Substitutional Self-Assembly of Alkanethiol and Selenol SAMs from a Lying-Down Doubly Tethered Butanedithiol SAM on Gold

Substitutional self-assembly of thiol and selenol SAMs from a lying-down phase of butanedithiol (C4DT) (SAM) were investigated using thiols, disulfide, and diselenide molecules. The intent was to address the question if formation of a lying-down dithiol phase is an impediment to formation of standing-up dithiol phases as it has been assumed. It is demonstrated that this is not the case, and the C4DT SAM, where both the sulfur atoms are chemisorbed on gold, is removed and replaced in all cases. Differences in substitution kinetics are observed.

Dynamics of the reaction between the free end of a tethered self-avoiding polymer and a flat penetrable surface: A renormalization group study

The average time tau(r) for one end of a long, self-avoiding polymer to interact for the first time with a flat penetrable surface to which it is attached at the other end is shown here to scale essentially as the square of the chain's contour length N. This result is obtained within the framework of the Wilemski-Fixman approximation to diffusion-limited reactions, in which the reaction time is expressed as a time correlation function of a ``sink'' term. In the present work, this sink-sink correlation function is calculated using perturbation expansions in the excluded volume and the polymer-surface interactions, with renormalization group methods being used to resum the expansion into a power law form. The quadratic dependence of tau(r) on N mirrors the behavior of the average time tau(c) of a free random walk to cyclize, but contrasts with the cyclization time of a free self-avoiding walk (SAW), for which tau(r) similar to N-2.2. A simulation study by Cheng and Makarov J. Phys. Chem. B 114, 3321 (2010)] of the chain-end reaction time of an SAW on a flat impenetrable surface leads to the same N-2.2 behavior, which is surprising given the reduced conformational space a tethered polymer has to explore in order to react. (C) 2014 AIP Publishing LLC.

Anomalous lifetime statistics of ligand-receptor binding in a tethered polymer system

In this paper, motivated by observations of non-exponential decay times in the stochastic binding and release of ligand-receptor systems, exemplified by the work of Rogers et al on optically trapped DNA-coated colloids (Rogers et al 2013 Soft Matter 9 6412), we explore the general problem of polymer-mediated surface adhesion using a simplified model of the phenomenon in which a single polymer molecule, fixed at one end, binds through a ligand at its opposite end to a flat surface a fixed distance L away and uniformly covered with receptor sites. Working within the Wilemski-Fixman approximation to diffusion-controlled reactions, we show that for a flexible Gaussian chain, the predicted distribution of times f(t) for which the ligand and receptor are bound is given, for times much shorter than the longest relaxation time of the polymer, by a power law of the form t(-1/4). We also show when the effects of chain stiffness are incorporated into this model (approximately), the structure of f(t) is altered to t(-1/2). These results broadly mirror the experimental trends in the work cited above.

A numerical investigation on the flow physics of koi carp (Cyprinus carpio koi) burst-and-coast swimming

Abstract—Burst-and-coast is the most common locomotion type in freely routine swimming of koi carps (Cyprinus carpio koi), which consists of a burst phase and a coast phase in each cycle and mostly leads to a straight-line trajectory. Combining with the tracking experiment, the flow physics of koi carp’s burst-andcoast swimming is investigated using a novel integrated CFD method solving the body-fluid interaction problem. The dynamical equations of a deforming body are formulated. Following that, the loose-coupled equations of the body dynamics and the fluid dynamics are numerically solved with the integrated method. The two burst modes, MT (Multiple Tail-beat) and HT (Half Tail-beat), which have been reported by the experiments, are investigated by numerical simulations in this paper. The body kinematics is predicted and the flow physics is visualized, which are in good agreement with the corresponding experiments. Furthermore, the optimization on the energy cost and several critical control mechanisms in burst-and-coast swimming of koi carps are explored, by varying the parameters in its selfpropelled swimming. In this paper, energetics is measured by the two mechanical quantities, total output power CP and Froude efficiency Fr. Results and discussion show that from the standpoint of mechanical energy, burst-and-coast swimming does not actually save energy comparing with steady swimming at the same average speed, in that frequently changing of speed leads to decrease of efficiency.

Developing effective restoration plans to tackle the widespread impairment of coastal swimming and shellfishing waters

Congress established a legal imperative to restore the quality of our surface waters when it enacted the Clean Water Act in 1972. The act requires that existing uses of coastal waters such as swimming and shellfishing be protected and restored. Enforcement of this mandate is frequently measured in terms of the ability to swim and harvest shellfish in tidal creeks, rivers, sounds, bays, and ocean beaches. Public-health agencies carry out comprehensive water-quality sampling programs to check for bacteria contamination in coastal areas where swimming and shellfishing occur. Advisories that restrict swimming and shellfishing are issued when sampling indicates that bacteria concentrations exceed federal health standards. These actions place these coastal waters on the U.S. Environmental Protection Agencies’ (EPA) list of impaired waters, an action that triggers a federal mandate to prepare a Total Maximum Daily Load (TMDL) analysis that should result in management plans that will restore degraded waters to their designated uses. When coastal waters become polluted, most people think that improper sewage treatment is to blame. Water-quality studies conducted over the past several decades have shown that improper sewage treatment is a relatively minor source of this impairment. In states like North Carolina, it is estimated that about 80 percent of the pollution flowing into coastal waters is carried there by contaminated surface runoff. Studies show this runoff is the result of significant hydrologic modifications of the natural coastal landscape. There was virtually no surface runoff occurring when the coastal landscape was natural in places such as North Carolina. Most rainfall soaked into the ground, evaporated, or was used by vegetation. Surface runoff is largely an artificial condition that is created when land uses harden and drain the landscape surfaces. Roofs, parking lots, roads, fields, and even yards all result in dramatic changes in the natural hydrology of these coastal lands, and generate huge amounts of runoff that flow over the land’s surface into nearby waterways. (PDF contains 3 pages)

Information collected in Teesdale concerning free-swimming stages of brown trout (Salmo trutta L.)

During 1978 and 1979, electrofishing surveys were made in Teesdale - both to provide background information for ecological work on the streams, and to provide data so that the influence of discharge regime on the fish population densities could be examined. The discharge regimes of the different streams were compared using the Base Flow Index (BFI) as developed by the Institute of Hydrology. (PDF contains 30 pages)

Effects of seasonal change on activity rhythms and swimming behavior of age-0 bluefish (Pomatomus saltatrix) and a description of gliding behavior

Daily and seasonal activity rhythms, swimming speed, and modes of swimming were studied in a school of spring-spawned age-0 bluefish (Pomatomus saltatrix) for nine months in a 121-kL research aquarium. Temperature was lowered from 20° to 15°C, then returned to 20°C to match the seasonal cycle. The fish grew from a mean 198 mm to 320 mm (n= 67). Bluefish swam faster and in a more organized school during day (overall mean 47 cm/s) than at night (31 cm/s). Swimming speed declined in fall as temperature declined and accelerated in spring in response to change in photoperiod. Besides powered swimming, bluefish used a gliding-upswimming mode, which has not been previously described for this species. To glide, a bluefish rolled onto its side, ceased body and tail beating, and coasted diagonally downward. Bluefish glided in all months of the study, usually in the dark, and most intensely in winter. Energy savings while the fish is gliding and upswimming may be as much as 20% of the energy used in powered swimming. Additional savings accrue from increased lift due to the hydrofoil created by the horizontal body orientation and slightly concave shape. Energy-saving swimming would be advantageous during migration and overwintering.

Duration of unassisted swimming activity for spotted dolphin (Stenella attenuata) calves: implications for mother-calf separation during tuna purse-seine sets

Size-related differences in power production and swim speed duration may contribute to the observed deficit of nursing calves in relation to lactating females killed in sets by tuna purse-seiners in the eastern tropical Pacific Ocean (ETP). Power production and swim-speed duration were estimated for northeastern spotted dolphins (Stenella attenuata), the species (neonate through adult) most often captured by the fishery. Power required by neonates to swim unassisted was 3.6 times that required of an adult to swim the same speed. Estimated unassisted burst speed for neonates is only about 3 m/s compared to about 6 m/s for adults. Estimated long-term sustainable speed is about 1 m/s for neonates compared to about 2.5 m/s for adults. Weight-specific power requirements decrease as dolphin calves increase in size, but power estimates for 2-year-old spotted dolphin calves are still about 40% higher than power estimates for adults, to maintain the same speed. These estimated differences between calves and adults are conservative because the calculations do not include accommodation for reduced aerobic capacity in dolphin calves compared to adults. Discrepancies in power production are probably ameliorated under normal circumstances by calves drafting next to their mothers, and by employing burst-coast or leap-burst-coast swimming, but the relatively high speeds associated with evasion behaviors during and after tuna sets likely diminish use of these energy-saving strategies by calves.

Hydrodynamic entrapment of bacteria swimming near a solid surface.

The near-surface motility of bacteria is important in the initial formation of biofilms and in many biomedical applications. The swimming motion of Escherichia coli near a solid surface is investigated both numerically and experimentally. A boundary element method is used to predict the hydrodynamic entrapment of E. coli bacteria, their trajectories, and the minimum separation of the cell from the surface. The numerical results show the existence of a stable swimming distance from the boundary that depends only on the shape of the cell body and the flagellum. The experimental validation of the numerical approach allows one to use the numerical method as a predictive tool to estimate with reasonable accuracy the near-wall motility of swimming bacteria of known geometry. The analysis of the numerical database demonstrated the existence of a correlation between the radius of curvature of the near-wall circular trajectory and the separation gap. Such correlation allows an indirect estimation of either of the two quantities by a direct measure of the other without prior knowledge of the cell geometry. This result may prove extremely important in those biomedical and technical applications in which the near-wall behavior of bacteria is of fundamental importance.

Swimming crab Callinectes amnicola (Decapoda-Portunidae) capture analysis of a lagoon with high continental influence (Aby Lagoon, Cote d'Ivoire, West Africa)

The study describes the main causes of captures and productions decreasing of swimming crab Callinectes amnicola (Decapoda Portunidae) in Aby lagoon complex. For that, docks of two Sub Prefectures of Adiaké and Assini-Mafia respectively including the villages of Adiaké, Anga, Assomlan, Epleman, Aby and Man-Man, M'Bratty, Assini-Ngouankro and Assini-Mafia were studied from 2006 to 2009 and completed with previous results obtained from 1988 to 2005. Field investigators were identified by site/village and they recorded daily activities of fishermen (number of effective fishermen, number of gears and area of fishing, duration of fishing, types and quantity of bait) and landing of swimming crabs. During recent period of the study, total production decreased from 3742 tons in 2006 to 1500 tons in 2009. Matrix correlations and correlation analysis indicated that this downward trend was due to the increase of the number of fishermen, number of fishing gear, the decrease in female crabs capture and degradation of the environment related to gradual closure of the Assini-Mafia channel. Despite this decline, total production in Aby lagoon remained high compared to the productions of some lagoons of the country and the region. Given the importance of fishing swimming crabs in Aby lagoon, since it concerns many young people and it is a source of income, stringent measures for sustainable and responsible management must be taken and implemented as part of a co-management plan involving all stakeholders to sustainably manage the resource

Swimming depth, ambient water temperature preference, and feeding frequency of young Pacific bluefin tuna (Thunnus orientalis) determined with archival tags

We investigated the migration and behavior of young Pacific Bluefin tuna (Thunnus orientalis) using archival tags. The archival tag measures environmental variables, records them in its memory, and estimates daily geographical locations based on measured light levels. Of 166 archival tags implanted in Pacific bluefin tuna that were released at the northeastern end of the East China Sea from 1995 to 1997, 30 tags were recovered, including one from a fish that migrated across the Pacific. This article describes swimming depth, ambient water temperature, and feeding frequency of young Pacific bluefin tuna based on retrieved data. Tag performance, effect of the tag on the fish, and horizontal movements of the species are described in another paper. Young Pacific bluefin tuna swim mainly in the mixed layer, usually near the sea surface, and swim in deeper water in daytime than at nighttime. They also exhibit a pattern of depth changes, corresponding to sunrise and sunset, apparently to avoid a specific low light level. The archival tags recorded temperature changes in viscera that appear to be caused by feeding, and those changes indicate that young Pacific bluefin tuna commonly feed at dawn and in the daytime, but rarely at dusk or at night. Water temperature restricts their distribution, as indicated by changes in their vertical distribution with the seasonal change in depth of the thermocline and by the fact that their horizontal distribution is in most cases confined to water in the temperature range of 14−20°C.

Local distribution and abundance of swimming crabs (Callinectes spp. and Arenaeus cribrarius) on a tropical arid beach

Distribution, abundance, and several population features were studied in Ensenada de La Vela (Venezuela) between 1993 and 1998 as a first step in the assessment of local fisheries of swimming crabs. Arenaeus cribrarius was the most abundant species at the marine foreshore. Callinectes danae prevailed at the estuarine location. Callinectes bocourti was the most abundant species at the offshore. Abundances of A. cribrarius and C. danae fluctuated widely and randomly. Ovigerous females were almost absent. Adults of several species were smaller than previously reported. This study suggests that fisheries based on these swimming crabs probably will be restricted to an artisanal level because abundances appear too low to support industrial exploitation.

Swimming direction reversal of flagella through ciliary motion of mastigonemes.

Bio-inspired designs can provide an answer to engineering problems such as swimming strategies at the micron or nano-scale. Scientists are now designing artificial micro-swimmers that can mimic flagella-powered swimming of micro-organisms. In an application such as lab-on-a-chip in which micro-object manipulation in small flow geometries could be achieved by micro-swimmers, control of the swimming direction becomes an important aspect for retrieval and control of the micro-swimmer. A bio-inspired approach for swimming direction reversal (a flagellum bearing mastigonemes) can be used to design such a system and is being explored in the present work. We analyze the system using a computational framework in which the equations of solid mechanics and fluid dynamics are solved simultaneously. The fluid dynamics of Stokes flow is represented by a 2D Stokeslets approach while the solid mechanics behavior is realized using Euler-Bernoulli beam elements. The working principle of a flagellum bearing mastigonemes can be broken up into two parts: (1) the contribution of the base flagellum and (2) the contribution of mastigonemes, which act like cilia. These contributions are counteractive, and the net motion (velocity and direction) is a superposition of the two. In the present work, we also perform a dimensional analysis to understand the underlying physics associated with the system parameters such as the height of the mastigonemes, the number of mastigonemes, the flagellar wave length and amplitude, the flagellum length, and mastigonemes rigidity. Our results provide fundamental physical insight on the swimming of a flagellum with mastigonemes, and it provides guidelines for the design of artificial flagellar systems.