Research Report: Phage Display Technology for Heavy Rare Earth Element Separation: A Comprehensive Analysis of Enhanced Selectivity and Environmental Sustainability

Date: 2025-12-03

Executive Summary

This report synthesizes extensive research to evaluate the extent to which phage display technology and genetically engineered bacteriophages can enhance the selectivity and environmental sustainability of separating heavy rare earth elements (HREEs) compared to traditional solvent extraction (SX) methods. The findings indicate that this emerging biotechnology represents not an incremental improvement but a transformative paradigm shift, offering profound advantages in both performance and ecological impact.

Key Findings on Selectivity: Phage display technology fundamentally surpasses the selectivity of traditional solvent extraction. Where SX relies on small, bulk thermodynamic differences requiring hundreds of energy-intensive stages, phage display leverages highly specific, evolved molecular recognition. Through a process of biopanning, peptides are identified and engineered onto the surface of bacteriophages to create binders with exceptional affinity and specificity for target HREE ions. This selectivity is driven by a combination of factors: (1) the precise chelation of HREEs by specific amino acid residues, primarily aspartic and glutamic acid; (2) the formation of three-dimensional binding pockets tailored to the unique ionic radii and coordination geometries of HREEs, effectively exploiting the lanthanide contraction; and (3) a powerful "avidity effect," where the high-density, multivalent display of thousands of peptides on the phage surface dramatically amplifies overall binding strength. Quantitatively, this approach has yielded separation factors up to 3.4, a level of discrimination that promises to simplify separation cascades, increase product purity, and reduce processing costs.

Key Findings on Environmental Sustainability: The environmental advantages of phage-based separation are profound and systemic. The technology operates in aqueous solutions, entirely eliminating the need for the vast quantities of volatile, toxic, and flammable organic solvents that are central to SX. This fundamentally mitigates the generation of hazardous waste streams, including contaminated wastewater, solvent residues, and toxic sludge. The incumbent process can generate up to 2,000 tonnes of toxic and radioactive tailings for every tonne of finished rare earth oxides; phage-based systems replace this with manageable and often biodegradable biological waste. Furthermore, the process is significantly more energy-efficient. It replaces the energy-intensive solvent distillation and recovery stages of SX—which can account for over 50% of the total process energy—with simple, low-energy pH or temperature shifts to release the bound HREEs. The phage-based biosorbents have demonstrated remarkable robustness and reusability over multiple cycles with no loss of function, aligning with the principles of a circular economy.

Scalability and Future Outlook: While still transitioning from laboratory to industrial scale, a clear and viable pathway for implementation exists. The production of engineered phages leverages established, inexpensive, and scalable bacterial fermentation technology. The successful large-scale application of biomining in the copper and gold industries provides a strong precedent for the commercial viability of this approach. Although challenges related to optimizing large-scale production, managing biological waste streams, and ensuring long-term operational stability remain, the technology has been successfully demonstrated on complex, real-world feedstocks like acid mine drainage.

Conclusion: Genetically engineered bacteriophages offer the potential to extensively enhance both the selectivity and environmental sustainability of HREE separation. By replacing a brute-force, chemically intensive process with an elegant, bio-inspired molecular engineering approach, phage display technology presents a credible and compelling solution to the critical economic and ecological challenges facing the rare earth element supply chain, paving the way for a cleaner, more efficient, and sustainable future for critical materials recovery.

Introduction

Heavy rare earth elements (HREEs)—including terbium, dysprosium, europium, and ytterbium—are indispensable components of modern high-technology applications, from permanent magnets in electric vehicles and wind turbines to phosphors in advanced electronics and lasers in medical devices. As global demand for these technologies accelerates, the security and sustainability of the HREE supply chain have become matters of significant economic and geopolitical concern.

The current global supply of HREEs is dominated by a production paradigm that is both technologically challenging and environmentally damaging. The incumbent industrial method, solvent extraction (SX), is a chemically intensive hydrometallurgical process. The fundamental challenge lies in the remarkable chemical similarity of the lanthanide series elements. Due to the "lanthanide contraction," adjacent HREEs have nearly identical ionic radii and chemical properties, making their separation a formidable task. Consequently, SX requires vast, complex industrial plants with hundreds of sequential mixer-settler stages, consuming enormous quantities of organic solvents, strong acids, and energy. The process generates a cascade of hazardous waste, including volatile organic compounds (VOCs), acidic wastewater laden with heavy metals, and vast quantities of toxic and often radioactive tailings.

This unsustainable model has created an urgent need for disruptive innovations that can provide a cleaner, more efficient, and more selective alternative. In this context, biotechnology, and specifically phage display technology, has emerged as a highly promising frontier. This approach repurposes biological systems—bacteriophages, which are viruses that infect bacteria—as highly customizable and selective separation agents. By genetically engineering these viruses to display specific HREE-binding peptides on their surfaces, researchers can create "biomining" platforms that selectively capture target elements from complex mixtures with unparalleled precision.

This comprehensive research report synthesizes the findings from an expansive investigation into this technology. It aims to answer the central research query: To what extent can phage display technology and genetically engineered bacteriophages enhance the selectivity and environmental sustainability of separating heavy rare earth elements compared to traditional solvent extraction methods? The report provides a detailed comparative analysis, delving into the fundamental separation mechanisms, molecular architecture of selectivity, environmental impact profiles, and the practical scalability of both the incumbent and the emerging biotechnological approaches.

Key Findings

This section consolidates the principal findings from the research, organized thematically to provide a comprehensive overview of the comparative advantages and operational principles of phage-based HREE separation.

1. The Incumbent Technology: Inefficiencies and Environmental Burdens of Solvent Extraction

• Low Intrinsic Selectivity: SX relies on small differences in partition coefficients between an aqueous phase and an organic extractant. Due to the chemical similarity of HREEs, single-stage separation is minimal, necessitating complex cascades of hundreds of mixer-settler units to achieve high purity.
• Massive Chemical and Resource Consumption: The process is defined by its high consumption of petrochemical-derived reagents, including vast quantities of organic solvents (e.g., kerosene), chemical extractants (e.g., D2EHPA, PC88A), and strong acids (hydrochloric, sulfuric) for stripping and pH control.
• Severe Environmental Impact: SX generates multiple hazardous waste streams. These include large volumes of acidic, metal-laden wastewater; used organic solvents that contribute to air pollution as VOCs; and toxic sludge. The associated mining and leaching processes can produce up to 2,000 tonnes of toxic and radioactive tailings per tonne of REE oxides.
• High Energy Demand: The operational footprint is energy-intensive, driven by the pumping of large liquid volumes through hundreds of stages, heating, chemical manufacturing, and, critically, the energy required for solvent recovery and recycling via distillation, which can account for over 50% of the plant's total energy budget.
• Operational Complexity and Inefficiency at Low Concentrations: The massive physical footprint, high capital expenditure, and operational complexity make SX economically unviable for processing low-grade ores or recovering HREEs from dilute secondary sources like industrial wastewater and electronic waste.

2. The Biotechnological Alternative: Principles of Phage Display Separation

• Genetically Encoded Specificity: Phage display repurposes bacteriophages (typically M13) as a separation platform. By fusing DNA encoding a specific peptide to a phage coat protein gene, the phage is engineered to "display" this peptide on its surface, creating a direct link between the binding function (phenotype) and the genetic code (genotype).
• Biopanning for Targeted Binders: Through a process called biopanning, vast libraries containing billions of phages with unique peptide sequences are screened against a target HREE ion. Iterative cycles of binding, washing, elution, and amplification enrich for phages that display peptides with the highest affinity and specificity for the target, effectively using directed evolution to create custom separation agents.
• Aqueous-Based Operation: The entire process—binding, separation, and elution—occurs in aqueous solutions, fundamentally eliminating the need for organic solvents and operating under mild temperature and pressure conditions.
• Tunable and Reversible Binding: The binding of HREEs to the engineered peptides is strong yet reversible. The captured elements can be released (eluted) by simple, non-destructive environmental triggers, most commonly a shift in pH or the introduction of a benign competing ligand like citrate. This allows for the recovery of a concentrated HREE product and the regeneration of the phage for reuse.

3. Enhanced Selectivity Through Advanced Molecular Recognition

• Specific Amino Acid Chelation: Selectivity is primarily driven by the specific amino acid composition of the displayed peptides. Negatively charged residues, particularly aspartic acid (Asp) and glutamic acid (Glu), act as powerful chelators, forming stable coordination bonds with trivalent HREE ions.
• Tailored 3D Binding Pockets: Peptides fold into specific three-dimensional conformations, creating binding pockets that are sterically and electronically complementary to the target ion. This allows for fine-tuned discrimination based on the subtle differences in ionic radii across the lanthanide series (the lanthanide contraction), enabling preferential binding for HREEs over LREEs.
• The Avidity Effect as a Force Multiplier: The high-density display of peptides on the phage surface (e.g., ~3,300 copies of the pVIII protein on M13 phage) creates a powerful multivalent binding effect known as avidity. The cumulative strength of thousands of simultaneous weak interactions results in an exceptionally strong and stable overall bond, enabling efficient capture even from dilute solutions.
• Quantifiable Improvement in Performance: Bio-inspired peptides have demonstrated superior separation factors (SFs) for HREEs, with selectivity values reaching up to 3.4. This level of discrimination is comparable to or exceeds that of many industrial extractants and is achieved through a fundamentally more precise mechanism.

4. Transformative Improvements in Environmental Sustainability

• Drastic Reduction in Hazardous Waste: By replacing petrochemical solvents and harsh acids with a recyclable, water-based biological system, phage technology drastically reduces or eliminates the generation of toxic liquid waste, air pollution, and contaminated sludge.
• Lower Energy Profile: The technology avoids the highly energy-intensive solvent recovery and distillation steps inherent to SX. The operational energy requirements are significantly lower, primarily involving mixing and simple pH adjustments or mild heating. Related biotechnologies have shown potential energy savings of up to 87% compared to conventional hydrometallurgy.
• Process Simplicity and Reusability: The phage-based process can be conceptually simple, requiring minimal equipment like a mixing tank. The phages have proven to be robust and highly reusable, capable of undergoing at least five adsorption-desorption cycles with no significant loss in binding capacity or selectivity, which is critical for economic viability and waste minimization.
• Enabling a Circular Economy: The high affinity and selectivity of the technology make it particularly effective for recovering HREEs from low-concentration and unconventional sources, including acid mine drainage, industrial wastewater, and e-waste leachates. This opens new, sustainable pathways for "urban mining" and reducing reliance on primary extraction.

5. Practical Viability and Pathway to Industrial Scale

• Proven Efficacy in Real-World Conditions: Engineered phages have been successfully demonstrated to selectively bind and recover HREEs from complex, real-world feedstocks such as acid mine drainage, proving their robustness and specificity in the presence of numerous competing metal ions.
• Scalable and Cost-Effective Production: The production of the core separation agent—the bacteriophage—leverages well-established, large-scale fermentation technology using common bacterial hosts like E. coli. This biological replication is described as easy and inexpensive, offering a significant cost advantage over the synthesis of complex organic chemical extractants.
• Industrial Precedent: Large-scale biomining is not a novel concept. Biological methods already account for a significant portion (e.g., 20%) of global copper and gold production, providing a powerful industrial precedent and de-risking the development pathway for phage-based REE separation.
• Identified Challenges: Despite the promising outlook, hurdles to industrial-scale implementation remain. These include optimizing the cost-effectiveness of large-scale phage production and purification, developing efficient methods for managing biological waste streams (e.g., spent culture media, endotoxins), and ensuring the long-term stability and performance of the phage materials under continuous industrial operating conditions.

Detailed Analysis

This section provides a deeper exploration of the key findings, contrasting the operational paradigms of solvent extraction and phage display, dissecting the molecular mechanisms of selectivity, evaluating the environmental impact, and assessing the prospects for industrial-scale implementation.

1. A Comparative Analysis of Separation Paradigms: Bulk Chemistry vs. Molecular Engineering

The fundamental difference between solvent extraction and phage display lies in their core separation philosophy. SX is a paradigm of bulk chemical equilibrium, while phage display represents a paradigm of programmed molecular engineering.

Solvent Extraction: A "Brute Force" Approach The SX process for HREEs is a testament to brute-force chemical engineering. It exploits minute differences in the Gibbs free energy of formation of REE-extractant complexes, which translate into slightly different partition coefficients between the aqueous and organic phases. To amplify this minimal separation factor, the process is repeated hundreds of times in a counter-current cascade. Each of the three main stages—extraction, scrubbing, and stripping—is an equilibrium-limited process.

• Extraction: Relies on general chelation by organic ligands (e.g., D2EHPA), which are not specifically designed for one HREE over its neighbor. Selectivity is a weak function of ionic radius and basicity.
• Scrubbing: Attempts to refine the loaded organic phase by washing away impurities, but this often leads to some loss of the target element.
• Stripping: Uses strong acids to break the REE-extractant bond, a chemically harsh process that requires subsequent regeneration of the solvent.

This reliance on amplifying small thermodynamic differences is the direct cause of SX's major liabilities: the immense physical and capital costs of hundreds of mixer-settler units, the massive consumption of chemicals and energy, and the generation of large waste streams.

Phage Display: An "Intelligent Design" Approach Phage display shifts the paradigm from manipulating bulk phases to programming specific molecular interactions. The separation agent is not a general-purpose chelator but a highly evolved, specific binder.

• Pre-Programmed Selectivity: The selectivity is genetically encoded into the peptide sequence before the separation process begins. The biopanning process acts as a form of directed evolution, selecting for peptides that are already highly optimized for the target HREE.
• High-Affinity Binding: The combination of specific chemical interactions and the avidity effect leads to extremely high binding affinities. This means that separation is not an equilibrium-limited process in the same way as SX. Binding can be driven to completion much more effectively, even at very low HREE concentrations where SX would fail.
• Controlled Release: The release mechanism is also programmed. The peptide-ion bond is designed to be sensitive to specific environmental triggers, like a change in pH. This allows for a controlled, gentle release of the product and regeneration of the sorbent without the need for harsh chemicals or high energy input.

This molecular engineering approach allows for a process that is inherently more precise, efficient, and requires far fewer stages, leading to a drastically smaller physical and environmental footprint.

2. The Molecular Architecture of HREE Selectivity

The remarkable selectivity of engineered phages is not a black box phenomenon; it is rooted in well-understood principles of biochemistry and coordination chemistry.

• The Dominance of Acidic Residues: The primary binding interaction is electrostatic and coordinative, driven by the carboxylate side chains of aspartic acid (Asp) and glutamic acid (Glu). These negatively charged groups act as hard Lewis bases, perfectly suited to coordinate with the hard Lewis acid character of trivalent HREE cations (Ln³⁺). Peptides derived from the natural REE-binding protein lanmodulin, which features EF-hand loop motifs rich in these acidic residues, exhibit picomolar dissociation constants—a level of affinity far beyond synthetic extractants.

• The Importance of 3D Structure and Pre-organization: Beyond simple charge interactions, the three-dimensional structure of the peptide is critical.

  • Binding Pockets: The peptide chain folds to create a specific binding pocket. The size and geometry of this pocket can be evolutionarily tuned to preferentially accommodate the smaller ionic radii of HREEs, a direct exploitation of the lanthanide contraction for achieving intra-lanthanide separation. High-affinity sites often adopt a specific coordination geometry, such as a pentagonal bipyramidal structure involving seven oxygen atoms, which discriminates against other metal ions with different coordination preferences.
  • Peptide Cyclization: Structural pre-organization significantly enhances affinity. For example, the peptide TB2 (ACVDWNNDGWYEGDECA) contains two cysteine residues that form a disulfide bond, cyclizing the peptide. This structural constraint reduces the entropic penalty of binding and optimally positions the binding residues, resulting in a 100-fold increase in affinity for Terbium (Tb³⁺) and achieving a nanomolar dissociation constant.

• The Avidity Effect as a Selectivity Amplifier: A single phage particle acts as a high-density scaffold. With ~3,300 copies of the pVIII coat protein, an M13 phage engineered to display a lanthanide-binding peptide (LBP) presents thousands of "molecular claws" simultaneously. While a single peptide-ion interaction might be reversible, the probability of thousands of bonds dissociating at the exact same moment is infinitesimally small. This multivalent effect, or avidity, creates an immensely stable phage-HREE complex, ensuring that once an ion is captured, it is held tightly. This robust binding is what enables the efficient recovery of HREEs from dilute and complex solutions, a key weakness of traditional SX.

3. A Paradigm Shift in Environmental Sustainability

The transition from a petrochemical-based process to a bio-based one results in a systemic improvement in environmental performance across the entire lifecycle.

Comparison of Waste Streams and Reagent Profiles

Feature	Traditional Solvent Extraction (SX)	Phage-Based Separation
Primary Reagent	Petrochemical-derived organic solvents (kerosene) and chemical extractants (D2EHPA, phosphonic acids)	Genetically engineered bacteriophages (biological, self-replicating)
Process Medium	Immiscible organic and aqueous phases	Aqueous solutions (water-based)
Elution/Stripping Agent	Strong mineral acids (e.g., HCl, H₂SO₄)	Mild pH change (e.g., pH 5 -> 2) or benign ligands (e.g., low-concentration citrate)
Primary Waste Streams	Volatile Organic Compounds (VOCs), acidic wastewater, spent solvents, toxic sludge, radioactive tailings	Spent bacterial culture media (biodegradable), residual biological components (non-toxic)
Reagent Recyclability	Energy-intensive distillation with degradation and loss	High; simple, low-energy regeneration for multiple cycles with minimal loss of function

Energy Footprint Analysis The energy profile of the two technologies is starkly different. SX is a highly energy-intensive process due to the continuous pumping of massive liquid volumes, heating for certain stages, and the enormous energy cost of solvent recovery via distillation. It has been estimated that this final step alone can consume over half of the entire plant's energy budget.

Phage-based separation operates at or near ambient temperature and pressure. The most significant energy advantage comes from the elimination of solvent recovery. The regeneration of the phage biosorbent via a simple pH shift is a low-energy process. While a full lifecycle analysis must account for the energy required for phage fermentation, the operational energy savings are expected to be substantial. Related biotechnological approaches for metal recovery have demonstrated energy consumption reductions of up to 87% (600 kWh/tonne) compared to conventional hydrometallurgy.

Enabling a Sustainable Circular Economy The high affinity of engineered phages makes them uniquely suited for "scavenging" valuable HREEs from sources that are inaccessible to SX. This includes:

• Industrial Effluents: Capturing parts-per-million concentrations of HREEs from manufacturing wastewater.
• Acid Mine Drainage: Selectively recovering HREEs from contaminated water at mining sites, simultaneously performing remediation.
• E-waste Recycling: Providing a highly selective tool for extracting HREEs from the complex chemical "soup" generated by leaching discarded electronics. By turning these waste streams into valuable resources, phage technology is a key enabler of a circular economy for critical materials, reducing the need for destructive primary mining.

4. Industrial Scalability: Prospects and Challenges

The transition from a laboratory proof-of-concept to an industrial reality is the ultimate test for any new technology. The research indicates a credible, albeit challenging, path forward for phage-based HREE separation.

The Foundation for Scale-Up The scalability of the technology is built on several strong foundations:

1. Established Production Methods: The M13 bacteriophage infects E. coli, one of the most well-understood and widely used organisms in industrial biotechnology. Decades of experience in large-scale fermentation mean that the production of the phage feedstock can be achieved easily and inexpensively at an industrial scale.
2. High Adsorption Capacity: The high-density display of binding peptides on the phage surface results in a material with a very high binding capacity per unit mass. This means a smaller volume of the biosorbent is needed to process a given amount of HREE-containing solution, improving process economics.
3. Industrial Precedent of Biomining: The global mining industry already relies on biotechnology. Approximately 20% of the world's copper and a significant fraction of its gold are produced using microbial leaching processes. This history demonstrates that biological systems can be robustly deployed at massive scales in harsh mining environments, providing a powerful analogue and de-risking the development of phage-based systems.

Remaining Hurdles and Future Research Directions Despite these advantages, significant engineering challenges must be addressed for widespread adoption:

• Cost-Effective Downstream Processing: While phage production via fermentation is inexpensive, the subsequent purification and immobilization of phages onto a solid support material can be costly. Research into simpler, more efficient methods for creating stable, reusable phage-based materials is critical.
• Biological Waste Management: While far more benign than chemical waste, large-scale fermentation will produce significant volumes of spent culture media and bacterial biomass. Efficient strategies for treating or valorizing this biological waste will be necessary for a truly sustainable process.
• Long-Term Stability and Biofouling: The performance and stability of the engineered phages must be validated over thousands of hours of continuous operation in industrial conditions. The potential for biofouling, where other microorganisms colonize the biosorbent material, must also be addressed.
• System Integration: Integrating a phage-based separation unit into a broader hydrometallurgical flowsheet—from initial ore leaching to final product precipitation—requires careful process design and optimization.

Discussion

The synthesis of the available research reveals a compelling case for phage display technology as a disruptive force in the HREE sector. The extent of its potential enhancement over solvent extraction is not merely incremental but systemic, touching every aspect of the separation process from molecular efficiency to environmental stewardship.

A critical insight is the interconnectedness of selectivity and sustainability. The superior selectivity achieved through molecular engineering is the direct driver of the technology's environmental benefits. Because the phages can target specific HREEs with high precision, the need for a long, repetitive cascade of separation stages is dramatically reduced. A shorter process inherently consumes less energy, requires a smaller physical footprint, uses fewer reagents, and generates less waste. This contrasts with SX, where low selectivity is the root cause of its massive environmental and economic costs.

Furthermore, the technology's potential extends beyond simply replacing existing SX plants for primary ore processing. Its unique ability to function effectively in dilute and complex solutions positions it as a key technology for diversifying the HREE supply chain. By enabling the economic recovery of HREEs from secondary sources like e-waste and industrial effluents, it can help mitigate the geopolitical risks associated with a highly concentrated primary supply chain and reduce the immense environmental burden of new mining operations. This represents a shift from a linear "take-make-dispose" model to a more resilient and sustainable circular one.

The platform nature of phage display is another significant implication. The same fundamental techniques of library generation and biopanning can be applied to identify peptides that bind to other critical materials, such as lithium, cobalt, platinum group metals, or even to remediate toxic metals like lead and cadmium. This presents phage display not as a single-purpose solution but as a versatile platform for advanced materials recovery and environmental management.

While the engineering challenges for industrial-scale implementation are non-trivial, they are not insurmountable. The path has been paved by the successful scaling of other biotechnologies in adjacent industries. The trajectory suggests that with continued research and development in bioprocess engineering, materials science, and genetic optimization, phage-based separation will become an economically competitive and technologically superior alternative to solvent extraction.

Conclusions

In direct response to the research query, the evidence overwhelmingly indicates that phage display technology and genetically engineered bacteriophages can enhance the selectivity and environmental sustainability of separating heavy rare earth elements to a profound and transformative extent when compared to traditional solvent extraction methods.

The enhancement in selectivity is achieved by shifting from a process governed by bulk chemical properties to one directed by specific, pre-programmed molecular recognition. The synergistic combination of tailored amino acid binding pockets, structural pre-organization of peptides, and the powerful avidity effect from multivalent display allows for a level of discrimination between chemically similar HREEs that is difficult, costly, and inefficient to achieve with conventional extractants. This promises higher purity products from simplified, shorter, and more cost-effective processing flowsheets.

The enhancement in environmental sustainability is systemic and multi-faceted. The technology fundamentally redesignes the separation process along the principles of green chemistry and the bioeconomy. It replaces a hazardous, petrochemical-dependent system with a renewable, water-based, and recyclable biological one. This substitution drastically reduces the consumption of toxic reagents, eliminates the generation of the most harmful waste streams, and significantly lowers the overall energy footprint of HREE production. By enabling the recovery of critical materials from waste, it pioneers a path toward a sustainable, circular economy for HREEs.

While solvent extraction remains the mature, incumbent technology, its future is constrained by its inherent inefficiencies and significant environmental liabilities. Genetically engineered bacteriophages represent a technologically and environmentally superior trajectory. Although further engineering and scale-up optimization are required, phage display technology is no longer a theoretical curiosity but a validated and highly promising platform poised to revolutionize the critical materials industry, offering a viable path to a secure, efficient, and environmentally responsible supply chain for heavy rare earth elements.

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