Search NASA⌕ Search

SEARCH · Search NASA

Results for “macromolecular dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

108 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Bottlebrush Polymers at Liquid Interfaces: Assembly Dynamics, Mechanical Properties, and All-Liquid Printed Constructs

Bottlebrush polymer surfactants (BPSs), formed by the interfacial interactions between bottlebrush polymers (BPs) with poly(acrylic acid) side chains dissolved in an aqueous phase and amine-functionalized ligands dissolved in the oil phase, assemble and bind strongly to the fluid-fluid interface. The ratio between N BB (backbone degree of polymerization) and N SC (side chain degree of polymerization) defines the initial assembly kinetics, interface packing efficiency, and stress relaxation. The equilibrium interfacial tension (γ) increases when N BB < N SC , but decreases when N BB $\gg$ N SC , correlating to a pronounced change in the effective shape of the BPs from being spherical to worm-like structures. The apparent surface coverage (ASC), i.e., the interfacial packing efficiency, decreases as N BB increases. The dripping-to-jetting transition of an injected polymer solution, as well as fluorescence recovery after photobleaching experiments, revealed faster initial assembly kinetics for BPs with higher N BB . Furhter, Euler buckling of BPS assemblies with different N BB values was used to characterize the stress relaxation behavior and bending modulus. The stress relaxation behavior was directly related to the ASC, reflecting the strong influence of macromolecular shape on packing efficiency. The bending modulus of BPSs decreases for N BB < N SC , but increased when N BB $\gg$ N SC , showing the effect of molecular architecture and multisite anchoring. All-liquid printed constructs with lower N BB BPs yielded more stable structured liquids, underscoring the importance of macromolecular packing efficiency at fluid interfaces. Overall, this work elucidates fundamental relationships between nanoscopic structures and macroscopic properties associated with various bottlebrush polymer architectures, which translate to the stabilization of all-fluidic printed constructs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Bioimaging Science Program: 2022 Principal Investigator Meetings Proceedings

The mission of the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program’s Bioimaging Science Program (BSP) is to understand the translation of genomic information into the mechanisms that power living cells, communities of cells, and whole organisms. The goal of BSP is to develop new imaging and measurement technologies to visualize the spatial and temporal relationships of key metabolic processes governing phenotypic expression in plants and microbes. The extended goal of dynamic imaging is to functionally connect cellular components and interdependent organisms. Information about the time and place of chemical reactions in situ can identify causal relationships between biological activators and downstream effectors. BSP held its annual PI meeting virtually February 28–March 1. Contributing investigators are convened to review progress and current state-of-the-art bioimaging research. Holding the 2022 BSP meeting as part of the broader Genomic Science Program (GSP) PI meeting allowed researchers to interact with the extended GSP community. This convergence provided a platform for networking and exchange of ideas with experts in other technologies and in target BSP application areas, helping to forge new multidisciplinary collaborations among investigators from the sister programmatic areas within BER’s Biological Systems Science Division. An important highlight of the BSP meeting was the keynote presentation by Nobel Laureate Dr. Joachim Frank on Time-Resolved Macromolecular Imaging using Cryo-EM. He discussed microfluidic mixing and fast freezing to capture nonequilibrium intermediate states during molecular binding and conformational changes. The action of molecular machines can be captured at nanometer resolution and millisecond discrimination. BSP PIs made presentations describing their research focus and progress in plenary sessions on bioimaging science and on quantum-enabled bioimaging science research projects. BSP research at universities and DOE laboratories is presented in this report. A final discussion of the BSP was organized by meeting plenary session chairs, who prepared the following Executive Summary of current BSP research, research challenges, future opportunities, and potential ideas for expanding the BSP’s impact and interactions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

Rein, Robert↗
NASA NTRS2003

Iron catalyst chemistry in modeling a high-pressure carbon monoxide nanotube reactor

The high-pressure carbon monoxide (HiPco) technique for producing single-wall carbon nanotubes (SWNTs) is analyzed with the use of a chemical reaction model coupled with flow properties calculated along streamlines, calculated by the FLUENT code for pure carbon monoxide. Cold iron pentacarbonyl, diluted in CO at about 30 atmospheres, is injected into a conical mixing zone, where hot CO is also introduced via three jets at 30 degrees with respect to the axis. Hot CO decomposes the Fe(CO)5 to release atomic Fe. Then iron nucleates and forms clusters that catalyze the formation of SWNTs by a disproportionation reaction (Boudouard) of CO on Fe-containing clusters. Alternative nucleation rates are estimated from the theory of hard sphere collision dynamics with an activation energy barrier. The rate coefficient for carbon nanotube growth is estimated from activation energies in the literature. The calculated growth was found be about an order of magnitude greater than measured, regardless of the nucleation rate. A study of cluster formation in an incubation zone prior to injection into the reactor shows that direct dimer formation from Fe atoms is not as important as formation via an exchange reaction of Fe with CO in FeCO.

Evaluation Studies↗
DOE OSTI2024

Bottlebrush Block Copolymers at the Interface of Immiscible Liquids: Adsorption and Lateral Packing

Amphiphilic bottlebrush block copolymers (BBCPs), having a hydrophilic bottlebrush polymer (BP) linked covalently to a hydrophobic BP, were found to segregate to liquid-liquid interfaces to minimize the free energy of the system. The key parameter influencing the outcome of the experiments is the ratio between the degree of polymerization of the backbone (NBB) and that of the side-chain brushes (NSC). Specifically, a spherical, star-like configuration results when NBB < NSC, while a cylindrical, bottlebrush-like shape is preferred when NBB > NSC. Dynamic interfacial tension (γ) and fluorescence recovery after photobleaching (FRAP) measurements show that the BBCP configuration influences the areal density and in-plane diffusion at the fluid interface. The characteristic relaxation times associated with BBCP adsorption (τA) and reorganization (τR) were determined by fitting time-dependent interfacial tension measurements to a sum of two exponential relaxation functions. Both τA and τR initially increased with NBB up to 92 repeat units, due to the larger hydrodynamic radius in solution and slower in-plane diffusivity, attributed to a shorter cross-sectional diameter of the side-chains near the block junction. This trend reversed at NBB = 190, with shorter τA and τR attributed to increased segregation strength and exposure of the bare water/toluene interface due to tilting and/or wiggling of the backbone chains, respectively. The adsorption energy barrier decreased with higher NBB, due to a reduced BBCP packing density at the fluid interface. In conclusion, this study provides fundamental insights into macromolecular assembly at fluid interfaces, as it pertains to unique bottlebrush block architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A previously uncharacterized divisome-associated lipoprotein, DalA, is needed for normal cell division in Rhodobacterales

ABSTRACT The bacterial cell envelope is a key subcellular compartment with important roles in antibiotic resistance, nutrient acquisition, and cell morphology. We seek to gain a better understanding of proteins that contribute to the function of the cell envelope in Alphaproteobacteria . Using Rhodobacter sphaeroides , we show that a previously uncharacterized protein, RSP_1200, is an outer membrane (OM) lipoprotein that non-covalently binds peptidoglycan (PG). Using a fluorescently tagged version of this protein, we find that RSP_1200 undergoes a dynamic repositioning during the cell cycle and is enriched at the septum during cell division. We show that the position of RSP_1200 mirrors the location of FtsZ rings, leading us to propose that RSP_1200 is a newly identified component of the R. sphaeroides ’ divisome. Additional support for this hypothesis includes the co-precipitation of RSP_1200 with FtsZ, the Pal protein, and several predicted PG L,D-transpeptidases. We also find that a ∆ RSP_1200 mutation leads to defects in cell division, sensitivity to PG-active antibiotics, and results in the formation of OM protrusions at the septum during cell division. Based on these results, we propose to name RSP_1200 DalA (for division-associated lipoprotein A) and postulate that DalA serves as a scaffold to position or modulate the activity of PG transpeptidases that are needed to form envelope invaginations during cell division. We find that DalA homologs are present in members of the Rhodobacterales order within Alphaproteobacteria . Therefore, we propose that further analysis of this and related proteins will increase our understanding of the macromolecular machinery and proteins that participate in cell division in Gram-negative bacteria. IMPORTANCE Multi-protein complexes of the bacterial cell envelope orchestrate key processes like growth, division, biofilm formation, antimicrobial resistance, and production of valuable compounds. The subunits of these protein complexes are well studied in some bacteria, and differences in their composition and function are linked to variations in cell envelope composition, shape, and proliferation. However, some envelope protein complex subunits have no known homologs across the bacterial phylogeny. We find that Rhodobacter sphaeroides RSP_1200 is a newly identified lipoprotein (DalA) and that loss of this protein causes defects in cell division and changes the sensitivity to compounds, affecting cell envelope synthesis and function. We find that DalA forms a complex with proteins needed for cell division, binds the cell envelope polymer peptidoglycan, and colocalizes with enzymes involved in the assembly of this macromolecule. The analysis of DalA provides new information on the cell division machinery in this and possibly other Alphaproteobacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Interfacial Inversion of Stealth Surfactants

Amphiphilic macromolecular surfactants segregate to liquid–liquid interfaces, thereby reducing the interfacial tension and free energy. Here, we investigated “stealth surfactants” in the form of core–shell bottlebrush polymers comprised of pH-responsive diblock copolymer side chains forming a hydrophilic core and a hydrophobic shell, enabling solubility in oil. At liquid–liquid interfaces, these polymers undergo a structural “inversion”, with hydrophilic blocks segregating into the aqueous phase and hydrophobic blocks residing in the oil phase. The reconfiguration kinetics and surfactant properties are influenced by multiple factors, including the molecular weights of the backbone and side chain components, the hydrophilic-to-hydrophobic balance of the side chains, and the pH of the aqueous phase. An observed nonmonotonic dependence of interfacial tension with time is attributed to a progressive structural inversion, where the projected area of the macromolecule onto the interface decreases. To validate this inversion hypothesis, interfacial properties were characterized by sum-frequency generation vibrational spectroscopy, which revealed configurational changes of the core–shell bottlebrush polymers at the fluid interface and revealed a pH-dependent interfacial coverage. Coarse-grained molecular dynamics simulations supported these experimental findings, showing that the pH-responsive core and hydrophobic shell assume a time-averaged configuration with orientations parallel and perpendicular to the plane of the interface, respectively. These findings open routes to design multistimuli-responsive polymeric surfactants and compatibilizers, expanding their potential applications in advanced interfacial systems.

Stealth surfactants↗
NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗
DOE OSTI2025

Redox Poise during Rhodospirillum rubrum Phototrophic Growth Drives Large-scale Changes in Macromolecular Synthesis Pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H2), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H 2 ), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H 2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sustainable Shape Memory Elastomers with Reduced Melt Viscosity and Enhanced Stiffness

Melt reactive processing of lignin with nitrile rubber is a promising approach to synthesizing shape memory materials. The strong intramolecular interactions in lignin macromolecular structures, caused by π–π stacking in aromatic rings and hydrogen bonding, often result in large phase separation or low miscibility with rubbers. In this study, we investigated the chemical and molecular characteristics, as well as the stiffness and complex viscosity, of modified kraft lignin melt-reacted with an acrylonitrile/butadiene copolymer containing 41% acrylonitrile (NBR41). To enhance the macromolecular compatibility of kraft lignin with NBR41, kraft lignin was cross-linked with poly(propylene glycol) diglycidyl ether (PPDE) and trimethylolpropane triglycidyl ether (TTE), both rich in epoxy reactive groups capable of forming chemical bonds with hydroxyl and carboxyl groups. Here, our findings demonstrate that the modification of kraft lignin with PPDE and TTE resulted in significantly increased stiffness of the composites. The elastic modulus of NBR41-Kraft lignin-PPDE and NBR41-Kraft lignin-TTE increased by 82 and 162%, respectively. Both the yield strength and Young’s modulus of these two samples showed dramatic improvements. Specifically, the yield strength and Young’s modulus of NBR41-Kraft lignin-TTE increased nearly 4 and 3-fold, respectively, compared to the control sample. Interestingly, despite significant improvements in mechanical properties, the viscosity of NBR41-Kraft lignin-PPDE was substantially lower than that of the control sample. At 210 °C and an angular frequency of 1 rad/s, the complex viscosity of NBR41-Kraft lignin was approximately 100.25 ± 4.77 kPa·s, while that of NBR41-Kraft lignin-PPDE was significantly lower at 56 ± 0.93 kPa·s. These findings were validated through Fourier transform infrared spectroscopy, scanning electron microscopy, dynamic mechanical analysis, thermal characterization, rheological tests, and quasi-elastic neutron scattering techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass

Abstract Nitrogen (N) is frequently limiting to plant growth, in part because most soil N is present as polymeric organic compounds that are not readily taken up by plants. Microbial depolymerization of these large macromolecular N-substrates gradually releases available inorganic N. While many studies have researched and modeled controls on soil organic matter formation and bulk N mineralization, the ecological—spatial, temporal and phylogenetic—patterns underlying organic N degradation remain unclear. We analyzed 48 time-resolved metatranscriptomes and quantified N-depolymerization gene expression to resolve differential expression by soil habitat and time in specific taxonomic groups and gene-based guilds. We observed much higher expression of extracellular serine-type proteases than other extracellular N-degrading enzymes, with protease expression of predatory bacteria declining with time and other taxonomic patterns driven by the presence (Gammaproteobacteria) or absence (Thermoproteota) of live roots and root detritus (Deltaproteobacteria and Fungi). The primary chitinase chit1 gene was more highly expressed by eukaryotes near root detritus, suggesting predation of fungi. In some lineages, increased gene expression over time suggests increased competitiveness with rhizosphere age (Chloroflexi). Phylotypes from some genera had protease expression patterns that could benefit plant N nutrition, for example, we identified a Janthinobacterium phylotype and two Burkholderiales that depolymerize organic N near young roots and a Rhizobacter with elevated protease levels near mature roots. These taxon-resolved gene expression results provide an ecological read-out of microbial interactions and controls on N dynamics in specific soil microhabitats and could be used to target potential plant N bioaugmentation strategies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Predictive coarse-grained (CG) modeling of morphologies in polymer nanocomposites with specific and directional intermolecular interactions (Final Report)

The overarching goal of the proposed work was to develop predictive models for investigating structure and dynamics in soft materials with chemistries that have specific and directional molecular interactions. The motivation behind studying materials with specific and directional interactions lies in the many desirable features these interactions provide when designing novel soft materials. Soft materials with specific and direction interactions (such as hydrogen bonds or H-bonds) can have a) thermally reversible phase behavior with different functions with varying temperature, b) precisely tuned nanostructure with desirable geometries that afford unique physical properties (e.g., color response, mechanical properties) and c) well-mixed/blended morphologies that are useful for variety of applications in energy field (e.g., materials for batteries require use of blended polymers where one domain gives superior mechanical properties and one domain promotes electrical conduction). Notably, biology makes extensive use of specific and directional interactions, in many cases based on H-bonds, to construct materials with precisely defined architectures and properties. Engineered soft materials with precisely tuned nanostructures and improved processiblity through thermoresponsive phase behavior are useful in numerous applications that are relevant to the Department of Energy (DOE) including high efficiency electronic devices, light-weight high-strength composite materials for batteries and fuel cells, and polymer membranes for separations, etc. While past computational studies have been tremendously useful in understanding molecular phenomena and guiding synthesis of new macromolecular soft materials for a wide variety of applications, the inability to capture small scale specific and directional interactions alongside macromolecular length and time scales represented a key limitation of most studies to date. Our work in this project addressed this grand challenge in computational materials chemistry, i.e., ability to model the anisotropic, directional, and specific interactions that govern the behavior of many macromolecular soft matter systems of interest, thus, has greatly expanded the predictive potential of simulations. Specifically the key outcomes were: successful development of new coarse-grained (CG) polymer models to study generic and specific polymer chemistries in which hydrogen-bonding interactions are dominant. These CG models were then used in molecular simulations to study structure and thermodynamics in polymer nanocomposites and blends; some studies were conducted in collaboration with experimentalists. We also published a perspective and a viewpoint which included some of the work we completed in this DOE project; we believe these perspective and viewpoint articles guide other researchers in the soft materials community on how to extend the computational approaches and models we have developed for the purposes of their studies.

36 MATERIALS SCIENCE↗
NASA NTRS2001

Crosstalk between p38, Hsp25 and Akt in spinal motor neurons after sciatic nerve injury

The p38 stress-activated protein kinase pathway is involved in regulation of phosphorylation of Hsp25, which in turn regulates actin filament dynamic in non-neuronal cells. We report that p38, Hsp25 and Akt signaling pathways were specifically activated in spinal motor neurons after sciatic nerve axotomy. The activation of the p38 kinase was required for induction of Hsp25 expression. Furthermore, Hsp25 formed a complex with Akt, a member of PI-3 kinase pathway that prevents neuronal cell death. Together, our observations implicate Hsp25 as a central player in a complex system of signaling that may both promote regeneration of nerve fibers and prevent neuronal cell death in the injured spinal cord.

NASA Discipline Developmental Biology↗
NASA NTRS2001

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

Models, Molecular↗
NASA NTRS2003

Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin microfilament system to be restructured in a controlled manner via polymerization, depolymerization, severing, cross-linking, and anchorage. The structure the semicrystalline state of profilin:actin will challenge and validate current models of muscle contraction and cell motility. The methodology and theory under development will be easily extendable to other systems.

Borgstahl, G.↗
NASA NTRS2011

Signatures of Chemical Evolution in Protostellar Nebulae

A decade ago observers began to take serious notice of the presence of crystalline silicate grains in the dust flowing away from some comets. While crystallinity had been seen in such objects previously, starting with the recognitions by Campins and Ryan (1990) that the 10 micron feature of Comet Halley resembled that of the mineral forsterite, most such observations were either ignored or dismissed as no path to explain such crystalline grains was available in the literature. When it was first suggested that an outward flow must be present to carry annealed silicate grains from the innermost regions of the Solar Nebula out to the regions where comets could form (Nuth, 1999; 2001) this suggestion was also dismissed because no such transport mechanism was known at the time. Since then not only have new models of nebular dynamics demonstrated the reality of long distance outward transport (Ciesla, 2007; 2008; 2009) but examination of older models (Boss, 2004) showed that such transport had been present but had gone unrecognized for many years. The most unassailable evidence for outward nebular transport came with the return of the Stardust samples from Comet Wild2, a Kuiper-belt comet that contained micron-scale grains of high temperature minerals resembling the Calcium-Aluminum Inclusions found in primitive meteorites (Zolensky et aI., 2006) that formed at T > 1400K. Now that outward transport in protostellar nebulae has been firmly established, a re-examination of its consequences for nebular gas is in order that takes into account both the factors that regulate both the outward flow as well as those that likely control the chemical composition of the gas. Laboratory studies of surface catalyzed reactions suggest that a trend toward more highly reduced carbon and nitrogen compounds in the gas phase should be correlated with a general increase in the crystallinity of the dust (Nuth et aI., 2000), but is such a trend actually observable? Unlike the Fischer-Tropsch or the Haber-Bosch reactions used in industry, the surface catalyzed reactions seen in our laboratory do not produce a simple product stream of methane or ammonia, respectively. Instead, such reactions produce a wide range of both aliphatic and aromatic hydrocarbons, as well as reduced nitrogen compounds such as ammonia, amines, amides and imides, as gas phase products together with a heavy, macromolecular, kerogen-like surface coating that remains on the grains. While CO and N2 will certainly be depleted by conversion into more complex and less volatile species via reaction on grain surfaces, it may be very difficult to monitor such changes from outside the system.

Nuth, Joseph A., III↗
DOE OSTI2025

Gerischer Electrochemistry Today

Semiconductor photoelectrochemistry is a dynamic and interdisciplinary field at the forefront of research in solar fuels, energy conversion, and catalysis. Here, this Perspective captures the collective insights from the second Gerischer Electrochemistry Today Symposium, held at Colorado State University in Fort Collins, CO, in August 2024, which convened leading researchers, early-career scientists, and industry partners to define the critical next steps for the field. Through interactive sessions, technical talks, panel discussions, and training initiatives─including a Semiconductor Electrochemistry Bootcamp─the symposium emphasized three pillars of advancement: (i) facilitating the exchange of new ideas in semiconductor electrochemistry and charge separation; (ii) fostering the development of future researchers, research topics, and participation in the semiconductor workforce; and (iii) building community. This Energy Focus distills key themes from the meeting and identifies major knowledge gaps in the following areas: mechanisms of charge separation and recombination, role of defects and disorder, dynamic and operando characterization methods, interfacial chemistry and surface passivation, theoretical and modeling limitations, and standardization and benchmarking. The inclusive and collaborative structure of the symposium enabled the generation of this comprehensive report that will serve as a roadmap for fundamental and applied research in the rapidly evolving field of semiconductor electrochemistry over the next decade.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗