Nucleon structure from basis light-front quantization
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72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
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Results for “structured light”
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Predicting partner fitness based on spatial structuring in a light-driven microbial community
Microbial communities have vital roles in systems essential to human health and agriculture, such as gut and soil microbiomes, and there is growing interest in engineering designer consortia for applications in biotechnology ( e . g ., personalized probiotics, bioproduction of high-value products, biosensing). The capacity to monitor and model metabolite exchange in dynamic microbial consortia can provide foundational information important to understand the community level behaviors that emerge, a requirement for building novel consortia. Where experimental approaches for monitoring metabolic exchange are technologically challenging, computational tools can enable greater access to the fate of both chemicals and microbes within a consortium. In this study, we developed an in-silico model of a synthetic microbial consortia of sucrose-secreting Synechococcus elongatus PCC 7942 and Escherichia coli W. Our model was built on the NUFEB framework for Individual-based Modeling (IbM) and optimized for biological accuracy using experimental data. We showed that the relative level of sucrose secretion regulates not only the steady-state support for heterotrophic biomass, but also the temporal dynamics of consortia growth. In order to determine the importance of spatial organization within the consortium, we fit a regression model to spatial data and used it to accurately predict colony fitness. We found that some of the critical parameters for fitness prediction were inter-colony distance, initial biomass, induction level, and distance from the center of the simulation volume. We anticipate that the synergy between experimental and computational approaches will improve our ability to design consortia with novel function.
59 BASIC BIOLOGICAL SCIENCES↗
Structural Diversity in Eukaryotic Photosynthetic Light Harvesting
Photosynthesis has been using energy from sunlight to assimilate atmospheric CO 2 for at least 3.5 billion years. Through evolution and natural selection, photosynthetic organisms have flourished in almost all aquatic and terrestrial environments. This is partly due to the diversity of light-harvesting complex (LHC) proteins, which facilitate photosystem assembly, efficient excitation energy transfer, and photoprotection. Structural advances have provided angstrom-level structures of many of these proteins and have expanded our understanding of the pigments, lipids, and residues that drive LHC function. In this review, we compare and contrast recently observed cryo-electron microscopy structures across photosynthetic eukaryotes to identify structural motifs that underlie various light-harvesting strategies. We discuss subtle monomer changes that result in macroscale reorganization of LHC oligomers. Additionally, we find recurring patterns across diverse LHCs that may serve as evolutionary stepping stones for functional diversification. Advancing our understanding of LHC protein–environment interactions will improve our capacity to engineer more productive crops.
60 APPLIED LIFE SCIENCES↗
Dimer Asymmetry and Light Activation Mechanism in Brucella Blue-Light Sensor Histidine Kinase
The ability to sense and respond to environmental cues is essential for adaptation and survival in living organisms. In bacteria, this process is accomplished by multidomain sensor histidine kinases that undergo autophosphorylation in response to specific stimuli, thereby triggering downstream signaling cascades. However, the molecular mechanism of allosteric activation is not fully understood in these important sensor proteins. Here, we report the full-length crystal structure of a blue light photoreceptor LOV histidine kinase (LOV-HK) involved in light-dependent virulence modulation in the pathogenic bacterium Brucella abortus. Joint analyses of dark and light structures determined in different signaling states have shown that LOV-HK transitions from a symmetric dark structure to a highly asymmetric light state. The initial local and subtle structural signal originated in the chromophore-binding LOV domain alters the dimer asymmetry via a coiled-coil rotary switch and helical bending in the helical spine. These amplified structural changes result in enhanced conformational flexibility and large-scale rearrangements that facilitate the phosphoryl transfer reaction in the HK domain.
59 BASIC BIOLOGICAL SCIENCES↗
Formation of pyrophosphates across grain boundaries induces the formation of mismatched but oriented interfaces in silver phosphate polypods
The interfaces and their misfit defects determine the materials properties for a wide range of applications, such as electronic devices, photocatalysis, and mechanical engineering, etc. However, current understanding of atomic interfacial structures is limited. Here we discover a special interfacial structure, mismatched but oriented interface via two distinct facets. Transmission and scanning electron microscopy results suggest that, in Ag 3 PO 4 polypods structures, interfaces of {1 0 0} and {1 1 0}, ({1 0 0}/(1 1 0}), {1 0 0}/{1 1 1}, {1 1 0}/{1 1 1}, and {1 0 0}/{1 0 0}, etc., have a certain orientation relationship, corresponding to the energy minima and coincident site lattice of interfacial atoms as demonstrated by molecular dynamics simulations. Density functional theory demonstrates that the formation of pyrophosphate and/or phosphates rotation to bond across the interface compensate the lattice mismatch at the interfaces, as well as deformations of Ag-O bonds. Furthermore, our work opens up a new avenue for a much wider range of interfacial structures, allow for a higher diversity of structures, and shine light on tailoring crystal structures, morphologies, and the resulting properties.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural insights into photoactivation of plant Cryptochrome-2
Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Vertically stacked photovoltaic and thermal solar cell
According to some embodiments, the present invention provides a novel photovoltaic solar cell system from photovoltaic modules that are vertically arrayed in a stack format using thin film semiconductors selected from among organic and inorganic thin film semiconductors. The stack cells may be cells that are produced in a planar manner, then vertically oriented in an angular form, also termed herein tilted, to maximize the light capturing aspects. The use of a stack configuration system as described herein allows for the use of a variety of electrode materials, such as transparent materials or semitransparent metals. Light concentration can be achieved by using fresnel lens, parabolic mirrors or derivatives of such structures. The light capturing can be controlled by being reflected back and forth in the photovoltaic system until significant quantities of the resonant light is absorbed. Light that passes to the very end and can be reflected back through the device by beveling or capping the end of the device with a different refractive index material, or alternatively using a reflective surface. The contacting between stacked cells can be done in series or parallel. According to some embodiments, the present invention uses a concentrator architecture where the light is channeled into the cells that contain thermal fluid channels (using a transparent fluid such as water) to absorb and hence reduce the thermal energy generation.
14 SOLAR ENERGY↗
Slow light in a 2D semiconductor plasmonic structure
Spectrally narrow optical resonances can be used to generate slow light, i.e., a large reduction in the group velocity. In a previous work, we developed hybrid 2D semiconductor plasmonic structures, which consist of propagating optical frequency surface-plasmon polaritons interacting with excitons in a semiconductor monolayer. Here, we use coupled exciton-surface plasmon polaritons (E-SPPs) in monolayer WSe 2 to demonstrate slow light with a 1300 fold decrease of the SPP group velocity. Specifically, we use a high resolution two-color laser technique where the nonlinear E-SPP response gives rise to ultra-narrow coherent population oscillation (CPO) resonances, resulting in a group velocity on order of 105 m/s. Our work paves the way toward on-chip actively switched delay lines and optical buffers that utilize 2D semiconductors as active elements.
42 ENGINEERING↗
De novo designed ice-binding proteins from twist-constrained helices
Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure–activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure–activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.
Science & Technology - Other Topics↗
Upconversion of Infrared Light by Graphitic Microparticles Due to Photoinduced Structural Modification
Recent reports of upconversion and white light emission from graphitic particles warrant an explanation of the physics behind the process. A model is offered, wherein the upconversion is facilitated by photoinduced electronic structure modification allowing for multiphoton processes. As per the prediction of the model, it is experimentally shown that graphite upconverts infrared light centered around 1.31 μm (0.95 eV) to broadband white light centered around 0.85 μm (1.46 eV). The results suggest that upconversion from shortwave infrared (≈3 μm, 0.45 eV) to visible region may be possible. The experiments show that the population dynamics of the electronic states involved in this upconversion process occur in the timescale of milliseconds.
Sharma, Rohin↗
Biomimetic Light Harvesting Complexes Based on Self-Assembled Dye-DNA Nanostructures (Final Technical Report)
A fundamental limitation in the development of artificial molecular light harvesting structures is that generally if one places pigment molecules close enough to achieve very high energy transfer efficiency and absorbance cross section, the dyes interact in such a way that self-quenching occurs. This limits both the optical cross section and the overall efficiency of light capture in such systems. Nature overcomes this problem and achieves efficient energy transfer without self-quenching by controlling the environment, vibration characteristics, orientation and dynamics of the pigments involved in light harvesting. Natural light harvesting systems have evolved highly intricate chromophore architectures of protein-bound organic molecules that absorb and funnel solar energy with high efficiency and fast transfer rates using elegant excitonic circuitries. Nature achieves this precise control over the properties of pigment complexes by using specific proteins as templates to guide the formation of very well-defined pigment aggregates, groups of pigment molecules that are in close enough contact to undergo excitonic interactions resulting in new electronic properties that were not present in the monomer. In synthetic systems, pigment aggregates are well known, and J-aggregates and H-aggregates have been long studied for their unique properties. In Nature, the chlorosomes of green bacteria form what appear to be classical J-aggregates and the light harvesting complexes of purple nonsulfur bacteria form ring structures that have many of the properties of J-aggregates such as a red-shifted absorbance spectrum and excited states that are delocalized over multiple pigment molecules. These photosynthetic systems leverage the spectral and enhanced transport properties of J-like aggregates to achieve fast exciton transport within the antenna and thus high light-harvesting efficiency. The close interaction of the pigments results in substantial electronic coupling that lifts the degeneracy of excitonic states and therefore modifies the absorption and emission spectra of the monomer. In the case of J-aggregation, lower energy excitonic states acquire significant oscillator strength, resulting in a characteristic bathochromic shift of the absorption and fluorescence and often superradiant delocalized exciton states.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Long-Term Stability of Ferri-/Ferrocyanide as an Electroactive Component for Redox Flow Battery Applications: On the Origin of Apparent Capacity Fade
We assess the suitability of potassium ferri-/ferrocyanide as an electroactive species for long-term utilization in aqueous organic redox flow batteries. A series of electrochemical and chemical characterization experiments was performed to distinguish between structural decomposition and apparent capacity fade of ferri-/ferrocyanide solutions used in the capacity-limiting side of a flow battery. Our results indicate that, in contrast with previous reports, no structural decomposition of ferri-/ferrocyanide occurs at tested pH values as high as 14 in the dark or in diffuse indoor light. Instead, an apparent capacity fade takes place due to a chemical reduction of ferricyanide to ferrocyanide, via chemical oxygen evolution reaction. We find that this parasitic process can be further exacerbated by carbon electrodes, with apparent capacity fade rates at pH 14 increasing with an increased ratio of carbon electrode surface area to ferricyanide in solution. Based on these results, we report a set of operating conditions that enables the long-duration cycling of alkaline ferri-/ferrocyanide electrolytes and demonstrate how apparent capacity fade rates can be engineered by the initial system setup. If protected from direct exposure to light, the structural stability of ferri-/ferrocyanide anions allows for their practical deployment as electroactive species in long duration energy storage applications.
25 ENERGY STORAGE↗
Study of light nuclei by polarization observables in electron scattering
Electron-induced proton, neutron and deuteron knock-out remains the most versatile probe of the electro-magnetic properties and spin structure of light nuclei. The advent of highly polarized beams and targets and improvements in recoil polarization methods, as well as analysis and simulation techniques, have enabled us to study the static and dynamical properties of few-body systems with unprecedented precision. Recent experiments at Jefferson Lab and MAMI are presented and put into perspective of state-of-the art Faddeev calculations, with focus on the ^\mathbf{3}\mathbf{He} 3 𝐇 𝐞 nucleus.
Sirca, Simon↗
Modeling the co-assembly of binary nanoparticles
Abstract In this work, we present a binary assembly model that can predict the co-assembly structure and spatial frequency spectra of monodispersed nanoparticles with two different particle sizes. The approach relies on an iterative algorithm based on geometric constraints, which can simulate the assembly patterns of particles with two distinct diameters, size distributions, and at various mixture ratios on a planar surface. The two-dimensional spatial-frequency spectra of the modeled assembles can be analyzed using fast Fourier transform analysis to examine their frequency content. The simulated co-assembly structures and spectra are compared with assembled nanoparticles fabricated using transfer coating method are in qualitative agreement with the experimental results. The co-assembly model can also be used to predict the peak spatial frequency and the full-width at half-maximum bandwidth, which can lead to the design of the structure spectra by selection of different monodispersed particles. This work can find applications in fabrication of non-periodic nanostructures for functional surfaces, light extraction structures, and broadband nanophotonics.
Mohanty, Saurav (ORCID:0009000302592855)↗
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. In this study we use time-resolved serial femtosecond crystallography using an X-ray free-electron laser 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.
59 BASIC BIOLOGICAL SCIENCES↗
The spontaneous symmetry breaking in Ta 2 NiSe 5 is structural in nature
The excitonic insulator is an electronically driven phase of matter that emerges upon the spontaneous formation and Bose condensation of excitons. Detecting this exotic order in candidate materials is a subject of paramount importance, as the size of the excitonic gap in the band structure establishes the potential of this collective state for superfluid energy transport. However, the identification of this phase in real solids is hindered by the coexistence of a structural order parameter with the same symmetry as the excitonic order. Only a few materials are currently believed to host a dominant excitonic phase, Ta 2 NiSe 5 being the most promising. Here, we test this scenario by using an ultrashort laser pulse to quench the broken-symmetry phase of this transition metal chalcogenide. Tracking the dynamics of the material’s electronic and crystal structure after light excitation reveals spectroscopic fingerprints that are compatible only with a primary order parameter of phononic nature. We rationalize our findings through state-of-the-art calculations, confirming that the structural order accounts for most of the gap opening. Our results suggest that the spontaneous symmetry breaking in Ta 2 NiSe 5 is mostly of structural character, hampering the possibility to realize quasi-dissipationless energy transport.
Science & Technology - Other Topics↗
The structure of Photosystem I acclimated to far-red light illuminates an ecologically important acclimation process in photosynthesis
Phototrophic organisms are superbly adapted to different light environments but often must acclimate to challenging competition for visible light wavelengths in their niches. Some cyanobacteria overcome this challenge by expressing paralogous photosynthetic proteins and by synthesizing and incorporating ~8% chlorophyll f into their Photosystem I (PSI) complexes, enabling them to grow under far-red light (FRL). We solved the structure of FRL-acclimated PSI from the cyanobacterium Fischerella thermalis PCC 7521 by single-particle, cryo–electron microscopy to understand its structural and functional differences. Four binding sites occupied by chlorophyll f are proposed. Subtle structural changes enable FRL-adapted PSI to extend light utilization for oxygenic photosynthesis to nearly 800 nm. This structure provides a platform for understanding FRL-driven photosynthesis and illustrates the robustness of adaptive and acclimation mechanisms in nature.
Science & Technology - Other Topics↗
Structural elucidation of the cis -prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation
Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme’s active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme’s active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.
59 BASIC BIOLOGICAL SCIENCES↗