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At least 73 records · Page 4

Biomaniac

Los Alamos National Laboratory researchers are developing a machine-learning based algorithm to revolutionize how biopolymers are designed and optimized. BioManIAC is a software platform that fills the gaps in data to gain insight into new potential polymer properties without making and testing them. Polymer engineers are able to use BioManIAC software to extrapolate and tune new biopolymer properties that allow the user to create small smart libraries, rather than largescale trial and error testing. This targeted design is expected to improve both time to market and R&D expenditure, as well as the resulting mechanical properties of biopolymers, enabling for more direct competition with traditional petroleum-based polymers. Los Alamos is seeking partners to further validate our software platform.

36 MATERIALS SCIENCE↗

Quantifying market volume sensitivity to material property modifications in polyhydroxybutyrate: A parametric analysis approach

Polyhydroxybutyrate (PHB), a biodegradable biopolymer, represents a promising alternative to petroleum-based thermoplastics. However, despite consistent market growth, PHB faces persistent commercialization challenges that limit widespread adoption. Existing research has focused predominantly on optimizing PHB production processes, leaving a critical gap in understanding which material property modifications would most effectively enhance market competitiveness. This study addresses this gap by systematically analyzing the relationship between polymer material properties and market performance using U.S. market data from 2008 to 2021 for 21 thermoplastic polymers across 19 material properties. We employed principal component regression to identify property modifications that could maximize market volume while reducing CO 2 emissions. Our parametric analysis revealed that two specific material properties – Hardness Shore A and Sheet Extrusion Temperature – significantly influence PHB marketability across different price points. Market simulations demonstrated that a 10% increase in Hardness Shore A could increase PHB market volume by 431.5 million kg while reducing emissions by 188.7 kg CO 2 . A similar 10% increase to Sheet Extrusion Temperature could yield a 297.5 million kg volume increase and a 99.2 kg CO 2 reduction in emissions. Critically, this approach is agnostic to the specific methods required to achieve these property changes, instead providing material scientists with quantitative, data-driven targets for R&D prioritization. Here, this framework offers a novel methodology for evaluating biopolymer competitiveness and supporting strategic decisions to accelerate PHB market adoption and contribute to decarbonization of the plastics industry.

09 BIOMASS FUELS↗

Materials Based on Technical Bulk Lignin

Lignin is the second most abundant biopolymer and the main source of aromatic structures on earth. Lignin has long been produced as a byproduct of the pulping process and utilized in low value-added applications like heat. However, lignin has received increased attention in recent years to improve its value through various chemical processes. This Review compiles recent progress in synthesis, properties, and applications of lignin-based materials. The lignin for material applications can often be classified into three categories: technical bulk lignin (TBL), lignin-derived oligomers (LDOs), and lignin-derived phenols (LDPs). Furthermore, this Review focuses on the chemical modifications of TBLs and their applications in novel smart materials like self-healing, stimulus responsive, and shape memory polymers. The conversion of TBL to polymers can be briefly divided into two steps: (1) introduction of polymerizable functional groups into the lignin backbone and (2) polymerization that achieves desired materials. Both lignin functionalization and polymerization approaches are discussed in detail. As such, this work attempts to provide a comprehensive overview that highlights the importance of these approaches for the utilization of the abundant but largely ignored biopolymer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enriched Molecular-Level View of Saline Wetland Soil Carbon by Sensitivity-Enhanced Solid-State NMR

Soil organic matter (SOM) plays a major role in mitigating greenhouse gas emission and regulating earth’s climate, carbon cycle, and biodiversity. Wetland soils account for one-third of all SOM; however, globally, coastal wetland soils are eroding faster due to increasing sea-level rise. Our understanding of carbon sequestration dynamics in wetlands lags behind that of upland soils. Here, we employ solid-state nuclear magnetic resonance (ssNMR) to investigate the molecular-level structure of biopolymers in wetland soils spanning 11 centuries. High-resolution multidimensional spectra, enabled by dynamic nuclear polarization (DNP), demonstrate enduring preservation of molecular structures within herbaceous plant cores, notably condensing aromatic motifs and carbohydrates, even over a millennium, with the preserved cores constituting a decreasing minority among molecules from decomposition and repolymerization with depth and age. Such preserved cores occur alongside molecules from the decomposition of loosely packed parent biopolymers. These findings emphasize the relative vulnerability of coastal wetland SOM when exposed to oxygenated water due to geological and anthropogenic changes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Chemical structure–property relationships in nanocelluloses

Abstract Nanocelluloses, nanoscale cellulosic particles or fibrils, are an appealing class of nanomaterials with enormous potential for sustainable development. They have great promise to target some of the 17 Sustainable Development Goals outlined by the United Nations. Nanocelluloses are derived from the most abundant biopolymer in the world, cellulose, which have multiple hydroxyl groups on their surface, enabling a vast range of chemical modifications. The interplay between the chemical structure and physicochemical properties of nanocelluloses is crucial to engineering the next generation of green, functional nanomaterials. In this review paper, we provide a comprehensive account of the structure–property relationships in nanocelluloses, which may establish the basis for the design of precision bio‐based materials. Chemical modifications of nanocelluloses, including hydrolysis, oxidation, esterification, amidation, and polymer grafting, provide an array of chemical and physical properties that open opportunities in a diverse spectrum of applications. We review how chemical modifications affect the physicochemical properties of nanocelluloses, such as thermal stability, hydrophobicity, and dispersibility in nonpolar media. Understanding nanocellulose chemical structure–property relationships is integral to the development of sustainable material platforms based on the most renewable biopolymer on earth.

59 BASIC BIOLOGICAL SCIENCES↗

CFD-DEM Modeling of Autothermal Pyrolysis of Corn Stover with a Coupled Particle- and Reactor-Scale Framework

Autothermal operation of fast pyrolysis is an efficient process-intensification technique wherein exothermic oxidation reactions are used to overcome the heat-transfer bottleneck of conventional pyrolysis. The development of accurate, reliable modeling toolsets is imperative to generating a deeper understanding of biomass autothermal pyrolysis systems to support scale-up and industrial deployment. This modeling effort describes the development of single-particle and reactor models which incorporate detailed reaction schemes and simultaneous exothermic oxidation reactions. The particle-scale model was parameterized for corn stover feedstock with particle morphology, density, ash content, and biopolymer composition, all of which impact the emergent conversion characteristics during pyrolysis. Results were then used to parameterize a reactor-scale autothermal pyrolysis model, which was developed using a coarse-grained computational fluid dynamic-discrete element method. The simulation results compared well with experimental results, with the predicted bio-oil, light gas, and biochar yield within 3.0 wt% of the experimental yields. Further analyses were performed to test the influence of equivalence ratio, biomass injection position, and particle size distribution on autothermal pyrolysis. The analysis of the physio-chemical properties of the fluid and solid phase inside the reactor and at the reactor outlet help reveal important process interactions of autothermal pyrolysis.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

Catabolism of lignin-related methoxylated compounds in white-rot fungi utilizes non-canonical oxidoreductases

White-rot fungi (WRF) are the most effective lignin-degrading organisms in nature, making them essential to Earth’s carbon cycle. Lignin is a highly methoxylated, heterogeneous biopolymer derived from plants. However, the pathways WRF use to metabolize methoxylated aromatic monomericcompounds as carbon sources remain unidentified. Here, we employ a systems biology approach to elucidate the intracellular catabolism of vanillate – a monomethoxylated aromatic compound – in two white-rot fungi (WRF), Gelatoporia subvermispora and Trametes versicolor. We identified and biochemically validated a four-enzyme pathway that converts vanillate into ß-ketoadipate – a metabolite that enters central carbon metabolism. This pathway deviates from typical bacterial pathways, where vanillate is initially demethylated and ring-cleaved by intradiol dioxygenases; instead, oxidative decarboxylation occurs prior to ring cleavage by extradiol dioxygenases. Thus, we conducted an in-depth investigation of ring cleavage and further downstream catabolism by the identified fungal enzymes using biochemical and structural approaches. This revealed non-canonical enzymes, including a highly substrate-specific extradiol dioxygenase and a metal-free, promiscuous reductase, the latter capable of acting on catabolic intermediates derived from both methoxylated and non-methoxylated aromatic compounds. This work emphasizes the potential of WRF and their enzymes to advance lignin valorization and enhance our understanding of their role during wood decay.

dioxygenase↗

Enzymatically hydrolyzed fluorescence-based chemical probe enables in situ mapping of chitinase activity in the rhizosphere

Rhizosphere microbiomes and root exudates play a pivotal biochemical role in helping to catalyze chitin catabolism. Chitin is a recalcitrant and ubiquitous soil biopolymer, estimated to be the second most abundant organic soil biopolymer on Earth. Despite its abundance, role as a source of C and N in soil, and importance to ecosystem function, the biochemical mechanisms controlling chitin fate in the rhizosphere are elusive and poorly understood. To enable spatial mapping of chitinase activity in the rhizosphere, we designed and synthesized an enzymatically activated fluorogenic substrate, chitotriose-TokyoGreen (chitotriose-TG), by incorporating a fluorescein derivative (TG) onto the trimeric unit of chitin. This non-fluorescent substrate is selectively hydrolyzed by chitinase to release TG and yield a high fluorescence signal, which can be used to spatially image and measure chitinase activity in the rhizosphere. To demonstrate the application of this technique, we grew switchgrass (Panicum virgatum) in rhizoboxes amended with a horizontal layer of chitin. We extracted mobile proteins from the rhizobox using a nitrocellulose membrane blotting technique which offer non-destructive enzyme extraction while preserving the 2D spatial position of the enzymes. We then subjected these membranes to the synthesized chitotriose-TG stain to spatially visualize the distribution of chitinase activity within the rhizosphere. Furthermore, we observed increased chitinase activity near plant roots and higher activity within the soil zone enriched in chitin, showing an adaptive response of chitinase activity with spatial focusing in areas of higher chitin abundance. Thus, the enzyme extraction and visualization strategy we describe here can help enlighten efforts to better understand spatial controls on chitin breakdown in rhizosphere, further elucidating the role of chitin as a C and N source in these systems.

59 BASIC BIOLOGICAL SCIENCES↗

Discovering and Designing a Chimeric Hyperthermophilic Chitinase for Crystalline Chitin Degradation

Chitin is one of the most abundant renewable biopolymers on earth. However, it is highly crystalline and recalcitrant to degrade. Here, we report a hyperthermophilic chitinase (ActChi) to directly hydrolyze crystalline chitin at its optimal temperature of 80 °C. It contains a malectin domain, a fibronectin type-III (Fn3) domain, and a catalytic domain (CD chi ). Both Fn3 and malectin have the function of chitin binding domain (ChBD) to increase the activity. Fn3 also significantly increases thermostability, but malectin decreases it. To enhance both activity and thermostability, here we introduced a heterogeneous and hyperthermophilic ChBD at the N-terminus of CD chi to obtain ChBD-CD chi . The activity of this hybrid enzyme is 201 U/μmol for crystalline chitin, which has increased 400% compared with that of ActChi. In addition, ChBD-CD chi can continuously degrade crystalline chitin for more than 4 days at 70 °C to increase the overall hydrolysis rate. The strategy is a good example of green sustainable degradation for crystalline biopolymer in nature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Range and strength of mechanical interactions of force dipoles in elastic fiber networks

Mechanical forces generated by myosin II molecular motors drive diverse cellular processes, most notably shape change, division and locomotion. These forces may be transmitted over long range through the cytoskeletal medium – a disordered, viscoelastic network of biopolymers. The resulting cell size scale force chains can in principle mediate mechanical interactions between distant actomyosin units, leading to self-organized structural order in the cell cytoskeleton. Inspired by such force transmission through elastic structures in the cytoskeleton, we consider a percolated fiber lattice network, where fibers are represented as linear elastic elements that can both bend and stretch, and the contractile activity of myosin motors is represented by force dipoles. Then, by using a variety of metrics, we show how two such contractile force dipoles interact with each other through their mutual mechanical deformations of the elastic fiber network. As a prelude to two-dipole interactions, we quantify how forces propagate through the network from a single anisotropic force dipole by analyzing clusters of nodes connected by highly strained bonds, as well as through the decay rate of strain energy with distance from a force dipole. We show that predominant fiber bending screens out force propagation, resulting in reduced and strongly network configuration-dependent dipole interactions. On the other hand, stretching-dominated networks support longer-ranged inter-dipole interactions that recapitulate the predictions of linear elasticity theory. By characterizing the differences between tensile and compressive force propagation in the fiber network, we show how inter-dipole interaction depends on the dipoles’ mutual separation and orientation. The resulting elastic interaction energy may mediate a force between multiple distant dipoles, leading to their self-organization into ordered configurations. In conclusion, this provides a potential pathway for active mechanical force-driven structural order in elastic biopolymer networks.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy

Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical interactions between carbohydrates, proteins, and lignin. Furthermore, these structural features provide an atomic-level understanding of many cellular processes, promoting the development of better biomaterials and inhibitors. It is anticipated that the capabilities of MAS-DNP in biomolecular and biomaterial research will be further enlarged by the rapid development of instrumentation and methodology.

36 MATERIALS SCIENCE↗

Intracellular pathways for lignin catabolism in white-rot fungi

White-rot fungi, the most efficient organisms at breaking down lignin from wood in Nature, utilize lignin degradation products as a carbon source. 15 Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in Nature. While lignin depolymerization by WRF has been exhaustively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here we employ 13C-labeling and systems biology approaches to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in 20 soil ecosystems, and furthermore establishes a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts – a key step towards enabling a sustainable bioeconomy.

Del Cerro, Carlos↗

Architecture of a catalytically active homotrimeric plant cellulose synthase complex

Cellulose is an essential plant cell wall component and represents the most abundant biopolymer on Earth. Supramolecular plant cellulose synthase complexes organize multiple linear glucose polymers into microfibrils as load-bearing wall components. We determined the structure of a poplar cellulose synthase CesA homotrimer that suggests a molecular basis for cellulose microfibril formation. This complex, stabilized by cytosolic plant-conserved regions and helical exchange within the transmembrane segments, forms three channels occupied by nascent cellulose polymers. Secretion steers the polymers toward a common exit point, which could facilitate protofibril formation. CesA’s N-terminal domains assemble into a cytosolic stalk that interacts with a microtubule-tethering protein and may thus be involved in CesA localization. Here, our data suggest how cellulose synthase complexes assemble and provide the molecular basis for plant cell wall engineering.

59 BASIC BIOLOGICAL SCIENCES↗

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.

Kordia↗

Data for The Stem Cell-Type Transcriptome of Bioenergy Sorghum Reveals the Spatial Regulation of Secondary Cell Wall Networks

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.

Software↗

Elucidation of Aromatic Catabolic Pathways in White-Rot Fungi

This project aims to investigate the hypothesis that white-rot fungi can simultaneously depolymerize lignin extracellularly and catabolize depolymerization products intracellularly as carbon and energy sources. Evaluating this hypothesis will provide deeper understanding of the role of white-rot fungi in facilitating carbon sequestration in Nature. Additionally, identifying the most promising fungal strains for lignin turnover and catabolism will catalyze future efforts in genetic tool development to enable metabolic engineering in white-rot fungi for lignin bioconversion to bioproducts. Lignin is the second most abundant plant-based biopolymer on Earth and represents up to 40% of the energy density of lignocellulosic biomass. Even though lignin is a massive natural carbon and energy reservoir, only a small group of basidiomycete fungi, namely white-rot fungi (WRF), have evolved the ability to efficiently depolymerize and mineralize lignin to CO2 and H2O. Considerable research efforts have been undertaken to understand how WRF depolymerize lignin but the biochemical reactions that convert lignin into CO2 have been largely neglected. In fact, it is unclear if WRF intracellularly catabolize lignin-derived aromatic compounds to utilize them as a carbon and energy source, or rather if lignin is depolymerized and mineralized extracellularly merely to facilitate access to cellulose and hemicellulose for use as a primary carbon source. To date, we have employed 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to definitively demonstrate that two WRF, Trametes versicolor and Gelatoporia (Ceriporiopsis) subvermispora, funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways [1]. Specifically, 13C-isotopic labeling approaches showed that these WRF utilize poplar-derived aromatic compounds (e.g. 4-hydroxybenzoic acid (4-HBA)) as a carbon source. In silico genome analysis led us to hypothesize a complete catabolic pathway for 4-HBA and identify multiple homologous sequences for enzymes with putative oxidative decarboxylase, hydroxylase, and ring-opening dioxygenase activities, which are among the main biochemical reactions acting on aromatic compounds. Spatial and differential proteomic and metabolomic analyses supported the proposed catabolic pathways and showed alternative catabolic steps in T. versicolor that were not present in G. subvermispora. Based on the in silico, proteomics, and transcriptomics results, we down-selected enzymes for further in vitro characterization, and we have assigned a function to six fungal enzymes (including oxidative decarboxylases, hydroxylases, and ring-opening dioxygenases). Interestingly, even though we selected homologous enzyme pairs from both WRF with similar -omics trends, in a few cases only one of the studied fungi showed activity for the proposed substrate. Based on all the observations from this study [1], we hypothesized that 4-HBA preferentially undergoes oxidative decarboxylation to hydroquinone and subsequent hydroxylation to 1,2,4-benzenetriol in G. subvermispora before ring cleavage, whereas 4-HBA would preferentially undergo hydroxylation to protocatechuate and further oxidative decarboxylation to 1,2,4-benzenetriol in T. versicolor. Examining additional decarboxylases and hydroxylases as well as enzymes from other protein families that can perform the same or similar oxidative reactions, such as cytochromes P450 with aromatic hydroxylation activity, will also be key for elucidating enzyme preferences for specific substrates. Overall, this work forms the foundation of a new research area based on lignin catabolism by WRF, which could be further exploited to convert the undervalued biopolymer lignin into value-added compounds.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

2.3.4.501 - Synthesis and Analysis of Performance-Advantaged Bioproducts

This project focuses on the synthesis and analysis of performance-advantaged bioproducts (PABPs). We have established collaborations with other BETO-funded projects and academic and industrial collaborators to source new molecules that have promising manufacturing pathways and that could be serve as performance-advantaged biochemicals or biopolymers. We conduct synthesis and characterization of biochemicals and biopolymers alongside techno-economic analysis and life cycle assessment to estimate their cost and environmental impacts relative to incumbent materials. As part of the project, Profs. Linda Broadbelt and Brent Shanks are developing computational pathway prediction tools to identify optimal production pathways for bio-based compounds via biological and chemo-catalytic transformations. When coupled to the polyID tool from the Inverse Design project, these tools will ultimately enable a narrowing of design space for PABPs. From FY21-FY23, we described a framework for benchmarking PAPBs, estimated the energy and GHG emissions for commodity organic chemicals, developed performance-advantaged nylons and polyesters from beta-ketoadipic acid, and produced lignin-based plasticizers. We have shown that aromatic amines can be used in performance thermosets and that polyhydroxyalkanoates with crosslinked side chains can exhibit rubber-like properties, along with repair and degradability. We are working actively with industry partners on scale-up and validation of multiple PABPs.

BIOMASS FUELS↗

Chitosan as a Canvas for Studies of Macromolecular Controls on CaCO 3 Biological Crystallization

A mechanistic understanding of how macromolecules, typically as an organic matrix, nucleate and grow crystals to produce functional biomineral structures remains elusive. Advances in structural biology indicate that polysaccharides (e.g., chitin) and negatively charged proteoglycans (due to carboxyl, sulfate, and phosphate groups) are ubiquitous in biocrystallization settings and play greater roles than currently recognized. This review highlights studies of CaCO 3 crystallization onto chitinous materials and demonstrates that a broader understanding of macromolecular controls on mineralization has not emerged. With recent advances in biopolymer chemistry, it is now possible to prepare chitosan-based hydrogels with tailored functional group compositions. By deploying these characterized compounds in hypothesis-based studies of nucleation rate, quantitative relationships between energy barrier to crystallization, macromolecule composition, and solvent structuring can be determined. Finally, this foundational knowledge will help researchers understand composition-structure-function controls on mineralization in living systems and tune the designs of new materials for advanced applications.

15 GEOTHERMAL ENERGY↗