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The three vibrational modes of the water molecule and their fundamental frequencies in liquid water: symmetric stretching (v1), bending (v2) and asymmetric stretching (v3). The atoms move in the directions indicated by arrows. (b) Absorption spectrum of pure water (Hale and Querry, 1973; Segelstein, 1981; Pope and Fry, 1997). Peaks in the absorption spectrum correspond to the fundamental frequencies and higher harmonics of the vibrations of the water molecules. (c) Absorption spectrum of pure water in the visible and infrared region. Shoulders in the absorption spectrum correspond to the third, fourth, fifth, sixth and seventh harmonics of the symmetric and asymmetric stretch vibrations, as indicated.

The three vibrational modes of the water molecule and their fundamental frequencies in liquid water: symmetric stretching (v1), bending (v2) and asymmetric stretching (v3). The atoms move in the directions indicated by arrows. (b) Absorption spectrum of pure water (Hale and Querry, 1973; Segelstein, 1981; Pope and Fry, 1997). Peaks in the absorption spectrum correspond to the fundamental frequencies and higher harmonics of the vibrations of the water molecules. (c) Absorption spectrum of pure water in the visible and infrared region. Shoulders in the absorption spectrum correspond to the third, fourth, fifth, sixth and seventh harmonics of the symmetric and asymmetric stretch vibrations, as indicated.

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The photosynthetic pigments of phototrophic microorganisms cover different regions of the solar light spectrum. Utilization of the light spectrum can be interpreted in terms of classical niche theory, as the light spectrum offers opportunities for niche differentiation and allows coexistence of species absorbing different colors of light. However,...

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... rotate and vibrate. Vibrations of water molecules occur in three modes, including symmetric stretching (v 1 ), asym- metric stretching (v 3 ) and bending (v 2 ) of the water molecule (Figure 2a; see also, for example, Braun and Smirnov, 1993;Pegau et al., 1997;Sogandares and Fry, 1997). The energy for these vibrations is obtained by absorption of radiation. ...
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... vibrations are most intense at wavelengths matching the specific energy requirements of these motions. These wavelengths can be recognized as peaks in the absorption spectrum of pure water (Figure 2b). Because the energy requirements for symmetric and asymmetric stretching are rather similar, their absorption peaks coalesce into a large absorption peak at around 3000 nm. ...
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... a result, harmonics of the bending and stretching vibrations can be recognized as shoulders in the visible and near-infrared range of the absorption spectrum of water. For instance, the distinct shoulders in Figure 2c, at 449, 514, 605, 742 and 972 nm have been identified as the seventh, sixth, fifth, fourth and third harmonics, respectively, of the symmetrical and asymmetrical stretch vibra- tion ( Braun and Smirnov, 1993;Pegau et al., 1997;Sogandares and Fry, 1997). The shoulder at 1130 nm has also been identified as a third harmonics, composed of the combination of a symmetrical, asymmetrical and bending vibration (v 1 þ v 2 þ v 3 ). ...
Context 4
... I(l,z) is the light intensity of wavelength l at depth z, I in (l) is the spectrum of the incident solar irradiance, K W (l) is the absorption spectrum of pure water (Figures 2b and c), K GT (l) is the absorp- tion spectrum of gilvin and tripton and K PH (l) is the absorption spectrum of the phytoplankton community. ...
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... dips in the incident solar spectrum are due to light absorption by oxygen and water molecules in the atmosphere (Kirk, 1994). Pure water mainly absorbs red and infrared light, with several distinct shoulders (Figure 2c). In contrast, gilvin and tripton absorb strongly in the blue region of the spectrum (Figures 3a-c). ...

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... Light was thus the primary limiting resource for microbial phototrophs in the mat. One strategy to remain competitive under light limitation is to complement light absorption by Chl a, the main light harvesting pigment in oxygenic photosynthesis, by metabolic investment in producing a range of accessory pigments absorbing a broader part of the available light spectrum and channeling it to the photosynthetic reaction centers (Stomp et al., 2007;Trampe and Kühl, 2016;Kühl et al., 2020). HPLC pigment analysis of the upper 0.5 mm of the microbial mat revealed that very efficient light absorption was achieved by a mixture of light harvesting pigments from cyanobacteria (Chl a, mixoxanthophyll, zeaxanthin, oscillaxanthin and β,ε-carotene) and anoxygenic phototrophs (BChl a), able to absorb light from the UV-B well into the NIR region (Figure 3). ...
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Microbial mats are diverse and stratified microbial biofilm communities characterized by steep gradients in light, temperature and chemical parameters. Their high optical density creates a competition for light among phototrophic microalgae and bacteria residing in the uppermost mat layers. Strategies to counter such resource limitation include metabolic investment in protective and light-harvesting pigments enabling exploitation of separate niches in terms of irradiance and spectral composition, or investment in motility to enable migration to an optimal light microenvironment. We used microsensor measurements of light, temperature and gross photosynthesis in coastal microbial mats dominated by motile cyanobacteria and colorless sulfur bacteria to study how migration affected their radiative energy-budgets and relative photosynthetic efficiency. The optical density of the microbial mat was extremely high, and >99% of incident irradiance of visible light (400-700 nm) was attenuated <0.4 mm below the surface. While energy conservation efficiency did not change dramatically with previous light acclimation, vertical profiles of photosynthetic efficiency showed a shift in the position of maximum efficiency of ∼0.2 mm, depending on light treatment. Besides avoidance of unfavorable chemical conditions such as high sulfide levels, vertical migration over short distances thus enable cyanobacteria to track zones with optimal light exposure thereby efficiently counteracting detrimental effects of excessive light at the surface and insufficient light deeper in the mat.
... Where E in situ is the in situ light spectra determined using a typical incident solar spectrum from Stomp et al. (2007a;2007b) and the spectrally dependent light attenuation coefficient following Morel et al. (2007). E LED is the spectral light distribution of the actinic light sources in the FastAct chamber as supplied by the manufacturer. ...
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Chlorophyll fluorescence, primarily used to derive phytoplankton biomass, has long been an underutilized source of information on phytoplankton physiology. Diel fluctuations in chlorophyll fluorescence are affected by both photosynthetic efficiency and non-photochemical quenching (NPQ), where NPQ is a decrease in fluorescence through the dissipation of excess energy as heat. NPQ variability is linked to iron and light availability, and has the potential to provide important diagnostic information on phytoplankton physiology. Here we establish a relationship between NPQsv (Stern-Volmer NPQ) and indices of iron limitation from nutrient addition experiments in the sub-Antarctic zone (SAZ) of the Atlantic Southern Ocean, through the derivation of NPQmax (the maximum NPQsv value) and αNPQ (the light limited slope of NPQsv). Significant differences were found for both Fv/Fm and αNPQ for iron versus control treatments, with no significant differences for NPQmax. Similar results from CTDs indicated that changes in NPQ were driven by increasing light availability from late July to December, but by both iron and light from January to February. We propose here that variability in αNPQ, which has removed the effect of light availability, can potentially be used as a proxy for iron limitation (as shown here for the Atlantic SAZ), with higher values being associated with greater iron stress. This approach was transferred to data from a buoyancy glider deployment at the same location by utilizing the degree of fluorescence quenching as a proxy for NPQGlider, which was plotted against in situ light to determine αNPQ. Seasonal increases in αNPQ are consistent with increased light availability, shoaling of the mixed layer depth (MLD) and anticipated seasonal iron limitation. The transition from winter to summer, when positive net heat flux dominates stratification, was coincident with a 24% increase in αNPQ variability and a switch in the dominant driver from incident PAR to MLD. The dominant scales of αNPQ variability are consistent with fine scale variability in MLD and a significant positive relationship was observed between these two at a ∼10 day window. The results emphasize the important role of fine scale dynamics in driving iron supply, particularly in summer when this micronutrient is limiting.
... This analysis was carried out using the Diamond soware -molecular crystal and structure visualization. 28 Fig. 1 34,35 The peak at about 3528 cm À1 is assigned to a vibration mode of H 2 O. 36 A slight reduction in the intensity of 2D peak was observed in the composite samples as compared to GF sample. This decrease in the 2D peak is a clear indication of the interaction between GF and the phosphate material because this mode is very sensitive to defects. ...
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Unique microstructured nickel ammonium phosphate Ni(NH4)2(PO3)4·4H2O and Ni(NH4)2(PO3)4·4H2O/GF composite were successfully synthesized through the hydrothermal method with different graphene foam (GF) mass loading of 30, 60 and 90 mg as a positive electrode for asymmetric supercapacitors. The crystal structure, vibrational mode, texture and morphology of the samples were studied with X-ray diffraction (XRD), Raman spectroscopy, Brunauer–Emmett–Teller (BET) surface area analysis and scanning electron microscopy (SEM). The prepared materials were tested in both 3-and 2-electrode measurements using 6 M KOH electrolyte. The composite material Ni(NH4)2(PO3)4·4H2O/60 mg exhibited a remarkable gravimetric capacity of 52 mA h g⁻¹, higher than the 34 mA h g⁻¹ obtained for the Ni(NH4)2(PO3)4·4H2O pristine sample, both at 0.5 A g⁻¹. For the fabrication of the asymmetric device, activated carbon from pepper seed (ppAC) was used as a negative electrode while Ni(NH4)2(PO3)4·4H2O/60 mg GF was adopted as the positive electrode. The Ni(NH4)2(PO3)4·4H2O/60 mg GF//ppAC asymmetric device delivered a specific energy of 52 Wh kg⁻¹ with an equivalent specific power of 861 W kg⁻¹ at 1.0 A g⁻¹ within a potential range of 0.0–1.5 V. Moreover, the asymmetric device displayed a capacity retention of about 76% for over 10 000 cycles at a high specific current of 10.0 A g⁻¹.
... As a result, harmonics of the bending and stretching vibrations can be recognized as shoulders in the visible and near-infrared range. For instance, the distinct shoulders are positioned at 449, 514, 605, 742 and 972 nm (see Figure 7), and can be identified as the third, fourth, fifth, sixth and seventh harmonics, respectively, of the bending and the related symmetrical and asymmetrical stretch vibrations of water molecules (Braun and Smirnov, 1993;Pegau et al., 1997;Sogandares and Fry, 1997;Stomp, 2007). We may understand this series of peaks as a specific water vibrational signature. ...
Article
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This paper addresses the question whether electromagnetic frequencies associated with pure water are similar to those of biological systems. A literature survey was performed on intrinsic frequencies of water molecules measured across the electromagnetic spectrum using various spectroscopic technologies. The registered frequencies were plotted on an algorithmic generalized music (GM) scale, described by a quantum entangled wave function, and compared with earlier detected electromagnetic frequency patterns revealed in various biological systems. The meta-analysis shows that semi-harmonic frequency patterns found in purified water are very similar to those found in biological systems. A meta-analysis of about 700 measured frequencies of pure water shows that 192 subsequent first and second derivatives of spectral frequency curves of water molecules can be precisely positioned at the proposed lines of the calculated pattern of coherent eigenfrequencies with an error of 0.45% and statistical significance of p < 0.02. A new order parameter characteristic for water molecule assembly has been revealed, which implies quantum coherency and en-tanglement. This is in line with the already evidenced and published universal order that we called the GM-scale. Following these findings, we may assume that water molecule assembly shows electromagnetic and electronic collective states that contain "quantum imprints or molds" for living cells. A potential explanation for this feature is that water molecules are ordered in a partially distorted tetrahedral geometry, which yields a specific network structure. Since water molecules have a comparable distribution of coherent electromagnetic field (EMF) bands to that of fluid assemblies in living cells, a resonant wave interaction is expected between the cytoplasm and surrounding water molecules. Evidence of a new quantum wave equation of coherence for water molecules has been found, that is defined as a physical principle: E n = ħ ω ref 2 n+p 3 m .
... Büchel 2019). Different photosynthetic organisms adopt distinct types of Chls with absorption properties matching the light spectrum available in their natural habitat (Croce and van Amerongen 2014;Stomp et al. 2007). In addition to Chls, photosynthetic organisms use carotenoids (Cars) and phycobilins to increase their absorption cross section in the green region (500-600 nm) (Beale 1993;Frank and Cogdell 1996), which is poorly absorbed by Chls. ...
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Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.
... 2−4 A feature of natural photosynthesis is that different organisms exploit different parts of the solar spectrum depending on their pigmentation. 5,6 Plants, algae, and cyanobacteria contain chlorophyll (Chl) as their principal photosynthetic pigment ( Figure S1A, Supporting Information) and exploit much of the visible spectrum. 3,5,7 In contrast, diverse anoxygenic photosynthetic bacteria utilize bacteriochlorophyll (BChl) ( Figure S1A, Supporting Information) and occupy complementary light niches in the near-ultraviolet and near-infrared. ...
Article
Many strategies for meeting mankind's future energy demands through the exploitation of plentiful solar energy have been influenced by the efficient and sustainable processes of natural photosynthesis. A limitation affecting solar energy conversion based on photosynthetic proteins is the selective spectral coverage that is the consequence of their particular natural pigmentation. Here we demonstrate the bottom-up formation of semisynthetic, polychromatic photosystems in mixtures of the chlorophyll-based LHCII major light harvesting complex from the oxygenic green plant Arabidopsis thaliana, the bacteriochlorophyll-based photochemical reaction center (RC) from the anoxygenic purple bacterium Rhodobacter sphaeroides and synthetic quantum dots (QDs). Polyhistidine tag adaptation of LHCII and the RC enabled predictable self-assembly of LHCII/RC/QD nanoconjugates, the thermodynamics of which could be accurately modeled and parametrized. The tricomponent biohybrid photosystems displayed enhanced solar energy conversion via either direct chlorophyll-to-bacteriochlorophyll energy transfer or an indirect pathway enabled by the QD, with an overall energy transfer efficiency comparable to that seen in natural photosystems.
... A sample of 5 mL of liquid culture was taken every two days to analyze culture absorbance (samples were diluted with water in order to adjust the readings between 0.2 and 1.0), pH and the concentration of TOC, IC, TN and volatile fatty acids (VFA), while 100 mL of the bottle headspace was drawn with gastight syringes (Hamilton, USA) to quantify the gas concentration of CO 2 , H 2 S, CH 4 . PPB growth was monitored using culture absorbance at 808 nm (OD 808 ), which represents a specific spectral niche for these phototrophic microorganisms compared to other phototrophic species (Stomp et al., 2007). Thus, although the organic matter present in PWW preferentially absorbs at wavelengths under 700 nm (Fig. S1), PPB mainly absorb with characteristic peaks above 800 nm (Hülsen et al., 2019), corresponding to bacteriochlorophyll a (Hunter et al., 2009). ...
Article
The increase in natural water bodies pollution caused by intensive animal farming requires the development of innovative sustainable treatment processes. This study assessed the influence of piggery wastewater (PWW) load, air dosing, CO2/NaHCO3− supplementation and pH control on PWW treatment by mixed cultures of purple phototrophic bacteria (PPB) under infrared radiation in batch photobioreactors. PPB was not able to grow in raw PWW but PWW dilution prevented inhibition and supported an effective light penetration. Despite the fact that PPB were tolerant to O2, carbon recovery decreased in the presence of air (induced by stripping). CO2 supplementation was identified as an effective strategy to maximize the removal of carbon during PPB-based PWW treatment with removal efficiencies of 72% and 74% for TOC and VFAs. However, the benefits derived from CO2 addition were induced by the indirect pH control exerted in the cultivation medium. Thus, PPB supported an optimal pollutant removal performance at pH 7, with removal efficiencies of 75%, 39% and 98% for TOC, TN and VFAs.
... The linearized Hamiltonian Eq. (4) describes three decoupled harmonic oscillators corresponding to the three vibrational modes of the planar triatomic molecule [31]: I 1 corresponds to the asymmetric stretch, I 2 to the bending mode and I 3 to the symmetric stretch (see Fig. 1). We note that the 1:1 resonance between I 1 and I 2 is a result of the symmetry of the system under consideration; changing, for example, one of the masses would remove this frequency degeneracy. ...
Article
The symmetric harmonic three-mass system with finite rest lengths, despite its apparent simplicity, displays a wide array of interesting dynamics for different energy values. At low energy the system shows regular behavior that produces a deformation-induced rotation with a constant averaged angular velocity. As the energy is increased this behavior makes way to a chaotic regime with rotational behavior statistically resembling Lévy walks and random walks. At high enough energies, where the rest lengths become negligible, the chaotic signature vanishes and the system returns to regularity, with a single dominant frequency. The transition to and from chaos, as well as the anomalous power-law statistics measured for the angular displacement of the harmonic three-mass system are largely governed by the structure of regular solutions of this mixed Hamiltonian system. Thus, a deeper understating of the system's irregular behavior requires mapping out its regular solutions. In this work we provide a comprehensive analysis of the system's regular regimes of motion, using perturbative methods to derive analytical expressions of the system as almost-integrable in its low- and high-energy extremes. The compatibility of this description with the full system is shown numerically. In the low-energy regime, the Birkhoff normal form method is utilized to circumvent the low-order 1:1 resonance of the system, and the conditions for Kolmogorov-Arnold-Moser theory are shown to hold. The integrable approximations provide the back-bone structure around which the behavior of the full nonlinear system is organized and provide a pathway to understanding the origin of the power-law statistics measured in the system.
... Based on a flux model from available pmf and ATP substrate parameters, Silverstein (Silverstein, 2014) estimated that, with similar previous experimentally measured pmf and DG ATP levels, the E. coli and bovine mitochondrial ATP synthases (c 10 and c 8 , respectively) should convert pmf to DG ATP with about 25% higher efficiency compared to the chloroplast ATP synthase (c 14 ), and speculated that because photosynthetic organisms have access to readily available sunlight as an energy source, there may have been less evolutionary selection pressure to maximize the thermodynamic efficiency for ATP synthesis compared to organisms that rely on more scarce energy sources (fixed organic molecules). However, it is well known that photosynthetic organisms have adapted to grow in lightlimiting conditions (Judd et al., 1964;Stomp et al., 2007;Scanlan et al., 2009), including low light requiring cyanobacteria which have been shown to also have large c-rings . ...
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The conversion of sunlight into useable cellular energy occurs via the proton–coupled electron transfer reactions of photosynthesis. Light is absorbed by photosynthetic pigments and transferred to photochemical reaction centers to initiate electron and proton transfer reactions to store energy in a redox gradient and an electrochemical proton gradient (proton motive force, pmf), composed of a concentration gradient (ΔpH) and an electric field (Δψ), which drives the synthesis of ATP through the thylakoid FoF1-ATP synthase. Although ATP synthase structure and function are conserved across biological kingdoms, the number of membrane–embedded ion–binding c subunits varies between organisms, ranging from 8 to 17, theoretically altering the H+/ATP ratio for different ATP synthase complexes, with profound implications for the bioenergetic processes of cellular metabolism. Of the known c–ring stoichiometries, photosynthetic c–rings are among the largest identified stoichiometries, and it has been proposed that decreasing the c-stoichiometry could increase the energy conversion efficiency of photosynthesis. Indeed, there is strong evidence that the high H+/ATP of the chloroplast ATP synthase results in a low ATP/nicotinamide adenine dinucleotide phosphate (NADPH) ratio produced by photosynthetic linear electron flow, requiring secondary processes such as cyclic electron flow to support downstream metabolism. We hypothesize that the larger c subunit stoichiometry observed in photosynthetic ATP synthases was selected for because it allows the thylakoid to maintain pmf in a range where ATP synthesis is supported, but avoids excess Δψ and ΔpH, both of which can lead to production of reactive oxygen species and subsequent photodamage. Numerical kinetic simulations of the energetics of chloroplast photosynthetic reactions with altered c–ring size predicts the energy storage of pmf and its effects on the photochemical reaction centers strongly support this hypothesis, suggesting that, despite the low efficiency and suboptimal ATP/NADPH ratio, a high H+/ATP is favored to avoid photodamage. This has important implications for the evolution and regulation of photosynthesis as well as for synthetic biology efforts to alter photosynthetic efficiency by engineering the ATP synthase.
... As a result, harmonics of the bending and stretching vibrations can be recognized as shoulders in the visible and near-infrared range. For instance, the distinct shoulders are positioned at 449, 514, 605, 742 and 972 nm (see Figure 7), and can be identified as the third, fourth, fifth, sixth and seventh harmonics, respectively, of the bending and the related symmetrical and asymmetrical stretch vibrations of water molecules (Braun and Smirnov, 1993;Pegau et al., 1997;Sogandares and Fry, 1997;Stomp, 2007). We may understand this series of peaks as a specific water vibrational signature. ...
Article
Full-text available
This paper addresses the question whether electromagnetic frequencies associated with pure water are similar to those of biological systems. A literature survey was performed on intrinsic frequencies of water molecules measured across the electromagnetic spectrum using various spectroscopic technologies. The registered frequencies were plotted on an algorithmic generalized music (GM) scale, described by a quantum entangled wave function, and compared with earlier detected electromagnetic frequency patterns revealed in various biological systems. The meta-analysis shows that semi-harmonic frequency patterns found in purified water are very similar to those found in biological systems. A meta-analysis of about 700 measured frequencies of pure water shows that 192 subsequent first and second derivatives of spectral frequency curves of water molecules can be precisely positioned at the proposed lines of the calculated pattern of coherent eigenfrequencies with an error of 0.45% and statistical significance of p < 0.02. A new order parameter characteristic for water molecule assembly has been revealed, which implies quantum coherency and en-tanglement. This is in line with the already evidenced and published universal order that we called the GM-scale. Following these findings, we may assume that water molecule assembly shows electromagnetic and electronic collective states that contain "quantum imprints or molds" for living cells. A potential explanation for this feature is that water molecules are ordered in a partially distorted tetrahedral geometry, which yields a specific network structure. Since water molecules have a comparable distribution of coherent electromagnetic field (EMF) bands to that of fluid assemblies in living cells, a resonant wave interaction is expected between the cytoplasm and surrounding water molecules. Evidence of a new quantum wave equation of coherence for water molecules has been found, that is defined as a physical principle: E n = ħ ω ref 2 n+p 3 m .