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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Single-Molecule Chemical Reactions Unveiled in Molecular Junctions

Understanding chemical processes at the single-molecule scale represents the ultimate limit of analytical chemistry. Single-molecule detection techniques allow one to reveal the detailed dynamics and kinetics of a chemical reaction with unprecedented accuracy. It has also enabled the discoveries of new reaction pathways or intermediates/transition states that are inaccessible in conventional ensemble experiments, which is critical to elucidating their intrinsic mechanisms. Thanks to the rapid development of single-molecule junction (SMJ) techniques, detecting chemical reactions via monitoring the electrical current through single molecules has received an increasing amount of attention and has witnessed tremendous advances in recent years. Research efforts in this direction have opened a new route for probing chemical and physical processes with single-molecule precision. This review presents detailed advancements in probing single-molecule chemical reactions using SMJ techniques. We specifically highlight recent progress in investigating electric-field-driven reactions, reaction dynamics and kinetics, host–guest interactions, and redox reactions of different molecular systems. Finally, we discuss the potential of single-molecule detection using SMJs across various future applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
NASA NTRSDate not supplied

AMMPER: a user-friendly agent-based model that recapitulates simple metabolic responses of yeast to deep-space radiation

For humans venturing to deep space, radiation exposure poses a major health risk. Fundamental research into the biological effects of space radiation are essential for enabling exploration, and the first experimental organisms we send to deep space will be microbial. Yet there are many ways in which microorganisms are likely to experience the effects of high-energy particle radiation (such as Galactic Cosmic Rays) differently from multicellular animals, partly due to the simple fact that microbes are small and unicellular-- less likely to get hit in the first place, and less likely to communicate damage between cells. Computational modeling can aid in designing experiments and predicting the biological effects of radiation, but thus far particle radiation models have not focused on microbes. Here we present the latest developments in AMMPER, the Agent-based Model for Microbial Populations Exposed to Radiation. Originally written in 2021, AMMPER is a Python-based model that incorporates radiation track data from NASA's RITRACKS software and simulates the growth, damage, and death of yeast cells in 3D. It is now freely available as an open-source package on NASA's GitHub repository. Recent improvements include the ability to simulate the dynamics of alamarBlue, a color-changing redox dye commonly used to track metabolic activity in microbial spaceflight experiments. We demonstrate that a simple blue-pink-clear transition model is able to recapitulate key features observed in empirical data from ground studies. AMMPER also includes a new graphical user interface and introductory tutorial to facilitate ease of use by a wider audience. AMMPER can help us to understand how spatially heterogeneous particle radiation damage at the single-cell level can translate to growth differences at the population level, ultimately allowing us to better interpret experiments using microbes as model organisms and how well their results apply to humans.

yeast↗
DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Competitive Pi-Stacking and H-Bond Piling Increase Solubility of Heterocyclic Redoxmers

Redoxmers are organic molecules that carry electric charge in flow batteries. In many instances, they consist of heteroaromatic moieties modified with appended groups to prevent stacking of the planar cores and increase solubility in liquid electrolytes. This higher solubility is desired as it potentially allows achieving greater energy density in the battery. However, the present synthetic strategies often yield bulky molecules with low molarity even when they are neat and still lower molarity in liquid solutions. Fortunately, there are exceptions to this rule. Here, we examine one well-studied redoxmer, 2,1,3-benzothiadiazole, which has solubility similar to 5.7 M in acetonitrile at 25 degrees C. We demonstrate computationally and prove experimentally that the competition between two packing motifs, face-to-face it-stacking and random N-H bond piling, introduces frustration that confounds nucleation in crowded solutions. Our findings and examples from related systems suggest a complementary strategy for the molecular design of redoxmers for high energy density redox flow cells.

25 ENERGY STORAGE↗
DOE OSTI2026

Ion-Electron Coupling-Driven Redox Behavior in Metal–Organic Frameworks

Redox-active metal–organic frameworks (MOFs) have long been proposed as electronic transport platforms, yet the microscopic origin of their conductivity remains debated. A theoretical demonstration reveals charge transport in a Zn(pyrazole–naphthalene diimide (NDI)) MOF arising not from delocalized band-like states but from redox hopping between discrete linker sites. Using ab initio molecular dynamics simulations combined with electronic structure analysis, we established a direct link among electron injection, structural reorganization, and transport. Electron accumulation proceeds sequentially and site-selectively from imide and carbonyl groups of the NDI core progressively involving pyrazole N atoms at higher reduction states, through a hierarchy of redox-active sites. In contrast, Zn nodes remain essentially redox-inactive, which confirms their structural role. Density-of-states analysis corroborates a transport regime dominated by linker-centered states with evolving p-character upon reduction, resulting in dynamically reconfigured conduction networks. Real-time trajectories reveal anisotropic linker-to-linker electron transfer modulated by counterion coordination. This cooperative ion–electron regime emerges from potential energy surface collapse into a single low-barrier transition (ΔG ‡ ≈ 45 meV), where ionic and electronic motions evolve adiabatically on the same free-energy landscape. Elucidating redox conductivity in Zn(pyrazole–NDI) MOFs provides a theoretical framework for use in neuromorphic computing and related technologies.

Charge transfer↗
DOE OSTI2024

Impact of surface hydrophilicity on the ordering and transport properties of bicontinuous microemulsions

Microemulsions (MEs) have many industrial applications, where recent developments have shown that MEs can be utilized for electrochemical applications, including potentially in redox flow batteries. However, understanding the structure and dynamics of these systems, including at a surface, is needed to direct and rationally control their electrochemical behavior. While bulk solution measurements have provided insight into their structure, their assembly at an interface also impacts the electron (to the electrode) and ion (across the surfactant) charge transfer processes in the system. To address this shortcoming, neutron reflectivity experiments and molecular simulations have been completed that document the near surface structure of a series of deuterated water (D 2 O)/polysorbate-20/toluene MEs on hydrophilic and amphiphilic surfaces. These results show that the microemulsions form complex layered structures near a hard electrode surface, where most layers are not purely one component. Decreasing the D 2 O concentration in the ME increases the number of and purity of the layers established on the solid surface. These lamellar-type layers transition from the surface to the bulk microemulsion as a series of mixed layers (i.e., containing oil, water, and surfactant) that are consistent with perforated lamellae. Additionally, these mixed lamellae appear to become more perforated with oil and water pathways on an amphiphilic surface. Furthermore, the purity and thickness of these layers will influence the accessibility of an electrode by redox active species, as well as ion transport required to satisfy the electroneutrality condition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Insights on the structure and properties of sodium iron phosphate glasses from molecular dynamics simulations

Iron phosphate glasses are promising nuclear waste forms while more detailed understanding of their structures and structure-property relations are still needed to better design waste glass compositions. In this work we report studies of three series of sodium iron phosphate (NFP) glasses: 60P 2 O 5 -(40-x)Fe 2 O 3 -xNa 2 O (x = 0→40), (100–2x)P 2 O 5 -xFe 2 O 3 -xNa 2 O (x = 5→17.5) and one with different iron redox ratio, to understand the composition as well as the iron redox effects on the structure and properties of these glasses using molecular dynamics simulations with effective two-body and three-body potentials. Structural analyses, including pair distribution function, bond angle distribution, Q n distribution, and polyhedral connectivity, were performed to obtain in-depth information on short-range and medium-range structural features. The P-O pair distributions showed a first peak splitting with phosphorus-bridging and non-bridging oxygen contributions. This and the average P-O and other cation-oxygen bond distances are in excellent agreement with experiments. The coordination number of P 5+ remained four while that of Fe 3+ increased from 4.30 to 4.72 with decreasing Fe/Na ratio. Polyhedral linkage analysis showed [PO 4 ] units linked with [PO 4 ] and [FeO x ] through corner-sharing while the [PO 4 ]-[FeO x ] linkages become dominant for compositions with Fe 2 O 3 larger than 15 mol%. The effect of iron redox ratio on the structure of NFP glasses was also studied and it was found that bond lengths and coordination numbers were not strongly affected, while the reduction of iron introduced higher network distortions, as evident by O-P-O bond angle and Q n distribution. The glass transition temperature (T g ) showed a monotonic increase with Fe 2 O 3 in the first series, in good agreement with experiments, while those of the second series showed a maximum at P 2 O 5 = 82 mol%. Here, calculated elastic moduli were found to increase with Fe 2 O 3 in the first glass series, which was be explained by the increase of network connectivity, while those of the second series decrease with Fe 2 O 3 due to decrease of P 2 O 5 .

36 MATERIALS SCIENCE↗
DOE OSTI2024

Breaking up CO 2 through pressure-induced redox reaction with rhenium

We present results from density-functional-theory (DFT) based molecular dynamics simulations of fluid mixtures of carbon dioxide (CO 2 ) and rhenium (Re) metal at pressures up to 45 GPa and a temperature of 4000 K. Covalently-bonded carbon chains form as a result of a redox reaction between CO 2 and Re, whereas a pure CO 2 fluid is stable against decomposition at the same conditions. Furthermore, these findings have implications in reducing CO 2 by pressure-induced redox reactions with transition metals, which may play a role in CO 2 destruction and carbon storage as related to possible solutions to the current climate crisis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Surface-Initiated Atom Transfer Radical Polymerization Using Hydrogel Reactors

Atom transfer radical polymerization (ATRP) is a controlled radical polymerization method that enables the synthesis of tailored polymeric materials with low dispersity, highlighting its immense potential for green fabrication of advanced materials. However, its broader implementation is limited by challenges in product isolation, maintaining catalyst activity, and mitigating atmospheric sensitivity arising from oxygen-sensitive metal catalysts. Here, gelatin hydrogels (GHs) are introduced as a soft “reactor” matrix for interfacial ATRP, operating with minimal metal-catalyst loading while exhibiting possibly an organoreductive behavior. This strategy leverages activator regeneration via electron transfer through a ligand–metal charge-transfer (LMCT) mechanism to reduce oxidized metal catalysts within the GH network. Polymerization is evaluated by growing polymer brushes at an active interface formed between GHs swollen in monomer solution and an initiating surface, and sequential growth experiments confirmed that GH-mediated ATRP preserves living character. Under UV illumination, LMCT is activated, producing polymers both at the desired interface and within the GH bulk. UV–Vis spectroscopy revealed active reduction of Cu(II) to Cu(I) along with concentration-dependent complex formation, indicating dynamic coordination chemistry within the hydrogel. The redox-active arginine- and glutamic acid-rich gelatin backbone coordinates and reduces the metal center, enabling ATRP at ppm-level catalyst concentrations. While polymerization proceeds in GH-Cu(II) reactors, adding external mobile ligands to the GH results in longer polymer brushes. Here, the results reported here are exploratory. More experiments are needed to characterize polymer brush growth in GHs and compare it to conventional surface-initiated polymerization in solution.

Absorption↗
DOE OSTI2025

Thiol- and Disulfide-Functionalized Polycyclooctene: Metathesis Polymerization, Degradation, and Reformation

The enormous global production and use of polymers and plastics, combined with slower and less efficient disposal and recycling methods, have led to a worldwide growth in plastic waste. Here, we describe an approach that builds degradability into macromolecular polyolefins through the design of telechelic oligomers with reactive functional groups that enables control over polymer deconstruction and reconstruction. Our work exploits disulfide-containing polymers that have emerged as promising cyclable materials due to their dynamic reversibility (bond formation and cleavage) driven by redox chemistry under mild conditions. Specifically, we describe the synthesis of a telechelic α,ω-dithiopolycyclooctene (PCOE) by ring-opening metathesis polymerization using a dithioacetate chain transfer agent, followed by deprotection to convert the chain-end thioacetates to thiols. This process was studied towards control over the degree of oxidation to yield disulfide-containing PCOE, followed by an evaluation of reductive degradation and oxidative repolymerization. Overall, this approach facilitates the production of disulfide-containing unsaturated polyolefins and the integration of degradable and reformable moieties into soluble, processable, metathesis-derived polymers.

Lee, Kyoungwon↗
DOE OSTI2022

Modeling Absolute Redox Potentials of Ferrocene in the Condensed Phase

Absolute thermodynamic quantities for critical chemical reactions are needed to determine the role of solvents and reactive environments in catalysis and electrocatalysis beyond the relative scales typically employed. In principle, theoretical methods can provide such quantification but are often hindered by the innate complexity of strong electron correlation and dynamic relaxation of solvent environments. Here, we present and validate a protocol for calculating the redox potentials of ferrocene/ferrocenium redox pair in the acetonitrile. Equation-of-motion ionization potential coupled-cluster single-double (EOM-IP-CCSD) and effective fragment potential (EFP) methods are used to characterize the adiabatic and vertical ionization potentials (IP) as well as the electron affinity processes. We benchmark molecular mechanics against the EFP model to show the differences in ferrocene electronic polarizability in two redox states. Our best estimate of the redox potential (4.94 eV) agrees well with the experimental value (4.93 eV). This demonstrated the ability of modern computational methods to predict absolute redox potentials quantitatively and, more critically, quantify the correlation of dynamic effects, which underlie their origin.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Stabilized Oxygen Vacancy Chemistry toward High-Performance Layered Oxide Cathodes for Sodium-Ion Batteries

Anionic redox has emerged as a transformative paradigm for high-energy layered transition-metal (TM) oxide cathodes, but it is usually accompanied by the formation of anionic redox-mediated oxygen vacancies (OVs) due to irreversible oxygen release. Additionally, external factor-induced OVs (defined as intrinsic OVs) also play a pivotal role in the physicochemical properties of layered TM oxides. However, an in-depth understanding of the interplay between intrinsic and anionic redox-mediated OVs and the corresponding regulation mechanism of the dynamic evolution of OVs is still missing. Herein, we disclose the strong interrelationship between these OVs and demonstrate that the presence of intrinsic OVs in the TMO2 layers could induce weak integrity of the TM-O frameworks and unlock additional diffusion paths to trigger the generation and migration of anionic redox-mediated OVs. Accordingly, an OV stabilization strategy is proposed by deliberately introducing high-valence Nb5+, which could serve as an important building block in anchoring the oxygen sublattice and preventing the formation of a percolating OV migration network, thereby suppressing the formation/diffusion of anionic redox-mediated OVs. Consequently, superb structural integrity and improved electrochemical performance with reversible anionic redox chemistry are achieved. This work advances our understanding of the role of OVs for developing high-performance energy storage systems utilizing anionic redox.

anionic redox↗
DOE OSTI2024

Systems and methods for dynamically reconfigurable artificial synapses and neurons with tunable activation functions

An ionic redox transistor comprises a solid channel, a solid reservoir layer, and a solid electrolyte layer disposed between the channel and the reservoir layer. The channel exhibits a substantially linear current-voltage relationship in a first range of voltages, and a nonlinear current-voltage relationship in a second range of voltages that is greater than the first range of voltages. One or both of the substantially linear current-voltage relationship or the nonlinear current-voltage relationship of the channel is varied by changing the concentration of ions such as oxygen vacancies in the channel. Ion or vacancy transport between the channel and the reservoir layer across the electrolyte layer occurs in response to applying a voltage between the channel and the reservoir layer. Subject to the first range of voltages, the channel can function as a synapse device. Subject to the second range of voltages, the channel can function as a neuron device.

Talin, Albert Alec↗
DOE OSTI2025

Probing Electrode Transformation under Dynamic Operation for Alkaline Water Electrolysis

Alkaline water electrolyzers (AWEs) play a pivotal role in the realm of large-scale hydrogen production. However, AWEs face significant challenges in electrode degradation particularly under dynamic operating conditions, induced by reverse current phenomenon during frequent startup/shutdown. Herein, this study aims to rationalize the degradation mechanisms of AWEs under these conditions. A three-electrode membrane electrode assembly (MEA) setup is first utilized to decouple polarization behaviors of anode and cathode in AWEs. Following a proposed accelerated stress testing protocol, the setup allows for tracking individual electrode performance transformations during frequent reverse current operation. Integrating operando cell studies with in situ and post-mortem characterizations, it is showed that continuous formation of highly active species, nickel (oxy)hydroxides, improves the anode performance for oxygen evolution reaction. On the contrary, irreversible oxidation of nickel to β-nickel hydroxide results in a severe degradation of cathode, leading to material dissolution, poor electrical conductivity and loss of catalytic activity for hydrogen evolution reaction. These results provide insights in nickel-based electrode transformation mechanisms for alkaline water electrolysis and indicate that cathode with higher redox reversibility can potentially improve durability of AWEs under dynamic conditions.

08 HYDROGEN↗
DOE OSTI2025

Multi-Omics Reveals Temporal Scales of Carbon Metabolism in Synechococcus Elongatus PCC 7942 Under Light Disturbance

Central carbon metabolism in model cyanobacteria involves multiple pathways to adapt to energy-light limitations across diel cycles. However, the success in mechanistic modeling for phenotypic prediction of the protein regulators in the metabolic state depends on capturing the vast possibilities emerging from multiple regulatory pathways in complex biological processes. Here, we developed a physics-informed machine learning approach based on energy-landscape concepts to predict regulatory proteins responding to cyclic circadian and unforeseen light perturbations in cyanobacterial metabolic networks. Our approach provides interpretable de novo models for inferring gene expression dynamics from Synechococcus elongatus over diel cycles and using redox proteome analysis to distinguish immediate light-responsive elements from circadian-regulated processes in carbon metabolism pathways. We identified distinct temporal signatures with the analysis of the redox proteome: there was an immediate shift in cysteine redox states accompanied by a limited change in protein abundance under constant illumination and after 2 hours of darkness. This discovery indicates that the generation of reductants coordinates photoinduced electron transport with redox metabolic pathways in two discernable molecular mechanisms: fast redox-based protein modifications occur immediately after the light disturbance, followed by slow transcriptional regulations across networks. This temporal regulation reveals how metabolic networks integrate rapid light responses with programmed circadian rhythms to maintain cellular homeostasis under the light-energy limitations over the diel cycle.

Biomolecular & subcellular processes↗
DOE OSTI2022

Effective Storage of Electrons in Water by the Formation of Highly Reduced Polyoxometalate Clusters

Aqueous solutions of polyoxometalates (POMs) have been shown to have potential as high-capacity energy storage materials due to their potential for multi-electron redox processes, yet the mechanism of reduction and practical limits are currently unknown. Herein, we explore the mechanism of multi-electron redox processes that allow the highly reduced POM clusters of the form {MO 3 } y to absorb y electrons in aqueous solution, focusing mechanistically on the Wells-Dawson structure X 6 [P 2 W 18 O 62 ], which comprises 18 metal centers and can uptake up to 18 electrons reversibly (y = 18) per cluster in aqueous solution when the countercations are lithium. This unconventional redox activity is rationalized by density functional theory, molecular dynamics simulations, UV-vis, electron paramagnetic resonance spectroscopy, and small-angle X-ray scattering spectra. These data point to a new phenomenon showing that cluster protonation and aggregation allow the formation of highly electron-rich meta-stable systems in aqueous solution, which produce H 2 when the solution is diluted. Finally, we show that this understanding is transferrable to other salts of [P 5 W 30 O 110 ] 15- and [P 8 W 48 O 184 ] 40- anions, which can be charged to 23 and 27 electrons per cluster, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Correlative operando microscopy of oxygen evolution electrocatalysts

Transition metal (oxy)hydroxides are promising electrocatalysts for the oxygen evolution reaction.1–3 The properties of these materials evolve dynamically and heterogeneously4 with applied voltage through ion insertion redox reactions, converting inactive materials at open-circuit into active electrocatalysts during operation.5 Thus, the catalytic state is inherently far-from-equilibrium, complicating its direct observation. Here, we establish the link between the oxygen evolution activity and the local operational chemical, physical, and electronic nanoscale structure of single-crystalline β-Co(OH)2 platelet particles through a suite of newly developed correlative operando scanning probe and X-ray microscopy techniques. At pre-catalytic voltages, the particles swell to form an α-CoO2H1.5·0.5H2O-like structure with associated Co2.5+ oxidation state produced through hydroxide intercalation. With increasing voltage to drive oxygen evolution, interlayer water and protons de-intercalate to form contracted β-CoOOH particles with Co3+ species. While these transformations manifest heterogeneously through the bulk of the particles, the electrochemical current is primarily restricted to the particle edge facets. The observed Tafel behavior is correlated to the local concentration of Co3+ at these reactive edge sites, demonstrating the link between bulk ion-insertion and surface catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Effect of fluctuating redox conditions on trace metal release from wetland soils from South Carolina and stream sediments from Tennessee

Natural aquatic systems undergo fluctuating redox conditions due to microbial activity, varying water saturation levels, and nutrients dynamics. With fluctuating oxic and anoxic conditions, trace metals can be mobilized or sequestered in response to changes in iron and sulfur speciation and the concentrations and lability of organic carbon. We conducted a systematic laboratory-based microcosm study to examine the effect of redox fluctuations on trace metal mobility in samples collected from two different natural aquatic systems: riparian wetlands and a stream. We incubated water-saturated soils under three cycles of anoxic-oxic conditions (τanoxic:τoxic = 3) spanning 24 days and monitored the change in dissolved and bioavailable metal (copper (Cu), nickel (Ni), zinc (Zn), cobalt (Co), iron (Fe), and manganese (Mn)) concentrations. The dataset includes the results of the variation in metal concentrations due to redox fluctuations in wetland soils and stream sediments. Additionally, the variation in the bioavailable concentration of metals obtained using passive samplers based on diffuse gradient in thin-films technique is included in the dataset. We have also reported the change in the pH values and dissolved oxygen concentrations in the microcosms during the entire study of 24 days. The dataset also contains the dissolved organic carbon and sulfate concentrations, and the data on fractions of metals bound to reducible and oxidizable phases. For materials from both the wetlands and the stream, anoxic conditions favored Co and Zn release, which corresponded with the reductive dissolution of iron oxides. In contrast, dissolved Cu concentrations increased under oxic conditions for both sites and correlated positively with the release of sulfate. In wetland soils, dissolution of Fe (hydr)oxides increased Ni solubility; however, in stream sediments, Ni release occurred when sulfides or organic matter were oxidized. For stream sediments, each subsequent redox cycle increased the bioavailability of trace metals. Upon redox fluctuations in wetland soils, the bioavailability of Zn and Cu increased, whereas bioavailable Ni and Co decreased. This study illustrates that different trace metals display distinct bioavailability patterns during oxic-anoxic fluctuations in natural environments. The biogeochemical cycling of carbon and nitrogen in systems with redox fluctuations may be influenced by these patterns in trace metal availability in addition to the availability of electron donors and acceptors.

54 ENVIRONMENTAL SCIENCES↗