Search Results (39)

Prion diseases such as chronic wasting disease involve the conformational conversion of the cellular prion protein (PrP^C) into its misfolded, β-rich isoform (PrP^Sc). While chemical denaturants such as guanidine hydrochloride (GdnHCl) and urea are commonly used to study this process in vitro, their distinct molecular effects on native and misfolded PrP conformers remain incompletely understood. In this study, we employed 500 ns all-atom molecular dynamics simulations and essential collective dynamics analysis to investigate the differential effects of GdnHCl and urea on a composite PrP^C/PrP^Sc system, where white-tailed deer PrP^C interfaces with a corresponding PrP^Sc conformer. GdnHCl was found to preserve interfacial alignment and enhance β-sheet retention in PrP^Sc, while urea promoted partial β-strand dissolution and interfacial destabilization. Both denaturants formed transient contacts with PrP, but urea displaced water hydrogen bonds more extensively. Remarkably, we also observed long-range dynamical coupling across the PrP^C/PrP^Sc interface and between transiently bound solutes and distal protein regions. These findings highlight distinct, denaturant-specific mechanisms of protein destabilization and suggest that localized interactions may propagate non-locally via mechanical or steric pathways. Our results provide molecular-scale insights relevant to prion conversion mechanisms and inform experimental strategies using GdnHCl and urea to modulate misfolding processes in vitro. Full article

The cubic phase of the high-entropy alloy AgBi_1−xSb_xSe_0.8S_0.6Te_0.6 compound, characterized by the substitution of Sb for Bi in the structure to enhance phonon scattering, has been analyzed for local atomic displacements and electronic structure using a combination of X-ray absorption and X-ray photoelectron spectroscopy techniques. Notably, Ag K-edge and Bi L₃-edge X-ray absorption measurements demonstrate a contraction of bond distances upon substitution due to the smaller size of Sb. Conversely, X-ray photoelectron spectroscopy reveals that, while Ag remains predominantly in the Ag¹⁺ state across all samples, Bi and Sb exhibit a single valence state only for minimal Sb substitution. At higher Sb substitution levels, both Bi and Sb manifest mixed valence states, indicating complex electronic behavior that potentially influences the thermoelectric properties of the system. These findings suggest that optimizing the local structure through Sb substitution can be beneficial in enhancing the material’s thermoelectric performance. Full article

CoCrNi medium-entropy alloy (MEA) coatings prepared using laser cladding (LC) with unique properties have aroused great interest in recent years and have been widely studied. However, limited studies have been conducted on the effect of adding Al/Fe on the wear properties of CoCrNi MEA coatings prepared on the surface of stainless steel. In this study, AlCoCrFeNi, CoCrFeNi, and CoCrNi MEA LC coatings were prepared on a stainless steel substrate. The grain structures and microscopic morphologies of coatings were characterized, and the wear mechanisms were analyzed using the nano-indentation and wear tests. The hardness-strengthening mechanism was theoretically investigated using phase diagrams and molecular dynamics (MD). The phase diagram results show that the addition of Al lowered the nucleation initiation temperature, thereby increasing the nucleation rate and forming more grains. Moreover, according to the Voronoi volumes and mean–square atomic displacements (MASD) results using MD, the addition of Al makes the appearance of severe localized lattice distortions, while the addition of Fe tends to form short-range ordered structures. In summary, fine-grain strengthening and the hardness strengthening caused by local lattice distortion were the main strengthening mechanisms of AlCoCrFeNi. These findings are highly significant for expanding the application potential and provide profound insights into the wear properties of the CoCrNi MEA coatings. Full article

As talk grows about billions or even trillions of dollars being directed toward potential “Net Zero” activities, it is imperative that the chemistry inherent in or driving those actions make scientific sense. The challenge is to close the mass and energy balances to the carbon and oxygen cycles in the Earth’s atmosphere and oceans. Several areas of climate science have been identified that chemists can investigate through methods that do not require a supercomputer or a climate model for investigation, most notably the following: (1) The carbon cycle, which still needs to be balanced, as many known streams, such as carbon to landfills, carbon in human-enhanced sewage and land runoff streams, and carbon stored in homes and other material, do not seem to have been accounted for in carbon balances used by the IPCC. (2) Ocean chemistry and balances are required to explain the causes of regional and local-scale salinity, pH, and anoxic conditions vs. global changes. For example, local anoxic conditions are known to be impacted by changes in nutrient discharges to oceans, while large-scale human diversions of fresh water streams for irrigation, power, and industrial cooling must have regional impacts on oceanic salinity and pH. (3) Carbon Capture and Storage (CCS) schemes, if adopted on the large scales being proposed (100s to 1000s of Gt net injection by 2100), should impact the composition of the atmosphere by reducing free oxygen, adding more water from combustion, and displacing saline water from subsurface aquifers. Data indicate that atmospheric oxygen is currently dropping at about twice the rate of CO₂ concentrations increasing, which is consistent with combustion chemistry with 1.5 to 2 molecules of oxygen being converted through combustion to 1 molecule of CO₂ and 1 to 2 molecules of H₂O, with reverse reactions occurring as a result of oxygenic photosynthesis by increased plant growth. The CCS schemes will sabotage these reverse reactions of oxygenic photosynthesis by permanently sequestering the oxygen atoms in each CO₂ molecule. Full article

In this study, molecular dynamics (MD) simulations were used to investigate how alloying tungsten (W) with molybdenum (Mo) and local strain affect the primary defect formation and interstitial dislocation loops (IDLs) in W–Mo alloys. While the number of Frenkel pairs (FPs) in the W–Mo alloy is similar to pure W, it is half that of pure Mo. The W–20% Mo alloy, chosen for further analysis, showed minimal FP variance after collision cascades induced by primary knock-on atoms (PKAs) at 10 to 80 keV. The research examined hydrostatic strains from −1.4% to 1.6%, finding that higher strains correlated with increased FP counts and cluster formation, including IDLs. The following two types of IDLs were identified: majority ½ <111> loops as well as <100> IDLs that formed within the initial picoseconds of the simulations under higher tensile strain (1.6%) and larger PKA energies (80 keV). The strain effects also correlated with changes in threshold displacement energy (TDE), with higher FP formation under tensile strain. This study highlights the impact of strain and alloying on radiation damage, particularly in low-temperature, high-energy environments. Full article

This study presents a molecular dynamics (MD) investigation of the evolution of local atomic environments (LAEs) in a Cu₆₆Zr₃₄ bulk metallic glass (BMG), both at rest and under constant shear deformation. LAEs were characterized using Voronoi polyhedra analysis. Even in the absence of external load, LAEs frequently transformed into one another due to short-ranged atomic position fluctuations. However, as expected, each transition from one polyhedra to another was balanced by the reverse transition, thereby preserving the proportions of the different polyhedra. Cu-centered icosahedral LAEs were observed to preferentially transform into and from <1,0,9,3,0>, <0,1,10,2,0>, and <0,2,8,2,0> LAEs. Upon applying pure shear, the simulation box was first deformed in one direction up to a strain of 25% and then in the opposite direction to the same strain level. Shear deformation induced large nonaffine atomic displacements in the directions parallel to the shear, which were concentrated in specific regions of the BMG, forming band-like regions. From the onset, shear deformation led to the destabilization of Cu-centered icosahedral LAEs, as indicated by more frequent transitions to and from other polyhedra. Unlike other Cu-centered LAEs, icosahedra were also found to be more sensitive to yielding. The destruction of Cu-centered icosahedra was primarily a result of net transformations into <1,0,9,3,0> and <0,2,8,2,0> LAEs in the BMG subjected to pure shear, with a minor contribution of transformations involving the <0,1,10,2,0> polyhedra. Full article

Time-dependent deformation in nuclear graphite is influenced by the creation and migration of radiation-induced defects in the reactor environment. This study investigates the role of pre-existing defects such as point defect clusters and Mrozowski cracks in nuclear graphite IG-110. Separate specimens were irradiated with a 2.8 MeV Au²⁺ beam with a fluence of 4.38 × 10¹⁴ cm⁻² and an 8 MeV C²⁺ beam with a fluence of 1.24 × 10¹⁶ cm⁻². Microscopic specimens were either mechanically loaded inside a transmission electron microscope (TEM) or subjected to ex situ indentation-based creep loading. In situ TEM tests showed significant plasticity in regions highly localized around the Mrozowski cracks, resembling slip or ripplocation bands. Slip bands were also seen near regions without pre-existing defects but at very high stresses. Ex situ self-ion irradiation embrittled the specimens and decreased the creep displacement and rate, while heavy ion irradiation resulted in the opposite behavior. We hypothesize that the large-sized gold ions (compared to the carbon atoms) induced interplanar swelling as well as cross-plane channels for increased defect mobility. These findings illustrate the role of pre-existing defects in the dynamic relaxation of stresses during irradiation and the need for more studies into the radiation environment’s impact on the mechanical response of nuclear graphite. Full article

Carbon-based novel low-dimensional XC/YC (with X, Y ≡ Si, Ge, and Sn) heterostructures have recently gained considerable scientific and technological interest in the design of electronic devices for energy transport use in extreme environments. Despite many efforts made to understand the structural, electronic, and vibrational properties of XC and X_xY_1−xC alloys, no measurements exist for identifying the phonon characteristics of superlattices (SLs) by employing either an infrared and/or Raman scattering spectroscopy. In this work, we report the results of a systematic study to investigate the lattice dynamics of the ideal ${\left(\mathrm{X}\mathrm{C}\right)}_{\mathrm{m}}$/${\left(\mathrm{Y}\mathrm{C}\right)}_{\mathrm{n}}$ as well as graded ${\left(\mathrm{X}\mathrm{C}\right)}_{10-∆}/{\left({\mathrm{X}}_{0.5}{\mathrm{Y}}_{0.5}\mathrm{C}\right)}_{∆}/{\left(\mathrm{Y}\mathrm{C}\right)}_{10-∆}/{\left({\mathrm{X}}_{0.5}{\mathrm{Y}}_{0.5}\mathrm{C}\right)}_{∆}$ SLs by meticulously including the interfacial layer thickness $∆$ (≡1–3 monolayers). While the folded acoustic phonons (FAPs) are calculated using a Rytov model, the confined optical modes (COMs) and FAPs are described by adopting a modified linear-chain model. Although the simulations of low-energy dispersions for the FAPs indicated no significant changes by increasing $∆$, the results revealed, however, considerable “downward” shifts of high frequency COMs and “upward” shifts for the low energy optical modes. In the framework of a bond polarizability model, the calculated results of Raman scattering spectra for graded SLs are presented as a function of $∆.$ Special attention is paid to those modes in the middle of the frequency region, which offer strong contributions for enhancing the Raman intensity profiles. These simulated changes are linked to the localization of atomic displacements constrained either by the XC/YC or YC/XC unabrupt interfaces. We strongly feel that this study will encourage spectroscopists to perform Raman scattering measurements to check our theoretical conjectures. Full article

The studies of polaronic centers in a homologous series of scheelite-type compounds AWO₄ (A = Ca, Sr, Ba) were performed using the W L₃-edge and Sr K-edge X-ray absorption spectroscopy combined with the reverse Monte Carlo simulations, X-ray photoelectron spectroscopy (XPS), and first-principles calculations. Protonated scheelites H_xAWO₄ were produced using acid electrolytes in a one-step route at ambient conditions. The underlying mechanism behind this phenomenon can be ascribed to the intercalation of H⁺ into the crystal structure of tungstate, effectively resulting in the reduction of W⁶⁺ to W⁵⁺, i.e., the formation of polaronic centers, and giving rise to a characteristic dark blue-purple color. The emergence of the W⁵⁺ was confirmed by XPS experiments. The relaxation of the local atomic structure around the W⁵⁺ polaronic center was determined from the analysis of the extended X-ray absorption fine structures using the reverse Monte Carlo method. The results obtained suggest the displacement of the W⁵⁺ ions from the center of [W⁵⁺O₄] tetrahedra in the structure of AWO₄ scheelite-type tungstates. This finding was also supported by the results of the first-principles calculations. Full article

NbAs is a Weyl semimetal and belongs to the group of topological phases that exhibit distinct quantum and topological attributes. Topological phases have a fundamentally different response to external perturbations, such as magnetic fields. To obtain insights into the response of such phases to pressure, we conducted a comprehensive study on the pressure-induced electronic and structural transitions in NbAs. We used micro-X-ray diffraction (XRD) and micro-X-ray spectroscopy (XAS) techniques to elucidate the changes at different atomic and electronic length scales (local, medium, and bulk) as combined with theoretical calculations. High-pressure XRD measurements revealed a rather common compression behavior up to ~12 GPa that could be fitted to an equation of state formalism with a bulk modulus of $⟨K_0⟩=$ 179.6 GPa. Complementary Nb K-edge XAS data unveiled anomalies at pressure intervals of ~12–15 and ~25–26 GPa in agreement with previous literature data from XRD studies. We attribute these anomalies to a previously reported topological Lifshitz transition and the tetragonal-to-hexagonal phase transition, respectively. Analysis of EXAFS results revealed slight changes in the mean next-nearest neighbor distance Nb–As₍₁₎ (~2.6 Å) at ~15 GPa, while the second nearest neighboring bond Nb–Nb₍₁₎ (~3.4 Å) shows a pronounced anomaly. This indicates that the electronic changes across the Lifshitz transition are accommodated first in the medium-range atomic structure and then at the local range and bulk. The variances of these bonds show anomalous but progressive evolutions close to the tetragonal-to-hexagonal transition at ~25 GPa, which allowed us to derive the evolution of vibration properties in this material. We suggest a prominent displacive character of the $I{4}_{1}md\to P\overline{6}m2$ transition facilitated by phonon modes. Full article

The formation of intrinsic point defects in the N-sublattice of semi-insulating Mg-doped GaN crystals grown by the ammonothermal method (SI AT GaN:Mg) was investigated for the first time. The grown-in defects produced by the displacement of nitrogen atoms were experimentally observed as deep traps revealed by the Laplace transform photoinduced transient spectroscopy in the compensated p-type crystals with the Mg concentrations of 6 × 10¹⁸ and 2 × 10¹⁹ cm⁻³ and resistivities of ~10¹¹ Ωcm and ~10⁶ Ωcm, respectively. In both kinds of materials, three closely located traps with activation energies of 430, 450, and 460 meV were revealed. The traps, whose concentrations in the stronger-doped material were found to be significantly higher, are assigned to the (3+/+) and (2+/+) transition levels of nitrogen vacancies as well as to the (2+/+) level of nitrogen split interstitials, respectively. In the material with the lower Mg concentration, a middle-gap trap with the activation energy of 1870 meV was found to be predominant. The results are confirmed and quantitatively described by temperature-dependent Hall effect measurements. The mechanism of nitrogen atom displacement due to the local strain field arising in SI AT GaN:Mg is proposed and the effect of the Mg concentration on the charge compensation is discussed. Full article

Systematic results of lattice dynamical calculations are reported as a function of m and n for the novel (SiC)_m/(GeC)_n superlattices (SLs) by exploiting a modified linear-chain model and a realistic rigid-ion model (RIM). A bond polarizability method is employed to simulate the Raman intensity profiles (RIPs) for both the ideal and graded (SiC)_10-Δ/(Si_0.5Ge_0.5C)_Δ/(GeC)_10-Δ/(Si_0.5Ge_0.5C)_Δ SLs. We have adopted a virtual-crystal approximation for describing the interfacial layer thickness, Δ (≡0, 1, 2, and 3 monolayers (MLs)) by selecting equal proportions of SiC and GeC layers. Systematic variation of Δ has initiated considerable upward (downward) shifts of GeC-(SiC)-like Raman peaks in the optical phonon frequency regions. Our simulated results of RIPs in SiC/GeC SLs are agreed reasonably well with the recent analyses of Raman scattering data on graded short-period GaN/AlN SLs. Maximum changes in the calculated optical phonons (up to ±~47 cm⁻¹) with Δ = 3, are proven effective for causing accidental degeneracies and instigating localization of atomic displacements at the transition regions of the SLs. Strong Δ-dependent enhancement of Raman intensity features in SiC/GeC are considered valuable for validating the interfacial constituents in other technologically important heterostructures. By incorporating RIM, we have also studied the phonon dispersions [${{{\mathsf{\omega }}_{}}_{\mathrm{j}}^{\mathrm{S}\mathrm{L}}}_{}\left(\overrightarrow{\mathbf{q}}\right)$] of (SiC)_m/(GeC)_n SLs along the growth [001] as well as in-plane [100], [110] directions [i.e., perpendicular to the growth]. In the acoustic mode regions, our results of ${{{\mathsf{\omega }}_{}}_{\mathrm{j}}^{\mathrm{S}\mathrm{L}}}_{}\left(\overrightarrow{\mathbf{q}}\right)$ have confirmed the formation of mini-gaps at the zone center and zone edges while providing strong evidences of the anti-crossing and phonon confinements. Besides examining the angular dependence of zone-center optical modes, the results of phonon folding, confinement, and anisotropic behavior in (SiC)_m/(GeC)_n are compared and contrasted very well with the recent first-principles calculations of (GaN)_m/(AlN)_n strained layer SLs. Full article

A detailed comprehension of protein function requires information on the spatial structure of the protein, which is often gathered from X-ray crystallography. However, conformational dynamics often also plays an important functional role in proteins and can be directly investigated by complementary quasielastic neutron scattering. A classic example for dynamics–function correlations is Photosystem II, which is a multimeric pigment–protein complex responsible for catalyzing the light-induced photosynthetic water splitting into protons and oxygen. Several functional subprocesses of photosynthetic electron transfer and water splitting are strongly dependent on temperature and hydration, two factors also known to affect protein dynamics. Photosystem II is often investigated in the form of membrane fragments, where the protein complex remains embedded into its native lipid environment. However, experiments on protein function are often carried out in solution state, while direct investigations of molecular dynamics by quasielastic neutron scattering are mainly performed using specifically hydrated membrane fragments only. The present study provides the first quasielastic neutron scattering investigation of the molecular dynamics of Photosystem II membrane fragments (PSIImf) in solution over a wide temperature range from 50 to 300 K. At physiological temperatures above the melting point of water, we observed that the dynamics of PSIImf are significantly activated, leading to larger atomic mean square displacement values compared to those of specifically hydrated membrane stacks. The QENS data can be described by two dynamical components: a fast one, most probably corresponding to methyl group rotation; and a slower one, representing localized conformational dynamics. The latter component could be fitted by a jump-diffusion model at 300 K. The dynamics observed characterize the level of flexibility necessary for the proper PS II functionality under physiological conditions. In contrast, we observe a severe restriction of molecular dynamics upon freezing of the solvent below ~276 K. We associate this unexpected suppression of dynamics with a substantial aggregation of PSIImf caused by ice formation. Full article

The Raman scattering, infrared absorption, and reflection spectra of hexagonal non-centrosymmetric BaZnBO₃F and BaAlBO₃F₂ and centrosymmetric BaZn₃BO₃F₂ and BaZnCO₃F₂ are calculated using the standard procedures of the CRYSTAL package with the basis of localized orbitals and the B3LYP hybrid functional within the framework of the Hartree-Fock conjugate perturbation method. It is shown that the layered structure of crystals manifests itself in the spectra of vibrational modes polarized along and perpendicular to the c axis with wavenumbers for the lattice region formed by displacements of atoms in [BaF]∞ and [MAO₃]∞ (M: Zn, Al; A: B, C) layers, for molecular deformation outside and in the plane of anions BO₃ and CO₃. The quantitative and qualitative composition of the spectra is determined by the symmetry of the crystal lattice. Full article

Austenitic stainless steel D9 is a candidate for Generation IV nuclear reactor structural materials due to its enhanced irradiation tolerance and high-temperature creep strength compared to conventional 300-series stainless steels. But, like other austenitic steels, D9 is susceptible to irradiation-induced clustering of Ni and Si, the mechanism for which is not well understood. This study utilizes atom probe tomography (APT) to characterize the chemistry and morphology of Ni–Si nanoclusters in D9 following neutron or proton irradiation to doses ranging from 5–9 displacements per atom (dpa) and temperatures ranging from 430–683 °C. Nanoclusters form only after neutron irradiation and exhibit classical coarsening with increasing dose and temperature. The nanoclusters have Ni₃Si stoichiometry in a Ni core–Si shell structure. This core–shell structure provides insight into a potentially unique nucleation and growth mechanism—nanocluster cores may nucleate through local, spinodal-like compositional fluctuations in Ni, with subsequent growth driven by rapid Si diffusion. This study underscores how APT can shed light on an unusual irradiation-induced nanocluster nucleation mechanism active in the ubiquitous class of austenitic stainless steels. Full article