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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural insights into VRC01-class bnAb precursors with diverse light chains elicited in the IAVI G001 human vaccine trial

The development of germline-targeting vaccines represents a potentially transformative strategy to elicit broadly neutralizing antibodies (bnAbs) against HIV and other antigenically diverse pathogens. Here, we report on structural characterization of vaccine-elicited VRC01-class bnAb precursors in the IAVI G001 Phase 1 clinical trial with the eOD-GT8 60mer nanoparticle as immunogen. High-resolution X-ray structures of eOD-GT8 monomer complexed with Fabs of five VRC01-class bnAb precursors with >90% germline identity revealed a conserved mode of binding to the HIV CD4-binding site via IGHV1-2-encoded heavy chains, mirroring mature bnAb interactions. The light-chain V-gene diversity emulated VRC01 bnAbs and stabilized antigen engagement, while their conserved five-residue LCDR3 motifs prevented steric clashes. Notably, the VRC01-class bnAb precursors accommodated the N276 glycan, a key barrier in HIV Env recognition, through structural rearrangements in HCDR3 or LCDR1, despite its absence in the immunogen. Surface plasmon resonance analysis showed that 87% of elicited antibodies retained glycan binding capacity, albeit with reduced affinity. These findings validate the ability of eOD-GT8 60mer nanoparticles to prime VRC01-class bnAb precursors with native-like paratopes but with intrinsic glycan adaptability. Structural mimicry of mature bnAbs was observed even with limited somatic hypermutation, indicating that critical features are encoded in the germline repertoire. The structures highlight how germline-encoded features drive bnAb-like recognition at early stages. This work provides molecular evidence supporting germline targeting in humans and provides guidance for designing booster immunogens to shepherd affinity maturation toward broad neutralization.

Science & Technology - Other Topics↗
DOE OSTI2024

Mechanisms of a novel regulatory light chain–dependent cardiac myosin inhibitor

Hypertrophic cardiomyopathy (HCM) is a genetic disease of the heart characterized by thickening of the left ventricle (LV), hypercontractility, and impaired relaxation. HCM is caused primarily by heritable mutations in sarcomeric proteins, such as β myosin heavy chain. Until recently, medications in clinical use for HCM did not directly target the underlying contractile changes in the sarcomere. Here, we investigate a novel small molecule, RLC-1, identified in a bovine cardiac myofibril high-throughput screen. RLC-1 is highly dependent on the presence of a regulatory light chain to bind to cardiac myosin and modulate its ATPase activity. In demembranated rat LV trabeculae, RLC-1 decreased maximal Ca2+-activated force and Ca2+ sensitivity of force, while it increased the submaximal rate constant for tension redevelopment. In myofibrils isolated from rat LV, both maximal and submaximal Ca2+-activated force are reduced by nearly 50%. Additionally, the fast and slow phases of relaxation were approximately twice as fast as DMSO controls, and the duration of the slow phase was shorter. Structurally, x-ray diffraction studies showed that RLC-1 moved myosin heads away from the thick filament backbone and decreased the order of myosin heads, which is different from other myosin inhibitors. In intact trabeculae and isolated cardiomyocytes, RLC-1 treatment resulted in decreased peak twitch magnitude and faster activation and relaxation kinetics. In conclusion, RLC-1 accelerated kinetics and decreased force production in the demembranated tissue, intact tissue, and intact whole cells, resulting in a smaller cardiac twitch, which could improve the underlying contractile changes associated with HCM.

Physiology↗
DOE OSTI2022

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes

Abstract Cytochromes are electron transfer (ET) proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electrons outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis, and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and to elucidate the stepwise ET along the respiratory paths. However, investigating direct ET events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. Nuclear magnetic resonance (NMR) spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor ET within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of ET between c-type cytochromes, using as model a triheme periplasmic cytochrome and a membrane-associated monoheme cytochrome from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional ET within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory ET chains.

Morgado, Leonor (ORCID:0000000237605180)↗
DOE OSTI2022

Applying Crystallography and 19 F NMR to investigate dynamics and partner protein interactions in a long chain Flavodoxin

Flavodoxin (Fld) is a small FMN containing protein that is involved in single electron transfer. The long‐chain flavodoxin in Rhodopseudomonas palustris bacteria replaces ferredoxin as a low‐potential electron carrier when iron is scarce. Thus it is proposed to interact with the bifurcating electron transfer flavoprotein (ETF) that yields low‐potential electrons. A surface loop on Fld interacts with another of Fld's partner proteins, so we hypothesize that it also mediates Fld's interaction with ETF. To monitor interactions with ETF directly and investigate dynamics in this loop, we are using 19 F NMR in solution. 19 F is hyperresponsive to changes in its chemical environment with a chemical shift range of >300 ppm. To provide a static reference point and assess structural heterogeneity, we are also exploiting X‐ray crystallography. In this study we selectively fluorinated the five tyrosine residues in Fld. We obtained resonance assignments from 19 F spectra of Fld variants in which individual tyrosine residues have been replaced. We obtain well resolved signals for each residue, but the resonances' linewidths indicate dynamics that affects some resonances more than others. Y90 residue displays two resonances demonstrating two different conformations that interconvert slowly on an NMR time scale. Meanwhile the crystal structure solved at 2.1Å resolution reveals two molecules per asymmetric unit providing two perspectives on the details of the structure. The crystal symmetry is monoclinic in contrast to most of the other Flds, which are orthorhombic. Interestingly, the long loop bearing Y121 and Y123 is not well resolved in chain B of the crystal structure, and the NMR line of Y123 is exceptionally broad, both indicating that the loop is dynamic and capable of altering its conformation to accomodate binding to a partner protein. Future directions include monitoring the changes in the 19 F NMR of the Fld when titrated with the partner protein, temperature dependence of the NMR spectrum and relaxation studies to evaluate time scales of motions.

Khan, Sharique↗
DOE OSTI2020

Complex magnetic order in the decorated spin-chain system Rb 2 Mn 3 ( MoO 4 ) 3 ( OH ) 2

The macroscopic magnetic properties and microscopic magnetic structure of Rb 2 Mn 3 (MoO 4 ) 3 (OH) 2 (space group Pn ma) are investigated by magnetization, heat capacity, and single-crystal neutron diffraction measurements. The compound's crystal structure contains bond-alternating [Mn 3 O 11 ] ∞ chains along the b axis, formed by isosceles triangles of Mn ions occupying two crystallographically nonequivalent sites (the Mn1 site on the base and Mn2 site on the vertex). These chains are only weakly linked to each other by nonmagnetic oxyanions. Both superconducting quantum interference device magnetometry and neutron diffraction experiments show two successive magnetic transitions as a function of temperature. On cooling, it transitions from a paramagnetic phase into an incommensurate phase below 4.5 K with a magnetic wave vector near k 1 = ( 0 , 0.46 , 0 ). An additional commensurate antiferromagnetically ordered component arises with k 2 = ( 0, 0, 0), forming a complex magnetic structure below 3.5 K with two different propagation vectors of different stars. On further cooling, the incommensurate wave vector undergoes a lock-in transition below 2.3 K. The experimental results suggest that the magnetic superspace group is Pnma. 1' (0b0) s0ss for the single- k incommensurate phase and is Pn' m a ( 0 b 0 ) 00 s for the two- k magnetic phase. We propose a simplified magnetic structure model taking into account the major ordered contributions, where the commensurate k 2 defines the ordering of the c-axis component of the Mn1 magnetic moment, while the incommensurate k 1 describes the ordering of the ab -plane components of both Mn1 and Mn2 moments into elliptical cycloids.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Lyapunov growth in quantum spin chains

The Ising spin chain with longitudinal and transverse magnetic fields is often used in studies of quantum chaos, displaying both chaotic and integrable regions in its parameter space. However, even at a strongly chaotic point this model does not exhibit Lyapunov growth of the commutator squared of spin operators, as this observable saturates before exponential growth can manifest itself (even in situations where a spatial suppression factor makes the initial commutator small). In this work, we extend this model from the spin 1/2 Ising model to higher spins, demonstrate numerically that a window of exponential growth opens up for sufficiently large spin, and extract a quantity which corresponds to a notion of a Lyapunov exponent. In the classical infinite-spin limit, we identify and compute the appropriate classical analog of the commutator squared, and show that the corresponding exponent agrees with the infinite-spin limit extracted from the quantum spin chain.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Beyond universal behavior in the one-dimensional chain with random nearest-neighbor hopping

Here, we study the one-dimensional nearest-neighbor tight-binding model of electrons with independently distributed random hopping and no on-site potential (i.e., off-diagonal disorder with particle-hole symmetry, leading to sublattice symmetry, for each realization). For nonsingular distributions of the hopping, it is known that the model exhibits a universal, singular behavior of the density of states $ρ(E) ~ 1/|E\: \text{ln}^3 |E||$ and of the localization length $ξ(E) ~ |\text{ln}|E||$, near the band center $\textit{E}$ = 0 . (This singular behavior is also applicable to random $\textit{XY}$ and Heisenberg spin chains; it was first obtained by Dyson for a specific random harmonic oscillator chain.) Simultaneously, the state at$\textit{E}$ = 0 shows a universal, subexponential decay at large distances $\sim \text{exp}[–\sqrt{r/r_0}]$. In this study, we consider singular, but normalizable, distributions of hopping, whose behavior at small $\textit{t}$ is of the form $\sim 1/[t \text{ln}^{λ+1}(1/t)]$, characterized by a single, continuously tunable parameter λ > 0. We find, using a combination of analytic and numerical methods, that while the universal result applies for λ > 2, it no longer holds in the interval 0 < λ < 2. In particular, we find that the form of the density of states singularity is enhanced (relative to the Dyson result) in a continuous manner depending on the nonuniversal parameter λ; simultaneously, the localization length shows a less divergent form at low energies and ceases to diverge below λ = 1. For λ < 2, the fall-off of the $\textit{E}$ = 0 state at large distances also deviates from the universal result and is of the form $\sim\text{exp}[–(r/r_0)^{1/λ}]$ , which decays faster than an exponential for λ < 1.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Spinon excitations in the quasi-one-dimensional $S = \frac{1}{2}$ chain compound Cs 4 CuSb 2 Cl 12

The spin-$\frac{1}{2}$ Heisenberg antiferromagnetic chain is ideal for realizing one of the simplest gapless quantum spin liquids (QSLs), supporting a many-body ground state whose elementary excitations are fractional fermionic excitations called spinons. Here we report the discovery of such a one-dimensional (1D) QSL in Cs 4 CuSb 2 Cl 12 . Compared to previously reported $S = \frac{1}{2}$ 1D chains, this material possesses a wider temperature range over which the QSL state is stabilized. In this work, we identify spinon excitations extending at $\textit{T}$ > 0.8 K, with a large $\textit{T}$-linear contribution to the specific heat, γ = 31.5(2)mJ mol –1 K –2 , which contribute itinerantly to thermal transport up to temperatures as high as $\textit{T}$ = 35 K. At $\textit{T}$ = 0.7 K , we find a second-order phase transition that is unchanged by a $μ_0H = 5T$ magnetic field. Cs 4 CuSb 2 Cl 12 reveals new phenomenology deep in the 1D QSL regime, supporting a gapped QSL phase over a wide temperature range compared to many other experimental realizations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Low-energy physics of isotropic spin-1 chains in the critical and Haldane phases

Using a matrix product state algorithm with infinite boundary conditions, we compute high-resolution dynamic spin and quadrupolar structure factors in the thermodynamic limit to explore the low-energy excitations of isotropic bilinear-biquadratic spin-1 chains. Haldane mapped the spin-1 Heisenberg antiferromagnet to a continuum field theory, the nonlinear sigma model (NLσM). In this work, we find that the NLσM fails to capture the influence of the biquadratic term and provides only an unsatisfactory description of the Haldane phase physics. But several features in the Haldane phase can be explained by noninteracting multimagnon states. The physics at the Uimin-Lai-Sutherland point is characterized by multisoliton continua. Moving into the extended critical phase, we find that these excitation continua contract, which we explain using a field-theoretic description. New excitations emerge at higher energies and, in the vicinity of the purely biquadratic point, they show simple cosine dispersions. Using block fidelities, we identify them as elementary one-particle excitations and relate them to the integrable Temperley-Lieb chain.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Nonlinear soliton confinement in weakly coupled antiferromagnetic spin chains

In this work, we analyze the low-energy dynamics of quasi-one-dimensional, large-$\textit{S}$ quantum antiferromagnets with easy-axis anisotropy, using a semiclassical nonlinear sigma model. The saddle point approximation leads to a sine-Gordon equation which supports soliton solutions. These correspond to the movement of spatially extended domain walls. Long-range magnetic order is a consequence of a weak interchain coupling. Below the ordering temperature, the coupling to nearby chains leads to an energy cost associated with the separation of two domain walls. From the kink-antikink two-soliton solution, we compute the effective confinement potential. At distances large compared to the size of the solitons the potential is linear, as expected for pointlike domain walls. At small distances the gradual annihilation of the solitons weakens the effective attraction and renders the potential quadratic. From numerically solving the effective one-dimensional Schrödinger equation with this nonlinear confinement potential we compute the soliton bound state spectrum. We apply the theory to CaFe 2 O 4 , an anisotropic $\textit{S}$ = 5/2 magnet based upon antiferromagnetic zigzag chains. Using inelastic neutron scattering, we are able to resolve seven discrete energy levels for spectra recorded slightly below the Néel temperature $T_N$ ≈ 200 K. These modes are well described by our nonlinear confinement model in the regime of large spatially extended solitons.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

One-directional polarization transport in electron/nuclear spin chains with loss and gain

Understanding the joint dynamics of electron and nuclear spins is central to core concepts in solid-state magnetic resonance such as spin-lattice relaxation and dynamic nuclear polarization, but a generalization that capitalizes on competing polarization loss and gain channels is still lacking. Here, we study theoretically the non-Hermitian dynamics of hybrid electron/nuclear spin systems in the simultaneous presence of electron spin pumping and spin-lattice relaxation. Focusing on periodic, one-dimensional chains, we find that, by adjusting the electron spin pumping to a critical level, it is possible to steer the flow of nuclear polarization to create site-dependent distributions where either end of the array polarizes in opposite ways, irrespective of the initial state. By contrast, we show that ring-like patterns—where the limit nuclear polarization is uniform—exhibit a non-decaying, externally driven nuclear spin current. Interestingly, cyclic magnetic field modulation can render these processes largely robust to defects in the chain, a response featuring some interesting similarities—and differences—with recent findings in other non-Hermitian physical platforms.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Spin dynamics of the spin-chain antiferromagnet RbFeS 2

In this work, we report transport and inelastic neutron scattering studies on electronic properties and spin dynamics of the quasi-one-dimensional spin-chain antiferromagnet RbFeS 2 . An antiferromagnetic phase transition at TN≈195 K and dispersive spin waves with a spin gap of 5 meV are observed. By modeling the spin excitation spectra using linear spin wave theory, intra and interchain exchange interactions are found to be SJ 1 =100(5) meV and SJ 3 =0.9(3) meV, respectively, together with a small single-ion anisotropy of SD zz =0.04(1) meV. Comparison with previous results for other materials in the same class of Fe 3+ spin-chain systems reveals that although the magnetic order sizes show significant variation from 1.8 to 3.0μ B within the family of materials, the exchange interactions SJ are nevertheless quite similar, analogous to the iron pnictide superconductors where both localized and delocalized electrons contribute to the spin dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Constructing Hubbard models for the hydrogen chain using sliced-basis density matrix renormalization group

Sliced-basis DMRG(sb-DMRG) is used to simulate a chain of hydrogen atoms and to construct low-energy effective Hubbard-like models. The downfolding procedure first involves a change of basis to a set of atom-centered Wannier functions constructed from the natural orbitals of the exact DMRG one-particle density matrix. The Wannier function model is then reduced to a fewer-parameter Hubbard-like model, whose parameters are determined by minimizing the expectation value of the Wannier Hamiltonian in the ground state of the Hubbard Hamiltonian. This indirect variational procedure not only yields compact and simple models for the hydrogen chain, but also allows us to explore the importance of constraints in the effective Hamiltonian, such as the restricting the range of the single-particle hopping and two-particle interactions, and to assess the reliability of more conventional downfolding. The entanglement entropy for a model's ground state, cut in the middle, is an important property determining the ability of DMRG and tensor networks to simulate the model, and here we study its variation with the range of the interactions. Counterintuitively, we find that shorter ranged interactions often have larger entanglement.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Prediction of orbital-selective Mott phases and block magnetic states in the quasi-one-dimensional iron chain Ce 2 O 2 FeSe 2 under hole and electron doping

The recent detailed study of quasi-one-dimensional iron-based ladders, with the 3d iron electronic density n=6, has unveiled surprises, such as orbital-selective phases. However, similar studies for n=6 iron chains are still rare. Here a three-orbital electronic Hubbard model was constructed to study the magnetic and electronic properties of the quasi-one-dimensional n=6 iron chain Ce 2 O 2 FeSe 2 , with focus on the effect of doping. Specifically, introducing the Hubbard U and Hund J H couplings and studying the model via the density matrix renormalization group, we report the ground-state phase diagram varying the electronic density away from n=6. For the realistic Hund coupling J H /U=1/4, several electronic phases were obtained, including a metal, orbital-selective Mott, and Mott insulating phases. Doping away from the parent phase, the competition of many tendencies leads to a variety of magnetic states, such as ferromagnetism, as well as several antiferromagnetic and magnetic “block” phases. In the hole-doping region, two different interesting orbital-selective Mott phases were found: OSMP1 (with one localized orbital and two itinerant orbitals) and OSMP2 (with two localized orbitals and one itinerant orbital). Moreover, charge disproportionation phenomena were found in special doping regions. We argue that our predictions can be tested by simple modifications in the original chemical formula of Ce 2 O 2 FeSe 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Topological edge modes without symmetry in quasiperiodically driven spin chains

Here we construct an example of a 1d quasiperiodically driven spin chain whose edge states can coherently store quantum information, protected by a combination of localization, dynamics, and topology. In a sharp departure from topological phases in static and periodically driven (Floquet) spin chains, this model does not rely upon microscopic symmetry protection: Instead, the edge states are protected purely by emergent dynamical symmetries. We explore the dynamical signatures of this emergent dynamical symmetry-protected topological (EDSPT) order through exact numerics, time evolving block decimation, and analytic high-frequency expansion, finding evidence that the EDSPT is a stable dynamical phase protected by bulk many-body localization up to (at least) stretched-exponentially long timescales, and possibly beyond. We argue that EDSPTs are special to the quasiperiodically driven setting, and cannot arise in Floquet systems. Moreover, we find evidence of a type of boundary critical with no known static or Floquet analogue, in which the edge spin dynamics transition from quasiperiodic to chaotic, leading to bulk thermalization.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Dynamics and transport in the boundary-driven dissipative Klein-Gordon chain

Motivated by experiments on chains of superconducting qubits, we consider the dynamics of a classical Klein-Gordon chain coupled to coherent driving and subject to dissipation solely at its boundaries. As the strength of the boundary driving is increased, this minimal classical model recovers the main features of the "dissipative phase transition" seen experimentally. Between the transmitting and non-transmitting regimes on either side of this transition (which support ballistic and diffusive energy transport respectively), we observe additional dynamical regimes of interest. These include a regime of superdiffusive energy transport at weaker driving strengths, together with a "dissipative breather crystal" regime at stronger driving strengths, which is characterized by emergent translation symmetry, ballistic energy transport, and coherent oscillations of a nonlinear normal mode. Here, we propose a non-local Lyapunov exponent as an experimentally measurable diagnostic of many-body chaos in this system, and more generally in open systems that are only coupled to an environment at their boundaries.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Topological quantum computation on a chiral Kondo chain

We describe the chiral Kondo chain model based on the symplectic Kondo effect and demonstrate that it has a quantum critical ground state populated by non-Abelian anyons. We show that the fusion channel of two arbitrary anyons can be detected by locally coupling the two anyons to an extra single channel of chiral current and measuring the corresponding conductance at a finite frequency. Based on such measurements, we propose that the chiral Kondo chain model with symplectic symmetry can be used for the implementation of measurement-only topological quantum computations, and it possesses several distinct features favorable for such applications. Furthermore, the sources and effects of errors in the proposed system are analyzed and possible material realizations are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗