Engineering topics

Han, Jimei

Publications and source records attributed to Han, Jimei.

9 records

DOE OSTI2023

From remotely-sensed solar-induced chlorophyll fluorescence to ecosystem structure, function, and service: Part II—Harnessing data

Although our observing capabilities of solar-induced chlorophyll fluorescence (SIF) have been growing rapidly, the quality and consistency of SIF datasets are still in an active stage of research and development. As a result, there are considerable inconsistencies among diverse SIF datasets at all scales and the widespread applications of them have led to contradictory findings. The present review is the second of the two companion reviews, and data oriented. It aims to (1) synthesize the variety, scale, and uncertainty of existing SIF datasets, (2) synthesize the diverse applications in the sector of ecology, agriculture, hydrology, climate, and socioeconomics, and (3) clarify how such data inconsistency superimposed with the theoretical complexities laid out in may impact process interpretation of various applications and contribute to inconsistent findings. We emphasize that accurate interpretation of the functional relationships between SIF and other ecological indicators is contingent upon complete understanding of SIF data quality and uncertainty. Additionally, biases and uncertainties in SIF observations can significantly confound interpretation of their relationships and how such relationships respond to environmental variations. Built upon our syntheses, we summarize existing gaps and uncertainties in current SIF observations. Further, we offer our perspectives on innovations needed to help improve informing ecosystem structure, function, and service under climate change, including enhancing in-situ SIF observing capability especially in “data desert” regions, improving cross-instrument data standardization and network coordination, and advancing applications by fully harnessing theory and data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

From remotely sensed solar-induced chlorophyll fluorescence to ecosystem structure, function, and service: Part I—Harnessing theory

Solar-induced chlorophyll fluorescence (SIF) is a remotely sensed optical signal emitted during the light reactions of photosynthesis. The past two decades have witnessed an explosion in availability of SIF data at increasingly higher spatial and temporal resolutions, sparking applications in diverse research sectors (e.g., ecology, agriculture, hydrology, climate, and socioeconomics). These applications must deal with complexities caused by tremendous variations in scale and the impacts of interacting and superimposing plant physiology and three-dimensional vegetation structure on the emission and scattering of SIF. At present, these complexities have not been overcome. To advance future research, the two companion reviews aim to (1) develop an analytical framework for inferring terrestrial vegetation structures and function that are tied to SIF emission, (2) synthesize progress and identify challenges in SIF research via the lens of multi-sector applications, and (3) map out actionable solutions to tackle these challenges and offer our vision for research priorities over the next 5-10 years based on the proposed analytical framework. This paper is the first of the two companion reviews, and theory oriented. It introduces a theoretically rigorous yet practically applicable analytical framework. Guided by this framework, we offer theoretical perspectives on three overarching questions: (1) The forward (mechanism) question—How are the dynamics of SIF affected by terrestrial ecosystem structure and function? (2) The inference question: What aspects of terrestrial ecosystem structure, function, and service can be reliably inferred from remotely sensed SIF and how? (3) The innovation question: What innovations are needed to realize the full potential of SIF remote sensing for real-world applications under climate change? In conclusion, the analytical framework elucidates that process complexity must be appreciated in inferring ecosystem structure and function from the observed SIF; this framework can serve as a diagnosis and inference tool for versatile applications across diverse spatial and temporal scales.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

An exploratory steady–state redox model of photosynthetic linear electron transport for use in complete modelling of photosynthesis for broad applications

A photochemical model of photosynthetic electron transport (PET) is needed to integrate photophysics, photochemistry, and biochemistry to determine redox conditions of electron carriers and enzymes for plant stress assessment and mechanistically link sun-induced chlorophyll fluorescence to carbon assimilation for remotely sensing photosynthesis. Towards this goal, we derived photochemical equations governing the states and redox reactions of complexes and electron carriers along the PET chain. These equations allow the redox conditions of the mobile plastoquinone pool and the cytochrome b 6 f complex (Cyt) to be inferred with typical fluorometry. The equations agreed well with fluorometry measurements from diverse C 3 /C 4 species across environments in the relationship between the PET rate and fraction of open photosystem II reaction centres. We found the oxidation of plastoquinol by Cyt is the bottleneck of PET, and genetically improving the oxidation of plastoquinol by Cyt may enhance the efficiency of PET and photosynthesis across species. Redox reactions and photochemical and biochemical interactions are highly redundant in their complex controls of PET. Although individual reaction rate constants cannot be resolved, they appear in parameter groups which can be collectively inferred with fluorometry measurements for broad applications. The new photochemical model developed enables advances in different fronts of photosynthesis research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Granal thylakoid structure and function: explaining an enduring mystery of higher plants

Summary In higher plants, photosystems II and I are found in grana stacks and unstacked stroma lamellae, respectively. To connect them, electron carriers negotiate tortuous multi‐media paths and are subject to macromolecular blocking. Why does evolution select an apparently unnecessary, inefficient bipartition? Here we systematically explain this perplexing phenomenon. We propose that grana stacks, acting like bellows in accordions, increase the degree of ultrastructural control on photosynthesis through thylakoid swelling/shrinking induced by osmotic water fluxes. This control coordinates with variations in stomatal conductance and the turgor of guard cells, which act like an accordion's air button. Thylakoid ultrastructural dynamics regulate macromolecular blocking/collision probability, direct diffusional pathlengths, division of function of Cytochrome b 6 f complex between linear and cyclic electron transport, luminal pH via osmotic water fluxes, and the separation of pH dynamics between granal and lamellar lumens in response to environmental variations. With the two functionally asymmetrical photosystems located distantly from each other, the ultrastructural control, nonphotochemical quenching, and carbon‐reaction feedbacks maximally cooperate to balance electron transport with gas exchange, provide homeostasis in fluctuating light environments, and protect photosystems in drought. Grana stacks represent a dry/high irradiance adaptation of photosynthetic machinery to improve fitness in challenging land environments. Our theory unifies many well‐known but seemingly unconnected phenomena of thylakoid structure and function in higher plants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The physiological basis for estimating photosynthesis from Chl>em>a fluorescence

We report solar-induced Chl fluorescence (SIF) offers the potential to curb large uncertainties in the estimation of photosynthesis across biomes and climates, and at different spatiotemporal scales. However, it remains unclear how SIF should be used to mechanistically estimate photosynthesis. In this study, we built a quantitative framework for the estimation of photosynthesis, based on a mechanistic light reaction model with the Chla fluorescence of Photosystem II (SIFPSII) as an input (MLR-SIF). Utilizing 29 C 3 and C 4 plant species that are representative of major plant biomes across the globe, we confirmed the validity of this framework at the leaf level. The MLR-SIF model is capable of accurately reproducing photosynthesis for all C 3 and C 4 species under diverse light, temperature, and CO 2 conditions. We further tested the robustness of the MLR-SIF model using Monte Carlo simulations, and found that photosynthesis estimates were much less sensitive to parameter uncertainties relative to the conventional Farquhar, von Caemmerer, Berry (FvCB) model because of the additional independent information contained in SIF PSII . Once inferred from direct observables of SIF, SIF PSII provides ‘parameter savings’ to the MLR-SIF model, compared to the mechanistically equivalent FvCB model, and thus avoids the uncertainties arising as a result of imperfect model parameterization. Our findings set the stage for future efforts to employ SIF mechanistically to improve photosynthesis estimates across a variety of scales, functional groups, and environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Inference of photosynthetic capacity parameters from chlorophyll a fluorescence is affected by redox state of PSII reaction centers

Solar-induced chlorophyll fluorescence (SIF) has been used to infer photosynthetic capacity parameters (e.g., the maximum carboxylation rate V cmax , and the maximum electron transport rate J max ). However, the precise mechanism and practical utility of such approach under dynamic environments remain unclear. In this study, we used the balance between the light and carbon reactions to derive theoretical equations relating chlorophyll a fluorescence (ChlF) emission and photosynthetic capacity parameters, and formulated testable hypotheses regarding the dynamic relationships between the true total ChlF emitted from PSII (SIF PSII ) and V cmax and J max . We employed concurrent measurements of gas exchanges and ChlF parameters for 15 species from six biomes to test the formulated hypotheses across species, temperatures, and limitation state of carboxylation. Our results revealed that SIF PSII alone is incapable of informing the variations in V cmax and J max across species, even when SIF PSII is determined under the same environmental conditions. In contrast, the product of SIF PSII and the fraction of open PSII reactions q L , which indicates the redox state of PSII, is a strong predictor of both V cmax and J max , although their precise relationships vary somewhat with environmental conditions. Our findings suggest the redox state of PSII strongly influences the relationship between SIF PSII and V cmax and J max .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Leafweb: Dataset in Support of Coupled Modeling of Photophysics, Photochemistry, and Biochemistry of Photosynthesis, December 2022 Release

This data set contains measurements of leaf gas exchange and Pulse-Amplitude Modulated (PAM) fluorometry of light, carbon dioxide (CO2), oxygen (O2), and temperature responses from 26 C3 photosynthetic and four C4 photosynthetic species measured by independent researchers in Canada, China, Finland, Netherlands, and United States in the field, garden, or greenhouse. Data were collected between 1987 and 2021, however data for individual species only provide coverage over a few hours to one year. Species include three lianas, three shrubs, two boreal deciduous trees, two boreal evergreen needle-leaf tree, three temperate deciduous trees, four tropical deciduous trees, three tropical evergreen trees, one C3 grass, three C4 grasses, and six crop varieties. These measurements are conducted according to standard protocols in gas exchange (Long and Bernacchi 2003) and PAM fluorometry (Baker 2008). The Scots pine (Pinus sylvestris) dataset contains one-year continuous fluorometry observations made at intervals of 10 or 30 minutes in the field under natural environments using Walz monitoring PAM. Measurements from all other 29 species include simultaneous PAM fluorometry and gas exchange observations. Among these 29 species, seven species were measured with light response curves only (i.e., light intensity varied systematically with ambient CO2 concentration controlled at a constant level, e.g., 400 ppm). All the other 22 species were measured with both the light response and CO2 response (i.e., ambient CO2 concentration varied systematically with light intensity controlled at a constant level, e.g., 1200 µmolm-2s-1). For most species, measurements were made with temperature controlled at ~ 25 degrees Celsius (C) with the exceptions of Scots pine (natural diurnal and seasonal variations), tomato cultivar Basket Vee (~ 21 degrees C), and cotton which contained temperature stress experiments (9 to 40 degrees C). All measurements were made at ambient O2 concentration except for the tomato cultivar Basket Vee and cotton which used two O2 levels (2 and 21%) and rice and tomato cultivar Growdena which used five O2 levels (2, 10, 21, 35, and 50%). This dataset supports the complete modeling of photosynthesis at the leaf scale, including photophysical, photochemical, and biochemical reactions. It will support research in the applications of remotely sensed solar induced chlorophyll fluorescence and the responses of energy dissipation pathways to environmental variations across species and climates. This dataset contains 260 data files in comma separate (.csv) format contained inside 11 compressed (*.zip) files. Additional metadata are provided: one data dictionary, a species information table, and a file-level metadata file in comma separate (.csv) format and a user guide in PDF (*.pdf) format.

air temperature↗

DOE OSTI2021

The roles of photochemical and non-photochemical quenching in regulating photosynthesis depend on the phases of fluctuating light conditions

We report the induction and relaxation of photochemistry and non-photochemical quenching (NPQ) are not instantaneous and require time to respond to fluctuating environments. There is a lack of integrated understanding on how photochemistry and NPQ influence photosynthesis in fluctuating environments. We measured the induction and relaxation of chlorophyll a fluorescence and gas exchange in poplar and cotton at varying temperatures under saturating and fluctuating lights. When the light shifted from dark to high, the fraction of open reaction centers in photosystem II (q L ) gradually increased while NPQ increased suddenly and then remained stable. Temperature significantly changed the response of q L but not that of NPQ during the dark to high light transition. Increased q L led to higher photosynthesis but their precise relationship was affected by NPQ and temperature. q L was significantly related to biochemical capacity. Thus, q L appears to be a strong indicator of the activation of carboxylase, leading to the similar dynamics between q L and photosynthesis. When the light shifted from high to low intensity, NPQ is still engaged at a high level, causing a stronger decline in photosynthesis. Our finding suggests that the dynamic effects of photochemistry and NPQ on photosynthesis depend on the phases of environmental fluctuations and interactive effects of light and temperature. Across the full spectra of light fluctuation, the slow induction of q L is a more important limiting factor than the slow relaxation of NPQ for photosynthesis in typical ranges of temperature for photosynthesis. The findings provided a new perspective to improve photosynthetic productivity with molecular biology under natural fluctuating environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Unpacking the drivers of diurnal dynamics of sun-induced chlorophyll fluorescence (SIF): Canopy structure, plant physiology, instrument configuration and retrieval methods

Sun-induced chlorophyll fluorescence (SIF) from spaceborne sensors is a promising tool for global carbon cycle monitoring, but its application is constrained by insufficient understanding of the drivers underlying diurnal SIF dynamics. SIF measurements from ground-based towers can reveal diurnal SIF dynamics across biomes and environmental conditions; however, meaningful interpretation of diurnal variations requires disentangling impacts from canopy structure, plant physiology, instrument configuration and retrieval methods, which often interact with and confound each other. This study aims to unpack these drivers using 1) concurrent ground and airborne canopy-scale and leaf-scale measurements at a corn field, 2) a mechanistic SIF model that explicitly considers the dynamics of photochemistry (via the fraction of open photosystem II reaction centers, qL) and photoprotection (via nonphotochemical quenching, NPQ) as well as their interactive dependence on the sub-canopy light environment, and 3) cross-comparison of SIF instrument configurations and retrieval methods. We found that crop row orientations and sun angles can introduce a distinctive midday dip in SIF in absence of stress, due to a midday drop of absorbed photosynthetically active radiation (APAR) when crop rows are north-south oriented. Canopy structure caused distinctive responses in both qL and NPQ at different positions within the vertical canopy that collectively influenced fluorescence quantum yield (Φ F ) at the leaf scale. Once integrated at the canopy scale, diurnal dynamics of both APAR and canopy escape probability (ε) are critical for accurately shaping diurnal SIF variations. While leaf-level qL and NPQ exhibited strong diurnal dynamics, their influence was attenuated at the canopy scale due to opposing effects on SIF at different canopy layers. Furthermore, different system configurations (i.e., bi-hemispherical vs. hemispherical-conical) and retrieval methods can bias the SIF magnitude and distort its diurnal shapes, therefore confounding the interpretation of inherent strength and dynamics of SIF emission. Our findings demonstrate the importance of crop row structures, interactive variations in canopy structure and plant physiology, instrument configuration, and retrieval method in shaping the measured dynamics of diurnal SIF. This study highlights the necessity to account for these factors to accurately interpret satellite SIF, and informs future synthesis work with different SIF instrumentation and retrieval methods across sites.

59 BASIC BIOLOGICAL SCIENCES↗