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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 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Excited State Dynamics of a Conformationally Fluxional Copper Coordination Complex

The conversion of solar energy into chemical fuel represents a capstone goal of the 21st century and has the potential to supply terawatts of power in a globally distributed manner. However, the disparate time scales of photodriven charge separation (~fs) and steps in chemical reactions (~μs) represent an inherent bottleneck in solar-to-fuels technology. Here to address this discrepancy, we are developing earth-abundant coordination complexes that undergo light-induced conformational rearrangements such that charge separation (CS) is hastened, while charge recombination (CR) is slowed. To these ends, we report the preparation and characterization of a new series of conformationally fluxional copper coordination complexes that contain a twisted intramolecular charge transfer (TICT) fluorophore as part of their ligand scaffold. Structural and spectroscopic characterization of the Cu(I) and Cu(II) complexes formed with these ligands in their ground states establish oxidation state-dependent conformational dynamicity, while time-resolved emission and transient absorption spectroscopies define the photopysical parameters of photo-induced excited states. Building on initial reports with a related set of molecules, the improved ligand design presented here greatly simplifies the observed photophysics, effectively shutting down unwanted ligand-centered excited states previously observed. Finally, time-dependent density functional theory (TDDFT) analyses reveal an unusual metal-to-TICT electronic transition only reported once before, and though the formation of a CS state is not observed directly through experiments, TDDFT geometry optimizations in the excited states support the formation of transient Cu(II) CS species, lending credence to the potential success of our approach. These studies establish a clear model for the excited state dynamics at play in proof-of-concept systems and clarify key design parameters for future optimizations toward achieving long-lived CS via photoinduced conformational gating.

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

Energy coupling and stoichiometry of Zn 2+ /H + antiport by the prokaryotic cation diffusion facilitator YiiP

YiiP from Shewanella oneidensis is a prokaryotic Zn 2+ /H + antiporter that serves as a model for the Cation Diffusion Facilitator (CDF) superfamily, members of which are generally responsible for homeostasis of transition metal ions. Previous studies of YiiP as well as related CDF transporters have established a homodimeric architecture and the presence of three distinct Zn 2+ binding sites named A, B, and C. In this study, we use cryo-EM, microscale thermophoresis and molecular dynamics simulations to address the structural and functional roles of individual sites as well as the interplay between Zn 2+ binding and protonation. Structural studies indicate that site C in the cytoplasmic domain is primarily responsible for stabilizing the dimer and that site B at the cytoplasmic membrane surface controls the structural transition from an inward facing conformation to an occluded conformation. Binding data show that intramembrane site A, which is directly responsible for transport, has a dramatic pH dependence consistent with coupling to the proton motive force. A comprehensive thermodynamic model encompassing Zn 2+ binding and protonation states of individual residues indicates a transport stoichiometry of 1 Zn 2+ to 2–3 H + depending on the external pH. This stoichiometry would be favorable in a physiological context, allowing the cell to use the proton gradient as well as the membrane potential to drive the export of Zn 2+ .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Modular Commutators in Conformal Field Theory

The modular commutator is a recently discovered entanglement quantity that quantifies the chirality of the underlying many-body quantum state. In this Letter, we derive a universal expression for the modular commutator in conformal field theories in 1 + 1 dimensions and discuss its salient features. We show that the modular commutator depends only on the chiral central charge and the conformal cross ratio. We test this formula for a gapped (2 + 1)-dimensional system with a chiral edge, i.e., the quantum Hall state, and observe excellent agreement with numerical simulations. Furthermore, we propose a geometric dual for the modular commutator in certain preferred states of the AdS/CFT correspondence. Finally, for these states, we argue that the modular commutator can be obtained from a set of crossing angles between intersecting Ryu-Takayanagi surfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Holographic BCFT with a Defect on the End-of-the-World brane

In this paper, we propose a new gravity dual for a 2d BCFT with two conformal boundaries by introducing a defect that connects the two End-of-the-World branes. We demonstrate that the BCFT dual to this bulk model exhibits a richer lowest spectrum. The corresponding lowest energy eigenvalue can continuously interpolate between - πc 24 Δ x and 0 where Δ x is the distance between the boundaries. This range was inaccessible to the conventional AdS/BCFT model with distinct boundary conditions. We compute the holographic entanglement entropy and find that it exhibits three different phases, one of which breaks the time reflection symmetry. We also construct a wormhole saddle, analogous to a 3d replica wormhole, which connects different boundaries through the AdS bulk. This saddle is present only if the BCFT is non-unitary and is always subdominant compared to the disconnected saddle.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Initial Simulations of Empty Room Collapse and Reconsolidation at the Waste Isolation Pilot Plant

The Waste Isolation Pilot Plant (WIPP) is a geologic repository for defense-related nuclear waste. If left undisturbed, the virtually impermeable rock salt surrounding the repository will isolate the nuclear waste from the biosphere. If humans accidentally intrude into the repository in the future, then the likelihood of a radionuclide release to the biosphere will depend significantly on the porosity and permeability of the repository itself. Room ceilings and walls at the WIPP tend to collapse over time, causing rubble piles to form on floors of empty rooms. The surrounding rock formation will gradually compact these rubble piles until they eventually become solid salt, but the length of time for a rubble pile to reach a certain porosity and permeability is unknown. This report details the first efforts to build models to predict the porosity and permeability evolution of an empty room as it closes. Conventional geomechanical numerical methods would struggle to model empty room collapse and rubble pile consolidation, so three different meshless methods, the Immersed Isogeometric Analysis Meshfree, Reproducing Kernel Particle Method (RKPM), and the Conformal Reproducing Kernel method, were assessed. First, the meshless methods and the finite element method each simulated gradual room closure, without ceiling or wall collapse. All three methods produced equivalent room closure predictions with comparable computational speed. Second, the Immersed Isogeometric Analysis Meshfree method and RKPM simulated two-dimensional empty room collapse and rubble pile consolidation. Both methods successfully simulated large viscoplastic deformations, fracture, and rubble pile rearrangement to produce qualitatively realistic results. In addition to geomechanical simulations, the flow channels in damaged salt and crushed salt were measured using micro-computed tomography, and input into a computational fluid dynamics simulation to predict the salt's permeability. Although room for improvement exists, the current simulation approaches appear promising.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Narrow Slot Gasket Grooves And Step Changes In Width

We provide corrections to the slot capacitance and inverse inductance per unit length for slot gasket groove geometries using an approximate conformal mapping approach. We also provide corrections for abrupt step changes in slot width along with boundary discontinuity conditions for implementation in the various slot models.

42 ENGINEERING↗
DOE OSTI2022

Slip velocity boundary conditions for the lattice Boltzmann modeling of microchannel flows

Abstract Slip flows in ducts are important in numerous engineering applications, most notably in microchannel flows. Compared to the standard no‐slip Dirichlet condition, the case of slip formulates as a Robin‐type condition for the fluid tangential velocity. Such an increase in mathematical complexity is accompanied by a more challenging numerical transcription. The present work concerns with this topic, addressing the modeling of the slip velocity boundary condition in the lattice Boltzmann method (LBM) applied to steady slow viscous flows inside ducts of nontrivial shapes. As novelty, we extend the newly revised local second‐order boundary (LSOB) Dirichlet fluid flow method [ Philos. Trans. R. Soc. A 378, 20190404 (2020)] to implement the slip velocity condition within the two‐relaxation‐time (TRT) framework. The LSOB follows an in‐node philosophy where its operation principle seeks to explicitly reconstruct the unknown boundary populations in the form of a third‐order accurate Chapman–Enskog expansion, where the wall slip condition is built‐in as a normal Taylor‐type condition. The key point of this approach is that the required first‐ and second‐order momentum derivatives, rather than computed through nonlocal finite difference approximations, are locally determined through a simple local linear algebra procedure, whose formulation is particularly aided by the TRT symmetry argument. To express the obtained derivatives, two approaches are considered, called and , which operate with node and wall variables, respectively. These two formulations are developed to prescribe the physical slip condition over plane and curved walls, including the corners. Their consistency and accuracy characteristics are examined against alternative linkwise strategies to impose the wall slip velocity, such as the kinetic‐based diffusive bounce‐back scheme, the central linear interpolation slip scheme, and the multireflection slip scheme. The several slip schemes are tested over different 3D microchannel configurations, with walls not conforming with the LBM uniform mesh. Numerical tests confirm the advanced accuracy characteristics of the proposed LSOB slip boundary scheme, revealing the added challenge of the wall slip modeling, and that parabolic accuracy is a necessary requirement to reach second‐order accuracy within this problem class.

Silva, Goncalo↗
DOE OSTI2020

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

An Evolve-Then-Correct Reduced Order Model for Hidden Fluid Dynamics

In this paper, we put forth an evolve-then-correct reduced order modeling approach that combines intrusive and nonintrusive models to take hidden physical processes into account. Specifically, we split the underlying dynamics into known and unknown components. In the known part, we first utilize an intrusive Galerkin method projected on a set of basis functions obtained by proper orthogonal decomposition. We then present two variants of correction formula based on the assumption that the observed data are a manifestation of all relevant processes. The first method uses a standard least-squares regression with a quadratic approximation and requires solving a rank-deficient linear system, while the second approach employs a recurrent neural network emulator to account for the correction term. We further enhance our approach by using an orthonormality conforming basis interpolation approach on a Grassmannian manifold to address off-design conditions. The proposed framework is illustrated here with the application of two-dimensional co-rotating vortex simulations under modeling uncertainty. The results demonstrate highly accurate predictions underlining the effectiveness of the evolve-then-correct approach toward real-time simulations, where the full process model is not known a priori.

long short-term memory↗
DOE OSTI2024

Relevance of anisotropy in the Kondo effect: Lessons from the symplectic case

A Kondo model with symplectic symmetry was recently put forward as the effective low-energy theory of a superconducting-island device coupled to multiple leads. This model, which possesses non-Fermi liquid physics and effective anyons, was argued to belong to the class of topological Kondo effects. Here, we clarify the extent of stability of its exotic fixed point using perturbative and numerical renormalization group in conjunction with bosonization and conformal field theory. In contrast to previous claims, we show that asymmetry in the coupling to the leads destabilizes the non-Fermi liquid. Other destabilizing perturbations include asymmetry in the superconducting pairing or internal energy of the individual quantum dots in the island. Nevertheless, these perturbations all generate the same relevant operators. Thus, only a small number of couplings need to be tuned individually, and these can be selected according to experimental convenience. Our results highlight a common misconception that anisotropy in single-channel Kondo couplings is always irrelevant. As demonstrated, relevant terms will emerge whenever the group generators do not span the full space of impurity operators. This calls for a more detailed inspection of models that exhibit this property, such as large-spin impurities and SO⁡( M ) Kondo models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Chain trajectories, domain shapes, and terminal boundaries in block copolymers

The packing geometry of macromolecules in complex mesophases is of key importance to self-organization in synthetic and biological soft materials. While approximate or heuristic models rely on often-untested assumptions about how flexible molecules “fit in” to distinct locations of complex assemblies, physical assemblies derive from ensembles of fluctuating conformations, obscuring the connection between mesophase geometry and the underlying arrangements. Here, we present an approach to extract and analyze features of molecular packing in diblock block copolymer (BCP) melts, a prototypical soft matter system, based on the statistical description of chain conformations in self-consistent field (SCF) theory. We show how average BCP chain trajectories in ordered morphologies can be analyzed from the SCF-derived orientational order parameter of chain segments. We use these extracted trajectories to analyze the features of local packing geometry, including chain bending and tilt, as well as the terminal boundaries that delineate distinct domains in ordered BCP morphologies. In conclusion, we illustrate this analysis by focusing on measurable features of packing frustration in 2D (columnar) and 3D (spherical and bicontinuous) morphologies, notably establishing an explicit link between chain conformations in complex morphologies and their medial geometry.

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

Three-Dimensional Topological Field Theories and Nonunitary Minimal Models

We find an intriguing relation between a class of three-dimensional nonunitary topological field theories (TFTs) and Virasoro minimal models M ( 2 , 2 r + 3 ) with r ≥ 1 . The TFTs are constructed by topologically twisting 3D N = 4 superconformal field theories (SCFTs) of rank-0, i.e., having zero-dimensional Coulomb and Higgs branches. We present ultraviolet (UV) field theory descriptions of the SCFTs with manifest N = 2 supersymmetry, which we argue is enhanced to N = 4 in the infrared. From the UV description, we compute various partition functions of the TFTs and reproduce some basic properties of the minimal models, such as their characters and modular matrices. We expect more general correspondence between topologically twisted 3d N = 4 rank-0 SCFTs and 2D nonunitary rational conformal field theories. Published by the American Physical Society 2024

Physics↗
DOE OSTI2021

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases

Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Finally, our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations

Abstract Molecular analysis of interactions between IgE antibody and allergen allows the structural basis of IgE recognition to be defined. Human IgE (hIgE) epitopes of respiratory lipocalin allergens, including Can f 1, remain elusive due to a lack of IgE‐allergen complexes. This study aims to map the structure of allergenic epitopes on Can f 1. The fragment antigen‐binding (Fab) regions of Can f 1 specific human IgE monoclonal antibodies (hIgE mAb) were used to determine the structures of IgE epitopes. Epitope mutants were designed to target Can f 1 epitopes. Immunoassays and a human FcεRIαtransgenic mouse model of passive anaphylaxis in vivo were used to assess the functional activity of epitope mutants. Crystal structures of natural or recombinant Can f 1 complexed with two hIgE mAb 1J11 and 12F3 Fabs, respectively, were determined. The hIgE mAb bound to two partially overlapping epitopes and recognized two different Can f 1 conformations. The hIgE mAb 12F3 showed an unusual mode of binding by protruding its heavy chain CDR3 inside the Can f 1 calyx. Epitope mutants generated based on the structural analyses displayed a 64%–89% reduction in IgE antibody binding and failed to induce passive anaphylaxis in a human FcεRIαtransgenic mouse model. In summary, the structures of Can f 1‐hIgE Fab complexes revealed two unique and partially overlapping epitopes on Can f 1. The modification of the identified IgE epitopes provides a pathway for the design of hypoallergens to treat dog allergies.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Impact of Polymer Rheology on Gel Treatment Performance of Horizontal Wells with Severe Channeling

Summary Gel treatment has been a cost-effective method to control the conformance of a reservoir with severe heterogeneity problems. The water channels in such reservoirs can be classified as open fractures or high permeability porous media with pore-throat network. Many simulation studies have been conducted to discuss gel treatment performance for conformance control. However, nobody considered the polymer rheology difference in open fractures and porous media in simulation. Previous simulation studies also ignored the residual resistance factor as a function of rock permeability rather than a constant parameter. In this study, a conceptual simulation model was established to simulate the linear flow system for the reservoir with horizontal wells considering the two factors mentioned above. The results demonstrate that the gel treatment always provides the better placement results in the open fracture type channel than pore-throat network type channel. Moreover, it is very necessary to consider residual resistance factor as a function of permeability, which is based on the experimental results and can provide much greater plugging efficiency in the higher permeable channels than constant residual resistance factor. Sensitivity analysis studies and multifactor analysis indicate that increasing oil viscosity and permeability ratio has a strong positive influence on conformance control results, which indicate in-situ gel treatment can be better applied in heavy or viscous oil reservoirs with fracture-like channels. Besides, the results also indicate that in reservoirs with severe channeling problem where channel velocity was high, the differences of gelant placement and profile improvement in models with two different types of channels could be enlarged greatly.

Engineering↗