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At least 307 records · Page 17

Comparison of interband related optical transitions and excitons in ZnGeN 2 and GaN

The optical dielectric function of ZnGeN 2 is calculated from the interband transitions using the energy bands calculated in the quasiparticle self-consistent (QS)GW^ method using two different levels of approximation: the independent particle approximation (IPA) and the Bethe-Salpeter Equation (BSE) approach. The first allows us to relate peaks in ε 2 to specific bands and k-points but does not include electron-hole interaction effects. The second includes electron-hole interaction or excitonic effects. The corresponding changes in the shape of ε 2 (ω) are found to be similar to those in GaN. The screened Coulomb interaction W^ is here calculated including electron-hole interactions in the polarization function and gives a band structure already going beyond the random phase approximation. The static dielectric constants including only electronic screening, commonly referred to as ε∞ , were calculated separately by extrapolating the wave vector dependent macroscopic dielectric function in the long-wavelength limit. Below the quasiparticle gap, we find three bound excitons optically active for different polarization. The convergence of these bound excitons with respect to the density of the k-mesh used in the BSE is studied and found to require a fine mesh. It is also found that these bound excitons originate from only the lowest conduction band and the top three valence bands. To incorporate the lattice screening, we include a scaling factor (ε∞/ε 0 ) 2 , which allows us to obtain exciton binding energies of the correct order of magnitude similar to those in GaN. Here, the excitons are related to each of the three fold split valence bands and the splittings of the latter are also studied as function of strain. Finally, a relation between the anisotropic effective masses and the valence band splitting is pointed out and explained.

36 MATERIALS SCIENCE↗

θ -dependence of light nuclei and nucleosynthesis

We investigate the impact of the QCD vacuum at nonzero θ on the properties of light nuclei, Big Bang nucleosynthesis, and stellar nucleosynthesis. Our analysis starts with a calculation of the θ-dependence of the neutron-proton mass difference and neutron decay using chiral perturbation theory. We then discuss the θ-dependence of the nucleon-nucleon interaction using a one-boson-exchange model and compute the properties of the two-nucleon system. Using the universal properties of four-component fermions at large scattering length, we then deduce the binding energies of the three-nucleon and four-nucleon systems. Based on these results, we discuss the implications for primordial abundances of light nuclei, the production of nuclei in stellar environments, and implications for an anthropic view of the universe.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Rational design of photosynthetic reaction center protein maquettes

New technologies for efficient solar-to-fuel energy conversion will help facilitate a global shift from dependence on fossil fuels to renewable energy. Nature uses photosynthetic reaction centers to convert photon energy into a cascade of electron-transfer reactions that eventually produce chemical fuel. The design of new reaction centers de novo deepens our understanding of photosynthetic charge separation and may one day allow production of biofuels with higher thermodynamic efficiency than natural photosystems. Recently, we described the multi-step electron-transfer activity of a designed reaction center maquette protein (the RC maquette), which can assemble metal ions, tyrosine, a Zn tetrapyrrole, and heme into an electron-transport chain. Here, we detail our modular strategy for rational protein design and show that the intended RC maquette design agrees with crystal structures in various states of assembly. A flexible, dynamic apo-state collapses by design into a more ordered holo-state upon cofactor binding. Crystal structures illustrate the structural transitions upon binding of different cofactors. Spectroscopic assays demonstrate that the RC maquette binds various electron donors, pigments, and electron acceptors with high affinity. We close with a critique of the present RC maquette design and use electron-tunneling theory to envision a path toward a designed RC with a substantially higher thermodynamic efficiency than natural photosystems.

09 BIOMASS FUELS↗

Structures of a phycobilisome in light-harvesting and photoprotected states

Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae 1,2 . These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching 3-6 . Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Further, only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties 7 , we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.

59 BASIC BIOLOGICAL SCIENCES↗

Be₂C as a neutron moderator for molten salt reactors: A first-principles study of structural, electronic, and defect properties

Beryllium carbide (Be 2 C), valued for its high neutron moderation efficiency and low absorption cross section, is a promising high-temperature neutron moderator for molten salt reactors. Its practical adoption, however, demands significant technological maturation, requiring comprehensive theoretical and experimental studies of its response to different conditions, including high temperature and irradiation. Here, we report initial results on the fundamental properties and radiation-induced defects of Be 2 C, focusing on antisites, vacancies, interstitial atoms, and Frenkel pairs in the Be and C sublattices. Using density functional theory (DFT) and ab initio molecular dynamics (AIMD), we calculate the defects formation and binding energies, evaluating their dependence on the supercell size, charge states, and chemical environment. In general, carbon defects exhibit higher formation energies, greater sensitivity to cell size, and stronger impacts on the density of states compared to beryllium defects, with charged state the effects being more pronounced. Static DFT reveals multiple metastable interstitial configurations, while AIMD identifies ground states as C-C <100> dumbbells and octahedral Be interstitials. In conclusion, the diversity of metastable configurations and defect states complicates the diffusion mechanisms, requiring further molecular dynamics analysis to elucidate the mechanisms and rates of radiation-induced atomic transport, as well as the structural stability of Be2C.

Ab initio modeling↗

Design of stimulus-responsive two-state hinge proteins

In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here, in this work, we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.

59 BASIC BIOLOGICAL SCIENCES↗

Star cluster evolution with primordial binaries. 3: Effect of the Galactic tidal field

We present the results of N-body simulations of tidally limited star clusters with an initial population of 0%-20% binaries. We find that (1) if enough binaries are initially present, the binary fraction may fall to a minimum value, then increase at late times; (2) the cluster evaporation timescale is quite insensitive to the details of the initial binary distribution; (3) the cluster core radius stabilizes at a few percent of the half-mass radius when binaries are present, just as in the case of isolated clusters; and (4) there may be a marked difference between the spatial distribution of low-energy and high-energy binaries as the cluster evolves. Specifically, the spatial distribution of the lower energy systems is often substantially more extended than that of the more tightly bound pairs. At no time are our simulated clusters well described by simple dynamical models that neglect the close coupling between the binding energies and the center-of-mass energies of the binaries they contain.

Mcmillan, Steve↗

Molecular dynamics simulations of fission gas xenon (Xe) diffusion at UO 2 grain-boundaries (Rev.1)

The diffusivity of fission gas xenon (Xe) at UO 2 grain-boundaries is one of the most important parameters in mechanistic modeling of fission gas diffusion in UO 2 based nuclear fuels. In this report, we use molecular dynamics simulations to investigate the Xe diffusivity in UO 2 grain-boundaries, employing the many-body potential developed by Cooper, Rushton and Grimes for UO 2 . Three different types of grain-boundaries are investigated, twist Σ5, tilt Σ5, and a random grain-boundary. Diffusion activation energies in the range of 0.39 – 1.46 eV are obtained for the Xe diffusivity. Comparison to results for the uranium vacancy diffusivity from MD simulations employing the same methodology suggests a weak to moderate attractive Xe-uranium vacancy binding energy depending on the grain-boundary type.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

The linker protein ApcI regulates light harvesting under red light in Synechocystis sp. PCC 6803

Phycobilisomes (PBSs) are versatile cyanobacterial antenna complexes that harvest light energy to drive photosynthesis. They can adapt to various light conditions; for example, dismantling under high light to prevent photo-oxidation and arranging in rows under low light to increase light harvesting efficiency. Light quality also influences PBS structure and function, as observed under far-red light exposure. Here, we describe a PBS linker protein, ApcI (previously hypothetical protein Sll1911), expressed specifically under red light (620 nm) or upon chemically induced reduction of the plastoquinone pool. We characterized ApcI in Synechocystis sp. PCC 6803 using mutant analyses, PBS binding experiments, and protein interaction studies. Deletion of apcI conferred high light tolerance on Synechocystis sp. PCC 6803 compared to the wild-type strain, leading to reduced energy transfer from PBSs to the photosystems under high light. Binding experiments revealed that ApcI replaces the linker protein ApcG at the membrane-facing side of the PBS core via a paralogous C-terminal motif. Additionally, the N-terminal region of ApcI interacts with photosystem II. Our findings highlight the importance of PBS remodeling for adaptation to different light conditions. The characterization of ApcI provides insight into the mechanisms by which cyanobacteria optimize light harvesting in response to varying light conditions.

Photosystem↗

B 2 H 6 splitting on catalytic surfaces and role of BH 3 towards hydrogen spillover

A fundamental understanding of the spillover mechanism is an open and challenging problem and plays an important role in catalysis. In particular, bond-exchange spillover mechanism is considered to be effective for reversible storage and release of hydrogen at near ambient conditions. For this, three critical steps are needed: finding the right support (acceptor), the right catalyst to split H 2 , and ensuring that once H 2 is split, the H atoms can migrate on the surface with the help of secondary catalysts and eventually hydrogenate the entire material. In this paper we address these challenges using density functional theory. Here we show that BH 3 , a secondary catalyst, can be produced by symmetrically splitting its stable precursor, B 2 H 6 , on doped metal-free surfaces such as graphene and h-BN as well as on MOF5. In addition, to reduce computational cost, we develop structural descriptor and predictive model equation to effectively screen potential BH 3 binding sites. Symmetrical splitting of B 2 H 6 on different types of materials can address the hydrogen spillover challenge, making efficient storage of hydrogen possible.

08 HYDROGEN↗

Revealing EDL-driven reduction mechanisms in binary, ternary, and quaternary fluorinated electrolytes via an integrated MD–DFT–ML framework

Accurately predicting solid electrolyte interphase (SEI) formation requires explicitly resolving the electric double layer (EDL) structure, which deviates significantly from that of the bulk electrolyte. Although an established molecular dynamics (MD) and Density Functional Theory (DFT) framework can model SEI formation by evaluating reduction reactions of local clusters in the EDL, it suffers from a combinatorial computational bottleneck. To overcome this limitation, we introduce a machine-learning-accelerated simulation workflow (MD–DFT–ML), integrating a gradient-boosted regression model trained on EDL composition data to efficiently predict reduction potentials. We apply this framework to seven fluorinated electrolytes comprising fluorinated anions, a fluorinated ester solvent, two types of diluent (ion-solvating ester vs. non-solvating ether), and an FEC additive. The analysis shows that the EDL selectively accumulates cation-binding species; consequently, the non–cation-binding ether diluent rarely enters the EDL and makes minimal contributions to SEI formation. DFT calculations on statistically representative EDL clusters provide reduction potentials and fluorine-release pathways, while the ML model, which substantially reduces the DFT workload, predicts cluster reduction energies with a mean absolute error of 0.1 eV. The combined MD–DFT–ML approach also quantifies contributions from different sources to LiF formation in the SEI. This methodology establishes a generalizable route for multiscale modeling electrolyte and interphase design for next-generation electrochemical energy-storage systems.

DFT-MD-ML workflow↗

Toward Quantum Chemical Free Energy Simulations of Platinum Nanoparticles on Titania Support

Platinum nanoparticles (Pt-NPs) supported on titania surfaces are costly but indispensable heterogeneous catalysts because of their highly effective and selective catalytic properties. Therefore, it is vital to understand their physicochemical processes during catalysis to optimize their use and to further develop better catalysts. However, simulating these dynamic processes is challenging due to the need for a reliable quantum chemical method to describe chemical bond breaking and bond formation during the processes but, at the same time, fast enough to sample a large number of configurations required to compute the corresponding free energy surfaces. Density functional theory (DFT) is often used to explore Pt-NPs; nonetheless, it is usually limited to some minimum-energy reaction pathways on static potential energy surfaces because of its high computational cost. In this work, we report a combination of the density functional tight binding (DFTB) method as a fast but reliable approximation to DFT, the steered molecular dynamics (SMD) technique, and the Jarzynski equality to construct free energy surfaces of the temperature-dependent diffusion and growth of platinum particles on a titania surface. In particular, we present the parametrization for Pt-X (X = Pt, Ti, or O) interactions in the framework of the second-order DFTB method, using a previous parametrization for titania as a basis. The optimized parameter set was used to simulate the surface diffusion of a single platinum atom (Pt 1 ) and the growth of Pt 6 from Pt 5 and Pt 1 on the rutile (110) surface at three different temperatures (T = 400, 600, 800 K). The free energy profile was constructed by using over a hundred SMD trajectories for each process. We found that increasing the temperature has a minimal effect on the formation free energy; nevertheless, it significantly reduces the free energy barrier of Pt atom migration on the TiO 2 surface and the transition state (TS) of its deposition. In a concluding remark, the methodology opens the pathway to quantum chemical free energy simulations of Pt-NPs’ temperature-dependent growth and other transformation processes on the titania support.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

LHCSR1 Functions as a Dimmer Switch for Light Harvesting

In oxygenic photosynthesis, high light leads to a set of photoprotective processes, known as nonphotochemical quenching, that are required for fitness. In moss and algae, the pigment−protein complex, light-harvesting stress-related (LHCSR), is crucial for photoprotection. Acidification of the thylakoid lumen under high light triggers the activation of LHCSR and the conversion of the xanthophyll violaxanthin into zeaxanthin, which is found within LHCSR. These interrelated molecular components combine to turn on a safety valve that dissipates excess energy as heat. Previous studies of detergent-solubilized LHCSR1 found that pH and zeaxanthin regulate distinct quenching sites via the protein conformation. However, protein function in the native membrane environment can be significantly different. In this work, we applied single-molecule fluorescence spectroscopy to LHCSR1 in membrane nanodiscs. The membrane environment enhanced total quenching, regardless of pH or zeaxanthin-binding. pH-dependent quenching was still observed whereas zeaxanthin-dependent quenching was suppressed. Conformational changes also increased in the membrane, establishing that the local environment can change the nature of the equilibrium between light harvesting and photoprotection.

Hoffmann, Madeline P. [Massachusetts Inst. of Tech↗

Xenon–metal pair formation in UO 2 investigated using DFT + U

A recent experimental study on a spent uranium dioxide (UO 2 ) fuel sample from Belgium Reactor 3 identified a unique pair structure formed by the noble metal phase (NMP) and fission gas [xenon (Xe)] precipitate. However, the fundamental mechanism behind this structure remains unclear. The present study aims to provide an understanding of the interaction between five different metal precipitates [molybdenum (Mo), ruthenium (Ru), palladium (Pd), technetium (Tc), and rhodium (Rh)] and the Xe fission gas atoms in UO 2 , by using density functional theory (DFT) in combination with the Hubbard U correction to compute the formation energies involved. All DFT + U calculations were performed with occupation matrix control to ensure antiferromagnetic ordering of UO 2 . The calculated formation and binding energies of the Xe and solid fission products in the NMP reveal that these metal precipitates form stable pair structures with Xe. Notably, the formation energy of Xe–metal pairs is lower than that of the isolated single defects in all instances, with Pd and Mo showing the most favorable binding energy, likely accounting for the observed pair structure formation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Recombination of 𝐵 𝑐 mesons in ultrarelativistic heavy-ion collisions

High-energy heavy-ion collisions have been suggested as a favorable environment for the production of 𝐵 𝑐 mesons, due to a much larger abundance of charm and bottom quarks compared to elementary reactions. Motivated by recent CMS data for 𝐵$^{+}_{𝑐}$ production in Pb-Pb(5.02 TeV) collisions at the Large Hadron Collider (LHC), we deploy a previously developed transport approach for charmonia and bottomonia to evaluate the kinetics of 𝐵 𝑐 mesons throughout the fireball formed in these reactions. The main inputs to our approach are two transport parameters: the 𝐵 𝑐 's reaction rate and equilibrium limit. Both quantities are determined by previous calculations via a combination of charm and bottom sectors. In-medium binding energies of 𝐵 𝑐 mesons are calculated from a thermodynamic 𝑇 matrix with a lattice-QCD constrained potential, and figure in their inelastic reaction rates. Temperature-dependent equilibrium limits include charm- and bottom-quark fugacities based on their initial production. We compute the centrality dependence of inclusive 𝐵 𝑐 production and transverse-momentum (𝑝 𝑇 ) spectra using two different recombination models: instantaneous coalescence and resonance recombination. The main uncertainty in the resulting nuclear modification factors, 𝑅 AA , is currently associated with the 𝐵 𝑐 cross section in elementary 𝑝⁢𝑝 collisions, caused by the uncertainty in the branching ratio for the 𝐵$^{−}_{𝑐}$ → 𝐽/𝜓⁢𝜇 − ⁢$\overline{𝜈}$ decay. Our results indicate a large enhancement of the 𝑅 AA at low 𝑝 𝑇 , with significant regeneration contributions up to 𝑝 𝑇 ≃ 20GeV. Comparisons to CMS data are carried out but firm conclusions will require a more accurate value of the branching ratio, or alternative channels to measure the 𝐵 𝑐 production in 𝑝⁢ collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Comparing the Expense and Accuracy of Methods to Simulate Atomic Vibrations in Rubrene

Atomic vibrations can inform about materials properties from hole transport in organic semiconductors to correlated disorder in metal–organic frameworks. Currently, there are several methods for predicting these vibrations using simulations, but the accuracy–efficiency tradeoffs have not been examined in depth. In this work, rubrene is used as a model system to predict atomic vibrational properties using six different simulation methods: density functional theory, density functional tight binding, density functional tight binding with a Chebyshev polynomial-based correction, a trained machine learning model, a pretrained machine learning model called ANI-1, and a classical forcefield model. The accuracy of each method is evaluated by comparison to the experimental inelastic neutron scattering spectrum. All methods discussed here show some accuracy across a wide energy region, though the Chebyshev-corrected tight-binding method showed the optimal combination of high accuracy with low expense. We then offer broad simulation guidelines to yield efficient, accurate results for inelastic neutron scattering spectrum prediction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metal–Metal Bonding in Actinide Dimers: U 2 and U 2 –

Understanding direct metal–metal bonding between actinide atoms has been an elusive goal in chemistry for years. Here we report for the first time the anion photoelectron spectrum of U 2 – . The threshold of the lowest electron binding energy (EBE) spectral band occurs at 1.0 eV, which corresponds to the electron affinity (EA) of U 2 , whereas the vertical detachment energy of U 2 – is found at EBE ~ 1.2 eV. Electronic structure calculations on U 2 and U 2 – were carried out with state-of-the-art theoretical methods. The computed values of EA(U 2 ) and EA(U) and the difference between the computed dissociation energies of U 2 and U 2 – are found to be internally consistent and consistent with experiment. Analysis of the bonds in U 2 and U 2 – shows that while U 2 has a formal quintuple bond, U 2 – has a quadruple bond, even if the effective bond orders differ only by 0.5 unit instead of one unit. Furthermore, the resulting experimental-computational synergy elucidates the nature of metal–metal bonding in U 2 and U 2 – .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Projecting the likely importance of weak-interaction-driven bulk viscosity in neutron star mergers

ABSTRACT In this work, we estimate how much bulk viscosity driven by Urca processes is likely to affect the gravitational wave signal of a neutron star coalescence. In the late inspiral, we show that bulk viscosity affects the binding energy at fourth post-Newtonian order. Even though this effect is enhanced by the square of the gravitational compactness, the coefficient of bulk viscosity is likely too small to lead to observable effects in the waveform during the late inspiral, when only considering the orbital motion itself. In the post-merger, however, the characteristic time-scales and spatial scales are different, potentially leading to the opposite conclusion. We post-process data from a state-of-the-art equal-mass binary neutron star merger simulation to estimate the effects of bulk viscosity (which was not included in the simulation itself). In that scenario, we find that bulk viscosity can reach high values in regions of the merger. We compute several estimates of how much it might directly affect the global dynamics of the considered merger scenario, and find that it could become significant. Even larger effects could arise in different merger scenarios or in simulations that include non-linear effects. This assessment is reinforced by a quantitative comparison with relativistic heavy-ion collisions where such effects have been explored extensively.

79 ASTRONOMY AND ASTROPHYSICS↗