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At least 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Dynamical Signatures of Thermotoga maritima Maltose-Binding Proteins Affected by Ligand Binding

Functional segregation among protein isoforms depends on the interplay of their overall structures and the molecular dynamics of these structures. Thermotoga maritima maltose-binding protein (tmMBP) isoforms show size-dependent differential binding of maltose and malto-oligomers while maintaining remarkable fold conservation. This differential behavior needs detailed characterization in native-like aqueous conditions to understand the effects of protein dynamics on ligand binding and recognition. Small-angle neutron scattering (SANS), neutron spin echo (NSE) spectroscopy, and dynamic light scattering (DLS) were used in conjunction with previously published computational molecular dynamics (MD) simulations to understand the dynamic behavior of tmMBPs experimentally. SANS provided information on the overall structure of the molecules, while NSE was used to determine the dynamics in the nanosecond time scale. Both tmMBP2 and tmMBP3 have a bidomain architecture linked with a flexible hinge, with the binding pocket sitting in the cleft between the two domains. tmMBP2 and tmMBP3 showed different solution dynamics, with the translational and rotational components dominating the dynamics of both systems, resulting in a clear differentiation of their diffusion pattern. A faster dynamics component was also observed and was attributed to segmental dynamics. Differences observed between the ligand-free (apo) and ligand-bound (holo) states of the two proteins are attributed to conformational entropy. Our results highlight the intricacies of how structure and dynamics can together shape binding to a repertoire of substrates in structurally similar proteins.

Diffusion↗
DOE OSTI2024

Microsecond dynamics control the HIV-1 Envelope conformation

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Probing the Core–Shell Organization of Nanoconfined Methane in Cylindrical Silica Pores Using In Situ Small-Angle Neutron Scattering and Molecular Dynamics Simulations

Determining the structure of nanoconfined fluids is essential for predicting the fate of these fluids in subsurface geologic formations with nanoporous features and for engineering novel nanoporous materials for storing compressed gases. In this study, we probe the structure of nanoconfined methane at pressures in the range of 15–100 bar using in situ small-angle neutron scattering (SANS) measurements and molecular dynamics (MD) simulations. The structure of methane is probed in MCM-41 and SBA-15 with cylindrical pores and diameters of 3.3 and 6.8 nm, respectively. In situ SANS measurements and MD simulations showed that the confined methane molecules are organized in a core–shell structure, with the shell arising from the adsorption of methane molecules on the silica surface. The shell thicknesses of the adsorbed deuterated methane (CD4) molecules in MCM-41 obtained by SANS measurements are 1.4 ± 0.5, 2.1 ± 0.1, 3.2 ± 0.8, 4.0 ± 0.3, and 6.0 ± 0.7 Å at equilibrated pressures of 15.6, 35.6, 55.5, 73.3, and 95.7 bar, respectively. The shell thicknesses of the adsorbed CD4 layer in SBA-15 pores are 2.7 ± 0.5, 4.3 ± 0.7, 6.6 ± 0.7, 10.2 ± 0.3, and 14.6 ± 0.8 Å at equilibrated pressures of 15.5, 32.7, 52.4, 70, and 99.5 bar, respectively. These experimental results are in close agreement with the results predicted from MD simulations. Adsorption of methane molecules on the silica surfaces is primarily driven by van der Waals interactions between the methane molecules and the hydroxyl groups on the silica surface, while electrostatic interactions play a minor role. In conclusion, the experimental and simulation approaches described in this study provide fundamental insights into the organization of confined gases using methane as a specific example in the context of compressed fluid storage in natural and engineered materials for adaptive energy use.

03 NATURAL GAS↗
DOE OSTI2020

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.

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

Energy-Resolved Femtosecond Hot Electron Dynamics in Single Plasmonic Nanoparticles

Efficient excitation and harvesting of hot carriers from nanoscale metals is central to many emerging photochemical, photovoltaic, and ultrafast optoelectronic applications. Nevertheless, direct experimental evidence of the energy-dependent femtosecond dynamics in ubiquitous tens-of-nanometer gold structures remains elusive, despite the potentially rich interplay between interfacial and internal plasmonic fields, excitation distributions, and scattering processes. To explore the effects of nanoscale structure on these dynamics, we employ simultaneous time-, angle-, and energy-resolved photoemission spectroscopy of single plasmonic nanoparticles. Photoelectron velocity and electric field distributions reveal bulk-like ballistic hot electron transport in different geometries, lacking any signatures of surface effects. Energy-resolved dynamics are measured in the 1–2 eV range and extrapolated to lower energies via Boltzmann theory, providing a detailed view of hot electron lifetimes within nanoscale gold. Here, we find that particles with relevant dimensions as small as 10 nm serve as exemplary platforms for studying intrinsic metal dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior

Manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. We develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and predicts experimental conditions that allow the actuation temperature of the nano-hinge to be tuned over a range of temperatures from 30 °C to 45 °C. Additionally, the model identifies microscopic interactions that are important to the macroscopic behavior of the system, revealing surprising features of the system. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures or use strand binding interactions to control dynamic DNA origami behavior. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Decoding the 2D IR spectrum of the aqueous proton with high-level VSCF/VCI calculations

The aqueous proton is a common and long-studied species in chemistry, yet there is currently intense interest devoted to understanding its hydration structure and transport dynamics. Typically described in terms of two limiting structures observed in gas-phase clusters, the Zundel H 5 O 2 + and Eigen H 9 O 4 + ions, the aqueous structure is less clear due to the heterogeneity of hydrogen bonding environments and room-temperature structural fluctuations in water. The linear infrared (IR) spectrum, which reports on structural configurations, is challenging to interpret because it appears as a continuum of absorption, and the underlying vibrational modes are strongly anharmonically coupled to each other. Recent two-dimensional IR (2D IR) experiments presented strong evidence for asymmetric Zundel-like motifs in solution, but true structure–spectrum correlations are missing and complicated by the anharmonicity of the system. In this study, we employ high-level vibrational self-consistent field/virtual state configuration interaction calculations to demonstrate that the 2D IR spectrum reports on a broad distribution of geometric configurations of the aqueous proton. We find that the diagonal 2D IR spectrum around 1200 cm –1 is dominated by the proton stretch vibrations of Zundel-like and intermediate geometries, broadened by the heterogeneity of aqueous configurations. There is a wide distribution of multidimensional potential shapes for the proton stretching vibration with varying degrees of potential asymmetry and confinement. In conclusion, we find specific cross peak patterns due to aqueous Zundel-like species. These studies provide clarity on highly debated spectral assignments and stringent spectroscopic benchmarks for future simulations.

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

HYDRODYNAMIC ANALYSIS OF MACROALGAE LOCAL MODEL USING COMPUTATIONAL FLUID DYNAMICS

In this article, a local scale, fully nonlinear coupled fluid-structural interaction (FSI) sugar kelp model has been developed using a computational fluid dynamics (CFD) method. In this model, to be consistent with available experimental data, the sugar kelp is approximated as elongated rectangles with smoothed isosceles triangles at the ends and a single kelp model with one end fixed in a channel with constant current model is developed. Several different current speeds are simulated, and the resulting drag forces and calculated drag coefficients are validated by comparison with experimental data from the literature. In a previous study, a global scale model was developed using a computational structural dynamics (CSD) method to simulate macroalgae farming system and guide the system configuration design. In the global scale model, the hydrodynamic forces are calculated using Morison’s equation and the kinematics and dynamics of the sugar kelp are simplified and the group of kelps attached to the long line is modeled as a slender structure with the same length and an effective diameter such that the volumes are consistent with the real physical system. This simplified model matches the weight and buoyancy but adjusting the hydrodynamic properties when the general hydrodynamic coefficients are employed. Therefore, optimal hydrodynamic coefficients used in global scale model were determined to obtain the hydrodynamic force more accurately. The validated local scale model is then be applied to determine the hydrodynamic coefficients of the simplified sugar kelp model for global dynamic analysis.

hydrodynamic modeling, macroalgae, CFD model↗
DOE OSTI2020

Experimental and theoretical study of energy transfer in a chromophore triad: What makes modeling dynamics successful?

Simulation of electronic dynamics in realistically large molecular systems is a demanding task that has not yet achieved the same level of quantitative prediction already realized for its static counterpart. This is particularly true for processes occurring beyond the Born–Oppenheimer regime. Non-adiabatic molecular dynamics (NAMD) simulations suffer from two convoluted sources of error: numerical algorithms for dynamics and electronic structure calculations. While the former has gained increasing attention, particularly addressing the validity of ad hoc methodologies, the effect of the latter remains relatively unexplored. Indeed, the required accuracy for electronic structure calculations to reach quantitative agreement with experiment in dynamics may be even more strict than that required for static simulations. In this study, we address this issue by modeling the electronic energy transfer in a donor–acceptor–donor (D–A–D) molecular light harvesting system using fewest switches surface hopping NAMD simulations. In the studied system, time-resolved experimental measurements deliver complete information on spectra and energy transfer rates. Subsequent modeling shows that the calculated electronic transition energies are “sufficiently good” to reproduce experimental spectra but produce over an order of magnitude error in simulated dynamical rates. We further perform simulations using artificially shifted energy gaps to investigate the complex relationship between transition energies and modeled dynamics to understand factors affecting non-radiative relaxation and energy transfer rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Nonadiabatic molecular dynamics analysis of hybrid Dion–Jacobson 2D leads iodide perovskites

The past six years have witnessed the rapid growth of interest in Dion–Jacobson (DJ) phase two-dimensional (2D) hybrid halide perovskites as optoelectronic materials with considerable intrinsic stability. The precise relationships between structural variations and the resulting charge carrier dynamics at finite temperature in these materials are keys to practical applications and are not yet completely understood. Here, we study 3-(aminomethyl) piperidinium (3AMP) and 4-(aminomethyl) piperidinium (4AMP) spacer cation-based lead iodide DJ phase systems and find these spacer cations to have a profound impact on the structural dynamics. Particularly, large conformational dynamics of the 3AMP-based perovskite compared to that of the 4AMP at room temperature leads to pronounced state energy fluctuation near band edges and further results in a shorter quantum coherence. The faster quantum decoherence of the 3AMP spacer-based perovskite underpins a longer nonradiative lifetime, offering insight into its superior performance as an optoelectronic material. This work sheds light on the relationship between structural fluctuations and charge carrier dynamics that can help in designing 2D perovskites with superior photophysical properties.

Wang, Ying (ORCID:0000000349048227)↗
DOE OSTI2024

Solid, structured composite neutron detectors with high dynamic range capability

Neutron detectors are essential across disciplines such as fundamental science, nuclear security, safeguards, and civilian applications. While 3 He-filled gas proportional counters have long been revered for their efficacy in detecting thermal neutrons and praised for their efficiency, neutron/gamma discrimination, and stability, the scarcity of 3He has spurred a search for alternatives. Here, we explore a solid structured scintillating particle composite (SPC) consisting of 6 Li-containing scintillating glass particles within an acrylic matrix as a neutron detector for high dynamic range applications. We show for the first time that an SPC neutron detector can boast an intrinsic detection efficiency of 0.261% for pure 252 Cf fission neutrons and an overall neutron detection efficiency of (0.546 ± 0.003)% at the Neutron Free-in-Air facility while being able to function in an intense gamma-ray environment. We also show that the SPC neutron detector supports fast neutron capture times and enables a dual-readout scheme that extends the detector dynamic range to high incident neutron fluxes. A scalable fabrication process allows for tailoring the SPC detector properties to the requirements of specific applications. Good agreement is found between the experimental results taken with a National Institute of Standards and Technology traceable 252 Cf source and the coupled MCNP6 and optical-ray-tracing simulations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Scattering theory in noncanonical phase space: A Drift-Kinetic collision operator for weakly collisional plasmas

After developing a scattering theory for grazing collisions in general noncanonical phase spaces, we introduce a guiding center collision operator in five-dimensional phase space designed for plasma regimes characterized by long wavelengths (relative to the Larmor radius), low frequencies (relative to the cyclotron frequency), and weak collisionality (where repeated Coulomb collisions induce cumulatively small changes in particle magnetic moment). The collision operator is fully determined by the noncanonical Hamiltonian structure of guiding center dynamics and exhibits a metriplectic structure, ensuring the conservation of particle number, momentum, energy, and interior Casimir invariants. It also satisfies an H-theorem, allowing for deviations from an equilibrium Maxwellian distribution due to the nontrivial kernel of the noncanonical guiding center Poisson tensor, spanned by the magnetic moment. We propose that this collision operator and its underlying mathematical structure may offer valuable insight into the study of turbulence, transport, and self-organizing phenomena in both laboratory and astrophysical plasmas.

Hamiltonian mechanics↗
DOE OSTI2023

Polymorphic structure of $\langle a \rangle$-type screw dislocation cores in $\alpha$-Ti

The dislocation core structure has a significant role in determining the dominant slip plane and the magnitude of the Peierls stress for a dislocation. An important challenge when studying dislocation cores is to determine the stable and metastable core morphologies, and then relate these structures to the dynamics of the dislocations. ere this study introduces a method for identifying core structures that are metastable at zero temperature. Application of this method to $\langle$a$\rangle$-type screw dislocations in α-Ti (as described using an empirical potential) reveals a multitude of (meta)stable nonplanar cores. Molecular dynamics studies show how the competing metastable core structures determine the properties of the dislocations at temperature and under a range of non-Schmid stresses.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Reconfigurable structure and tunable transport in synchronized active spinner materials

Ensembles of actuated colloids are excellent model systems to explore emergent out-of-equilibrium structures, complex collective dynamics, and design rules for the next generation materials. Here, we demonstrate that ferromagnetic microparticles suspended at an air-water interface and energized by an external rotating magnetic field spontaneously form dynamic ensembles of synchronized spinners in a certain range of the excitation field parameters. Each spinner generates strong hydrodynamic flows, and collective interactions of the multiple spinners promote a formation of dynamic lattices. On the basis of experiments and simulations, we reveal structural transitions from liquid to nearly crystalline states in this novel active spinner material and demonstrate that dynamic spinner lattices are reconfigurable, capable of self-healing behavior and that the transport of embedded inert cargo particles can be remotely tuned by the parameters of the external excitation field. Our findings provide insights into the behavior of active spinner materials with reconfigurable structural order and tunable functionalities.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Direct Observation of Ultrafast Hydrogen Bond Strengthening in Liquid Water

Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network, including unusually efficient vibrational energy redistribution and relaxation. An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here we measured the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04 Å on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of ~1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on the femtosecond timescales. Our experiment and simulations unveiled the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

36 MATERIALS SCIENCE↗
DOE OSTI2022

How arsenic makes amorphous GeSe a robust chalcogenide glass for advanced memory integration

The 3D integration technology in semiconductor fabrication requires a key component, the ovonic threshold switching (OTS) selector, to suppress the current leakage. The As doped amorphous (a-) GeSe glass is a commercialized OTS material in 3D phase-change memory, but the understanding of such a doping mechanism is still inadequate. Here we systematically explore the effect of As doping on the structural, bonding, and dynamics properties of a-GeAsSe using ab initio molecular dynamics simulations. The results reveal that As atoms form strong bonds with both Ge and Se atoms. The distorted octahedral structures and the 5-fold rings linked by atoms are increased. All of these structural features lead to a more disordered configuration. Moreover, as atoms have notably slowed down the atomic mobility, rendering a-GeAsSe a high stability. Overall, our studies offer insightful understanding of As-doping in OTS materials, paving the way for the design and application of advanced selector devices.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Mesoscopic two-point collective dynamics of glass-forming liquids

The collective density–density and hydrostatic pressure–pressure correlations of glass-forming liquids are spatiotemporally mapped out using molecular dynamics simulations. It is shown that the sharp rise of structural relaxation time below the Arrhenius temperature coincides with the emergence of slow, nonhydrodynamic collective dynamics on mesoscopic scales. The observed long-range, nonhydrodynamic mode is independent of wave numbers and closely coupled to the local structural dynamics. Below the Arrhenius temperature, it dominates the slow collective dynamics on length scales immediately beyond the first structural peak in contrast to the well-known behavior at high temperatures. Furthermore, these results highlight a key connection between the qualitative change in mesoscopic two-point collective dynamics and the dynamic crossover phenomenon.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A glossary of plant cell structures: Current insights and future questions

Abstract In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.

Biochemistry & Molecular Biology↗