Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “species dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,027 records · Page 57

Imaging the photochemistry of cyclobutanone using ultrafast electron diffraction: Experimental results

We investigated the ultrafast structural dynamics of cyclobutanone following photoexcitation at λ = 200 nm using gas-phase megaelectronvolt ultrafast electron diffraction. Our investigation complements the simulation studies of the same process within this special issue. It provides information about both electronic state population and structural dynamics through well-separable inelastic and elastic electron scattering signatures. We observe the depopulation of the photoexcited S 2 state of cyclobutanone with n3s Rydberg character through its inelastic electron scattering signature with a time constant of (0.29 ± 0.2) ps toward the S 1 state. The S 1 state population undergoes ring-opening via a Norrish Type-I reaction, likely while passing through a conical intersection with S 0 . The corresponding structural changes can be tracked by elastic electron scattering signatures. These changes appear with a delay of (0.14 ± 0.05) ps with respect to the initial photoexcitation, which is less than the S 2 depopulation time constant. This behavior provides evidence for the ballistic nature of the ring-opening once the S 1 state is reached. The resulting biradical species react further within (1.2 ± 0.2) ps via two rival fragmentation channels yielding ketene and ethylene, or propene and carbon monoxide. Furthermore, our study showcases the value of both gas-phase ultrafast diffraction studies as an experimental benchmark for nonadiabatic dynamics simulation methods and the limits in the interpretation of such experimental data without comparison with such simulations.

Carbon monoxide↗

From chromatin to crop: epigenetic innovations in bioenergy systems

Energy crops encompass a diverse array of plant species cultivated primarily as a source of biomass for energy generation and biofuel production. As such, they play a pivotal role in the transition to sustainable energy systems. However, their productivity is often limited by environmental stresses, nutrient availability, and the need for optimized yield. While traditional breeding and genetic engineering have driven improvements, challenges such as narrow genetic diversity, long development cycles, trait instability, and unexpected gene interactions remain. Epigenetics offers a largely untapped opportunity to overcome these constraints by regulating gene expression through mechanisms that are dynamic, finely tuned, and responsive to environmental and developmental cues. Epigenetic modifications including DNA methylation, histone post-translational changes, and small non-coding RNAs influence nearly all aspects of plant development and physiology, including traits central to bioenergy crops. While these mechanisms are well characterized in model species such as Arabidopsis thaliana, they remain underexplored in many purpose-grown energy crops. This review summarizes the current state of knowledge of epigenetic regulation in bioenergy species, explores how these mechanisms can be leveraged to enhance crop resilience and productivity, and identifies gaps in our understanding. By characterizing epigenetic mechanisms and harnessing epigenetic variation, we can expand the toolkit for developing resilient, high-yielding bioenergy crops to meet future environmental and energy demands.

09 BIOMASS FUELS↗

Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors

Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors.

16S rRNA↗

Regulatory Coordination of Photophysical, Photochemical, and Biochemical Reactions in the Photosynthesis of Land Plants

Balance among the sequential photophysical, photochemical, and biochemical reactions of photosynthesis is needed for converting fleeting energy in light to stable energy in chemical bonds. Any imbalance acts as either a bottleneck for limiting photosynthetic efficiency or an agent for inducing structural and functional damage to photosynthetic apparatus. Not only must each reaction be carefully regulated, but regulatory processes must also be coordinated across the reactions. However, regulations of different stages of photosynthesis have rarely been studied jointly. Non-photochemical quenching (NPQ) and stomatal conductance (g s ) are key regulators of photophysical and biochemical reactions, respectively. Existing evidence suggests that the redox state of plastoquinone regulates g s and that the photochemical reactions are partially regulated by the ultrastructural dynamics of thylakoids induced by osmotic water fluxes in chloroplasts of land plants. To examine how these regulations are coordinated and feedback to each other, we simultaneously measured NPQ and gs and inferred the redox state of plastoquinone and the light-induced thylakoid swelling/shrinking on numerous C 3 and C 4 species. For all species measured, NPQ and gs covary with the redox states of the electron transport chain, particularly plastoquinone, and increase as thylakoid swelling is inferred. NPQ has the maximal sensitivity at the light intensity at which thylakoid is inferred to be fully swollen. Our findings suggest that plant energy and water use strategies are intimately linked by evolution, and studying the regulations of different photosynthetic stages as a whole can lead to new insights of the functioning of photosynthetic machinery in dynamic environments.

59 BASIC BIOLOGICAL SCIENCES↗

Extending a land-surface model with <i>Sphagnum</i> moss to simulate responses of a northern temperate bog to whole ecosystem warming and elevated CO<sub>2</sub>

Abstract. Mosses need to be incorporated into Earth system models to better simulate peatland functional dynamics under the changing environment. Sphagnum mosses are strong determinants of nutrient, carbon, and water cycling in peatland ecosystems. However, most land-surface models do not include Sphagnum or other mosses as represented plant functional types (PFTs), thereby limiting predictive assessment of peatland responses to environmental change. In this study, we introduce a moss PFT into the land model component (ELM) of the Energy Exascale Earth System Model (E3SM) by developing water content dynamics and nonvascular photosynthetic processes for moss. The model was parameterized and independently evaluated against observations from an ombrotrophic forested bog as part of the Spruce and Peatland Responses Under Changing Environments (SPRUCE) project. The inclusion of a Sphagnum PFT with some Sphagnum-specific processes in ELM allows it to capture the observed seasonal dynamics of Sphagnum gross primary production (GPP) albeit with an underestimate of peak GPP. The model simulated a reasonable annual net primary production (NPP) for moss but with less interannual variation than observed, and it reproduced aboveground biomass for tree PFTs and stem biomass for shrubs. Different species showed highly variable warming responses under both ambient and elevated atmospheric CO2 concentrations, and elevated CO2 altered the warming response direction for the peatland ecosystem. Microtopography is critical: Sphagnum mosses on hummocks and hollows were simulated to show opposite warming responses (NPP decreasing with warming on hummocks but increasing in hollows), and hummock Sphagnum was modeled to have a strong dependence on water table height. The inclusion of this new moss PFT in global ELM simulations may provide a useful foundation for the investigation of northern peatland carbon exchange, enhancing the predictive capacity of carbon dynamics across the regional and global scales.

54 ENVIRONMENTAL SCIENCES↗

Anomalously slow hot carrier cooling and insulator-to-metal transition in a photo-doped Mott insulator

Photo-doped Mott insulators can exhibit novel photocarrier transport and relaxation dynamics and non-equilibrium phases. However, time-resolved real-space imaging of these processes are still lacking. Here, we use scanning ultrafast electron microscopy (SUEM) to directly visualize the spatial-temporal evolution of photoexcited species in a spin-orbit assisted Mott insulator α-RuCl 3 . At low optical fluences, we observe extremely long hot photocarrier transport time over one nanosecond, almost an order of magnitude longer than any known values in conventional semiconductors. At higher optical fluences, we observe nonlinear features suggesting a photo-induced insulator-to-metal transition, which is unusual in a large-gap Mott insulator. Our results demonstrate the rich physics in a photo-doped Mott insulator that can be extracted from spatial-temporal imaging and showcase the capability of SUEM to sensitively probe photoexcitations in strongly correlated electron systems.

42 ENGINEERING↗

Measuring Metapopulation Characteristics of the Southeastern Beach Mouse on Kennedy Space Center using a Dynamic Habitat Occupancy Approach

The Cape Canaveral Barrier Island Complex (CCBIC) represents the largest (72 km) continuous coastal habitat supporting the core population of the threatened southeastern beach mouse (Peromyscus polionotus niveiventris) in Florida. Despite protection throughout the subspecies’ remaining range, storm activity during the past two decades has de-stabilized coastal dune and coastal strand habitat required for beach mouse survival. Our long-term goal is to provide information to the management process to ensure a sustainable population on the CCBIC in light of sea-level rise, extreme storm events, and continued land development supporting the multi-user spaceport.Because beach mice populations are affected by storms (hurricanes, tropical storms, nor’easters), it is important to understand the species-habitat relations during periods with and without storm impacts. Conventional wisdom is that coastal dune and coastal strand are the preferred habitats, but coastal scrub habitat may be important because it is less affected by storm impacts (e.g., overwash, escarpment, sand deposition, etc.) and thus may serve as a refugia. In addition, genetic studies have shown some evidence for reduced dispersal between regions on CCBIC (Kalkvik et al., 2012; Zimmerman et al., 2015). We compared site occupancy dynamics for coastal dune, coastal strand, and coastal scrub habitat over three quarters (seasons) and determined the pattern of spatial correlation in habitat occupancy dynamics for locations at a range of distances in coastal dune, coastal strand, and coastal scrub habitats along the Kennedy Space Center (KSC) coastline (Figures1 and 2). Although habitat occupancy is very useful for understanding species-habitat relationships,in its simplest form it ignores differences in abundance between sites. Because information on abundance may inform management efforts and provide knowledge regarding status of the population, we tested measuring abundance state based on the number of detections in tracking tubes. Small mammal populations often fluctuate in a cyclic manner over time. These fluctuations make populations more susceptible to extinction and make trend detection more difficult. Efficient methods of measuring abundance across time and space are needed for monitoring trends.The purpose of this project was to:1.Estimate southeastern beach mouse habitat occupancy parameters in coastal dune, coastal strand, and coastal scrub habitats using a combination of tracking tubes and traps; 2.Model the spatial relationships of the effect of habitat (coastal dune, coastal strand, and coastal scrub) on parameters as a function of distance; and 3.Compare the reliability and efficiency of our survey methods and evaluate the potential to develop an abundance index.

Eric Douglas Stolen↗

Evidence for Photoinduced Polaron Generation in a High Persistence Length Low Bandgap Conjugated Polymer in Solution

Using ultrafast time-resolved infrared (TRIR) spectroscopy, we studied the solution-phase excited-state structural evolution of an indacenodithiophene-co-benzothiadiazole polymer (C8-IDTBT). Following band gap excitation, the TRIR spectra reveal vibrational features that develop within 10 ps and decay over 4 ns. Using pulse radiolysis measurements, charge-modulation spectroscopy, and quantum-chemical calculations, the IR features are assigned to polaron pairs. Interestingly, these features appear on an evolving broad mid-IR electronic absorption background, with kinetics correlating with the formation and decay of the cationradical vibrational bands. A three-state kinetic model successfully reproduces the spectral evolution, revealing that the polaron and exciton populations exist in dynamic equilibrium on picosecond time scales, with time constants for exciton dissociation in the range of 3− 5 ps and polaron-to-exciton reformation between 20 and 100 ps, while both species decay to the ground state on much slower nanosecond time scales (∼1 ns), yielding a remarkably high polaron-generation efficiency, higher than 50%. These findings provide fundamental insights into intramolecular charge photogeneration mechanisms in conjugated polymers, demonstrating efficient bound-polaron formation in isolated polymer chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of Collective Dynamics and Anharmonicity on Entropy in Heterogenous Catalysis: Building the Case for Advanced Molecular Simulations

In this paper, we present a perspective on the computational determination of entropy and its effects and consequences on heterogeneous catalysis. Special attention is paid to the role of anharmonicity and the deviations from the standard harmonic oscillator approximations which can fail to provide a reliable assessment of entropy. To address these challenges, advanced methodologies are needed that can explicitly account for these thermodynamic drivers through the appropriate statistical sampling of reactive free energy surfaces. We discuss where anharmonicity should be expected, where it has been observed from a theoretical perspective, and the methods currently employed to address it. We concentrate on three types of systems where we have observed major, nonnegligible anharmonic effects: (1) supported nanoparticles, where the migration of metal atoms, complexes, and entire clusters exhibit anharmonic behavior in their dynamic motion; (2) porous solids where confinement effects distort potential energy surfaces and hinder molecular motions resulting in large entropic terms; and (3) solid/liquid interfaces, where interactions between solvent molecules and adsorbed species can result in large solvent organization free energy and unique reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Gene loss during a transition to multicellularity

Multicellular evolution is a major transition associated with momentous diversification of multiple lineages and increased developmental complexity. The volvocine algae comprise a valuable system for the study of this transition, as they span from unicellular to undifferentiated and differentiated multicellular morphologies despite their genomes being similar, suggesting multicellular evolution requires few genetic changes to undergo dramatic shifts in developmental complexity. Here, the evolutionary dynamics of six volvocine genomes were examined, where a gradual loss of genes was observed in parallel to the co-option of a few key genes. Protein complexes in the six species exhibited novel interactions, suggesting that gene loss could play a role in evolutionary novelty. This finding was supported by gene network modeling, where gene loss outpaces gene gain in generating novel stable network states. These results suggest gene loss, in addition to gene gain and co-option, may be important for the evolution developmental complexity.

59 BASIC BIOLOGICAL SCIENCES↗

Study of toxicological evaluation of fire suppressants and extinguishers

The application of fluorocarbons as possible candidates for fire extinguishers and/or suppressants in confined spaces (such as spacecraft, aircraft, or submarines) was investigated, with special emphasis on their safety to man since they would be inhaled on an almost continuous basis. Short-term exposure experiments, using various animal species, were devised to look at specific parameters in order to determine which of the candidate compounds were sufficiently non-toxic to warrant long-term investigations. The following physiologic criteria were examined; tissue distribution, fluoride concentration, effect on mitochondria, microsomes, liposomes, and liver cell nuclei, erythrocyte fragility, clinical chemistry values, hematology, pathology, cardiac sensitization, behavioral effects. Various rodent species were used for initial investigations, with non-human primate exposures for Freon 116 which was warranted for negative results on rodents. Various types of exposure chambers were used, including closed dynamic chambers allowing for a recirculating atmosphere.

Source record↗

The Middle Atmosphere Program: Winter In Northern Europe (MAP/WINE)

The goals of map/wind (winter in Northern Europe) are to better understand: (1) the interaction of planetary waves of tropospheric origin; (2) the temporal and spatial development of sudden stratospheric warmings; (3) the temporal and spatial development of mesospheric cooling events in conjunction with stratospheric warmings; (4) the vertical and horizontal transport of minor constituents; (5) the effects on the chemistry of neutral and charged species of the large temperature changes occurring during stratospheric warmings and mesospheric cooling; (6) sources of turbulent energy; (7) the temporal and spatial development of turbulent layers; and (8) the contributions of dynamical processes to the heating and cooling of the mesospheric and turbopause region.

Vonzahn, U.↗

Effects of Radiative and Diffusive Transport Processes on Premixed Flames near Flammability Limits

A study of the mechanisms of flammability limits and the dynamics of flame extinguishment in premixed gas flames is described, a novel feature of which is the use of diluent gases having a wide range of radiative and diffusive transport properties. This feature enables an assessment of the importance of volumetric heat losses and Lewis number effects on these mechanisms. Additionally, effects of flame dynamics and flame front curvature are studied by employing spherically expanding flames obtained in a microgravity environment whereby natural convection is eliminated. New diagnostics include chamber pressure measurements and the first reported species concentration measurements in a microgravity combustion experiment. The limit mechanisms and extinguishment phenomena are found to be strongly influenced by the combined effects of radiant heat loss, Lewis number and flame curvature. Two new and as yet not well understood phenomena are reported: 'double flames' in rich H2-O2-CO2 mixtures and an 'inverse flammability region' in rich C3H8-O2-CO2 mixtures.

Abbud-Madrid, Angel↗

Single-shot ultrafast dynamics of nanosecond pulsed plasmas: Transition from ps–ns nonequilibrium to near-full ionization

The ultrafast multi-stage evolution of state-defining properties in atmospheric-pressure nanosecond pulsed plasmas is quantified using single-discharge, jitter-free, continuous streak-sweep spectroscopy of N 2 (C → B) molecular and N + /O + ionic species with a single-shot time resolution as short as ∼160 ps. An early period of extreme nonequilibrium is observed with vibrational temperatures [T V (C)] dropping from ∼8000 K at <200 ps after plasma breakdown to <4000 K within ∼1 ns, with near-ambient rotational temperatures [T R (C)] ∼ 300 K due to limited collisional energy transfer. This early-time T V (C) trend is representative of a direct and unquenched look into the high-energy tail of the electron energy distribution function; thus, it tracks real-time changes in the mean electron energy via the N2(C) emission signatures. This is followed by the rapid onset of N + /O + ionic emission after a distinct time delay of ∼14.9 ns due to multistep chemical kinetics. The ionic emission enables determination of electron densities (n e ) >2 × 10 19 cm −3 and electron temperatures (T e ) >36 000 K, indicating the transition to a nearly fully ionized regime. The ps–ns temporal dynamics are also compared between air and N 2 plasmas to assess the influence of collisional partners, as well as across the anode, cathode, and central gap regions to identify spatial variations in plasma behavior. Finally, this work demonstrates versatile continuously probing approach capable of spectro-temporal and spatially resolved single-shot measurements of key state variables in the ps–ns evolution of atmospheric-pressure nanosecond pulsed plasmas.

Electric discharges↗

Analytical population dynamics underlying harmful algal blooms triggered by prey avoidance

A modified version of the NPZD ecosystem model is used to analytically examine the effects of predation avoidance, a possible mechanism for triggering harmful algal blooms (HAB). To resolve HAB development caused by predation avoidance, an additional phytoplankton functional group is considered, one that has slower nutrient uptake and better predation avoidance characteristics than the non-harmful phytoplankton group used in traditional NPZD models. Because the two phytoplankton groups (one non-harmful and one HAB) compete for only one resource within the same system, steady state (equilibrium) conditions cannot occur without the presence of zooplankton; only the non-harmful phytoplankton group, which defeats the HAB group in the resource competition, can survive in the equilibrium. The presence of sufficient zooplankton effectively acts to replenish the nutrient pool by consuming the non-harmful phytoplankton. When this occurs, two equilibrium states are found: one with both phytoplankton groups coexisting, and one that only includes the HAB group. Further, the condition required for equilibrium is that the total nitrogen within the system should be larger than a threshold determined by model coefficients. The threshold and feasibility of the equilibrium are sensitive to the relative HAB predation avoidance coefficient. If the coefficient is larger than the ratio of net growth rates between the HAB and non-harmful phytoplankton group, the threshold becomes infinite, and an equilibrium is not feasible. The time scale for the system to reach an equilibrium state that includes a HAB group is determined asymptotically. The dependence of a threshold condition as a controlling factor may explain the regime shift of dominant species causing HABs. The ecosystem model is fully implemented into the Regional Ocean Modeling System and applied to an idealized coastal embayment (with depths and geometry taken from San Francisco Bay) to show numerically the dominance of prey avoidance dynamics in a natural shallow water environment that includes advection and diffusion. The analytical results improve strategies for HAB modeling and provide guidance for setting model coefficients necessary to resolve a HAB event.

54 ENVIRONMENTAL SCIENCES↗

Free-Energy Landscapes and Surface Dynamics in Methane Activation on Ni(511) via Machine Learning and Enhanced Sampling

Methane activation on stepped Ni(511) surfaces involves the rearrangement of surface atoms as the chemical reaction proceeds. This process is particularly sensitive to temperature. Using machine-learned interatomic potentials (MLIPs) coupled with enhanced sampling techniques, we investigate the activation of methane under realistic operando conditions. Our analysis reveals that methane dissociation occurs predominantly at step-edge nickel atoms. As CH x (where x = 3 or 4) species bind to additional surface nickel atoms, their reduced mobility leads to entropic penalties that suppress certain configurations and transition states. This is reflected in the underlying free energy surfaces, where configurations such as methyl binding to hollow sites and activation routes involving two nickel atoms become unfavorable as temperature increases. At elevated temperatures, methane activation extends from step-edge sites to terrace regions because of reduced free-energy barriers and enhanced surface dynamics. By decomposing the free-energy into enthalpic and entropic contributions, we uncover temperature-dependent shifts in the preferences of methane for the relevant active sites and arrive at a detailed molecular picture of methane activation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulating Forest Dynamics of Lowland Rainforests in Eastern Madagascar

Ecological modeling and forecasting are essential tools for the understanding of complex vegetation dynamics. The parametric demands of some of these models are often lacking or scant for threatened ecosystems, particularly in diverse tropical ecosystems. One such ecosystem and also one of the world's biodiversity hotspots, Madagascar's lowland rainforests, have disappeared at an alarming rate. The processes that drive tree species growth and distribution remain as poorly understood as the species themselves. We investigated the application of the process-based individual-based FORMIND model to successfully simulate a Madagascar lowland rainforest using previously collected multi-year forest inventory plot data. We inspected the model's ability to characterize growth and species abundance distributions over the study site, and then validated the model with an independently collected forest-inventory dataset from another lowland rainforest in eastern Madagascar. Following a comparative analysis using inventory data from the two study sites, we found that FORMIND accurately captures the structure and biomass of the study forest, with r(squared) values of 0.976, 0.895, and 0.995 for 1:1 lines comparing observed and simulated values across all plant functional types for aboveground biomass (tonnes/ha), stem numbers, and basal area (m(squared)/ha), respectively. Further, in validation with a second study forest site, FORMIND also compared well, only slightly over-estimating shade-intermediate species as compared to the study site, and slightly under-representing shade-tolerant species in percentage of total aboveground biomass. As an important application of the FORMIND model, we measured the net ecosystem exchange (NEE, in tons of carbon per hectare per year) for 50 ha of simulated forest over a 1000-year run from bare ground. We found that NEE values ranged between 1 and -1 t Cha(exp -1)year(exp -1), consequently the study forest can be considered as a net neutral or a very slight carbon sink ecosystem, after the initial 130 years of growth. Our study found that FORMIND represents a valuable tool toward simulating forest dynamics in the immensely diverse Madagascar rainforests.

Forest Productivity↗

Mechanism of Tyrosine-Driven Deprotonation in Photosystem II Revealed by Multiscale Simulations

Photosystem II (PSII) drives light-induced water oxidation via stepwise redox transitions of its oxygen-evolving complex (OEC), a Mn 4 Ca cluster advancing through five intermediate S-states (S 0 –S 4 ). The S 2 → S 3 transition involves a redox event in which a Mn ion donates an electron to the redox-active tyrosine YZ, coupled to deprotonation of an OEC-bound water ligand─yet the underlying coupling mechanism remains unresolved. Time-resolved serial femtosecond crystallography (TR-SFX) has revealed transient electron density shifts near the redox-active tyrosine Y Z , interpreted as sequential oxidation and reduction, with reduction initiating ∼1 μs after excitation and substantially progressed by 30 μs. However, this interpretation conflicts with kinetics from photothermal beam deflection (PBD), time-resolved X-ray absorption spectroscopy (TR-XAS), and electron paramagnetic resonance (EPR), which place electron transfer at 190–400 μs and proton transfer around 30 μs. Here, we reconcile these discrepancies using quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations. We show that oxidation of P680 and Y Z breaks the symmetry of the nearby hydrogen bonds involving water molecule W4, displacing Y Z and replicating the TR-SFX features of Y Z and Q165 observed at 1 μs. This local perturbation propagates through a hydrogen-bond network, transmitting the electrostatic signal from Y Z to the E65-E312 dyad and triggering redox-coupled deprotonation via the Cl1 channel. By 30 μs, the hydrogen-bond symmetry is restored through deprotonation of W2 (or alternatively W1), reproducing the disappearance of TR-SFX density differences around Y Z and Q165 without requiring Y Z reduction. Our proposed mechanism also gives molecular insights into the O6* density, assigning it to water reorganization rather than a discrete Ca-bound hydroxide species. Here, our results reveal a detailed atomistic mechanism linking Y Z oxidation to long-range proton release and suggest a functional role for the nearby Cl – ion in proton transfer. More broadly, this study underscores the importance of hydrogen-bond dynamics in mediating redox-driven proton transport and demonstrates how integrative simulations can resolve mechanistic ambiguities.

Deprotonation↗