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DOE OSTI2025

Smart culture medium optimization for recombinant protein production: Experimental, modeling, and AI/ML-driven strategies

Recombinant protein production (RPP) is central to biotechnology, where recombinant proteins are used as either end products or catalysts in the synthesis of chemicals, fuels, and materials. Among the major cost drivers, culture medium plays a pivotal role in determining protein yield and quality. This review presents a comprehensive perspective on the critical stages of “smart” culture medium optimization: planning, screening, modeling, optimization, and validation. In the planning stage, we examine the nutritional and energetic roles of medium components, including carbon, nitrogen, amino acids, salts, and trace metals, and their impacts on culture parameters such as pH, oxidative state, and osmolality. We highlight the variability in trace metal content due to water sources, culture vessels, and raw materials, which can substantially influence RPP. The screening stage covers Design of Experiments (DoE) approaches, assessing their theoretical basis, implementation, and limitations. For modeling, we describe methods that integrate experimental data to develop predictive models for smart medium formulation. Model-based optimization strategies can then be employed to select optimal media compositions for a given application. The validation stage aims to evaluate model predictions and provide feedback for model training and refinement. Finally, we survey mechanistic and artificial intelligence/machine learning (AI/ML)-driven models as integrated, transformational tools for predictive modeling of bioprocess conditions, nutrient availability, cellular metabolism, and protein quality, with the goal of optimizing culture media to enhance protein yields while reducing costs and environmental impact. We conclude by addressing the challenges of translating laboratory-scale medium optimization to industrial-scale settings and exploring future AI/ML-driven approaches that may overcome current bottlenecks and accelerate medium design for RPP. Overall, this review provides a unified framework for advancing smart medium design in RPP.

Artificial Intelligence/Machine Learning (AI/ML)↗

DOE OSTI2022

Novel cis-regulatory elements as synthetic promoters to drive recombinant protein expression from the Chlamydomonas reinhardtii nuclear genome

Eukaryotic green microalgae represent a sustainable, photosynthetic biotechnology platform for generating high-value products. The model green alga Chlamydomonas reinhardtii has already been used to generate high value bioproducts such as recombinant proteins and terpenoids. However, low, unstable, and variable nuclear transgene expression has limited the ease and speed of metabolic engineering and recombinant protein expression in this system. Here, novel genetic devices for transgene expression in C. reinhardtii have been developed by identifying cis-regulatory DNA elements capable of driving high transgene expression in C. reinhardtii promoters using de novo motif discovery informatics approaches. Thirteen putative motifs were synthesized as concatemers, linked to a common minimal basal promoter, and assayed for their activity to drive expression of a yellow fluorescent protein reporter gene. Following transformation of the vectors into C. reinhardtii by electroporation, in vivo measurements of yellow fluorescent protein expression by flow cytometry revealed that five of the DNA motifs analyzed displayed significantly higher reporter expression compared to the basal promoter control. Two of the concatemerized motifs, despite being much smaller minimal cis-regulatory elements, drove reporter expression at levels approaching that of the conventionally-used AR1 promoter. This analysis provides insight into C. reinhardtii promoter structure and gene regulation, and provides a new toolbox of cis-regulatory elements that can be used to drive transgene expression at a variety of expression levels.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Acceleration of Biexciton Radiative Recombination at Low Temperature in CdSe Nanoplatelets

Colloidal semiconductor nanocrystals offer bandgap tunability, high photoluminescence quantum yield, and colloidal processing of benefit to optoelectronics, however rapid nonradiative Auger recombination (AR) deleteriously affects device efficiencies at elevated excitation intensities. AR is understood to transition from temperature-dependent behavior in bulk semiconductors to temperature-independent behavior in zero-dimensional quantum dots (QDs) as a result of discretized band structure that facilitates satisfaction of linear momentum conservation. For nanoplatelets (NPLs), two-dimensional morphology renders prediction of photophysical behaviors challenging. Here, in this study, we investigate and compare the temperature dependence of excited-stated lifetime and fluence-dependent emission of CdSe NPLs and QDs. For NPLs, upon temperature reduction, biexciton lifetime surprisingly decreases (even becoming shorter lived than trion emission) and emission intensity increases nearly linearly with fluence rather than saturating, consistent with dominance of radiative recombination rather than AR. CdSe NPLs thus differ fundamentally from core-only QDs and foster increased utility of photogenerated excitons and multiexcitons at low temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

CdSe Magic-Size Clusters Deviate from Nanocrystal-Size Scalings for Ultrafast Intraband Relaxation and Auger Recombination

The cluster regime of colloidal semiconductor quantum dots (QDs) occupies an interesting space on the continuum from molecule to bulk material and allow the study of QD properties at extreme quantum confinement limits. For typical QDs, several size-dependent property trends are well established including intraband relaxation rates and universal scaling of Auger recombination with particle volume. Advances in synthesis now allow isolation of atomically precise semiconductor magic-size clusters (MCs), which offer experimental insight regarding how electronic structure changes with particle size in the ultrasmall limit. Here, we report intraband cooling and Auger recombination for several stable CdSe MCs as a function of particle size and observe deviation from QD response in the cluster regime. We additionally show optical signatures ascribed to transient disordering 2 that appear in the single exciton regime for MCs, which point to complexities regarding their implementation.

Auger recombination↗

DOE OSTI2023

Green Additive Limits Runaway Crystallinity in PM6:Y6 Organic Solar Cells but Causes Field-Independent Geminate Recombination

Solvent additives are well-established for improving device performance of organic solar cells by enhancing nanodomain phase separation and crystallization. However, optimum additive concentrations are typically at trace amounts with slight fluctuations causing runaway crystallinity that short the device and limit scale-up potential. Furthermore, we show that a nonhalogenated solvent additive 1-phenylnaphthalene (PN) can be used to optimize high-performance PM6:Y6 devices, but without runaway crystallinity even at concentrations 10× above the optimum. Our holistic analysis of device losses shows that PN increases photoabsorption while decreasing bimolecular recombination. However, above the optimum, charge generation is reduced due to field-independent geminate recombination of charge transfer states that overcomes the other benefits. Rotated Y6 crystallite orientation is a likely culprit, where the device electric field is ineffective at separating the charges. Despite this, device performance remains higher than that of traditional additives, indicating a route to avoiding the high sensitivity of performance to processing conditions.

14 SOLAR ENERGY↗

DOE OSTI2021

Impact of Photon Recycling, Grain Boundaries, and Nonlinear Recombination on Energy Transport in Semiconductors

Energy carrier transport and recombination in semiconductors can be directly monitored with optical microscopy, revealing key insights into fundamental photophysics and informs efficient optoelectronic device design. Oftentimes, energy transport is measured by monitoring a time-resolved expanding carrier profile after optical excitation under a focused laser beam. Although this approach has gained widespread adoption, the presence of competing dynamic processes, such as diffusion and photon recycling, has made it difficult to accurately extract and understand important semiconductor properties. Here, we develop and apply a new framework for modeling energy transport in both excitonic and free carrier semiconductors. Here, we demonstrate that processes such as nonlinear recombination and photon recycling can have a significant impact on the apparent energy carrier profiles, especially for excitonic materials with short radiative lifetimes. Additionally, we find that film microstructure can lead to unique transport profiles that strongly depends on material boundary behavior and the difference between feature size and diffusion length. Here, these findings provide a deeper understanding of energy transport in semiconducting materials and provide new strategies for the design and optimization of electronic and optoelectronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Strain dependence of Auger recombination in 3 μm GaInAsSb/GaSb type-I active regions

We differentiate the effect of strain induced by lattice-mismatched growth from strain induced by mechanical deformation on cubic nonradiative Auger recombination in narrow-gap GaInAsSb/GaSb quantum well (QW) heterostructures. The typical reduction in the Auger coefficient observed with lattice-mismatched growth appears to be due to the concomitant compositional change rather than the addition of strain, with implications for mid-IR semiconductor laser design. We induced a range of internal compressive strain in five samples from -0.90% to -2.07% by varying the composition during the growth and mechanically induced a similar range of internal strain in analogous quantum well membrane samples. We performed time-resolved photoluminescence and differential reflectivity measurements to extract the carrier recombination dynamics, taken at 300 K with carrier densities from 2.7 × 10 18 cm -3 to 1.4 × 10 19 cm -3 . We observed no change with strain in the cubic Auger coefficient of samples that were strained mechanically, but we did observe a trend with strain in samples that were strained by the QW alloy composition. Measured Auger coefficients ranged from 3.0 × 1 0 - 29 cm 6 s -1 to 3.0 × 1 0 - 28 cm 6 s -1 .

36 MATERIALS SCIENCE↗

DOE OSTI2021

Incorporation of GTR (generation–transport–recombination) in semiconductor simulations

With the emergence of phase change memory, where the devices experience extreme thermal gradients (~100 K/nm) during transitions between low and high resistive states, the study of thermoelectric effects at small scales becomes particularly relevant. We had earlier observed asymmetric melting of self-heated nano-crystalline silicon micro-wires, where current densities of ~10 7 A/cm 2 were forced through the wires by 1 μs, ~30 V pulses. The extreme asymmetry can be explained by the generation of considerable amount of minority carriers, transport under the electric field, and recombination downstream, a heat transfer process we termed as generation–transport–recombination, which is in opposite direction of the electronic-convective heat carried by the majority carriers. Here, we present a full semiconductor physics treatment of this carrier-lattice heat transport mechanism and the contribution of the minority carriers on the evolution of the melt–solid interface, which can be applied to various high-temperature electronic devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Tracking structural solvent reorganization and recombination dynamics following e – photoabstraction from aqueous I – with femtosecond x-ray spectroscopy and scattering

Here we present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I–(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L 1 -edge of the generated nascent iodine atoms (I 0 ) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine–electron recombination model without the need for a long-lived (I 0 :e–) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H 2 O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1 ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3 ps time constant for the mean iodine–oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I–) to an expanded cavity around I 0 with a more random orientation of the H 2 O molecules in a broadened first solvation shell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Inverted organic tandem solar cells with a charge recombination stack employing spatially confined p-type electrical doping

We report on the application of solution-based p-type electrical doping using 12-molybdophosphoric acid hydrate (PMA) to the fabrication of organic tandem solar cells. Such a doping approach leads to a spatially confined vertical doping profile down to a limited depth from the surface of polymer films, thus allowing the hole-collecting component of the charge recombination stack to be embedded in the photoactive layer of the bottom sub-cell. This simplifies the device architecture by removing the need for an extra dedicated hole-collecting layer. It is shown that this novel charge recombination stack comprising a PMA-doped bottom photoactive layer and a trilayer of Ag/AZO/PEIE is compatible with a solution-processed top photoactive layer. Here, the fabricated inverted organic tandem solar cells exhibit an open-circuit voltage that is close to the sum of the open-circuit voltages of the individual sub-cells, and a fill factor that is close to the better fill factor of the two sub-cells.

14 SOLAR ENERGY↗

DOE OSTI2023

Strain effects on Auger–Meitner recombination in silicon

We study the effects of compressive and tensile biaxial strain on direct and phonon-assisted Auger–Meitner recombination (AMR) in silicon using first-principles calculations. We find that the application of strain has a non-trivial effect on the AMR rate. For most AMR processes, the application of strain increases the AMR rate. However, the recombination rate for the AMR process involving two holes and one electron is suppressed by 38% under tensile strain. We further analyze the specific phonon contributions that mediate the phonon-assisted AMR mechanism, demonstrating the increased anisotropy under strain. In conclusion, our results indicate that the application of tensile strain increases the lifetime of minority electron carriers in p-type silicon and can be leveraged to improve the efficiency of silicon devices.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Improved VOC in RbF-Treated Cu(In,Ga)Se2 Solar Cells via Passivation of Recombination Centers

Cu(In,Ga)Se 2 (CIGS) solar cells have benefited in recent years from the addition of heavy alkali elements, such as Rb, which increase the solar cell open-circuit voltage ( V OC ). To investigate the source of this improvement, here, we compare samples with and without Rb to perform a quantitative comparison of electronic defects and minority carrier lifetime. Deep-level transient and optical spectroscopy measurements were performed on two sets of rubidium fluoride (RbF)-treated and untreated CIGS, and three distinct traps were identified regardless of RbF treatment. The RbF treatment was found to reduce the concentration of the H2 trap, which was previously found to act as a recombination center and is located preferentially at CIGS grain boundaries. Time-resolved photoluminescence measurements showed an increase in effective lifetime after RbF and nearly all lifetime improvement resulted from reductions in bulk recombination. The observed V OC improvement is well correlated with increased minority carrier lifetime and acceptor concentration, which led to increases and decreases in electron and hole quasi-Fermi levels, respectively.

Cu(In Ga)Se2 (CIGS)↗

DOE OSTI2020

Passivated Interfaces and Surface Recombination Velocities in Halide Perovskites

Surfaces and charge-extracting contacts remain major sources of non-radiative recombination loss; limiting the performance of perovskite PV compared to theoretical limits. We investigate mixed-cation mixed-halide perovskites and demonstrate that, with chemical surface passivation, they can achieve >4 μs minority carrier lifetimes, and >20% external PL quantum yields (PLQY), and nearly single-exponential decay kinetics. This high PLQY observed corresponds to ~97% of the Shockley-Queisser theoretical quasi-fermi level splitting, a first for MA-free mixed-cation mixed-halide compositions. The high PLQY and long PL lifetimes allow us to measure average surface recombination velocities (SRV) <10cm/s, with a champion low of ~1cm/s (a conservative estimate). We show how such improvements in SRV should lead to an absolute improvement in PCE of >4% even with the best of contact alignments. We investigate different MA-free high bandgap compositions, including bandgaps relevant for tandem applications (1.7-1.8eV), and demonstrate performance improvements across all these compositions with our surface passivation strategy. Lastly, using a combination of surface characterization techniques, we show Lewis base interactions of the passivating agent with the perovskite surfaces.

passivation↗

DOE OSTI2020

Radiative and Nonradiative Recombinations in Organic Radical Emitters: The Effect of Guest–Host Interactions

Radical-carrying organic molecules have received significant attention to bypass the issue related to harvesting triplet excitons in current light-emitting materials. While the computational efforts conducted so far have treated these radical emitters as isolated entities, in actual devices, they are embedded in a host matrix and subject to emitter–host interactions. In this study, by combining molecular dynamics simulations and density functional theory calculations, the impact of the host matrix on the optoelectronic performance of radical emitters is evaluated, taking as a representative example the (4-ncarbazolyl-2,6-dichlorophenyl)bis(2,4,6-trichlorophenyl)-methyl (TTM-3NCz) radical emitter dispersed in a 4,4-bis(carbazol-9-yl)biphenyl (CBP) host. A morphological analysis shows that steric effects around the radical centers, carried by the TTM electron-poor moieties of the emitters, disfavor π–π interactions with the host molecules, which leads to random intermolecular orientations around the TTM moieties. The 3NCz electron-rich moieties of the emitters, however, have much lesser spatial hindrance for intermolecular π–π stacking, which modulates the structural and electronic properties of the emitters in the host matrix. The influence of dynamic and static disorders on the radiative and nonradiative recombination processes is also investigated and it is found that the rates of nonradiative recombination are small, which opens the way to 100% internal quantum efficiency for the doublet-based emission process.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Retarded Charge-Carrier Recombination in Photoelectrochemical Cells from Plasmon-Induced Resonance Energy Transfer

N-type metal oxides such as hematite (α-Fe 2 O 3 ) and bismuth vanadate (BiVO 4 ) are promising candidate materials for efficient photoelectrochemical water splitting; however, their short minority carrier diffusion length and restricted carrier lifetime result in undesired rapid charge recombination. In this paper, a 2D arranged globular Au nanosphere (NS) monolayer array with a highly ordered hexagonal hole pattern (hereafter, Au array) is introduced onto the surface of photoanodes comprised of metal oxide films via a facile drying and transfer-printing process. Through plasmon-induced resonance energy transfer, the Au array provides a strong electromagnetic field in the near-surface area of the metal oxide film. The near-field coupling interaction and amplification of the electromagnetic field suppress the charge recombination with long-lived photogenerated holes and simultaneously enhance the light harvesting and charge transfer efficiencies. Consequently, an over 3.3-fold higher photocurrent density at 1.23 V versus reversible hydrogen electrode (RHE) is achieved for the Au array/α-Fe 2 O 3 . Furthermore, the high versatility of this transfer printing of Au arrays is demonstrated by introducing it on the molybdenum-doped BiVO 4 film, resulting in 1.5-fold higher photocurrent density at 1.23 V versus RHE. The tailored metal film design can provide a potential strategy for the versatile application in various light-mediated energy conversion and optoelectronic devices.

2D pattern array↗

DOE OSTI2021

Immobilization of transgenic plant cells towards bioprinting for production of a recombinant biodefense agent

Abstract Transgenic rice cells ( Oryza sativa ) producing recombinant butyrylcholinesterase (BChE) as a prophylactic/therapeutic against organophosphate nerve agent poisoning, cocaine toxicity, and neurodegenerative diseases like Alzheimer's were immobilized in a polyethylene glycol‐based hydrogel. The cells were sustained for 14 days in the semi‐solid matrix, undergoing a growth phase from days 0–6, a BChE production phase in sugar‐free medium from days 6–12, and a growth/recovery phase from days 12–14. Throughout this period, the cells maintained similar viability to those in suspension cultures and displayed analogous sugar consumption trends. The rice cells in the hydrogel also produced a significant amount of active BChE, comparable to the levels produced in liquid cultures. A considerable fraction of this BChE was secreted into the media, allowing for easier product separation. To the best of our knowledge, this proof‐of‐concept is the first report of immobilization of recombinant plant cells for continuous production of high‐value heterologous proteins. This work serves as a foundation for further investigation towards plant cell bioprinting and the development of a simple, efficient, robust, modular, and potentially field‐deployable bioreactor system for the manufacture of biologics.

Varma, Anika↗

DOE OSTI2021

Subacute safety assessment of recombinant Lactococcus lactis on the gut microbiota of male Sprague–Dawley rats

Abstract BACKGROUND Lactococcus lactis strain pGSMT/MG1363 is a genetically modified microorganism (GMM) that constitutively expresses human metallothionein‐I fusion protein to combine with intracellular lead. Unlike traditional probiotics, pGSMT/MG1363 lacks a history of safe use in food. Administration of microorganism could influence the gut microbial community and consequently confer health benefits or cause disadvantages to the host. To date, little has been done to assess the influence of recombinant strain pGSMT/MG1363 on the stability of gut microbiota. RESULTS Liver, testis and kidney sections of male Sprague–Dawley rats orally administered pGSMT/MG1363 for 6 weeks showed normal structure and no pathological damage. There were no adverse effects on the analyzed serum biochemical parameters between the pGSMT/MG1363 group and the MG1363 group. Principal coordinate analysis showed that, compared with the MG1363 group, the 6‐week‐old fecal gut microbiota of rats fed with pGSMT/MG1363 was not significantly different (Adonis, P = 0.802). pGSMT/MG1363 treatment for 6 weeks did not significantly change the relative abundance of gut microbiota at the phylum and genus levels in comparison with MG1363 treatment. CONCLUSION Compared to the non‐GM strain MG1363 group, administration of the recombinant strain pGSMT/MG1363 for 6 weeks showed no adverse effects on the analyzed physiological parameters and gut microbial compositions of male Sprague–Dawley rats. The results suggested that, in terms of gut microbiota stability, pGSMT/MG1363 could be considered as safe as MG1363, at least for short‐term intake. Further toxicological evaluations still need to be considered before drawing a definite conclusion concerning the safe use of pGSMT/MG1363. © 2021 Society of Chemical Industry.

Chen, Guowei↗

DOE OSTI2020

Understanding the adsorption and potential tear film stability properties of recombinant human lubricin and bovine submaxillary mucins in an in vitro tear film model

The wetting and adsorption properties for two glycoproteins, recombinant human lubricin and bovine submaxillary mucins (BSM) were evaluated on hydrophilic and hydrophobic glass dome surfaces in a simplified in vitro tear film model. Herein, we show that both recombinant human lubricin (rh-lubricin) and BSM solutions render surfaces hydrophilic and when the fluid films reach 500 nm or less, the fluids resist evaporation-driven breakup through a volumetric flux across the surface, which we believe is due to evaporation-driven solutocapillary flows. rh-Lubricin was able to maintain a wet film without spontaneous breakup for longer periods of time than BSM at lower concentrations, which we attribute to differences in adsorption properties, measured by QCM-D, that result from surface charge and structural differences (confirmed by zeta potential, DLS, and SAXS measurements).

60 APPLIED LIFE SCIENCES↗