Time-resolved Structure Research Articles

Time-Resolved Chemical Bonding Structure Evolution by Direct-Dynamics Chemical Simulations.

Direct-dynamics simulations monitor atomic nuclei trajectories during chemical reactions, where chemical bonds are broken and new ones are formed. While they provide valuable information about the ongoing nuclear dynamics, the evolution of the chemical bonds is customarily overlooked, thus, hindering key information about the reaction mechanism. Here we examine the evolution of the chemical bonds for the three main mechanisms of the F- + CH3CH2Cl reaction using quasi-classical trajectories for the nuclei, and global natural orbitals for the electrons. Key findings include (i) bimolecular nucleophilic substitution (SN2) resembles a one-step bond breaking and formation process; (ii) the elimination mechanisms (syn- and anti-E2) feature a sequential two-step process of proton abstraction and Cl- elimination; and (iii) the anti-E2 mechanism is slower, exhibits rebound effects, and gets activated by specific vibrational modes. This study highlights the importance of correctly describing and thoroughly analyzing the dynamical evolution of chemical bonds for chemical reaction mechanistic studies.

Multi-scale and time-resolved structure analysis of relaxor ferroelectric crystals under an electric field

Lead-based relaxor ferroelectrics exhibit giant piezoelectric properties owing to their heterogeneous structures. The average and local structures measured by single-crystal X-ray diffraction under DC and AC electric fields are reviewed in this article. The position-dependent local lattice strain and the distribution of polar nanodomains and nanoregions show strong electric field dependence, which contributes to the giant piezoelectric properties.

Transient X-Ray Absorption Near Edge Structure Spectroscopy Using Broadband Free-Electron Laser Pulses.

A new method for time-resolved X-ray absorption near edge structure (XANES) spectroscopy that enables faster data acquisition and requires smaller sample quantities for high-quality data, thus allowing the analysis of more samples in a shorter time is introduced. The method uses large bandwidth free electron laser pulses to measure laser-excited XANES spectra in transmission mode. A beam-splitting grating configuration allows simultaneous measurements of the spectra of the incoming X-ray Free Electron Laser (XFEL) pulses and transmission XANES, which is crucial for compensating the pulse-dependent intensity and spectrum fluctuations due to the self-amplified spontaneous emission operation. The implementation of this new methodology is applied on a liquid solution of ammonium iron(III) oxalate jet and is compared to previous results, showing great improvements in the speed of acquisition and spectral resolution, and the ability to measure a large 2-D spectral-time map quickly.

Nonoxidative dehydrogenation of propane using boron-incorporated silica-supported Pt Sites synthesized by atomic layer deposition.

Nonoxidative dehydrogenation of propane to propylene using Pt-based supported catalysts is an active research area in catalysis because catalyst attributes of Pt sites can be controlled by careful design of active sites. One way to achieve this is by the addition of a second metal that may impart a change in the electron density of active sites, which in turn affects catalytic performance. In this study, bimetallic Pt and B sites were deposited on powder SiO2 using atomic layer deposition (ALD). Boron was first deposited on SiO2 via half-cycle ALD using triisoproplyborate as the B source. Following calcination, Pt deposition was performed via half-cycle ALD using trimethyl(methylcyclopentadienyl)platinum(IV) as the Pt source. The synthesized catalysts were reduced under H2 at 550 °C and characterized using inductively coupled plasma optical emission spectroscopy for elemental analysis, diffuse reflectance infrared Fourier transform spectroscopy of adsorbed CO to examine the properties of Pt, and time-resolved X-ray absorption near edge structure spectroscopy to examine the changes in the reducibility of Pt sites. The samples were then tested for nonoxidative dehydrogenation of propane at 550 °C using a fixed-bed plug-flow reactor to examine the role of B on the catalytic performance. Characterization results showed that the addition of B imparted an increase in electron density and affected the reducibility of Pt sites. In addition, incorporating B on SiO2 created anchoring sites for Pt ALD. The amount of Pt deposited on B/SiO2 was 2.2 times that on SiO2. Catalytic activity results revealed the addition of B did not change the initial activity of Pt sites significantly, but improved propylene selectivity from 80% to 87% and stability almost threefold. The enhanced selectivity and stability of PtB/SiO2 is most presumably due to favored desorption of propylene and mitigating coke formation under reaction conditions, respectively.

Skyrmion lattice formation and destruction mechanisms probed with TR-SANS.

Magnetic skyrmions are topologically protected, nanoscale whirls of the spin configuration that tend to form hexagonally ordered arrays. As a topologically non-trivial structure, the nucleation and annihilation of the skyrmion, as well as the interaction between skyrmions, varies from conventional magnetic systems. Recent works have suggested that the ordering kinetics in these materials occur over millisecond or longer timescales, which is unusually slow for magnetic dynamics. The current work investigates the skyrmion ordering kinetics, particularly during lattice formation and destruction, using time-resolved small angle neutron scattering (TR-SANS). Evaluating the time-resolved structure and intensity of the neutron diffraction pattern reveals the evolving real-space structure of the skyrmion lattice and the timeframe of the formation. Measurements were performed on three prototypical skyrmion materials: MnSi, (Fe,Co)Si, and Cu2OSeO3. To probe lattice formation and destruction kinetics, the systems were prepared in the stable skyrmion state, and then a square-wave magnetic field modulation was applied. The measurements show that the skyrmions quickly form ordered domains, with a significant distribution in lattice parameters, which then converge to the final structure; the results confirm the slow kinetics, with formation times between 10 ms and 99 ms. Comparisons are made between the measured formation times and the fundamental material properties, suggesting the ordering temperature, saturation magnetization and magnetocrystalline anisotropy may be driving the timeframes. Micromagnetic simulations were also performed and support a scaling of the kinetics with sample volume, a behavior which is caused by the reconciling of misaligned domains.

SARS-CoV-2 proteins structural studies using synchrotron radiation.

In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp). This article provides a brief overview of structural analysis techniques, with focus on synchrotron radiation-based methods applied to the analysis of SARS-CoV-2 proteins.

Cavitation Rheology of Model Yield Stress Fluids Based on Carbopol

Measuring the surface tension of yield stress fluids has remained a critical challenge due to limitations of the traditional tensiometry techniques. Here, we overcome those limits and successfully measure the surface tension and mechanical properties of a model yield stress fluid based on Carbopol gels via a needle-induced cavitation (NIC) technique. Our results indicate that the surface tension is approximately 70 ± 3 mN/m, and is independent of the rheology of yield stress fluid over a wide range of yield stress values σy = 0.5-120 Pa. In addition, we demonstrate that a Young modulus smaller than E < 1 kPa can be successfully measured for Carbopol gels with NIC method. Finally, we present a time-resolved flow structure around the cavity in a host of yield stress fluids, and assess the impact of fluid rheology on the detailed form of flow around the cavity. Interestingly, prior to the critical point associated with cavitation, the yield stress fluid is weakly deformed suggesting that the measured surface tension data reflect the near equilibrium values. Beyond the critical point, the yield stress fluid experiences a strong flow that is controlled by both the critical pressure and the non-Newtonian rheology of the yield stress fluid.

Direct extraction of topological Zak phase with the synthetic dimension

Measuring topological invariants is an essential task in characterizing topological phases of matter. They are usually obtained from the number of edge states due to the bulk-edge correspondence or from interference since they are integrals of the geometric phases in the energy band. It is commonly believed that the bulk band structures could not be directly used to obtain the topological invariants. Here, we implement the experimental extraction of Zak phase from the bulk band structures of a Su-Schrieffer-Heeger (SSH) model in the synthetic frequency dimension. Such synthetic SSH lattices are constructed in the frequency axis of light, by controlling the coupling strengths between the symmetric and antisymmetric supermodes of two bichromatically driven rings. We measure the transmission spectra and obtain the projection of the time-resolved band structure on lattice sites, where a strong contrast between the non-trivial and trivial topological phases is observed. The topological Zak phase is naturally encoded in the bulk band structures of the synthetic SSH lattices, which can hence be experimentally extracted from the transmission spectra in a fiber-based modulated ring platform using a laser with telecom wavelength. Our method of extracting topological phases from the bulk band structure can be further extended to characterize topological invariants in higher dimensions, while the exhibited trivial and non-trivial transmission spectra from the topological transition may find future applications in optical communications.

Decomposing past and future: Integrated information decomposition based on shared probability mass exclusions.

A core feature of complex systems is that the interactions between elements in the present causally constrain their own futures, and the futures of other elements as the system evolves through time. To fully model all of these interactions (between elements, as well as ensembles of elements), it is possible to decompose the total information flowing from past to future into a set of non-overlapping temporal interactions that describe all the different modes by which information can be stored, transferred, or modified. To achieve this, I propose a novel information-theoretic measure of temporal dependency (Iτsx) based on the logic of local probability mass exclusions. This integrated information decomposition can reveal emergent and higher-order interactions within the dynamics of a system, as well as refining existing measures. To demonstrate the utility of this framework, I apply the decomposition to spontaneous spiking activity recorded from dissociated neural cultures of rat cerebral cortex to show how different modes of information processing are distributed over the system. Furthermore, being a localizable analysis, Iτsx can provide insight into the computational structure of single moments. I explore the time-resolved computational structure of neuronal avalanches and find that different types of information atoms have distinct profiles over the course of an avalanche, with the majority of non-trivial information dynamics happening before the first half of the cascade is completed. These analyses allow us to move beyond the historical focus on single measures of dependency such as information transfer or information integration, and explore a panoply of different relationships between elements (and groups of elements) in complex systems.

Biological function investigated by time-resolved structure determination.

Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length and time-scales, from fractions of Ångströms to micro-meters and from femtoseconds to hours.

Mix-and-Inject Serial Femtosecond Crystallography to Capture RNA Riboswitch Intermediates.

Time-resolved structure determination of macromolecular conformations and ligand-bound intermediates is extremely challenging, particularly for RNA. With rapid technological advances in both microfluidic liquid injection and X-ray free electron lasers (XFEL), a new frontier has emerged in time-resolved crystallography whereby crystals can be mixed with ligand and then probed with X-rays (mix-and-inject) in real time and at room temperature. This chapter outlines the basic setup and procedures for mix-and-inject experiments for recording time-resolved crystallographic data of riboswitch RNA reaction states using serial femtosecond crystallography (SFX) and an XFEL.

A study of the time-resolved structure of the vortices shed into the wake of an isolated F1 car wheel

A study of the time-resolved structure of the vortices shed into the wake of an isolated F1 car wheel

Observation of flat-band and band transition in the synthetic space

Constructions of synthetic lattices in photonics attract growingly attentions for exploring interesting physics beyond the geometric dimensionality, among which modulated ring resonator system has been proved as a powerful platform to create different kinds of connectivities between resonant modes along the synthetic frequency dimension with many theoretical proposals. Various experimental realizations are investigated in a single ring resonator, while building beyond simple synthetic lattices in multiple rings with different types remains lacking, which desires to be accomplished as an important step further. Here, we implement the experimental demonstration of generating the one-dimensional Lieb lattice along the frequency axis of light, realized in two coupled ring resonators while the larger ring undergoing dynamic modulation. Such synthetic photonic structure naturally exhibits the physics of flat band. We show that the time-resolved band structure read out from the drop-port output of the excited ring is the intensity projection of the band structure onto specific resonant mode in the synthetic momentum space, where gapless flat band, mode localization effect, and flat to non-flat band transition are observed in experiments and verified by simulations. Our work gives a direct evidence for the constructing synthetic Lieb lattice with two rings, which hence makes a solid step towards experimentally constructing more complicated lattices in multiple rings associated with synthetic frequency dimension.

Antiphase oscillations in the time-resolved spin structure factor of a photoexcited Mott insulator on a square lattice

We investigate momentum-dependent transient spin dynamics after photoirradiation in a two-dimensional Mott insulator described by a half-filled Hubbard model on a square lattice by using a numerically exact-diagonalization technique. We find a temporal oscillation in the static spin structure factor of a periodic lattice. The oscillation exhibits an antiphase behavior between, for example, two orthogonal momentum directions parallel and perpendicular to the electric field of a pump pulse. The origin of the antiphase oscillation is attributed to a photoexcited wave function that has overlap with eigenstates producing the B 1g bimagnon Raman intensity. Observing such antiphase oscillations will be a big challenge for time-resolved resonant elastic x-ray scattering experiments.

Laser-Induced Coulomb Explosion Imaging of Aligned Molecules and Molecular Dimers.

We discuss how Coulomb explosion imaging (CEI), triggered by intense femtosecond laser pulses and combined with laser-induced alignment and covariance analysis of the angular distributions of the recoiling fragment ions, provides new opportunities for imaging the structures of molecules and molecular complexes. First, focusing on gas phase molecules, we show how the periodic torsional motion of halogenated biphenyl molecules can be measured in real time by timed CEI, and how CEI of one-dimensionally aligned difluoroiodobenzene molecules can uniquely identify four structural isomers. Next, focusing on molecular complexes formed inside He nano-droplets, we show that the conformations of noncovalently bound dimers or trimers, aligned in one or three dimensions, can be determined by CEI. Results presented for homodimers of CS2, OCS, and bromobenzene pave the way for femtosecond time-resolved structure imaging of molecules undergoing bimolecular interactions and ultimately chemical reactions.

Lateral deformations of a crystal of potassium acid phthalate in an external electric field

The anisotropy of deformations in potassium acid phthalate crystals arising under the action of an external electric field up to 1 kV mm−1 applied along the [001] polar axis was studied using X-ray diffraction methods at room temperature. Electrical conductivity was measured and rocking curves for reflections 400, 070 and 004 were obtained by time-resolved X-ray diffractometry in Laue and Bragg geometries. Two saturation processes were observed from the time dependences of the electrical conductivity. A shift in the diffraction peaks and a change in their intensity were found, which indicated a deformation of the crystal structure. Rapid piezoelectric deformation and reversible relaxation-like deformation, kinetically similar to the electrical conductivity of a crystal, were revealed. The deformation depended on the polarity and strength of the applied field. The deformation was more noticeable in the [100] direction and was practically absent in the [001] direction of the applied field. X-ray diffraction analysis revealed a disordered arrangement of potassium atoms, i.e. additional positions and vacancies. The heights of potential barriers between the positions of K+ ions and the paths of their possible migration in the crystal structure of potassium acid phthalate were determined. The data obtained by time-resolved X-ray diffractometry and X-ray structure analysis, along with additional electrophysical measurements, allow the conclusion that the migration of charge carriers (potassium cations) leads to lateral deformation of the crystal structure of potassium phthalate in an external electric field.

Time-resolved structure analysis of vibrating gallium phosphate under alternating electric field

Time-resolved structure analysis of vibrating gallium phosphate under alternating electric field

Antiphase Oscillations in the Time-Resolved Spin Structure Factor of a Photoexcited Mott Insulator.

Motivated by the recent development of time-resolved resonant-inelastic x-ray scattering (TRRIXS) in photoexcited antiferromagnetic Mott insulators, we numerically investigate momentum-dependent transient spin dynamics in a half-filled Hubbard model on a square lattice. After turning off a pumping photon pulse, the intensity of a dynamical spin structure factor temporally oscillates with frequencies determined by the energy of two magnons in the antiferromagnetic Mott insulator. We find an antiphase behavior in the oscillations between two orthogonal momentum directions, parallel and perpendicular to the electric field of a pump pulse. The phase difference comes from the B_{1g} channel of the two-magnon excitation. Observing the antiphase oscillations will be a big challenge for TRRIXS experiments when their time resolution will be improved by more than an order of magnitude.

Beyond X-rays: an overview of emerging structural biology methods.

Structural biologists rely on X-ray crystallography as the main technique for determining the three-dimensional structures of macromolecules; however, in recent years, new methods that go beyond X-ray-based technologies are broadening the selection of tools to understand molecular structure and function. Simultaneously, national facilities are developing programming tools and maintaining personnel to aid novice structural biologists in de novo structure determination. The combination of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) now enable time-resolved structure determination that allows for capture of dynamic processes, such as reaction mechanism and conformational flexibility. XFEL and SFX, along with microcrystal electron diffraction (MicroED), help side-step the need for large crystals for structural studies. Moreover, advances in cryogenic electron microscopy (cryo-EM) as a tool for structure determination is revolutionizing how difficult to crystallize macromolecules and/or complexes can be visualized at the atomic scale. This review aims to provide a broad overview of these new methods and to guide readers to more in-depth literature of these methods.

Detecting seasonal transient correlations between populations of the West Nile Virus vector Culex sp. and temperatures with wavelet coherence analysis

Cullex sp. is one of the most important mosquito disease vector and climate is considered to be a key factor affecting its population dynamics. In this study we use straightforward techniques based on correlations and wavelet analysis to determine the non-trivial associations between Culex sp. mosquito abundance and weather variables (lagged population abundance, mean temperatures, rain and wind speed) in Northern Greece during two successive years. In particular, mosquito abundances were examined for collinearity using Pearson's correlation matrices and redundant or low correlated variables were excluded from further analyses. Multiple linear regression analysis was performed to fit normalized mosquito abundance weekly counts as the dependent variable to the independent variables including: mean temperatures, rain as well as lagged mosquito populations. There was a high and positive correlation between temperature and mosquito abundance during both observation years (r = 0.6). However, a very poor correlation was observed between rain and weekly mosquito abundances (r = 0.29), as well as between wind speed (r = 0.29), respectively. Additionally, according to the multiple linear regression model the effect of temperature, was significant. The continuous power spectrum of the mosquito abundance counts and mean temperatures depict in most cases similar power for periods which are close to 1 week, indicating the point of the lowest variance of the time series, although appearing on slight different moments of time. The cross wavelet coherent analysis showed that inter weekly cycles with a period between 2 and 3 weeks between mosquito abundance and temperature were coherent mostly during the first and the last weeks of the season. Hence, the wavelet analysis show a progressive oscillation in mosquito occurrences with time, which is higher at the start and the end of the season. Moreover, in contrast with standard methods of analysis, wavelets can provide useful insights into the time-resolved oscillation structure of mosquito data and accompanying revealing a non-stationary association with temperature.