore injured or lost sanctuary resources within the FKNMS. The restoration monitoring program tracks patterns of biological recovery, determines the success of restoration measures, and assesses the resiliency to environmental and anthropogenic disturbances of the site over time. To evaluate restoration success, reference habitats adjacent to the restoration site are concurrently monitored to compare the condition of restored reef areas with “natural” coral reef areas unimpacted by the vessel grounding or other injury. Restoration of the site was completed on July 22, 2002, and thus far two monitoring events have occurred; one in the Fall of 2004, and one in the Summer/Fall of 2006. The monitoring has consisted of: assessment of the structural stability of restoration modules and comparison of the coral recruitment conditions of the modules and reference sites. Corals are divided into Gorgonians, Milleporans, and Scleractinians and (except where noted) recruits are defined as follows: Gorgonians—maximum size (height) 150 mm at first monitoring event, 270 mm at second; Milleporans—maximum size (height) 65 mm at first event, 125 mm at second; Scleractinians—maximum size (greatest diameter) 50 mm at second event (only one species was size-classed at first event, at smaller size). Recruit densities at the restored and reference areas for each event are compared, as are size-class frequency distributions. For the Scleractinians, number and percentage of recruits by species, as well as several common biodiversity indices are provided. Finally, a qualitative comparison of recruit substrate settlement preference is indicated. Generally, results indicate that restored areas are converging on reference areas, based on almost all parameters examined, with one noted exception. Further monitoring is planned and the trends are anticipated to continue; close attention will be paid to the indicated anomaly. (PDF contains 63 pages.

M/V CONNECTED Coral Reef Restoration Monitoring Report, Monitoring Events 2004-2005. Florida Keys National Marine Sanctuary Monroe County, Florida

This document presents the results of the monitoring of a repaired coral reef injured by the M/V Connected vessel grounding incident of March 27, 2001. This grounding occurred in Florida state waters within the boundaries of the Florida Keys National Marine Sanctuary (FKNMS). The National Oceanic and Atmospheric Administration (NOAA) and the Board of Trustees of the Internal Improvement Trust Fund of the State of Florida, (“State of Florida” or “state”) are the co-trustees for the natural resources within the FKNMS and, thus, are responsible for mediating the restoration of the damaged marine resources and monitoring the outcome of the restoration actions. The restoration monitoring program tracks patterns of biological recovery, determines the success of restoration measures, and assesses the resiliency to environmental and anthropogenic disturbances of the site over time. The monitoring program at the Connected site was to have included an assessment of the structural stability of installed restoration modules and biological condition of reattached corals performed on the following schedule: immediately (i.e., baseline), 1, 3, and 6 years after restoration and following a catastrophic event. Restoration of this site was completed on July 20, 2001. Due to unavoidable delays in the settlement of the case, the “baseline” monitoring event for this site occurred in July 2004. The catastrophic monitoring event occurred on August 31, 2004, some 2 ½ weeks after the passage of Hurricane Charley which passed nearby, almost directly over the Dry Tortugas. In September 2005, the year one monitoring event occurred shortly after the passage of Hurricane Katrina, some 70 km to the NW. This report presents the results of all three monitoring events. (PDF contains 37 pages.

M/V JACQUELYN L Coral Reef Restoration Monitoring Report, Monitoring Events 2004-2005. Florida Keys National Marine Sanctuary Monroe County, Florida

This document presents the results of the monitoring of a repaired coral reef injured by the M/V Jacquelyn L vessel grounding incident of July 7, 1991. This grounding occurred in Florida state waters within the boundaries of the Florida Keys National Marine Sanctuary (FKNMS). The National Oceanic and Atmospheric Administration (NOAA) and the Board of Trustees of the Internal Improvement Trust Fund of the State of Florida, (“State of Florida” or “state”) are the co-trustees for the natural resources within the FKNMS and, thus, are responsible for mediating the restoration of the damaged marine resources and monitoring the outcome of the restoration actions. The restoration monitoring program tracks patterns of biological recovery, determines the success of restoration measures, and assesses the resiliency to environmental and anthropogenic disturbances of the site over time. The monitoring program at the Jacquelyn L site was to have included an assessment of the structural stability of installed restoration modules and biological condition of reattached corals performed on the following schedule: immediately (i.e., baseline), 1, 3, and 6 years after restoration and following a catastrophic event. Restoration of this site was completed on July 20, 2000. Due to unavoidable delays in the settlement of the case, the “baseline” monitoring event for this site occurred in July 2004. The catastrophic monitoring event occurred on August 31, 2004, some 2 ½ weeks after the passage of Hurricane Charley which passed nearby, almost directly over the Dry Tortugas. In September 2005, the year one monitoring event occurred shortly after the passage of Hurricane Katrina, some 70 km to the NW. This report presents the results of all three monitoring events. (PDF contains 31 pages.

Isolating the hydrodynamic triggers of the dive response in eastern oyster larvae

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography 60 (2015): 1332–1343, doi:10.1002/lno.10098.Understanding the behavior of larval invertebrates during planktonic and settlement phases remains an open and intriguing problem in larval ecology. Larvae modify their vertical swimming behavior in response to water column cues to feed, avoid predators, and search for settlement sites. The larval eastern oyster (Crassostrea virginica) can descend in the water column via active downward swimming, sinking, or “diving,” which is a flick and retraction of the ciliated velum to propel a transient downward acceleration. Diving may play an important role in active settlement, as diving larvae move rapidly downward in the water column and may regulate their proximity to suitable settlement sites. Alternatively, it may function as a predator-avoidance escape mechanism. We examined potential hydrodynamic triggers to this behavior by observing larval oysters in a grid-stirred turbulence tank. Larval swimming was recorded for two turbulence intensities and flow properties around each larva were measured using particle image velocimetry. The statistics of flow properties likely to be sensed by larvae (fluid acceleration, deformation, vorticity, and angular acceleration) were compared between diving and non-diving larvae. Our analyses showed that diving larvae experienced high average flow accelerations in short time intervals (approximately 1–2 s) prior to dive onset, while accelerations experienced by non-diving larvae were significantly lower. Further, the probability that larvae dove increased with the fluid acceleration they experienced. These results indicate that oyster larvae actively respond to hydrodynamic signals in the local flow field, which has ecological implications for settlement and predator avoidance.This work was supported by NSF grant OCE-0850419, NOAA Sea Grant NA14OAR4170074, grants from the WHOI Coastal Ocean Institute, discretionary WHOI funds, a WHOI Ocean Life Fellowship to LM, and a Grove City College Swezey Fellowship to EA

M/V ELPIS Coral Reef Restoration Monitoring Report Monitoring Events 2004-2007 Florida Keys National Marine Sanctuary, Monroe County, Florida

This document presents the results of the first three monitoring events to track the recovery of a repaired coral reef injured by the M/V Elpis vessel grounding incident of November 11, 1989. This grounding occurred within the boundaries of what at the time was designated the Key Largo National Marine Sanctuary (NMS), now designated the Key Largo NMS Existing Management Area within the Florida Keys National Marine Sanctuary (FKNMS). Pursuant to the National Marine Sanctuaries Act (NMSA) 16 U.S.C. 1431 et seq., and the Florida Keys National Marine Sanctuary and Protection Act (FKNMSPA) of 1990, NOAA is the federal trustee for the natural and cultural resources of the FKNMS. Under Section 312 of the NMSA, NOAA has the authority to recover monetary damages for injury, destruction, or loss of Sanctuary resources, and to use the recovered monies to restore injured or lost sanctuary resources within the FKNMS. The restoration monitoring program tracks patterns of biological recovery, determines the success of restoration measures, and assesses the resiliency to environmental and anthropogenic disturbances of the site over time. To evaluate restoration success, reference habitats adjacent to the restoration site are concurrently monitored to compare the condition of restored reef areas with natural coral reef areas unimpacted by the vessel grounding. Restoration of the site was completed September 1995, and thus far three monitoring events have occurred; one in the summer of 2004, one in the summer of 2005, and the latest in the summer of 2007. The monitoring in 2004 was in the nature of a “pilot project,” or proof of concept. Only the quantitative results of the 2005 and 2007 monitoring are presented and discussed. Monitoring has consisted of assessment of the structural stability of limestone boulders used in the restoration and comparison of the coral communities on the boulders and reference areas. Corals are divided into Gorgonians, Milleporans, and Scleractinians. Coral densities at the Restored and Reference areas for the 2005 and 2007 events are compared, and it is shown that the densities of all taxa in the Restored area are greater by 2007, though not significantly so. For the Scleractinians, number and percentage of colonies by species, as well as several common biodiversity indices are provided. The greater biodiversity of the Restored area is evidenced. Also, size-class frequency distributions for Agaricia spp. (Scleractinia) are presented. These demonstrate the approaching convergence of the Restored and Reference areas in this regard. An inter-annual comparison of densities, within both areas, for all three Orders, is presented. The most noteworthy finding was the relative consistency across time for all taxa in each area. Finally, certain anomalies regarding species settlement patterns are presented. (PDF contains 48 pages.

Ontogenetic changes in larval swimming and orientation of pre-competent sea urchin Arbacia punctulata in turbulence

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Experimental Biology 219 (2016): 1303-1310, doi:10.1242/jeb.129502.Many marine organisms have complex life histories, having sessile adults and relying on the planktonic larvae for dispersal. Larvae swim and disperse in a complex fluid environment and the effect of ambient flow on larval behavior could in turn impact their survival and transport. However, to date, most studies on larvae–flow interactions have focused on competent larvae near settlement. We examined the importance of flow on early larval stages by studying how local flow and ontogeny influence swimming behavior in pre-competent larval sea urchins, Arbacia punctulata. We exposed larval urchins to grid-stirred turbulence and recorded their behavior at two stages (4- and 6-armed plutei) in three turbulence regimes. Using particle image velocimetry to quantify and subtract local flow, we tested the hypothesis that larvae respond to turbulence by increasing swimming speed, and that the increase varies with ontogeny. Swimming speed increased with turbulence for both 4- and 6-armed larvae, but their responses differed in terms of vertical swimming velocity. 4-Armed larvae swam most strongly upward in the unforced flow regime, while 6-armed larvae swam most strongly upward in weakly forced flow. Increased turbulence intensity also decreased the relative time that larvae spent in their typical upright orientation. 6-Armed larvae were tilted more frequently in turbulence compared with 4-armed larvae. This observation suggests that as larvae increase in size and add pairs of arms, they are more likely to be passively re-oriented by moving water, rather than being stabilized (by mechanisms associated with increased mass), potentially leading to differential transport. The positive relationship between swimming speed and larval orientation angle suggests that there was also an active response to tilting in turbulence. Our results highlight the importance of turbulence to planktonic larvae, not just during settlement but also in earlier stages through morphology–flow interactions.This work was supported by the National Science Foundation [OCE-0850419] and the National Oceanic and Atmospheric Administration Sea Grant [NA14OAR4170074]. K.Y.K.C. was supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation and the Royal Swedish Academy of Sciences. K.Y.K.C. is currently funded by the Croucher Foundation. Additional funding was provided to L.S.M. through the WHOI Ocean Life Fellowship and discretionary WHOI funds, and to E.J.A. through the faculty sabbatical program at Grove City College

The hydrodynamic footprint of a benthic, sedentary fish in unidirectional flow

Author Posting. © Acoustical Society of America, 2007. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 122 (2007): 1227-1237, doi:10.1121/1.2749455.Mottled sculpin (Cottus bairdi) are small, benthic fish that avoid being swept downstream by orienting their bodies upstream and extending their large pectoral fins laterally to generate negative lift. Digital particle image velocimetry was used to determine the effects of these behaviors on the spatial and temporal characteristics of the near-body flow field as a function of current velocity. Flow around the fish's head was typical for that around the leading end of a rigid body. Flow separated around the edges of pectoral fin, forming a wake similar to that observed for a flat plate perpendicular to the flow. A recirculation region formed behind the pectoral fin and extended caudally along the trunk to the approximate position of the caudal peduncle. In this region, the time-averaged velocity was approximately one order of magnitude lower than that in the freestream region and flow direction varied over time, resembling the periodic shedding of vortices from the edge of a flat plate. These results show that the mottled sculpin pectoral fin significantly alters the ambient flow noise in the vicinity of trunk lateral line sensors, while simultaneously creating a hydrodynamic footprint of the fish's presence that may be detected by the lateral line of nearby fish.This work was funded in part by an NIDCD program project grant to the Parmly Hearing Institute, Loyola University Chicago (W. Yost, PI, S. Coombs, Co-PI)

Criticality in one dimension with inverse square-law potentials

It is demonstrated that the scaled order parameter for ferromagnetic Ising and three-state Potts chains with inverse-square interactions exhibits a universal critical jump, in analogy with the superfluid density in helium films. Renormalization-group arguments are combined with numerical simulations of systems containing up to one million lattice sites to accurately determine the critical properties of these models. In strong contrast with earlier work, compelling quantitative evidence for the Kosterlitz--Thouless-like character of the phase transition is provided.Comment: To appear in Phys. Rev. Let

Enhanced skeletal muscle ribosome biogenesis, yet attenuated mTORC1 and ribosome biogenesis-related signalling, following short-term concurrent versus single-mode resistance training

Combining endurance training with resistance training (RT) may attenuate skeletal muscle hypertrophic adaptation versus RT alone; however, the underlying mechanisms are unclear. We investigated changes in markers of ribosome biogenesis, a process linked with skeletal muscle hypertrophy, following concurrent training versus RT alone. Twenty-three males underwent eight weeks of RT, either performed alone (RT group, n = 8), or combined with either high-intensity interval training (HIT+RT group, n = 8), or moderate-intensity continuous training (MICT+RT group, n = 7). Muscle samples (vastus lateralis) were obtained before training, and immediately before, 1 h and 3 h after the final training session. Training-induced changes in basal expression of the 45S ribosomal RNA (rRNA) precursor (45S pre-rRNA), and 5.8S and 28S mature rRNAs, were greater with concurrent training versus RT. However, during the final training session, RT further increased both mTORC1 (p70S6K1 and rps6 phosphorylation) and 45S pre-rRNA transcription-related signalling (TIF-1A and UBF phosphorylation) versus concurrent training. These data suggest that when performed in a training-accustomed state, RT induces further increases mTORC1 and ribosome biogenesis-related signalling in human skeletal muscle versus concurrent training; however, changes in ribosome biogenesis markers were more favourable following a period of short-term concurrent training versus RT performed alon