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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Effect of Solvents on Lignin–Surface Interactions via Molecular Dynamics Simulations

Lignin, an essential building block of lignocellulosic biomass, is a potential abundant source of aromatic monomers for the polymer and chemical industry. Reductive catalytic fractionation (RCF) is one promising process that can produce high yields of phenolic monomers and oligomers from lignin under different catalytic conditions. An important choice in optimizing RCF is the selection of solvent; however, detailed insights into solvent effects on lignin behaviors and interactions remain limited. Here, in this work, we perform all-atom molecular dynamics simulations to study the solvation of lignin, solvent-mediated conformational changes, and the interaction of solvated lignin oligomers with model surfaces. We focus on the behavior of an oligomeric lignin model compound in methanol, ethanol, a binary mixture of ethanol and water, and water at both the RCF reaction temperature (473 K) and room temperature. Analysis of structural features of lignin suggests that these three organic solvent systems favorably solvate lignin, resulting in a more extended conformation suitable for catalytic conversion to valuable chemicals. We further introduce model palladium (Pd) and carbon (C) surfaces to understand how solvent choice impacts adsorption onto a representative catalytic surface and support, and to quantify the competition among the reactant and solvent molecules for the surface. Unbiased simulations suggest strong adsorption of lignin on both Pd and C surfaces at 473 K, with notable solvent-mediated differences in adsorption energies. Additionally, our findings indicate that lignin adsorption is promoted by the entropy change resulting from the displacement of solvent molecules from the surface. This study provides a molecular perspective of adsorption of lignin onto varying surfaces, which is a step towards understanding and optimizing the catalytic conversion of lignin into valuable chemicals.

adsorption↗
DOE OSTI2026

Tracking the protein conformational motions driving HIV-1 membrane fusion

HIV-1 Env (trimeric gp120/gp41) is the surface protein responsible for membrane fusion. The Env binds to the receptor proteins, which induces gp120 shedding leading to conformational changes of gp41 from the pre-fusion to post-fusion state, allowing its fusion peptide to embed in the host cell membrane and bringing the viral and host cell membranes together. The gp41 refolding is a target of several peptide inhibitors. Yet, the molecular mechanism of this dynamic process is still not well understood. In this study, we successfully simulate the conformational change of gp41 from pre-fusion to post-fusion state in atomistic resolution using all-atom structure-based models. We reveal that maintaining the directionality of protomer interactions in both pre-fusion and post-fusion states is crucial for gp41 refolding. Additionally, we find that HR1 inherently extends as a three-helical bundle toward the host-cell membrane without any bias. Importantly, we identify native contacts in the pre-fusion state that are critical for the proper refolding of gp41 towards the post-fusion state. Lastly, by incorporating the membrane-fusion inhibitors, T20 and SFT, we identify the most vulnerable stage in the fusion pathway that exhibits the greatest sensitivity to these drugs, which could aid in a better understanding of drug resistance mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

STEPs-SOL, a Peptoid Force Field Parameterization to Include Solvent Effects

As peptoids (N-substituted glycines) continue to gain popularity as a class of biomimetic polymers, the importance and demand for accurate force fields in molecular simulations also grow. Building on the vacuum-optimized Systematic and Extensible Force Field for Peptoids (STEPs) force field, here we present STEPs-SOL, a novel peptoid force field parametrization that effectively incorporates solvent effects to enhance the accuracy of peptoid simulations. The development of STEPs-SOL is based on the need for precise electrostatic modeling achieved through solvent-specific partial charge optimization. Here, our systematic approach significantly improves agreement with experimental measurements, reducing the mean absolute error in cis/trans ratio predictions (ΔG c/t ) by an average of 38% across multiple peptoid residues and solvent environments. This improved parametrization addresses computational challenges associated with nonbonded energies while maintaining a workflow that relies on high-level quantum mechanical data rather than depending solely on limited experimental equilibrium properties. By evaluating the effects of conformational bias in restrained electrostatic potential (RESP) charge generation and examining their impact on peptoid conformations in various solvents, we enhance our understanding of peptoid structural dynamics while providing a more accurate modeling framework.

force field↗
DOE OSTI2025

Shear-Induced Conformations of Salt-Free Polyelectrolytes in Semidilute Solutions

Here, we present coarse-grained molecular dynamics simulations of salt-free polyelectrolyte chains in semidilute solutions under simple shear flow, with full hydrodynamic interactions and explicit dipolar solvent. At equilibrium, chain orientation statistics follow a pseudo-Voigt distribution, and the structural correlation length and chain end-to-end vector autocorrelation function exhibit scaling behavior consistent with theoretical predictions for polyelectrolytes. Under shear, chains transition from coiled to stretched states and the end-to-end vector autocorrelation function reveals oscillatory dynamics at high Weissenberg numbers. Analysis of the gyration tensor and shear strain distributions identified three distinct chain populations with directional alignment along and against the shear gradient. Compared with their neutral polymer counterparts, polyelectrolytes exhibit stronger shear thinning and enhanced chain alignment under the same Weissenberg number, which is attributed to electrostatic interactions and shear-induced counterion release. These findings provide molecular insight into the distinct flow response of charged polymers and have implications for tailoring the rheological properties of polyelectrolyte-based materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

How Rigid Are Anthranilamide Molecular Electrets?

As important as molecular electrets are for electronic materials and devices, conformational fluctuations strongly impact their macrodipoles and intrinsic properties. Herein, we employ molecular dynamics (MD) simulations with the polarizable charge equilibrium (PQEq) method to investigate the persistence length (L P ) of molecular electrets composed of anthranilamide (Aa) residues. The PQEq-MD dissipates the accepted static notions about Aa macromolecules, and L P represents the shortest Aa rigid segments. The classical model with a single L P value does not describe these oligomers. Introducing multiple L P values for the same macromolecule follows the observed trends and discerns the enhanced rigidity in their middle sections from the reduced stiffness at their terminal regions. Furthermore, L P distinctly depends on solvent polarity. The Aa oligomers maintain extended conformations in nonpolar solvents with L P exceeding 4 nm, while in polar media, increased conformational fluctuations reduce L P to about 2 nm. These characteristics set key guidelines about the utility of Aa conjugates for charge-transfer systems within organic electronics and energy engineering.

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

Genetic control of morphological transitions in a coacervating protein template

Nature routinely exploits liquid–liquid phase separation (LLPS) of proteins to control the assembly and mineralization of hybrid materials. Here, we show that fusion of the Car9 silica-binding peptide to an elastin-like polypeptide (ELP) yields temperature- and sequence-programmable soft matter templates for the synthesis of silicified architectures ranging in size from nanometers to micrometers. Specifically, we demonstrate unprecedented control over the diameter of silica nanoparticles (SiNP) in the 30–60 nm range with 4 nm precision, show that a single arginine residue (R4) in the Car9 sequence underpins the transition from micelles to proteinosomes, and find that substitutions in other basic residues modulate electrostatic repulsion and solvation to enable access to kinetically trapped species. These structures, which include interconnected micelles, small (∼200 nm) and large (>5 µm) vesicles, are readily visualized by SEM imaging following silicification. Molecular dynamics (MD) simulations and AlphaFold predictions reveal that mutations in positively charged residues alter interfacial packing, hydration, and conformational freedom of the silica-binding segments. Overall, our results establish sequence and thermal energy as synergistic levers for morphological control across length scales using solid-binding ELPs and establish mineralization as a powerful tool to visualize the structure of dynamic soft matter assemblies.

hierarchy↗
DOE OSTI2024

Surface Dynamics of Selective Hydration of Rutile TiO 2 : A Kinetic Monte Carlo Approach

The utility of atomic layer deposition (ALD) continues to expand beyond conformal thin-film fabrication to include area- or site-selective ALD. We previously identified a strategy for site-selective ALD (SS-ALD) via the evaluation of thermodynamically preferred hydration of rutile TiO 2 surfaces, as deduced from electronic structure calculations. Here, we report a novel kinetic Monte Carlo (KMC) model that allows for the investigation of surface dynamics and kinetics that improves our understanding of and intuition for the selective hydration strategy. Here we demonstrate the validity of the strategy with respect to step-edge defects for the lowest energy (110) facet as well as report results for the other common facets which agree with experimental STM observations. The results here indicate that the selective hydration strategy is feasible both thermodynamically (evaluated in our previous publication) and kinetically (from the KMC model). Because diffusion has a slower rate than others, we find that any proximity effects between terrace and defect sites are unlikely to affect the selective hydration strategy for rutile TiO 2 . The KMC model further provides relevant timescales for achieving selectivity experimentally and establishes the kinetic viability of the selective hydration approach to SS-ALD.

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

Many roads to the seam: How conformational flexibility drives nonadiabatic relaxation in a prototypical tetrapyrrolic chromophore

Large and structurally flexible chromophores pose challenges for in silico modeling of photodeactivation due to the many vibrational modes that can funnel the system toward energy degeneracy. In this work, we examine how the multiple degrees of freedom in biliverdin, a prototypical tetrapyrrolic chromophore, cooperate to drive access to the S 1 /S 0 intersection seam in vacuo. We begin by mapping the ground-state potential energy surface to identify representative biliverdin conformers relevant to photoexcitation. We then use a CASSCF-based framework to map the excited-state landscape and characterize the intersection seam, identifying distinct conical-intersection types. Finally, we employ ab initio multiple spawning to resolve the dynamical pathways by which the system accesses these regions. DFT potential-energy and free-energy mappings indicate that, although several conformers are relevant, the “locked-helix” ZsZsZs conformer predominates in the ground state. The intersection seam comprises numerous geometrically distinct regions characterized by varying degrees and combinations of dihedral torsion, pyramidalization, and bond-length alternation. Yet only select regions lie within energetic reach, and moderate barriers separate them from the S 1 minimum. Nonadiabatic dynamics combined with multivariate analyses show that, despite extensive mode coupling during deactivation that guides the system toward multiple regions of the seam, a single dihedral torsion, together with bond-length alternation, predominantly drives energy degeneracy. This work offers new insight into biliverdin’s intrinsic photochemical response and underscores a general feature of flexible chromophores: many modes may participate during photorelaxation, but only a limited subset ultimately dictates seam accessibility.

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

ELG×LRG Distribution through Dark Matter Halo Dynamics

We investigate the clustering and halo occupation distribution (HOD) of DESI Y1 emission-line (ELGs) and luminous red (LRGs) galaxies at 0.8 < z < 1.1, including their cross-correlation (ELG×LRG), using the A BACUS S UMMIT suite and a new Halo Occupation Model (H OME ) for galaxy multitracers. This integrates intrahalo dynamics, halo exclusion, and quenching, bridging insights from hydrodynamical, HOD, abundance-matching, and semianalytic studies. Leveraging full phase-space information from the Uchuu N-body simulation, and sampling satellites from dark-matter particle positions via physically motivated prescriptions, Home reproduces the anisotropic clustering down to s = 200 h −1 kpc with unprecedented accuracy. Model parameters are inferred solely from two-point statistics using a two-level Bayesian framework, yielding high-fidelity ELG, LRG, and cross-reference catalogs. We find that satellite ELGs behave as incoherent flows within their parent halos, dominating the clustering below 4 h −1 Mpc. The HOD from the best-fit Home has the following properties: (i) 90.50% (85.91%) of ELGs (LRGs) are central galaxies without satellites, residing in halos of M vir ∼ 6.6 × 10 11 (1.2 × 10 13 ) h −1 M ⊙ ; (ii) the ELG×LRG cross-correlation is governed by central-central pairs and shaped by halo exclusion on 2–5 h −1 Mpc scales; (iii) 9.50% (14.09%) of ELGs (LRGs) are satellites, of which 1.09% (3.52%) inhabit halos with a central galaxy of the same species in a maximally conformal configuration, 7.02% (0.005%) orbit complementary hosts in a minimally conformal state, and 0.58% (10.57%) are orphans. The high sensitivity of Home precisely captures the dynamics of satellites in different host environments, opening a promising avenue for understanding systematics and the dynamical nature of dark matter, potentially distinguishing gravity models.

Favole, Ginevra [Universidad de La Laguna (Spain);↗
DOE OSTI2024

Tunable Growth of Layered Double Hydroxide Nanosheets through Hydrothermal Conversion of Atomic Layer Deposition Seed Layers

To enable the design and manufacturing of hierarchical nanomaterial architectures, there is a need for synthesis and processing methods that can enable tunable geometric control at the nanoscale while maintaining conformality on complex 3-D templates. Here, in this study, we explore the programmable control of vertically oriented Zn-Al layered double hydroxide (LDH) nanosheet arrays using atomic layer deposition (ALD) to deposit a seed layer of Al 2 O 3 , which is subsequently consumed and converted into the LDH phase under hydrothermal growth conditions. We demonstrate tunable control over the spacing and length of the nanosheets by varying the thickness of the initial ALD seed layer with subnanometer precision. This can be viewed as a nanoscale titration reaction, where Al acts as the limiting reagent during the hydrothermal synthesis of the nanosheets. Elemental mapping demonstrates the dynamic evolution of the resulting morphology, which is driven by surface diffusion and nucleation processes. The conformal nature of ALD allows for hierarchical growth of nanosheets on the surface of a variety of nonplanar substrate geometries, including microposts, paper fibers, and porous ceramic supports. This illustrates the power of ALD to enable bottom-up growth of 3-D nanoarchitectures with tunable geometries by controlling nucleation and growth in subsequent solution reactions.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Can black holes preserve 𝒩 > 4 supersymmetry?

The dynamics of near-BPS black holes are governed by the breaking of the conformal symmetry that emerges near their horizons. Using the classification of superconformal symmetries, we systematically classify and quantize all effective theories that can arise in the near-BPS limit of black holes. Using these results, we argue — under certain physical assumptions — that BPS black holes cannot preserve more than four supercharges. This conclusion is consistent with existing constructions in string theory.

Black Holes in String Theory↗
DOE OSTI2025

Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers

Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.

Disulfides↗
DOE OSTI2024

Distinct binding conformations of epinephrine with α- and β-adrenergic receptors

Abstract Agonists targeting α 2 -adrenergic receptors (ARs) are used to treat diverse conditions, including hypertension, attention-deficit/hyperactivity disorder, pain, panic disorders, opioid and alcohol withdrawal symptoms, and cigarette cravings. These receptors transduce signals through heterotrimeric Gi proteins. Here, we elucidated cryo-EM structures that depict α 2A -AR in complex with Gi proteins, along with the endogenous agonist epinephrine or the synthetic agonist dexmedetomidine. Molecular dynamics simulations and functional studies reinforce the results of the structural revelations. Our investigation revealed that epinephrine exhibits different conformations when engaging with α-ARs and β-ARs. Furthermore, α 2A -AR and β 1 -AR (primarily coupled to Gs, with secondary associations to Gi) were compared and found to exhibit different interactions with Gi proteins. Notably, the stability of the epinephrine–α 2A -AR–Gi complex is greater than that of the dexmedetomidine–α 2A -AR–Gi complex. These findings substantiate and improve our knowledge on the intricate signaling mechanisms orchestrated by ARs and concurrently shed light on the regulation of α-ARs and β-ARs by epinephrine.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2026

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗
DOE OSTI2024

Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms

Abstract Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant unusually preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employ static and dynamic structural methods and observe that, compared to R132H, the R132Q active site adopts a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling reveals a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4

PIP 3 -dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP 3 and heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP 3 , we discovered that Ins(1,3,4,5)P 4 (IP 4 ) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP 4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH–DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH–DEP1 and PH–4HB interfaces were disturbed exhibited enhanced activity during chemokineinduced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP 3 -containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP 4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crystalline Peptoid Nanofibers with a Single-Unit Cell Cross Section

Ultranarrow crystalline one-dimensional nanostructures formed from soft materials facilitate precise structural control in nanomaterial design, which is essential for biomedicine and nanotechnology applications. Systematic control of their hierarchical structure is challenging due to the complexities of simultaneously manipulating multiple noncovalent interactions at such small scales. We employed a polypeptoid crystal motif as a supramolecular synthon to engineer ultranarrow crystalline nanofibers constrained to a single lattice axis by incorporating a single ionizable side chain into the hydrophobic core of a nanosheet-forming peptoid. Cryogenic transmission electron microscopy of the nanofibers revealed detailed molecular arrangements of a unit-cell cross-section and the presence of distinct pH-dependent lattice isoforms that resulted in morphological transformations. Molecular dynamics simulations demonstrated that the ionizable side chain plays a critical role in changing the local conformation of the unit cell, which further impacts the dimensionality of hierarchical structures. Moreover, these fibers were readily functionalized with biological ligands to afford one-dimensional (1D) protein arrays. This approach for the high-precision bottom-up assembly of ultranarrow 1D nanostructures offers significant potential for developing novel biomimetic nanostructures.

Lee, Yen Jea↗