Engineering topics

Chan, Emory M. [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Molecular Foundry] (ORCID:0000000256550146)

Publications and source records attributed to Chan, Emory M. [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Molecular Foundry] (ORCID:0000000256550146).

7 records

All sources NASA NTRS DOE OSTI

DOE OSTI2026

CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization

Plant roots release a wide array of metabolites into the rhizosphere, shaping microbial communities and their functions. While metagenomics has expanded our understanding of these communities, little is known about the physiology of their members in host environments. Transcriptome analysis via RNA sequencing is a common approach to learning more, but its use has been challenging because of low bacterial biomass and interference from plant RNA. To overcome this, we developed a randomly-barcoded promoter-library insertion sequencing (RB-PI-seq) combined with chassis-independent recombinase-assisted genome engineering (CRAGE). Using Pseudomonas simiae WCS417 as a model rhizobacterium, this method enabled targeted amplification of barcoded transcripts, bypassing plant RNA interference and allowing measurement of thousands of promoter activities during Arabidopsis root colonization. Our analysis revealed temporally resolved transcriptional regulation, including those associated with cell growth, chemotaxis, plant immune suppression, biofilm formation, and stress responses, reflecting the coordinated physiological adaptation to the root environment. Additionally, we discovered that transcriptional activation of xanthine dehydrogenase and a lysozyme inhibitor is crucial for evading plant immune systems. This framework is scalable to other bacterial species and provides new opportunities for understanding rhizobacterial gene regulation in native environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Automated Nanocrystal Synthesis: Lessons from 25 Years of Robots, Microfluidics, and Machine Learning

Here, this perspective highlights the evolution of techniques for automating the synthesis of colloidal nanocrystals. Over the past 25 years, microfluidic reactors and robotic workflows have been developed to enhance the reproducibility of nanocrystal synthesis, facilitate rapid screening of reaction conditions, optimize material properties, and perform multistep syntheses of high-quality nanoparticles with complex heterostructures. Modern automated systems are now valued for their ability to generate robust data sets for validating physical models, supporting chemical mechanisms, training machine learning models, and for directing autonomous experimentation. We discuss the early challenges and limitations of these technologies and present key lessons for effectively utilizing automated and ML-guided tools to accelerate nanocrystal discovery for the next 25 years.

Nanocrystals↗

DOE OSTI2025

Gradient-based optimization of complex nanoparticle heterostructures enabled by deep learning on heterogeneous graphs

Applications of deep learning (DL) to design nanomaterials are hampered by a lack of suitable data representations and training data. Here, in this study, we report efforts to overcome these limitations and leverage DL to optimize the nonlinear optical properties of core–shell upconverting nanoparticles (UCNPs). UCNPs, which have applications in fields such as biosensing, super-resolution microscopy and three-dimensional printing, can emit visible and ultraviolet light from near-infrared excitations. We report a large-scale dataset of UCNP emission spectra based on accurate but expensive kinetic Monte Carlo simulations (N > 6,000) and use these data to train a heterogeneous graph neural network using a physically motivated representation of UCNP nanostructure. Applying gradient-based optimization on the trained graph neural network, we identify structures with 6.5× higher predicted emission under 800-nm illumination than any UCNP in our training set. Our work reveals design principles for UCNP heterostructures and presents a roadmap for DL-based inverse design of nanomaterials.

Sivonxay, Eric [Lawrence Berkeley National Laborat↗

DOE OSTI2025

Intrinsic optical bistability of photon avalanching nanocrystals

Optically bistable materials respond to a single input with two possible optical outputs, contingent on excitation history. Such materials would be ideal for optical switching and memory, but the limited understanding of intrinsic optical bistability (IOB) prevents the development of nanoscale IOB materials suitable for devices. Here we demonstrate IOB in Nd 3+ -doped KPb 2 Cl 5 avalanching nanoparticles, which switch with high contrast between luminescent and non-luminescent states, with hysteresis characteristic of bistability. Here we elucidate a non-thermal mechanism in which IOB originates from suppressed non-radiative relaxation in Nd 3+ ions and from the positive feedback of photon avalanching, resulting in extreme, >200th-order optical nonlinearities. The modulation of laser pulsing tunes the hysteresis widths, and dual-laser excitation enables transistor-like optical switching. This control over nanoscale IOB establishes avalanching nanoparticles for photonic devices in which light is used to manipulate light.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Direct Observation of Morphological and Chemical Changes during the Oxidation of Model Inorganic Ligand-Capped Particles

Functionalization and volatilization are competing reactions during the oxidation of carbonaceous materials and are important processes in many different areas of science and technology. Here, we present a combined ambient pressure X-ray photoelectron spectroscopy (APXPS) and grazing incidence X-ray scattering (GIXS) investigation of the oxidation of oleic acid ligands surrounding NaYF 4 nanoparticles (NPs) deposited onto SiO x /Si substrates. While APXPS monitors the evolution of the oxidation products, GIXS provides insight into the morphology of the ligands and particles before and after the oxidation. Our investigation shows that the oxidation of the oleic acid ligands proceeds at O 2 partial pressures of below 1 mbar in the presence of X-rays, with the oxidation eventually reaching a steady state in which mainly CH x and –COOH functional groups are observed. The scattering data reveal that the oxidation and volatilization reaction proceeds preferentially on the side of the particle facing the gas phase, leading to the formation of a chemically and morphologically asymmetric ligand layer. This comprehensive picture of the oxidation process could be obtained only by combining the X-ray scattering and APXPS data. The investigation presented here lays the foundation for further studies of the stability of NP layers in the presence of reactive trace gases and ionizing radiation and for other nanoscale systems where chemical and morphological changes happen simultaneously and cannot be understood in isolation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Automated Gold Nanorod Spectral Morphology Analysis Pipeline

The development of a colloidal synthesis procedure to produce nanomaterials with high shape and size purity is often a time-consuming, iterative process. This is often due to quantitative uncertainties in the required reaction conditions and the time, resources, and expertise intensive characterization methods required for quantitative determination of nanomaterial size and shape. Absorption spectroscopy is often the easiest method for colloidal nanomaterial characterization. However, due to the lack of a reliable method to extract nanoparticle shapes from absorption spectroscopy, it is generally treated as a more qualitative measure for metal nanoparticles. This work demonstrates a gold nanorod (AuNR) spectral morphology analysis tool, called AuNR-SMA, which is a fast and accurate method to extract quantitative structural information from colloidal AuNR absorption spectra. To demonstrate the practical utility of this model, we apply it to three distinct applications. First, we demonstrate this model's utility as an automated analysis tool in a high-throughput AuNR synthesis procedure by generating quantitative size information from optical spectra. Second, we use the predictions generated by this model to train a machine learning model to predict the resulting AuNR size distributions under specified reaction conditions. Third, we apply this model to spectra extracted from the literature where no size distributions are reported and impute unreported quantitative information on AuNR synthesis. This approach can potentially be extended to any other nanocrystal system where absorption spectra are size dependent, and accurate numerical simulation of absorption spectra is possible. In addition, this pipeline could be integrated into automated synthesis apparatuses to provide interpretable data from simple measurements, help explore the synthesis science of nanoparticles in a rational manner, or facilitate closed-loop workflows.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Advances in the photon avalanche luminescence of inorganic lanthanide-doped nanomaterials

Photon avalanche (PA)—where the absorption of a single photon initiates a ‘chain reaction’ of additional absorption and energy transfer events within a material—is a highly nonlinear optical process that results in upconverted light emission with an exceptionally steep dependence on the illumination intensity. Over 40 years following the first demonstration of photon avalanche emission in lanthanide-doped bulk crystals, PA emission has been achieved in nanometer-scale colloidal particles. The scaling of PA to nanomaterials has resulted in significant and rapid advances, such as luminescence imaging beyond the diffraction limit of light, optical thermometry and force sensing with (sub)micron spatial resolution, and all-optical data storage and processing. In this review, we discuss the fundamental principles underpinning PA and survey the studies leading to the development of nanoscale PA. Finally, we offer a perspective on how this knowledge can be used for the development of next-generation PA nanomaterials optimized for a broad range of applications, including mid-IR imaging, luminescence thermometry, (bio)sensing, optical data processing and nanophotonics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗