Local Structural Fluctuations Research Articles

Doping dependence of spin-momentum locking in bismuth-based high-temperature cuprate superconductors

Non-zero spin orbit coupling has been reported in several unconventional superconductors due to the absence of inversion symmetry breaking. This contrasts with cuprate superconductors, where such interaction has been neglected for a long time. The recent report of a non-trivial spin orbit coupling in overdoped Bi2212 cuprate superconductor, has re-opened an old debate on both the source and role of such interaction and its evolution throughout the superconducting dome. Using high-resolution spin- and angle-resolved photoemission spectroscopy, we reveal a momentum-dependent spin texture throughout the hole-doped side of the superconducting phase diagram for single- and double-layer bismuth-based cuprates. The universality of the reported effect among different dopings and the disappearance of spin polarization upon lead substitution, suggest a common source. We argue that local structural fluctuations of the CuO planes and the resulting charge imbalance may cause local inversion symmetry breaking and spin polarization, which might be crucial for understanding cuprates physics.

Structural fluctuations in thin cohesive particle layers in powder-based additive manufacturing

Producing dense and homogeneous powder layers with smooth free surface is challenging in additive manufacturing, as interparticle cohesion can strongly affect the powder packing structure and therefore influence the quality of the end product. We use the Discrete Element Method to simulate the spreading process of spherical powders and examine how cohesion influences the characteristics of the packing structure with a focus on the fluctuation of the local morphology. As cohesion increases, the overall packing density decreases, and the free surface roughness increases, which is calculated from digitized surface height distributions. Local structural fluctuations for both quantities are examined through the local packing anisotropy on the particle scale, obtained from Voronoï tessellation. The distributions of these particle-level metrics quantify the increasingly heterogeneous packing structure with clustering and changing surface morphology.

In search of a precursor for crystal nucleation of hard and charged colloids.

The interplay between crystal nucleation and the structure of the metastable fluid has been a topic of significant debate over recent years. In particular, it has been suggested that even in simple model systems such as hard or charged colloids, crystal nucleation might be foreshadowed by significant fluctuations in local structure around the location where the nucleus first arises. We investigate this using computer simulations of spontaneous nucleation events in both hard and charged colloidal systems. To detect local structural variations, we use both standard and unsupervised machine learning methods capable of finding hidden structures in the metastable fluid phase. We track numerous nucleation events for the face-centered cubic and body-centered cubic crystals on a local level and demonstrate that all signs of crystallinity emerge simultaneously from the very start of the nucleation process. We thus conclude that we observe no precursor for the crystal nucleation of hard and charged colloids.

Regulation Mechanism of Electron Transfer Reaction from Cytochrome C to Cytochrome C Oxidase

The respiratory chain in mitochondria is quite essential for the energy generation in cells, effectively producing “the energy currency in living organisms”, ATP. The driving force for this system is a series of electron transfers form Complex I (NADH:quinone oxidoreductase) to Complex IV (Cytochrome c Oxidase; CcO) in inner mitochondria membrane, and these electron transfer reactions promote the proton pumping from the matrix to the intermembrane space in mitochondria, and, by use of the resulting proton concentration gradient across the membrane, Complex V (ATP synthase) produces ATP. These series of electron transfer reactions terminate at CcO to reduce molecular oxygen to water molecules. The electrons required for this four-electron reduction of molecular oxygen in CcO are donated from a small soluble electron transfer hemoprotein, Cytochrome c (Cyt c), and this electron transfer is also associated with the proton pumping for the ATP generation in the respiratory chain. To examine the molecular regulation mechanism of the electron transfer reaction to terminate the electron transport chain for four-electron reduction of molecular oxygen and proton pumping for the ATP generation, we kinetically followed the electron transfer reaction and analyzed the electron transfer reaction by the Michaelis-Menten equation. By utilizing the Cyt c mutants, we identified the amino acid residues to regulate the electron transfer reactions (Biochem. J., 2020, 477,1565). The kinetic analysis of the electron transfer reaction also revealed that the apparent rate for the electron transfer reaction determined by the steady-state kinetics is much slower than the intramolecular electron transfer rate in the Cyt c – CcO complex. On the other hand, we successfully determined the interaction site between Cyt c and CcO by using NMR (Proc. Natl. Acad. Sci., 2011, 108, 12271) and protein-protein docking simulation (J. Biol. Chem., 2016, 291, 15320). The Cyt c – CcO complex structure estimated from the NMR and protein-protein docking simulation clearly showed that the two redox centers, heme iron in Cyt c and CuA in subunit II of CcO, were located more than 20 Å apart, and the complexes exhibiting shorter redox center distances were energetically unstable. Combined with the results from kinetic and structural studies, we proposed a “conformationally gated electron transfer mechanism”, where the thermal fluctuation of the protein structure controls the electron transfer rate. However, direct experimental evidence that protein conformational fluctuations regulate electron transfer reactions has not been obtained. In this study, we focused on the viscosity of the protein solution as a factor to regulate the conformational fluctuation of the proteins, based on the assumption that high viscosity of the solution suppresses the conformational fluctuation. The electron transfer reaction from Cyt c to CcO was examined in the high viscosity solution and NMR relaxation measurements under high viscosity were also performed to identify the local structural fluctuation responsible for the regulation of the electron transfer rate. Together with the transient complex structures between Cyt c and CcO estimated by the MD simulation, the regulation mechanism of the electron transfer from Cyt c to CcO based on the “conformational gating” will be discussed.

Critical behavior of the fluctuation heat capacity near the glass transition of metallic glasses

The high-frequency shear modulus of five Zr-, Pd-, Cu-based conventional and two high-entropy bulk metallic glasses was measured in a wide temperature range up to the beginning of crystallization. Using these data and general thermodynamic relations, the “fluctuation” heat capacity ΔCf determined by local structural fluctuations in the defect regions is introduced and calculated. It is found that ΔCf temperature dependence for all metallic glasses has a large peak located slightly below or above the glass transition temperature but clearly lower than the crystallization onset temperature. The form of this peak resembles the characteristic λ-peak typical for order–disorder phase transitions. It is suggested that this ΔCf-peak reflects certain underlying critical phenomenon. The critical temperature T0 (peak temperature) and corresponding critical index α are determined. Averaged over all seven metallic glasses under investigation in the initial and relaxed states, the critical index <α>=0.26. The results obtained indicate that the fluctuations of thermal energy near the glass transition bear the marks of a continuous phase transition. However, the derived critical index is between those corresponding to a second-order phase transition (α≈0.1) and a critical transition characterized by a tricritical point (α≈0.5).

Probing the Disorder Inside the Cubic Unit Cell of Halide Perovskites from First-Principles.

Strong deviations in the finite temperature atomic structure of halide perovskites from their average geometry can have profound impacts on optoelectronic and other device-relevant properties. Detailed mechanistic understandings of these structural fluctuations and their consequences remain, however, limited by the experimental and theoretical challenges involved in characterizing strongly anharmonic vibrational characteristics and their impact on other properties. We overcome some of these challenges by a theoretical characterization of the vibrational interactions that occur among the atoms in the prototypical cubic CsPbBr3. Our investigation based on first-principles molecular dynamics calculations finds that the motions of neighboring Cs-Br atoms interlock, which appears as the most likely Cs-Br distance being significantly shorter than what is inferred from an ideal cubic structure. This form of dynamic Cs-Br coupling coincides with very shallow dynamic potential wells for Br motions that occur across a locally and dynamically disordered energy landscape. We reveal an interesting dynamic coupling mechanism among the atoms within the nominal unit cell of cubic CsPbBr3 and quantify the important local structural fluctuations on an atomic scale.

Effect on intrinsic peroxidase activity of substituting coevolved residues from Ω-loop C of human cytochrome c into yeast iso-1-cytochrome c

Naturally-occurring variants of human cytochrome c (Cytc) that induce thrombocytopenia IV occur within Ω-loop C (residues 40–57). These variants enhance the peroxidase activity of human Cytc apparently by facilitating access to the heme by destabilizing Ω-loops C and D (residues 70–85). Given the importance of peroxidase activity in the early stages of apoptosis, we identified three sites with the EVmutation algorithm in or near Ω-loop C that coevolve and differ between yeast iso-1-Cytc and human Cytc. We prepared iso-1-Cytc variants with all possible combinations of the S40T, V57I and N63T substitutions to determine if these residues decrease the peroxidase activity of iso-1-Cytc to that of human Cytc producing an effective off state for a peroxidase signaling switch. At pH 6 and above, all variants significantly decreased peroxidase activity. However, the correlation of peroxidase activity with local and global stability, expected if cooperative unfolding of Ω-loops C and D is required for peroxidase activity, was generally poor. The m-values derived from the guanidine hydrochloride dependence of the kinetics of imidazole binding to horse Cytc, which is well-characterized by native-state hydrogen exchange methods, and K72A/K73A/K79A iso-1-Cytc show that local structural fluctuations and not subglobal cooperative unfolding of Ω-loops C and D are sufficient to permit binding of a small molecule like peroxide to the heme. A 2.46 Å structure of N63T iso-1-Cytc identifies a change to a hydrogen bond network linking Ω-loops C and D that could modulate the local fluctuations needed for the intrinsic peroxidase activity of Cytc.

Atomic-level characterization of free volume in the structure of Cu67Zr33 amorphous alloy

The structure of Cu67Zr33 amorphous alloy was investigated in terms of packing density and free volume by using neutron, x-ray diffraction and reverse Monte Carlo (RMC) modelling. The RMC model was analysed by a method of decomposing the three-dimensional atomic configuration into fundamental polyhedral units (termed as ‘holes’ referencing the Bernal’s works) of which faces are all triangles consisting of chemical bonds. Not only tetrahedral and octahedral holes but also other larger holes were identified. Moreover, the atomic packing fractions and free volumes in the respective polyhedral holes were evaluated with reference to those for the corresponding crystal structures. The results show that the distribution of free volumes for the larger holes can be described by the exponential function assuming that there are no energetic interactions between each other. On the other hand, the local structural fluctuations due to densely and loosely packed tetrahedral holes were observed, leading to the negative free volume spaces.

Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates

The series of RNA folding events that occur during transcription can critically influence cellular RNA function. Here, we present reconstructing RNA dynamics from data (R2D2), a method to uncover details of cotranscriptional RNA folding. We model the folding of the Escherichia coli signal recognition particle (SRP) RNA and show that it requires specific local structural fluctuations within a key hairpin to engender efficient cotranscriptional conformational rearrangement into the functional structure. All-atom molecular dynamics simulations suggest that this rearrangement proceeds through an internal toehold-mediated strand-displacementmechanism, which can be disrupted with a point mutation that limits local structural fluctuations and rescued with compensating mutations that restore these fluctuations. Moreover, a cotranscriptional folding intermediate could be cleaved invitro by recombinant E.coli RNase P, suggesting potential cotranscriptional processing. These results from experiment-guided multi-scale modeling demonstrate that even an RNA with a simple functional structure can undergo complex folding and processing during synthesis.

Single Ensemble Non-exponential Photoluminescent Population Decays from a Broadband White-Light-Emitting Perovskite.

The mechanism of white-light emission from layered Pb-X (X = Cl or Br) perovskites following UV excitation has generated considerable interest. Prior time-dependent studies indicated that the broadband photoluminescence (PL) from (110) perovskites arises from a distribution of self-trapped excitonic sites emitting in different regions of the visible spectrum with different decay dynamics. Here, using time-correlated single photon counting to study single crystals, we show that the white-light emission decay from the (110) perovskite (EDBE)PbBr4 (EDBE = 2,2'-(ethylenedioxy)bis(ethylammonium)) behaves as a single ensemble. Following the rapid decay (0.6 ns) of a small spectral side band, the broad emission line shape is constant to 100 ns. We propose that rapid local structural fluctuations cause the self-trapped excitons (STEs) to experience a wide range of energies, resulting in the very broad PL. The STEs sample fluctuating local environments on time scales fast compared to the PL, which averages the PL decay at all emission wavelengths, yielding single ensemble PL dynamics. Although emission occurs from a very wide, inhomogeneously broadened spectral line with time-averaged single ensemble luminescence dynamics, the decay is tri-exponential. Two heuristic models for the tri-exponential decay involving defects are discussed. Spin-coated films show faster non-exponential decays with the slowest component of the crystal PL absent. Like the crystals, the film PL decays as a single ensemble. These results demonstrate that the broadband emission decay of (EDBE)PbBr4 arises from a time-averaged single ensemble and not from a set of excited states emitting with distinct luminescence decays at different wavelengths.

Amorphous polymer dynamics and free volume element size distributions from ultrafast IR spectroscopy

A method for measuring the size and size probability distribution of free volume regions in polymeric materials using ultrafast infrared (IR) polarization-selective pump-probe experiments is presented. Measurements of the ultrafast dynamics of a vibrational probe (the CN stretch of phenyl selenocyanate) in poly(methyl methacrylate) show that the probe dynamics are highly confined. The degree of confinement was found to be both time-dependent and dependent on the vibrational frequency of the probe molecule. The experiments demonstrate that different vibrational frequencies correspond to distinct subensembles of probe molecules that have different dynamic properties determined by their local structural environments. By combining the degree of dynamical confinement with the molecular size of the probe molecule, the free volume element size probability distribution was determined and found to be in good agreement with the best established experimental measure of free volume. The relative probability of a free volume element size is determined by the amplitude of the nitrile absorption spectrum at the frequency of the measurement. The inhomogeneous broadening of the spectrum was linked to the vibrational Stark effect, which permits site selectivity. The observed dynamics at each frequency were then associated with a different size free volume element and distinct local electric field. The multiple timescales observed in the pump-probe experiments were connected to local structural fluctuations of the free volume elements.

Cation-Disordered Lithium-Excess Li-Fe-Ti Oxide Cathode Materials for Enhanced Li-Ion Storage.

Cation-disordered Li-excess lithium-transition metal (Li-TM) oxides designed based on the percolation theory are regarded as a promising new type of high-performance cathode material for Li-ion batteries. Herein, cation-disordered rocksalt-type Li-Fe-Ti oxides of Li0.89Fe0.44Ti0.45O2, Li1.18Fe0.34Ti0.45O2, and Li1.24Fe0.38Ti0.38O2 with different Li-to-transition metal ratios (Li/TM = 1, 1.49, or 1.63) are investigated to understand the effect of a Li excess on the electrochemical Li-ion storage properties. The Li excess leads to local structural fluctuations of the as-prepared Li-Fe-Ti oxides, contributing to the formation of 0-TM diffusion channels for rapid Li-ion migration. The as-prepared Li-excess Li-Fe-Ti oxide cathodes (Li/TM = 1.49 and Li/TM = 1.63) deliver a higher reversible capacity of over 220 mAh g-1 and a better rate capability compared to the Li/TM = 1 electrode, which possesses a maximum discharge capacity of only about 165 mAh g-1. The redox reactions of Fe2+/Fe3+ and O2-/O22- achieve the main capacity of the Li-excess Li-Fe-Ti oxide cathodes during cycling, as supported by 57Fe Mössbauer spectroscopy, O 1s X-ray photoelectron spectroscopy, and O K-edge soft X-ray absorption spectroscopy.

Modulus distribution in polyacrylonitrile-based carbon fiber monofilaments

Modulus distribution in carbon fiber (CF) monofilament plays a key role in bridging the microscopic heterogeneous structures to the macroscopic mechanical properties, and is critical to understand its performance. Here, we present a quantitative measurement of the modulus distributions for a series of commercially available polyacrylonitrile (PAN)-based CFs (T300, T700S, T800H, T1000G and M40J from Toray) using plasma-assisted radius profiling method. The distribution, which is unique for each kind of CFs, shows a strong correlation to monofilament tensile properties. Based on the observations, we propose a mechanical model that reveals the dependence of the tensile strength of CF monofilament on the local modulus gradient and the local structural fluctuations. The work is a great improvement to the traditional skin-core model, and facilitates the design of high strength and high modulus CFs. The mechanical model can be generally applied to all kinds of fiber-shaped structures and materials.

Heterogeneity at multiple length scales in halide perovskite semiconductors

Materials with highly crystalline lattice structures and low defect concentrations have classically been considered essential for high-performance optoelectronic devices. However, the emergence of high-efficiency devices based on halide perovskites is provoking researchers to rethink this traditional picture, as the heterogeneity in several properties within these materials occurs on a series of length scales. Perovskites are typically fabricated crudely through simple processing techniques, which leads to large local fluctuations in defect density, lattice structure, chemistry and bandgap that appear on short length scales ( 10 μm). Despite these variable and complex non-uniformities, perovskites maintain exceptional device efficiencies and are, as of 2018, the best-performing polycrystalline thin-film solar cell material. In this Review, we highlight the multiple layers of heterogeneity ascertained using high-spatial-resolution methods that provide access to the relevant length scales. We discuss the impact that the optoelectronic variations have on halide perovskite devices, including the prospect that it is this very disorder that leads to their remarkable power-conversion efficiencies. Despite their excellent macroscopic operational parameters, halide perovskites exhibit heterogeneity in materials properties at all lateral and vertical length scales. In this Review, we discuss the nature of heterogeneity in halide perovskites and assess the impact of these non-uniformities on their optoelectronic properties and how the heterogeneity may even be beneficial for device properties.

In-situ measurement of SiC/Si interfacial tensile strength of reaction bonded SiC/Si composite

Reaction bonded SiC/Si (RBSC) ceramic composites have been extensively used in applications calling for outstanding mechanical and thermal properties such as high energy laser (HEL) mirrors, advanced armors and semiconductor fabrication platforms. The phase components of RBSC generally include preexisting α-SiC, reaction formed β-SiC, and residual crystalline silicon (c-Si). In addition, however, a minor phase, amorphous Si (a-Si), is often observed near the SiC/Si interface due to local temperature and structural fluctuations that can occur during the composite fabrication. An in-situ tensile testing system composed of piezo stages, force sensor and specimen holders is integrated and accommodated inside a field emission scanning electron microscope (FE-SEM) for the nanoscale tensile testing. Tensile specimens containing the SiC/Si interface are successfully prepared by focused ion beam (FIB). The interfacial tensile strength is directly measured for the first time and it reaches as high as 7.1 GPa. The a-Si phase on the fracture surfaces is confirmed by high resolution transmission electron microscopy (HRTEM).

Co-emergence of magnetic order and structural fluctuations in magnetite

The nature of the Verwey transition occurring at TV ≈ 125 K in magnetite (Fe3O4) has been an outstanding problem over many decades. A complex low temperature electronic order was recently discovered and associated structural fluctuations persisting above TV are widely reported, but the origin of the underlying correlations and hence of the Verwey transition remains unclear. Here we show that local structural fluctuations in magnetite emerge below the Curie transition at TC ≈ 850 K, through X-ray pair distribution function analysis. Around 80% of the low temperature correlations emerge in proportion to magnetization below TC. This confirms that fluctuations in Fe-Fe bonding arising from magnetic order are the primary electronic instability and hence the origin of the Verwey transition. Such hidden instabilities may be important to other spin-polarised conductors and orbitally degenerate materials.

Monitoring Dynamics of Protein Nascent Chain on the Ribosome using PET-FCS

The ribosome synthesizes proteins according to the sequence of the messenger RNA (mRNA) by progressively adding amino acids to the C-terminus of the nascent peptide. For a protein to become fully functional, it has to fold into a specific three-dimensional structure, called the native state. Experimental work on protein folding in solution has shown several possible models of protein folding. However, currently there is no unifying model for protein folding on the ribosome. Recent experimental work has shown that in the cell nascent polypeptides begin to fold during ongoing translation and in the constrained space of the ribosomal peptide exit tunnel. Here we propose to utilize two novel experimental techniques, force profile assay (FPA) and photoinduced electron transfer with fluorescence correlation spectroscopy (PET-FCS) to map the folding trajectory and obtain temporal information on rapid local structural fluctuations of dynamic cotranslational intermediates. We studied how a small α-helical domain, the N-terminal domain of HemK, folds cotranslationally using a high-resolution force profile assay. FPA reveals that the protein starts to compact as soon as the N-terminal α-helical segments are synthesized. Compaction proceeds vectorially – as nascent chain grows, emerging helical segments dock onto the preceding structures and rearrangements continue after emergence out of the tunnel and near the ribosomal surface. PET-FCS shows that at each stage of translation the nascent peptide undergoes structural fluctuations on the µs time scale. As the domain grows in length and the complexity of tertiary interactions and moves away from the ribosome the fluctuations slow down. Native state destabilizing mutations have little effect on the folding pathway inside the ribosome exit tunnel, but disrupt the final domain stabilization. The results presented in this thesis show how FPA and PET-FCS method can be utilized in solving the trajectory of cotranslational protein folding and characterizing the dynamic properties of folding intermediates.

Disorder in Aqueous Solutions and Peak Broadening in X-ray Photoelectron Spectroscopy

The microscopic structure and photoelectron spectra of an aqueous solution are investigated with ab initio molecular dynamics simulations and ambient pressure X-ray photoelectron spectroscopy (AP-XPS). The simulation results show that the structural fluctuations in an aqueous solution can lead to remarkable peak broadening (∼1 eV) of ionic species, which is in good agreement with the results from AP-XPS experiments. We find that this broadening of the XPS peaks can be directly correlated with the local structural fluctuations in the aqueous solution, such as the evolution of solvation shells. This work demonstrates that the rich dynamics of solvation shells in aqueous solutions can be revealed by combining advanced simulations with in situ AP-XPS, and may stimulate new developments in the in situ XPS characterization of complex electrochemical reactions.

Quantifying structural dynamic heterogeneity in a dense two-dimensional equilibrium liquid.

We investigate local structural fluctuations in a model equilibrium fluid with the aim of better understanding the structural basis of locally heterogeneous dynamics identified in recent simulations and experimental studies of glass-forming liquids and other strongly interacting particle systems, such as lipid membranes, dusty plasmas, interfacial dynamics of crystals, the internal dynamics of proteins, etc. In particular, we utilize molecular dynamics simulation methods to study a single component Lennard-Jones condensed material at constant temperature in two dimensions over a range of densities covering both liquid and crystalline phase regimes. We identify three distinct structural classes of particles by examining the immediate neighborhood of individual particles relying on a solid-angle based tessellation technique. The area distribution of the neighborhoods reveals cages having hexagonal, pentagonal, and square symmetries. Pentagonal cells appear to be the predominant motif in the liquid phase, while the solid phase is dominated by hexagonal cells, as in the case of a perfect crystal. An examination of the spatial organization of particles belonging to each structural class further indicates that finite-size clusters of the hexagonal and pentagonal particle populations arise within both liquids and solids, and the size of these clusters grows in a complementary way as a function of density. Both particle populations form percolation clusters in the liquid-crystal coexistence regime. Interestingly, the populations of particles with different local structures, defined by the arrangement of neighboring particles, are found to maintain different diffusivities, as computed from the velocity autocorrelation function for each type of particle for all densities studied. Our analysis provides a new conceptual framework for understanding the structural origin of dynamical heterogeneity in soft materials.

Elastic and dynamical structural properties of La and Mn-doped SrTiO3 studied by neutron scattering and their relation with thermal conductivities

The electron-doped SrTiO3 exhibits good thermoelectric properties, which makes this material a promising candidate of an n-type oxide thermoelectric device. Recent studies indicated that only a few percent co-doping of La and Mn in SrTiO3 substantially reduces the thermal conductivity, thereby greatly improving the thermoelectric figure of merit at room temperature. Our time-of-flight neutron scattering studies revealed that by doping both La and Mn into SrTiO3, the inelastic scattering spectrum shows a momentum-independent increase in the low-energy spectral weight approximately below 10 meV. The increase in the low-energy spectral weight exhibits a clear correlation with thermal conductivity. The correlation is attributed to dynamical and local structural fluctuations caused by the Jahn-Teller instability in Mn3+ ions coupled with the incipient ferroelectric nature of SrTiO3, as the origin of the low thermal conductivity.