Ultrafast structural changes within a photosynthetic reaction centre.

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.

Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosines.

Proteins are commonly known to transfer electrons over distances limited to a few nanometers. However, many biological processes require electron transport over far longer distances. For example, soil and sediment bacteria transport electrons, over hundreds of micrometers to even centimeters, via putative filamentous proteins rich in aromatic residues. However, measurements of true protein conductivity have been hampered by artifacts due to large contact resistances between proteins and electrodes. Using individual amyloid protein crystals with atomic-resolution structures as a model system, we perform contact-free measurements of intrinsic electronic conductivity using a four-electrode approach. We find hole transport through micrometer-long stacked tyrosines at physiologically relevant potentials. Notably, the transport rate through tyrosines (105 s-1) is comparable to cytochromes. Our studies therefore show that amyloid proteins can efficiently transport charges, under ordinary thermal conditions, without any need for redox-active metal cofactors, large driving force, or photosensitizers to generate a high oxidation state for charge injection. By measuring conductivity as a function of molecular length, voltage, and temperature, while eliminating the dominant contribution of contact resistances, we show that a multistep hopping mechanism (composed of multiple tunneling steps), not single-step tunneling, explains the measured conductivity. Combined experimental and computational studies reveal that proton-coupled electron transfer confers conductivity; both the energetics of the proton acceptor, a neighboring glutamine, and its proximity to tyrosine influence the hole transport rate through a proton rocking mechanism. Surprisingly, conductivity increases 200-fold upon cooling due to higher availability of the proton acceptor by increased hydrogen bonding.

On the equivalence of scalar-pressure and vector-based acoustic dosage measures as derived from time-limited signal waveformsa).

The dynamic (acoustic pressure) and kinematic (acoustic acceleration and velocity) properties of time-limited signals are studied in terms of acoustic dose metrics as might be used to assess the impact of underwater noise on marine life. The work is relevant for the study of anthropogenic transient acoustic signals, such as airguns, pile driving, and underwater explosive sources, as well as more generic transient signals from sonar systems. Dose metrics are first derived from numerical simulations of sound propagation from a seismic airgun source as specified in a Joint Industry Programme benchmark problem. Similar analyses are carried out based on at-sea acoustic measurements on the continental shelf, made with a vector sensor positioned 1.45 m off the seabed. These measurements are on transient time-limited signals from multiple underwater explosive sources at differing ranges, and from a towed, sonar source. The study demonstrates, both numerically and experimentally, that under many realistic scenarios, kinematic based acoustic dosage metrics within the water column can be evaluated using acoustic pressure measurements.

Coherent reflection recovery in scattering from the ocean surface using the frequency-difference autoproducta).

The coherence of rough sea-surface-scattered acoustic fields decreases with increasing frequency. The frequency-difference autoproduct, a quadratic product of acoustic fields at nearby frequencies, mimics a genuine field at the difference frequency. In rough-surface scattering, the autoproduct's lower effective frequency decreases the apparent surface roughness, restoring coherent reflection. Herein, the recovery of coherent reflection in sea surface scattering via the frequency-difference autoproduct is examined for data collected off the coast of New Jersey during the Shallow Water '06 (SW06) experiment. An acoustic source at depth 40 m and receiver at depth 24.3 m and range 200 m interrogated 160 independent realizations of the ocean surface. The root mean square surface height h was 0.167 m, and broadcast frequencies were 14-20 kHz, so that 2.5 ≤kh cos θ≤ 3.7 for acoustic wavenumber k and incidence angle θ. Measured autoproducts, constructed from scattered constituent fields, show significant coherent reflection at sufficiently low difference frequencies. Theoretical results, using the Kirchhoff approximation and a non-analytic surface autocorrelation function, agree with experimental findings. The match is improved using a numerical strategy, exploiting the relationship between autoproduct-based coherence recovery, the ocean-surface autocorrelation function, and the ocean-surface height spectrum. Error bars computed from Monte Carlo scattering simulations support the validity of the measured coherence recovery.

Active intensity vortex and stagnation point singularities in a shallow underwater waveguide.

Vector acoustic properties of a narrowband acoustic field are observed as a function of range from a source towed in waters of depth 77 m on the New England Mud Patch. At the source frequency (43 Hz), the waveguide supported three trapped modes, with mode 2 weakly excited owing to the towed source depth. The receiving sensor was positioned 1.45 m above the seafloor with a sampling range aperture of 2500 m. The vector acoustics observations enabled study of vortex regions that encompass two singular points for active acoustic intensity: the vortex point, which is co-located with a dislocation, and stagnation point. Interpretative modeling, based on the normal modes and using a geoacoustic model consistent with those emerging from studies conducted at this location, is in agreement with these measurements. Model-data comparisons were based on the first-order variables of acoustic pressure and velocity along with inverse Hankel transforms, which yield normalized horizontal wavenumber spectra, and second-order variables in the form of horizontal and vertical intensity as well as non-dimensional intensity-based ratios. These measures provide a degree of observational confirmation of some vortex region properties. Both observations and modeling point to a gradual deepening of such regions with increasing range owing to sediment attenuation.

Electric field stimulates production of highly conductive microbial OmcZ nanowires.

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S cm-1) and threefold higher stiffness (1.5 GPa) than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function and observe pH-induced conformational switching to ß-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modeling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. These findings of biologically produced, highly conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.

Vector acoustic and polarization properties of underwater ship noise.

Vector acoustic field properties measured during the 2017 Seabed Characterization Experiment (SBCEX17) are presented. The measurements were made using the Intensity Vector Autonomous Recorder (IVAR) that records acoustic pressure and acceleration from which acoustic velocity is obtained. Potential and kinetic energies of underwater noise from two ship sources, computed in decidecimal bands centered between 25-630 Hz, are equal within calibration uncertainty of ±1.5 dB, representing a practical result towards the inference of kinematic properties from pressure-only measurements. Bivariate signals limited to two acoustic velocity components are placed in the context of the Stokes framework to describe polarization properties, such as the degree of polarization, which represents a statistical measure of the dispersion of the polarization properties. A bivariate signal composed of vertical and radial velocity components within a narrow frequency band centered at 63 Hz representing different measures of circularity and degree of polarization is examined in detail, which clearly demonstrates properties of bivariate signal trajectory. An examination of the bivariate signal composed of the two horizontal components of velocity within decidecimal bands centered at 63 Hz and 250 Hz demonstrates the importance of the degree of polarization in bearing estimation of moving sources.

Potential and kinetic energy of underwater noise measured below a passing ship and response to sub-bottom layering.

Observed near the seafloor, broadband noise emissions from a vessel passing directly above exhibit frequency bands where potential acoustic energy is greater than kinetic energy while the opposite occurs in neighboring frequency bands. The condition where the dynamic and kinematic energy forms differ in this manner is characteristic to interference involving steep angles or near-normal incidence reflection from the seafloor. Measurements are made at two experimental sites using a research vessel passing above a vector sensor, positioned ∼1.5 m above the seabed, resulting in a vessel horizontal range approaching ∼0. The data are expressed as a ratio of kinetic to potential energy in decibels and yield information on seabed properties. A model for kinetic and potential energy is developed from the method of images using a layered seabed and is used to invert data collected in Puget Sound. A higher-impedance seabed is identified via inversion, which is consistent with the thin Holocene sediments in the region. For data collected on the New England Mud Patch, the model is instead applied directly to nominal seabed parameters originating from prior studies that identify a low-speed mud layer atop a higher-speed transition layer separating the mud substrate from a sediment basement.

Physical effects of sound exposure from underwater explosions on Pacific mackerel (Scomber japonicus): Effects on non-auditory tissues.

Underwater explosions from activities such as construction, demolition, and military activities can damage non-auditory tissues in fishes. To better understand these effects, Pacific mackerel (Scomber japonicus) were placed in mid-depth cages with water depth of approximately 19.5 m and exposed at distances of 21 to 807 m to a single mid-depth detonation of C4 explosive (6.2 kg net explosive weight). Following exposure, potential correlations between blast acoustics and observed physical effects were examined. Primary effects were damage to the swim bladder and kidney that exceeded control levels at ≤333 m from the explosion [peak sound pressure level 226 dB re 1 µPa, sound exposure level (SEL) 196 dB re 1 µPa2 s, pressure impulse 98 Pa s]. A proportion of fish were dead upon retrieval at 26-40 min post exposure in 6 of 12 cages located ≤157 m from the explosion. All fish that died within this period suffered severe injuries, especially swim bladder and kidney rupture. Logistic regression models demonstrated that fish size or mass was not important in determining susceptibility to injury and that peak pressure and SEL were better predictors of injury than was pressure impulse.

Physical effects of sound exposure from underwater explosions on Pacific mackerel (Scomber japonicus): Effects on the inner ear.

Studies of the effects of sounds from underwater explosions on fishes have not included examination of potential effects on the ear. Caged Pacific mackerel (Scomber japonicus) located at seven distances (between approximately 35 and 800 m) from a single detonation of 4.5 kg of C4 explosives were exposed. After fish were recovered from the cages, the sensory epithelia of the saccular region of the inner ears were prepared and then examined microscopically. The number of hair cell (HC) ciliary bundles was counted at ten preselected 2500 µm2 regions. HCs were significantly reduced in fish exposed to the explosion as compared to the controls. The extent of these differences varied by saccular region, with damage greater in the rostral and caudal ends and minimal in the central region. The extent of effect also varied in animals at different distances from the explosion, with damage occurring in fish as far away as 400 m. While extrapolation to other species and other conditions (e.g., depth, explosive size, and distance) must be performed with extreme caution, the effects of explosive sounds should be considered when environmental impacts are estimated for marine projects.

Trends in low-frequency underwater noise off the Oregon coast and impacts of COVID-19 pandemic.

Approximately six years of underwater noise data recorded from the Regional Cabled Array network are examined to study long-term trends. The data originate from station HYS14 located 87 km offshore of Newport, OR. The results indicate that the third-octave band level centered at 63 Hz and attributable to shipping activity is reduced in the spring of 2020 by about 1.6 dB relative to the mean of the prior five years, owing to the reduced economic activity initiated by the COVID-19 pandemic. The results are subtle, as the noise reduction is less than the typical seasonal fluctuation associated with warming ocean surface temperatures in the summer that reduces mode excitation support at typical ship source depths, causing a repeated annual level change on the order of 4 dB at shipping frequencies. Seasonality of the noise contribution near 20 Hz from fin whales is also discussed. Corroboration of a COVID-19 effect on shipping noise is offered by an analysis of automatic identification system shipping data and shipping container activity for Puget Sound, over the same six-year period, which shows a reduction in the second quarter of 2020 by ∼19% and ∼17%, respectively, relative to the mean of the prior five years.

Polarization of ocean acoustic normal modes.

In ocean acoustics, shallow water propagation is conveniently described using normal mode propagation. This article proposes a framework to describe the polarization of normal modes, as measured using a particle velocity sensor in the water column. To do so, the article introduces the Stokes parameters, a set of four real-valued quantities widely used to describe polarization properties in wave physics, notably for light. Stokes parameters of acoustic normal modes are theoretically derived, and a signal processing framework to estimate them is introduced. The concept of the polarization spectrogram, which enables the visualization of the Stokes parameters using data from a single vector sensor, is also introduced. The whole framework is illustrated on simulated data as well as on experimental data collected during the 2017 Seabed Characterization Experiment. By introducing the Stokes framework used in many other fields, the article opens the door to a large set of methods developed and used in other contexts but largely ignored in ocean acoustics.

Power Law Behavior in Protein Desorption Kinetics Originating from Sequential Binding and Unbinding.

The study of protein adsorption at the single molecule level has recently revealed that the adsorption is reversible, but with a long-tailed residence time distribution which can be approximated with a sum of exponential functions putatively related to distinct adsorption sites. Here it is proposed that the shape of the residence time distribution results from an adsorption process with sequential and reversible steps that contribute to overall binding strength resembling "zippering". In this model, the survival function of the residence time distribution of single proteins varies from an exponential distribution for a single adsorption step to a power law distribution with exponent -1/2 for a large number of adsorption steps. The adsorption of fluorescently labeled fibrinogen to glass surfaces is experimentally studied with single molecule imaging. The experimental residence time distribution can be readily fit by the proposed model. This demonstrates that the observed long residence times can arise from stepwise adsorption rather than rare but strong binding sites and provides guidance for the control of protein adsorption to biomaterials.

Estimation of seabed properties and range from vector acoustic observations of underwater ship noise.

The Intensity Vector Autonomous Recorder (IVAR) simultaneously measures acoustic particle velocity and pressure. IVAR was deployed during the 2017 Seabed Characterization Experiment (SBCEX) with the primary objective to study sound propagation in fine-grained, muddy sediments. In this study a Bayesian inversion framework is applied to ship underwater noise recorded by IVAR. The data are relative phase of pressure and vertical particle velocity, a quantity that is independent of the ship noise source spectrum. Inversion estimates for the sediment layer and underlying basement properties are in agreement with other reports from SBCEX.

Seabed and range estimation of impulsive time series using a convolutional neural network.

In ocean acoustics, many types of optimizations have been employed to locate acoustic sources and estimate the properties of the seabed. How these tasks can take advantage of recent advances in deep learning remains as open questions, especially due to the lack of labeled field data. In this work, a Convolutional Neural Network (CNN) is used to find seabed type and source range simultaneously from 1 s pressure time series from impulsive sounds. Simulated data are used to train the CNN before application to signals from a single hydrophone signal during the 2017 Seabed Characterization Experiment. The training data includes four seabeds representing deep mud, mud over sand, sandy silt, and sand, and a wide range of source parameters. When applied to measured data, the trained CNN predicts expected seabed types and obtains ranges within 0.5 km when the source-receiver range is greater than 5 km, showing the potential for such algorithms to address these problems.

Physical effects of sound exposure from underwater explosions on Pacific sardines (Sardinops sagax).

Explosions from activities such as construction, demolition, and military activities are increasingly encountered in the underwater soundscape. However, there are few scientifically rigorous data on the effects of underwater explosions on aquatic animals, including fishes. Thus, there is a need for data on potential effects on fishes collected simultaneously with data on the received signal characteristics that result in those effects. To better understand potential physical effects on fishes, Pacific sardines (Sardinops sagax) were placed in cages at mid-depth at distances of 18 to 246 m from a single mid-depth detonation of C4 explosive (4.66 kg net explosive weight). The experimental site was located in the coastal ocean with a consistent depth of approximately 19.5 m. Following exposure, potential correlations between blast acoustics and observed physical effects were examined. Acoustic metrics were calculated as a function of range, including peak pressure, sound exposure level, and integrated pressure over time. Primary effects related to exposure were damage to the swim bladder and kidney. Interestingly, the relative frequency of these two injuries displayed a non-monotonic dependence with range from the explosion in relatively shallow water. A plausible explanation connecting swim bladder expansion with negative pressure as influenced by bottom reflection is proposed.

Copper release rate needed to inhibit fouling on the west coast of Sweden and control of copper release using zinc oxide.

How zinc oxide influences copper release has been tested and the lowest release rate of copper from various combinations of copper and zinc in a paint matrix evaluated, whilst still deterring macrofouling, including barnacles and bryozoans. Copper (I) oxide was added to a generic AF paint in 0, 8.5, 11.7 or 16.3 wt% copper oxide in combination with 0, 10 or 20 wt% zinc oxide and applied on PMMA panels. The results show that zinc influences the release rate of copper. When 10 and 20 wt% zinc was added, the total amount of copper released significantly increased by on average 32 and 47% respectively. All treatments that included copper were successful in deterring macrofouling, including the treatment with the lowest average Cu release rate, ie 4.68 µg cm-2 day-1.

Quantification of the Intracellular Life Time of Water Molecules to Measure Transport Rates of Human Aquaglyceroporins.

Orthodox aquaporins are transmembrane channel proteins that facilitate rapid diffusion of water, while aquaglyceroporins facilitate the diffusion of small uncharged molecules such as glycerol and arsenic trioxide. Aquaglyceroporins play important roles in human physiology, in particular for glycerol metabolism and arsenic detoxification. We have developed a unique system applying the strain of the yeast Pichia pastoris, where the endogenous aquaporins/aquaglyceroporins have been removed and human aquaglyceroporins AQP3, AQP7, and AQP9 are recombinantly expressed enabling comparative permeability measurements between the expressed proteins. Using a newly established Nuclear Magnetic Resonance approach based on measurement of the intracellular life time of water, we propose that human aquaglyceroporins are poor facilitators of water and that the water transport efficiency is similar to that of passive diffusion across native cell membranes. This is distinctly different from glycerol and arsenic trioxide, where high glycerol transport efficiency was recorded.

On the underwater sound field from impact pile driving: Arrival structure, precursor arrivals, and energy streamlines.

Underwater noise from impact pile driving is studied through measurements using a vertical line array (VLA) placed at range 120 m from the pile source (water depth 7.5 m) over which bathymetry varied gradually increasing to depth 12.5 m at the VLA. The data were modeled assuming the pile impact produces a radial expansion that acts as sound source and propagates along the pile at supersonic speed. This leads to the conceptualization of the pile as a discrete, vertical line source for which frequency- and source-depth-dependent complex phasing is applied. Dominant features of the pressure time series versus measurement depth are reproduced in modeled counterparts that are linearly related. These observations include precursor arrivals for which arrival timing depends on hydrophone depth and influence of a sediment sound speed gradient on precursor amplitude. Spatial gradients of model results are taken to obtain estimates of acoustic particle velocity and vector intensity for which active intensity is studied in the time domain. Evaluation of energy streamlines based on time-integrated active intensity, and energy path lines based on instantaneous (or very-short-time integrated) active intensity reveal interesting structure in the acoustic field, including an inference as to the source depth of the precursor.

Measurement of acoustic particle motion in shallow water and its application to geoacoustic inversion.

Within an underwater acoustic waveguide, the interference among multipath arrivals causes a phase difference in orthogonal components of the particle velocity. When two components of the particle velocity are not in phase, the fluid particles follow an elliptical trajectory. This property of the acoustic field can be readily detected by a vector sensor. A non-dimensional vector quantity, the degree of circularity, is used to quantify how much the trajectory resembles a circle. In this paper, vector sensor measurements collected during the 2013 Target and Reverberation Experiment are used to demonstrate the effect of multipath interference on the degree of circularity. Finally, geoacoustic properties representing the sandy sediment at the experimental site are inverted by minimization of a cost function, which quantifies the deviation between the measured and modeled degree of circularity.