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At least 487 records · Page 27

Advances in genetic tools for metabolic engineering of non-conventional yeasts

Non-conventional yeasts are emerging as powerful alternatives to Saccharomyces cerevisiae for metabolic engineering, owing to their innate stress tolerance, broad substrate utilization, and distinctive metabolic capabilities. These attributes position them as promising chassis for producing biofuels, pharmaceuticals, and specialty chemicals. This review synthesizes recent advances in genetic toolkits for four such species—Pichia kudriavzevii (Issatchenkia orientalis), Starmerella bombicola, Debaryomyces hansenii, and Pachysolen tannophilus—highlighting progress across plasmid architectures (episomal and integrative), identification of autonomously replicating sequences and centromeric elements, and the development of safe-harbor genomic loci. We summarize promoter and terminator libraries enabling tunable expression, the expansion of auxotrophic and antifungal selection markers with recycling strategies, and the rapid adaptation of CRISPR-based systems (Cas9 and Cas12a) with optimized guide RNA expression, multiplex editing, and approaches that enhance homologous recombination (e.g., KU70/80 disruption). We also review landing-pad platforms for modular, repeated integrations and transposon-based tools (e.g., piggyBac) that facilitate multigene pathway assembly. Collectively, these innovations are accelerating design-build-test-learn cycles and enabling precise, scalable engineering of non-conventional yeasts. Remaining challenges—including limited species-specific episomal systems, variable transformation efficiencies, genome-stability concerns, and alternative codon usage—define clear priorities for future toolkit development. Together, these advances and open needs chart a path toward robust, sustainable biomanufacturing using diverse non-conventional yeast chassis.

59 BASIC BIOLOGICAL SCIENCES↗

High-level co-production of 3-hydroxypropionic acid and 1,3-propanediol from glycerol: Metabolic engineering and process optimization

3-Hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3-PDO) are value-added chemicals with versatile applications in the chemical, pharmaceutical, and food industries. Nevertheless, sustainable production of 3-HP and 1,3-PDO is often limited by the lack of efficient strains and suitable fermentation configurations. We report attempts have been made to improve the co-production of both metabolites through metabolic engineering of Escherichia coli and process optimization. First, the 3-HP and 1,3-PDO co-biosynthetic pathways were recruited and optimized in E. coli, followed by coupling the pathways to the transhydrogenase-mediated cofactor regeneration systems that increased cofactor availability and product synthesis. Next, pathway rebalancing and block of by-product formation significantly improved 3-HP and 1,3-PDO net titer. Subsequently, glycerol flux toward 3-HP and 1,3-PDO synthesis was maximized by removing metabolic repression and fine-tuning the glycerol oxidation pathway. Lastly, the combined fermentation process optimization and two-stage pH-controlled fed-batch fermentation co-produced 140.50 g/L 3-HP and 1,3-PDO, with 0.85 mol/mol net yield.

1,3-propanediol↗

Systems-Level Modeling for CRISPR-Based Metabolic Engineering

The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. Here, the advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy

High levels of anthropogenic CO 2 emissions are driving the warming of global climate. If this pattern of increasing emissions does not change, it will cause further climate change with severe consequences for the human population. On top of this, the increasing accumulation of solid waste within the linear economy model is threatening global biosustainability. The magnitude of these challenges requires several approaches to capture and utilize waste carbon and establish a circular economy. Microbial gas fermentation presents an exciting opportunity to capture carbon oxides from gaseous and solid waste streams with high feedstock flexibility and selectivity. Here we discuss available microbial systems and review in detail the metabolism of both anaerobic acetogens and aerobic hydrogenotrophs and their ability to utilize C1 waste feedstocks. More specifically, we provide an overview of the systems-level understanding of metabolism, key metabolic pathways, scale-up opportunities and commercial successes, and the most recent technological advances in strain and process engineering. Finally, we also discuss in detail the gaps and opportunities to advance the understanding of these autotrophic biocatalysts for the efficient and economically viable production of bioproducts from recycled carbon.

59 BASIC BIOLOGICAL SCIENCES↗

Spatial Engineering Direct Cooperativity between Binding Sites for Uranium Sequestration

Preorganization is a basic design principle used by nature that allows for synergistic pathways to be expressed. Herein, a full account of the conceptual and experimental development from randomly distributed functionalities to a convergent arrangement that facilitates cooperative binding is given, thus conferring exceptional affinity toward the analyte of interest. The resulting material with chelating groups populated adjacently in a spatially locked manner displays up to two orders of magnitude improvement compared to a random and isolated manner using uranium sequestration as a model application. This adsorbent shows exceptional extraction efficiencies, capable of reducing the uranium concentration from 5 ppm to less than 1 ppb within 10 min, even though the system is permeated with high concentrations of competing ions. The efficiency is further supported by its ability to extract uranium from seawater with an uptake capability of 5.01 mg g -1 , placing it among the highest-capacity seawater uranium extraction materials described to date. The concept presented here uncovers a new paradigm in the design of efficient sorbent materials by manipulating the spatial distribution to amplify the cooperation of functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Data for Discovery, Characterization, and Application of Chromosomal Integration Sites for Stable Heterologous Gene Expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides . We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides . These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides .

Conversion↗

Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides

Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides. We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. Here, we validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides. These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides.

59 BASIC BIOLOGICAL SCIENCES↗

Generation of a highly attenuated strain of Pseudomonas aeruginosa for commercial production of alginate

Alginate is an important polysaccharide that is commonly used as a gelling agent in foods, cosmetics and healthcare products. Currently, all alginate used commercially is extracted from brown seaweed. However, with environmental changes such as increasing ocean temperature and the increasing number of biotechnological uses of alginates with specific properties, there is an emerging need for more reliable and customizable sources of alginate. An alternative to seaweed for alginate production is Pseudomonas aeruginosa, a common Gram-negative bacterium that can form alginate containing biofilms. However, P. aeruginosa is an opportunistic pathogen that can cause life-threatening infections in immunocompromised patients. Therefore, we sought to engineer a non-pathogenic P. aeruginosa strain that is safe for commercial production of alginate. Using a homologous recombination strategy, we sequentially deleted five key pathogenicity genes from the P. aeruginosa chromosome, resulting in the marker-free strain PGN5. Intraperitoneal injection of mice with PGN5 resulted in 0% mortality, while injection with wild-type P. aeruginosa resulted in 95% mortality, providing evidence that the systemic virulence of PGN5 is highly attenuated. Importantly, PGN5 produces large amounts of alginate in response to overexpression of MucE, an activator of alginate biosynthesis. The alginate produced by PGN5 is structurally identical to alginate produced by wildtype P. aeruginosa, indicating that the alginate biosynthetic pathway remains functional in this modified strain. The genetic versatility of P. aeruginosa will allow us to further engineer PGN5 to produce alginates with specific chemical compositions and physical properties to meet different industrial and biomedical needs.

60 APPLIED LIFE SCIENCES↗

Walking the ‘design–build–test–learn’ cycle: flux analysis and genetic engineering reveal the pliability of plant central metabolism

Oilseeds are of great economic importance for food and animal feed and their contribution to renewable energy production. Soybean seeds (Glycine max (L.) Merr.) contain c. 40% protein, 20% oil, and 30% carbohydrate (Song et al., 2023). Due to the massive scale of soybean production worldwide, even small improvements in seed protein and oil content make economic sense (Song et al., 2023). Successful manipulation of seed composition largely depends on a thorough understanding of the processes and pathways involved in the biosynthesis of fatty acids and amino acids, which are the building blocks of lipids and proteins. Rational engineering of the synthesis of storage reserves, that is, the rerouting of metabolic flux in central metabolism, is difficult to accomplish due to the complexity of the central metabolic network, the intricate regulation of its enzymes at multiple levels, and the often-unpredictable effects of genetic manipulation (Sweetlove et al., 2017). Therefore, the advancement of our understanding of central metabolism and its control of carbon partitioning requires following an iterative ‘design–build–test–learn’ (DBTL) cycle (Lin & Eudes, 2020) where metabolic flux analysis and hypothesis testing by transgenic approaches are important components. Previous metabolic studies on soybeans using isotopic tracers and metabolic flux analysis have provided insight into how lipid and protein biosynthesis occurs simultaneously during seed development (Allen et al., 2009; Allen & Young, 2013; Kambhampati et al., 2021). In an article published in this issue of New Phytologist, Morley et al. (2023; 1834–1851) put the insights they have gained into the delivery of metabolic precursors and energy cofactors to oil synthesis to the test and arrive at a successful metabolic engineering design. They show that an increase in seed oil content in soybeans can be achieved by overexpression of malic enzyme (ME) during seed development. Malic enzyme refers to a class of decarboxylating malate dehydrogenase enzymes that oxidize malate with NAD + or NADP + as redox cofactor while generating pyruvate and CO 2 . Like higher plants in general, soybean has distinct NADH- or NADPH-producing ME isoforms localized to the cytosol, plastid, or mitochondria (Gerrard Wheeler et al., 2016). As Morley et al. show, an increase in seed oil can be achieved in particular when a NADP+-dependent enzyme isoform (EC 1.1.1.40) is overexpressed in the plastid. Given the complex compartmentalization of pyruvate, malate, and redox metabolism (Fig. 1), increased oil production appears to depend on additional pyruvate and reducing equivalents being produced in the same compartment where de novo fatty acid biosynthesis occurs: the plastid.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of 2-Hydroxyacyl-CoA Synthases with High Acyloin Condensation Activity for Orthogonal One-Carbon Bioconversion

One-carbon (C1) compounds are emerging as cost-effective and potentially carbon-negative feedstocks for biomanufacturing, which require efficient, versatile metabolic platforms for the synthesis of value-added products. Synthetic formyl-CoA elongation (FORCE) pathways allow diverse product synthesis from C1 compounds via iterative C1 elongation, operating independently from the host metabolism with reduced engineering complexity and improved theoretical yields. However, a major bottleneck was identified as the suboptimal kinetics of the core C1–C1 condensation enzyme, 2-hydroxyacyl-CoA synthase (HACS), catalyzing the acyloin condensation reaction between formaldehyde and formyl-CoA. Furthermore, we used a combinatorial approach of bioprospecting and rational protein engineering to identify multiple HACS variants with significantly improved activities toward C1 substrates. Sequence and structure alignment of the active variants elucidated the key regions for the catalytic function, which were targeted for mutagenesis, leading to improved catalytic efficiency. In parallel, a consecutive round of bioprospecting for homologs with high similarity with active variants revealed a highly active HACS variant exhibiting up to 7-fold improvement in catalytic efficiency (k cat /K M ) and 14-fold improvement in the FORCE pathway flux in vivo compared to the previous reports. Upon further optimization of the downstream pathway, the orthogonal C1-to-product bioconversion system showed a metabolic flux of up to 700 μM glycolate OD –1 h –1 (2.1 mmol gDCW –1 h –1 ) and an industrially relevant glycolate titer, rate, and yield of 5.2 g L –1 (67.8 mM), 0.22 g L –1 h –1 , and 94% carbon yield, respectively.

2-hydroxyacyl-CoA synthase↗

Measuring the effectiveness of high-performance Co-Optima biofuels on suppressing soot formation at high temperature

Soot emissions in combustion are unwanted consequences of burning hydrocarbon fuels. The presence of soot during and following combustion processes is an indication of incomplete combustion and has several negative consequences including the emission of harmful particulates and increased operational costs. Efforts have been made to reduce soot production in combustion engines through utilizing oxygenated biofuels in lieu of traditional nonoxygenated feedstocks. The ongoing Co-Optimization of Fuels and Engines (Co-Optima) initiative from the US Department of Energy (DOE) is focused on accelerating the introduction of affordable, scalable, and sustainable biofuels and high-efficiency, low-emission vehicle engines. The Co-Optima program has identified a handful of biofuel compounds from a list of thousands of potential candidates. In this study, a shock tube was used to evaluate the performance of soot reduction of five high-performance biofuels downselected by the Co-Optima program. Current experiments were performed at test conditions between 1,700 and 2,100 K and 4 and 4.7 atm using shock tube and ultrafast, time-resolve laser absorption diagnostic techniques. The combination of shock heating and nonintrusive laser detection provides a state-of-the-art test platform for high-temperature soot formation under engine conditions. Soot reduction was found in ethanol, cyclopentanone, and methyl acetate; conversely, an α-diisobutylene and methyl furan produced more soot compared to the baseline over longer test times. For each biofuel, several reaction pathways that lead towards soot production were identified. The data collected in these experiments are valuable information for the future of renewable biofuel development and their applicability in engines.

09 BIOMASS FUELS↗

Establishing a clostridia foundry for biosystems design by integrating computational modeling, systems-level analyses, and cell-free engineering technologies (Final Report)

Rapid population growth, a rise in global living standards, and economic competitiveness have intensified the need for sustainable, low-cost biofuels and bioproducts production. Industrial biotechnology using microbial cell factories – and waste and/or renewable feedstocks – is one of the most attractive approaches for addressing this need, particularly when large-scale chemical synthesis is untenable. Unfortunately, designing, building, and optimizing biosynthetic pathways in cells remains a complex challenge. With support from the Department of Energy, we worked to address this challenge in a new interdisciplinary venture that established the world’s first clostridial Foundry for Biosystems Design (cBioFAB). Working both in vitro (cell-free) and in vivo, the goal of this project was to interweave and advance state-of-the-art computational modeling, genome editing, omics measurements, systems-biology analyses, and cell-free technologies to expand the set of platform organisms that meet DOE bioenergy goals. Specifically, we manufactured fuel and chemical intermediates via existing and de novo pathways. This report covers the outcomes of our research project.

09 BIOMASS FUELS↗

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

Bottlenecks in the efficient conversion of xylose into cost-effective biofuels have limited the widespread use of plant lignocellulose as a renewable feedstock. The yeast Saccharomyces cerevisiae ferments glucose into ethanol with such high metabolic flux that it ferments high concentrations of glucose aerobically, a trait called the Crabtree/Warburg Effect. In contrast to glucose, most engineered S. cerevisiae strains do not ferment xylose at economically viable rates and yields, and they require respiration to achieve sufficient xylose metabolic flux and energy return for growth aerobically. Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose. Through genome sequence comparisons and directed engineering, we determined that duplications of genes encoding engineered xylose metabolism enzymes, as well as TKL1, a gene encoding a transketolase in the pentose phosphate pathway, were the causative genetic changes for the evolved phenotype. Reengineered duplications of these enzymes, in combination with deletion mutations in HOG1, ISU1, GRE3, and IRA2, increased the rates of aerobic and anaerobic xylose fermentation. Importantly, we found that these genetic modifications function in another genetic background and increase the rate and yield of xylose-to-ethanol conversion in industrially relevant switchgrass hydrolysate, indicating that these specific genetic modifications may enable the sustainable production of industrial biofuels from yeast. We propose a model for how key regulatory mutations prime yeast for aerobic xylose fermentation by lowering the threshold for overflow metabolism, allowing mutations to increase xylose flux and to redirect it into fermentation products.

59 BASIC BIOLOGICAL SCIENCES↗

Polymer Deconstruction and Redesign Strategies for Plastics Recycling

Advancing plastics recycling requires both the selective deconstruction of existing polymers and the design of new materials that enable efficient reuse without loss of performance. This perspective highlights an integrated approach that is rooted in polymer chemistry, catalysis, and process engineering which can enable a circular plastics economy. Here, we outline recent advances in catalytic, solvolytic, and enzymatic pathways for plastic deconstruction, and examine the molecular design principles driving next-generation recyclable-by-design and bio-based polymers. Despite these advances, major knowledge gaps remain in understanding the evolution of polymer morphology and catalyst structure during deconstruction, assessing deconstruction processes with realistic polymers, and offering redesigned polymers with competitive cost and environmental advantage over conventional plastics. United States Department of Energy (U.S. DOE) national laboratories offer unique capabilities to address these challenges through in situ and operando characterization, high-throughput experimentation, environmental studies, technoeconomic and life cycle assessment, scale-up support, and collaboration networks. Advances made in understanding plastic deconstruction mechanisms and structure-property correlations of redesigned polymers inform emerging research directions including autonomous experimentation, real-time feedback-enabled process optimization, and protein engineering for enzymatic depolymerization.

36 MATERIALS SCIENCE↗

Data from Enhanced 2′-Fucosyllactose Production by Engineered Saccharomyces cerevisiae using Xylose as a Co-Substrate

2′-Fucosyllactose (2′-FL), a human milk oligosaccharide with confirmed benefits for infant health, is a promising infant formula ingredient. Although Escherichia coli , Saccharomyces cerevisiae , Corynebacterium glutamicum , and Bacillus subtilis have been engineered to produce 2′-FL, their titers and productivities need be improved for economic production. Glucose along with lactose have been used as substrates for producing 2′-FL, but accumulation of by-products due to overflow metabolism of glucose hampered efficient production of 2′-FL regardless of a host strain. To circumvent this problem, we used xylose, which is the second most abundant sugar in plant cell wall hydrolysates and is metabolized through oxidative metabolism, for the production of 2′-FL by engineered yeast. Specifically, we modified an engineered S. cerevisiae strain capable of assimilating xylose to produce 2′-FL from a mixture of xylose and lactose. First, a lactose transporter (Lac12) from Kluyveromyces lactis was introduced. Second, a heterologous 2′-FL biosynthetic pathway consisting of enzymes Gmd, WcaG, and WbgL from E. coli was introduced. Third, we adjusted expression levels of the heterologous genes to maximize 2′-FL production. The resulting engineered yeast produced 25.5 g/L of 2′-FL with a volumetric productivity of 0.35 g/L∙h in a fed-batch fermentation with lactose and xylose feeding to mitigate the glucose repression. Interestingly, the major location of produced 2′-FL by the engineered yeast can be changed using different culture media. While 72% of the produced 2′-FL was secreted when a complex medium was used, 82% of the produced 2′-FL remained inside the cells when a minimal medium was used. As yeast extract is already used as food and animal feed ingredients, 2′-FL enriched yeast extract can be produced cost-effectively using the 2′-FL-accumulating yeast cells.

Conversion↗

A Universal Design of Lithium Anode via Dynamic Stability Strategy for Practical All‐Solid‐State Batteries

Abstract All‐solid‐state Li‐metal battery (ASSLB) chemistry with thin solid‐state electrolyte (SSE) membranes features high energy density and intrinsic safety but suffers from severe dendrite formation and poor interface contact during cycling, which hampers the practical application of rechargeable ASSLB. Here, we propose a universal design of thin Li‐metal anode (LMA) via a dynamic stability strategy to address these issues. The ultra‐thin LMA (20 μm) is in situ constructed with uniform highly Li‐ion conductive solid‐electrolyte interphase and composite‐polymer interphase (CPI) via electroplating process. As a result, the passivation layer with poor Li‐ion conduction on Li anode can be dissolved and small surface resistance can be achieved due to the good compatibility of CPI to SSEs. The cycling of Li symmetric cell with Li 6 PS 5 Cl thin film electrolyte (<100 μm) shows a high critical current density of >2.0 mA cm −2 with excellent cycling stability at 1.0 mA cm −2 . The ASSLBs paring with Ni‐rich LiNi 0.6 Mn 0.2 Co 0.2 O 2 cathode demonstrated the feasibility of engineered LMA design by presenting good rate capability from 0.1 C to 1.0 C at room temperature, as well as long‐term cycling stability (81 % retention after 100 cycles). This work represents a general pathway to make thin dendrite‐free LMA available for high‐energy‐density ASSLBs.

Deng, Tao [Department of Chemical and Biomolecular↗

A Universal Design of Lithium Anode via Dynamic Stability Strategy for Practical All‐Solid‐State Batteries

Abstract All‐solid‐state Li‐metal battery (ASSLB) chemistry with thin solid‐state electrolyte (SSE) membranes features high energy density and intrinsic safety but suffers from severe dendrite formation and poor interface contact during cycling, which hampers the practical application of rechargeable ASSLB. Here, we propose a universal design of thin Li‐metal anode (LMA) via a dynamic stability strategy to address these issues. The ultra‐thin LMA (20 μm) is in situ constructed with uniform highly Li‐ion conductive solid‐electrolyte interphase and composite‐polymer interphase (CPI) via electroplating process. As a result, the passivation layer with poor Li‐ion conduction on Li anode can be dissolved and small surface resistance can be achieved due to the good compatibility of CPI to SSEs. The cycling of Li symmetric cell with Li 6 PS 5 Cl thin film electrolyte (<100 μm) shows a high critical current density of >2.0 mA cm −2 with excellent cycling stability at 1.0 mA cm −2 . The ASSLBs paring with Ni‐rich LiNi 0.6 Mn 0.2 Co 0.2 O 2 cathode demonstrated the feasibility of engineered LMA design by presenting good rate capability from 0.1 C to 1.0 C at room temperature, as well as long‐term cycling stability (81 % retention after 100 cycles). This work represents a general pathway to make thin dendrite‐free LMA available for high‐energy‐density ASSLBs.

Deng, Tao [Department of Chemical and Biomolecular↗

Quantum simulation of charge and exciton transfer in multi-mode models using engineered reservoirs

Quantum simulation enables studies of open-system dynamics in non-perturbative regimes by programming electronic, vibrational, and environmental interactions on comparable energy scales. Trapped ions offer this capability, combining spins, phonons, and tunable dissipation on one platform. We demonstrate an open-system quantum simulation of charge and exciton transfer in a multi-mode linear vibronic coupling model. Using tailored spin-phonon interactions with reservoir engineering, we emulate a system with two dissipative vibrational modes coupled to donor and acceptor sites and track its non-equilibrium dynamics. We continuously tune the system from the charge transfer regime to the vibrationally assisted exciton transfer regime and find that degenerate modes enhance transfer rates at large energy gaps, while non-degenerate modes activate pathways that reduce the energy-gap dependence. Thus, the presence of one additional vibration introduces interfering pathways and reshapes non-perturbative excitation transfer. Our results establish a scalable, hardware-efficient route to simulate vibronic processes with engineered environments.

74 ATOMIC AND MOLECULAR PHYSICS↗