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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.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs

RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A

Major Facilitator Superfamily Domain containing 2 A (MFSD2A) is a transporter that is highly enriched at the blood-brain and blood-retinal barriers, where it mediates Na + -dependent uptake of ω-3 fatty acids in the form of lysolipids into the brain and eyes, respectively. Despite recent structural insights, it remains unclear how this process is initiated, and driven by Na + . Here, we perform Molecular Dynamics simulations which demonstrate that substrates enter outward facing MFSD2A from the outer leaflet of the membrane via lateral openings between transmembrane helices 5/8 and 2/11. The substrate headgroup enters first and engages in Na + -bridged interactions with a conserved glutamic acid, while the tail is surrounded by hydrophobic residues. This binding mode is consistent with a “trap-and-flip” mechanism and triggers transition to an occluded conformation. Furthermore, using machine learning analysis, we identify key elements that enable these transitions. These results advance our molecular understanding of the MFSD2A transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces

The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.

catalysis (heterogeneous)↗
DOE OSTI2020

Adsorption of Non-Ionic Surfactant and Monoclonal Antibody on Siliconized Surface Studied by Neutron Reflectometry

The adsorption of monoclonal antibodies (mAbs) on hydrophobic surfaces is known to cause protein aggregation and degradation. Therefore, surfactants, such as Poloxamer 188, are widely used in therapeutic formulations to stabilize mAbs and protect mAbs from interacting with liquid-solid interfaces. Here, the adsorption of Poloxamer 188, one mAb and their competitive adsorption on a model hydrophobic siliconized surface is investigated with neutron scattering coupled with contrast variation to determine the molecular structure of adsorbed layers for each case. Small angle neutron scattering measurements of the affinity of Poloxamer 188 to this mAb indicate that there is negligible binding at these solution conditions. Neutron reflectometry measurements of the mAb show irreversible adsorption on the siliconized surface, which cannot be washed off with neat buffer. Poloxamer 188 can be adsorbed on the surface already occupied by mAb, which enables partial removal of some adsorbed mAb by washing with buffer. The adsorption of the surfactant introduces significant conformational changes for mAb molecules that remain on the surface. In contrast, if the siliconized surface is first saturated with the surfactant, no adsorption of mAb is observed. Competitive adsorption of mAb and Poloxamer 188 from solution leads to a surface dominantly occupied with surfactant molecules, whereas only a minor amount of mAb absorbs. These findings clearly indicate that Poloxamer 188 can protect against mAb adsorption as well as modify the adsorbed conformation of previously adsorbed mAb.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Water accelerated self-healing of hydrophobic copolymers

Previous studies have shown that copolymer compositions can significantly impact self-healing properties. This was accomplished by enhancement of van der Waals (vdW) forces which facilitate self-healing in relatively narrow copolymer compositional range. In this work we report the acceleration of self-healing in alternating/random hydrophobic acrylic-based copolymers in the presence of confined water molecules. Under these conditions competing vdW interactions do not allow H 2 O-diester H-bonding, thus forcing nBA side groups to adapt L-shape conformations, generating stronger dipole-dipole interactions resulting in shorter inter-chain distances compared to ‘key-and-lock’ associations without water. The perturbation of vdW forces upon mechanical damage in the presence of controllable amount of confined water is energetically unfavorable leading the enhancement of self-healing efficiency of hydrophobic copolymers by a factor of three. The concept may be applicable to other self-healing mechanisms involving reversible covalent bonding, supramolecular chemistry, or polymers with phase-separated morphologies.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Behavior of Water Near Multimodal Chromatography Ligands and Its Consequences for Modulating Protein–Ligand Interactions

Multimodal chromatography is a powerful approach for purifying proteins that uses ligands containing multiple modes of interaction. Recent studies have shown that selectivity in multimodal chromatographic separations is a function of the ligand structure and geometry. Here, we performed molecular dynamics simulations to explore how the ligand structure and geometry affect ligand–water interactions and how these differences in solution affect the nature of protein–ligand interactions. Our investigation focused on three chromatography ligands: Capto MMC, Nuvia cPrime, and Prototype 4, a structural variant of Nuvia cPrime. First, the solvation characteristics of each ligand were quantified via three metrics: average water density, fluctuations, and residence time. We then explored how solvation was perturbed when the ligand was bound to the protein surface and found that the probability of the phenyl ring dewetting followed the order: Capto MMC > Prototype 4 > Nuvia cPrime. To explore how these differences in dewetting affect protein–ligand interactions, we calculated the probability of each ligand binding to different types of residues on the protein surface and found that the probability of binding to a hydrophobic residue followed the same order as the dewetting behavior. This study illustrates the role that wetting and dewetting play in modulating protein–ligand interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Interactions of Polar and Nonpolar Groups of Alcohols in Zeolite Pores

Understanding the quantitative interactions among zeolite pore walls, Bro̷nsted acid sites, and molecules with both polar and nonpolar regions is essential for scoping out the potential of zeolites as sorbents and catalysts. Purely siliceous zeolites (MFI and Beta in the present study) are hydrophobic, whereas those containing aluminum are considered hydrophilic, preferentially adsorbing organic molecules even in aqueous environments. To characterize these interactions, we use primary alcohols of increasing molecular weight, quantifying their specific interactions in the confined pore space of the alkyl (CH x ) and OH groups. Three types of interactions were identified: (i) alkyl CH x groups interacting with the zeolite pore walls (approximately 10 kJ mol −1 per carbon), (ii) alcohol OH groups interacting with the pore walls (30−35 kJ mol −1 ), and (iii) alcohol OH groups interacting with Bro̷nsted acid sites (37 kJ mol −1 ). All three interactions were well mirrored by computational simulations. The contribution of the alkyl CH x groups was inferred from the incremental increase in sorption enthalpy with increasing molecular weight; the interaction strength of the OH groups was determined by extrapolating the global adsorption enthalpy of the alcohols to a hypothetical OH group without an alkyl group. This value was identical to the adsorption enthalpy of water. The experiments demonstrated that only water has an adsorption enthalpy on zeolite pore walls lower than its condensation enthalpy (30−35 kJ mol −1 vs 45 kJ mol −1 ), limiting the concentration of water that can be adsorbed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

SAN-Based Block Polymers as a Platform for Manufacturing Strong Isoporous Membranes

Ultrafiltration (UF) membranes are ubiquitous in water purification and bioprocessing. However, co-designing their mechanical and transport properties remains challenging because of the broad pore size distributions at the surface and within the bulk that result from nonsolvent-induced phase separation (NIPS) – their typical manufacturing process. These distributions influence the hydrodynamic resistance to water flow and the stress concentrations around the pores. Developing advanced UF membranes requires innovative molecular designs that offer control over the surface and bulk pores, as well as the mechanical properties of the load-bearing, polymer. Here, we introduce a platform for designing UF membranes by leveraging solution self-assembly of block polymers and chain architectures with pendant polar groups. The block polymers consist of a poly(styrene-co-acrylonitrile) hydrophobic block, which is known for its strength, and a poly(4-vinyl pyridine) hydrophilic block, which drives solution self-assembly. We focus on a series of block polymers with constant molecular weight, M n ≈ 115 kDa, SAN fraction, 75 wt.%, and varying acrylonitrile content, 0 to 40 mol%, to demonstrate that: (i) RAFT dispersion copolymerization of acrylonitrile and styrene provides a facile route to synthesize strong block polymers, (ii) incorporation of acrylonitrile into the hydrophobic block enhances membrane strength by facilitating chain entanglements and dipole-dipole interactions, and (iii) acrylonitrile alters the balance between membrane permeance and rejection, even when the membranes feature similar surface and bulk pores. Overall, our results provide insights into the molecular design of UF membranes with enhanced mechanical and separation properties, contributing to the development of materials for water and energy technologies.

deformation↗
DOE OSTI2025

Understanding the selectivity of nonsteroidal anti-inflammatory drugs for cyclooxygenases using quantum crystallography and electrostatic interaction energy

Quantum crystallography methods have been employed to investigate complex formation between nonsteroidal anti-inflammatory drugs (NSAIDs) and cyclooxygenase (COX) enzymes, with particular focus on the COX-1 and COX-2 isoforms. This study analyzed the electrostatic interaction energies of selected NSAIDs (flurbiprofen, ibuprofen, meloxicam and celecoxib) with the active sites of COX-1 and COX-2, revealing significant differences in binding profiles. Flurbiprofen exhibited the strongest interactions with both COX-1 and COX-2, indicating its potent binding affinity. Celecoxib and meloxicam showed a preference for COX-2, consistent with their known selectivity for this isoform, while ibuprofen showed comparable interaction energies with both isoforms, reflecting its nonselective inhibition pattern. Key amino-acid residues, including Arg120, Arg/His513 and Tyr355, were identified as critical determinants of NSAID selectivity and binding affinity. The findings highlight the complex interplay between interaction energy and selectivity, suggesting that while electrostatic interactions play a fundamental role, additional factors such as enzyme dynamics and the hydrophobic effect also contribute to the therapeutic efficacy and safety profiles of NSAIDs. These insights provide valuable guidance for the rational design of NSAIDs with enhanced therapeutic benefits and minimized adverse effects.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Discovery of unconventional and nonintuitive self-assembling peptide materials using experiment-driven machine learning

Prediction of peptide secondary structure is challenging because of complex molecular interactions, sequence-specific behavior, and environmental factors. Traditional design strategies, based on hydrophobicity and structural propensity, can be biased and could indeed prevent discovery of interesting, diverse, and unconventional peptides with desired nanostructure assembly. Using β sheet formation in pentapeptides as a case study, we used an integrated high-throughput experimental workflow and an artificial intelligence–driven active learning framework to improve prediction accuracy of self-assembly. By focusing on sequences where machine learning (ML) predictions deviate from conventional design strategies, we synthesized and tested 268 pentapeptides, successfully finding 96 forming β sheet assemblies, including unconventional sequences (e.g., ILFSM, LMISI, MITIY, MISIW, and WKIYI) not predicted by traditional methods. Our ML models outperformed conventional β sheet propensity tables, revealing useful chemical design rules. A web interface is provided to facilitate community access to these models. This work highlights the value of ML-driven approaches in overcoming the limitations of current peptide design strategies.

Talluri, Y. Nissi [Indian Inst. of Technology (IIT↗
DOE OSTI2024

Structural insights reveal interplay between LAG-3 homodimerization, ligand binding, and function

Lymphocyte activation gene-3 (LAG-3) is an inhibitory receptor expressed on activated T cells and an emerging immunotherapy target. Domain 1 (D1) of LAG-3, which has been purported to directly interact with major histocompatibility complex class II (MHCII) and fibrinogen-like protein 1 (FGL1), has been the major focus for the development of therapeutic antibodies that inhibit LAG-3 receptor-ligand interactions and restore T cell function. Here, we present a high-resolution structure of glycosylated mouse LAG-3 ectodomain, identifying that cis-homodimerization, mediated through a network of hydrophobic residues within domain 2 (D2), is critically required for LAG-3 function. Additionally, we found a previously unidentified key protein-glycan interaction in the dimer interface that affects the spatial orientation of the neighboring D1 domain. Mutation of LAG-3 D2 residues reduced dimer formation, dramatically abolished LAG-3 binding to both MHCII and FGL1 ligands, and consequentially inhibited the role of LAG-3 in suppressing T cell responses. Intriguingly, we showed that antibodies directed against D1, D2, and D3 domains are all capable of blocking LAG-3 dimer formation and MHCII and FGL-1 ligand binding, suggesting a potential allosteric model of LAG-3 function tightly regulated by dimerization. Furthermore, our work reveals unique epitopes, in addition to D1, that can be targeted for immunotherapy of cancer and other human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity

Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here, in this study, we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structures and Mechanisms of a Novel Bacterial Transport System for Fatty Acids

Abstract Bacterial acquisition of metabolites is largely facilitated by transporters with unique substrate scopes. The tripartite ATP‐independent periplasmic (TRAP) transporters comprise a large family of bacterial proteins that facilitate the uptake of a variety of small molecules. It has been reported that some TRAP systems encode a fourth protein, the T component. The T‐component, or TatT, is predicted to be a periplasmic‐facing lipoprotein that enables the uptake of metabolites from the outer membrane. However, no substrates were revealed for any TatT and their functional role(s) remained enigmatic. We recently identified a homolog in Methylococcus capsulatus that binds to sterols, and herein, we report two additional homologs that demonstrate a preference for long‐chain fatty acids. Our bioinformatics, quantitative analyses of protein‐ligand interactions, and high‐resolution crystal structures suggest that TatTs might facilitate the trafficking of hydrophobic or lipophilic substrates and represent a new class of bacterial lipid and fatty acid transporters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Impact of hydrophobic pendant phenyl groups on transport and co-transport of methanol and acetate in PEGDA-SPMAK cation exchange membranes

CO 2 reduction cells are innovative devices that reduce CO 2 into valuable chemicals (i.e. methanol (MeOH) and acetate (OAc – )) on the cathode. A major challenge with such devices is to develop ion exchange membranes that allow ion-selective transport (i.e., protons for cation exchange membranes, CEM) and suppress the crossover of CO 2 reduction products. To design such membranes, it is important to understand multi-solute transport behavior of these solutes. Previously, our group reported acetate diffusivities in co-transport with MeOH increase in sulfonated CEMs, where we speculated charge screening of the electrostatic interactions by co-diffusing MeOH has an impact. Here, crosslinked membranes fabricated by photopolymerization of poly(ethylene glycol) diacrylate (PEGDA), 3-sulfopropyl methacrylate potassium (SPMAK, SO 3 – -containing ionomer), and a phenyl-containing comonomer either phenoxyethyl acrylate (PEA) or poly(ethylene glycol) phenyl ether acrylate (PEGPEA)) are investigated. We observe OAc – diffusivities to both (1) PEGDA-SPMAK and (2) PEGDA-PEGPEA increase in co-diffusion with MeOH and those to (3) PEGDA-SPMAK/PEGPEA decrease. To rationalize this emergent co-transport behavior, we speculate (1) electrostatic interactions are interfered with by co-diffusing MeOH, (2) chain mobility (segmental dynamics) increases in the presence of MeOH and (3) for films with both hydrophobic (PEGPEA) and hydrophilic (SPMAK) comonomers chain mobility (segmental dynamics) decrease due to interactions between the comonomer sidechains depressing overall solute diffusivities. Finally, while further investigations are needed, this work contributes to improving our fundamental understanding of the relationships between polymer film chemistry, solute chemistry, and emergent cotransport behavior observed and described in this work (and others) towards enabling the design of improved membrane materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Polymorphism in Self-Assembly of Short Peptoid Sequences

Due to various applications enabled by diverse morphologies of self-assembled sequence-defined polymers, controlling the self-assembly of synthetic peptidomimetics into designed morphologies has emerged as a promising route for the development of bioinspired functional materials. Herein, we report morphological control over the assembly of a series of short peptoids, or poly-N-substituted glycines, that contain asymmetric hydrophobic domains. We demonstrate that the inherent flexibility of amphiphilic peptoid bilayers drives assembly polymorphism, resulting in the coexistence of nanosheets, twisted ribbons, and nanofibers three distinct morphologies. By tuning peptoid molecular interactions through variations in sequence design, solution pH, and temperature, we demonstrate precise control over the twisting and folding of peptoid bilayers, enabling the formation of well-defined nanosheets and nanohelices. Molecular dynamics simulations further unravel how the introduction of asymmetric hydrophobic domains enables the flexibility of peptoid bilayers and results in peptoid assembly polymorphism. By tuning peptoid molecular interactions through heating, we further demonstrate the transformation of nanosheets into nanohelices. We envision that our mechanistic investigation of peptoid assembly polymorphism provides a strong foundation for leveraging peptoid sequences and chemistries to achieve controlled molecular interactions, driving the creation of biomimetic materials with tailored morphologies and functionalities.

assembly polymorphism↗
DOE OSTI2023

Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions

Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye–DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye–DNA interactions on aggregate orientation and excitonic coupling.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Biobased Poly(dodecylene Furanoate) with Inherent Advantages in Performance and Circularity

Biobased polymers are gaining traction toward more sustainable flexible-film packaging, yet overcoming trade-offs between their performance properties and end-of-life (EoL) options still remains a challenge. Here, it is shown that biobased poly(dodecylene 2,5-furanoate) (PDDF), synthesized via both step-growth polycondensation and chain-growth ring-opening polymerization methods, exhibits advantages not only in gas barrier properties but also in EoL options due to its biodegradability and closed-loop chemical circularity. Specifically, PDDF displays significantly lower oxygen and carbon dioxide permeability than commercial poly(butylene adipate-co-terephthalate) (PBAT) and linear low-density polyethylene , alongside a markedly higher modulus (by ≈3 ×) and reduced water vapor transmission rate compared to PBAT. This superior performance is attributed to the inherently rigid, polar, H-bonding furan rings that enhance chain interaction, packing and crystallinity and thus reduce free volume impeding gas diffusion, while the long hydrophobic dodecylene segments inhibit water permeation. Furthermore, PDDF can be recycled back to its cyclic monomer by base-catalyzed depolymerization or diester and diol monomers by simple methanolysis. These superior barrier properties, coupled with biodegradation and closed-loop circularity, highlight the potential of the biobased PDDF as a more sustainable alternative for packaging.

Poly(dodecylene 2,5-furanoate) (PDDF)↗
DOE OSTI2025

Surface modification of cathode material enhances electrochemical performance in dry-processed Li-ion battery electrodes

The transition to electric vehicles (EVs) is pivotal for achieving energy security and integrating grid stability, with lithium-ion batteries (LIBs) playing a central role in this transformation. However, the conventional wet electrode manufacturing relying on N-methyl-2-pyrrolidone (NMP) solvent is energy intensive and costly. Dry processing (DP) has emerged as a promising alternative, eliminating solvents and using polytetrafluoroethylene (PTFE) binder for electrode fabrications. Despite its advantages, DP faces a critical challenge: poor interfacial adhesion between the hydrophobic PTFE binder and the hydrophilic cathode active material (CAM), particularly LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811), which undermines electrode performance. Here, to address this, we introduced a novel vapor-phase trimethoxymethylsilane (TMMS) coating to hydrophobize the CAM surface, enhancing compatibility with PTFE. This surface modification significantly enhances binder – CAM interactions, enabling uniform mixing and robust electrode integrity without damaging the CAM particles. Our findings advance the feasibility of environmentally sustainable and cost-effective dry processing, representing a significant step toward sustainable battery manufacturing.

Choi, Junbin [Oak Ridge National Laboratory (ORNL)↗