Knowledge about the structure and function of biomolecules continues to grow exponentially, enabling us to “see” structural snapshots of biomolecular interactions and functional assemblies. At PDB-101, the educational portal of the RCSB Protein Data Bank, we have taken a storytelling approach to make this body of knowledge accessible and comprehensible to a wide community of students, educators, and

Crystallography is an important science that impacts many areas of research. The number of users of crystallographic techniques has increased significantly over the past few decades, as diffractometers have become readily available and many commercial programs with user-friendly interfaces have been developed. The growth in computing power has led to the development of advanced methods that were unthinkable

We assess the performance of different protocols for simulating excited-state x-ray absorption spectra. We consider three different protocols based on equation-of-motion coupled-cluster singles and doubles, two of them combined with the maximum overlap method. The three protocols differ in the choice of a reference configuration used to compute target states. Maximum-overlap-method time-dependent density

In the past decade, there was increased research interest in studying internal motions of flexible proteins in solution using Neutron Spin Echo (NSE) as NSE can simultaneously probe the dynamics at the length and time scales comparable to protein domain motions. However, the collective intermediate scattering function (ISF) measured by NSE has the contributions from translational, rotational, and internal

In this paper, we investigate the femtosecond-optical-pulse-induced strain dynamics in relatively thin (100 nm) and thick (10 000 nm) silicon plates based on finite-element simulations. In the thin sample, almost spatially homogeneous excitation by the optical pulse predominantly generates a standing wave of the lowest-order acoustic resonance mode along the out-of-plane direction. At the same time

Phospholipid transbilayer movement (flip-flop) in the plasma membrane is regulated by membrane proteins to maintain cell homeostasis and interact with other cells. The promotion of flip-flop by phospholipid scramblases causes the loss of membrane lipid asymmetry, which is involved in apoptosis, blood coagulation, and viral infection. Therefore, compounds that can artificially control flip-flop in the

We use ultrafast x-ray diffraction to investigate the effect of expansive phononic and contractive magnetic stress driving the picosecond strain response of a metallic perovskite SrRuO3 thin film upon femtosecond laser excitation. We exemplify how the anisotropic bulk equilibrium thermal expansion can be used to predict the response of the thin film to ultrafast deposition of energy. It is key to consider

Room-temperature ionic liquids are promising candidates for applications ranging from electrolytes for energy storage devices to lubricants for food and cellulose processing to compounds for pharmaceutics, biotransformation, and biopreservation. Due to the ion complexity, many room-temperature ionic liquids readily form amorphous phases upon cooling, even at modest rates. Here, we investigate two commonly

Ultrafast, light-induced dynamics in copper–zinc–tin–sulfide (CZTS) photovoltaic nanoparticles are investigated through a combination of optical and x-ray transient absorption spectroscopy. Laser-pump, x-ray-probe spectroscopy on a colloidal CZTS nanoparticle ink yields element-specificity, which reveals a rapid photo-induced shift of electron density away from Cu-sites, affecting the molecular orbital

In order to address the loss of crystallographic training opportunities resulting from the cancelation of conventional schools around the world due to the COVID-19 pandemic, we have started an online crystallography school with live lectures and live Q&A using Zoom Webinar. Since we were trying to reach a large audience in a relatively short period, we have limited the school to ten 1 h lectures covering

Femtosecond x-ray and electron diffraction hold promise to image the evolving structures of single molecules. We present a unified quantum-electrodynamical formulation of diffraction signals, based on the exact many-body nuclear + electronic wavefunction that can be extracted from quantum chemistry simulations. This gives a framework for analyzing various approximate molecular dynamics simulations

Visualizing molecular transformations in real-time requires a structural retrieval method with Ångström spatial and femtosecond temporal atomic resolution. Imaging of hydrogen-containing molecules additionally requires an imaging method sensitive to the atomic positions of hydrogen nuclei, with most methods possessing relatively low sensitivity to hydrogen scattering. Laser-induced electron diffraction

An experimental technique that allows faster assessment of out-of-plane strain dynamics of thin film heterostructures via x-ray diffraction is presented. In contrast to conventional high-speed reciprocal space-mapping setups, our approach reduces the measurement time drastically due to a fixed measurement geometry with a position-sensitive detector. This means that neither the incident (ω) nor the

X-ray absorption near-edge structure (XANES) spectroscopy provides element specificity and is a powerful experimental method to probe local unoccupied electronic structures. In the soft x-ray regime, it is especially well suited for the study of 3d-metals and light elements such as nitrogen. Recent developments in vacuum-compatible liquid flat jets have facilitated soft x-ray transmission spectroscopy

Femtosecond carrier dynamics in layered 2H-MoTe2 semiconductor crystals have been investigated using soft x-ray transient absorption spectroscopy at the x-ray free-electron laser (XFEL) of the Pohang Accelerator Laboratory. Following above-bandgap optical excitation of 2H-MoTe2, the photoexcited hole distribution is directly probed via short-lived transitions from the Te 3d5/2 core level (M5-edge,

A promising new route for structural biology is single-particle imaging with an X-ray Free-Electron Laser (XFEL). This method has the advantage that the samples do not require crystallization and can be examined at room temperature. However, high-resolution structures can only be obtained from a sufficiently large number of diffraction patterns of individual molecules, so-called single particles. Here

Trehalose is chosen as a model molecule to investigate the dissolution mechanism of cellulose in NaOH/urea aqueous solution. The combination of neutron total scattering and empirical potential structure refinement yields the most probable all-atom positions in the complex fluid and reveals the cooperative dynamic effects of NaOH, urea, and water molecules in the dissolution process. NaOH directly interacts

A femtosecond plasma imaging modality based on a new development of ultrafast electron microscope is introduced. We investigated the laser-induced formation of high-temperature electron microplasmas and their subsequent non-equilibrium evolution. Based on a straightforward field imaging principle, we directly retrieve detailed information about the plasma dynamics, including plasma wave structures

Developing femtosecond resolution methods for directly observing structural dynamics is critical to understanding complex photochemical reaction mechanisms in solution. We have used two recent developments, ultrafast mega-electron-volt electron sources and vacuum compatible sub-micron thick liquid sheet jets, to enable liquid-phase ultrafast electron diffraction (LUED). We have demonstrated the viability

We present experimental evidence of a spin voltage—a difference between the chemical potentials of the two spin directions—in a thin iron film based on spin- and time-resolved photoemission spectroscopy. This voltage is the driving force for a spin current during the ultrafast demagnetization of the sample. The observed magnitude is on the order of 50 mV, a value that is quite consistent with predictions

An oil-swollen surfactant membrane is employed to measure the effects of incorporated hydrophobically functionalized gold nanoparticles (AuNPs) on the structure and dynamics of the membranes. While maintaining an average AuNP diameter of approximately 5 nm, the membrane thickness was varied from 5 nm to 7.5 nm by changing the amount of oil in the membrane. The membranes become softer as the proportion

Cationic lipid membranes have recently attracted huge attention both from a fundamental point of view and due to their practical applications in drug delivery and gene therapy. The dynamical behavior of the lipids in the membrane is a key parameter controlling various physiological processes and drug release kinetics. Here, we review the dynamical and thermotropic phase behavior of an archetypal cationic

We present the experimental end-station TRIXS dedicated to time-resolved soft x-ray resonant inelastic x-ray scattering (RIXS) experiments on solid samples at the free-electron laser FLASH. Using monochromatized ultrashort femtosecond XUV/soft x-ray photon pulses in combination with a synchronized optical laser in a pump-probe scheme, the TRIXS setup allows measuring sub-picosecond time-resolved high-resolution

Ultrafast phenomena on a femtosecond timescale are commonly examined by pump-probe experiments. This implies multiple measurements, where the sample under investigation is pumped with a short light pulse and then probed with a second pulse at various time delays to follow its dynamics. Recently, the principle of streaking extreme ultraviolet (XUV) pulses in the temporal domain has enabled recording

Time-resolved optical pump/X-ray probe experiments are often used to study structural dynamics. To ensure high temporal resolution, it is necessary to monitor the timing between the X-ray pulses and the laser pulses. The transition from a crystalline solid material to a disordered state in a non-thermal melting process can be used as a reliable timing monitor. We have performed a study of the non-thermal

The rapid growth of the field of time-resolved and ultrafast electron microscopy has been accompanied by the active development of new instrumentation. Recently, time-resolved microscopes equipped with a field emission gun have been introduced, demonstrating great potential for experiments that benefit from the high brightness and coherence of the electron source. Here, we describe a straightforward

Laser-driven non-local electron dynamics in ultrathin magnetic samples on a sub-10 nm length scale is a key process in ultrafast magnetism. However, the experimental access has been challenging due to the nanoscopic and femtosecond nature of such transport processes. Here, we present a scattering-based experiment relying on a laser-induced electro- and magneto-optical grating in a Co/Pd ferromagnetic

The transition from normal to malignant state in human cells is still a poorly understood process. Changes in the dynamical activity of intracellular water between healthy and cancerous human cells were probed as an innovative approach for unveiling particular features of malignancy and identifying specific reporters of cancer. Androgen-unresponsive prostate and triple-negative breast carcinomas were

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly

Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated

Like many soft materials, lipids undergo a melting transition associated with a significant increase in their dynamics. At temperatures below the main melting transition (Tm), all molecular and collective dynamics are suppressed, while above Tm the alkyl tail motions, lipid diffusivity, and collective membrane undulations are at least an order of magnitude faster. Here we study the collective dynamics

We applied shear to a silica nanoparticle dispersion in a microfluidic jet device and observed direction-dependent structure along and across the flow direction. The asymmetries of the diffraction patterns were evaluated by x-ray cross correlation analysis. For different Rayleigh nozzle sizes and shapes, we measured the decay of the shear-induced ordering after the cessation of the shear. At large

X-ray free electron lasers (XFELs) now routinely produce millijoule level pulses of x-ray photons with tens of femtoseconds duration. Such x-ray intensities gave rise to the idea that weakly scattering particles—perhaps single biomolecules or viruses—could be investigated free of radiation damage. Here, we examine elements from the past decade of so-called single particle imaging with hard XFELs. We

To date, alternating co-polymers based on electron-rich and electron-poor units are the most attractive materials to control functionality of organic semiconductor layers in which ultrafast excited-state processes play a key role. We present a computational study of the photoinduced excited-state dynamics of the 4-(2-thienyl)-2,1,3-benzothiadiazole (BT-1T) molecule, which is a common building block

Recently, coherent structural dynamics in the excited state of an iron photosensitizer was observed through oscillations in the intensity of Kα x-ray emission spectroscopy (XES). Understanding the origin of the unexpected sensitivity of core-to-core transitions to structural dynamics is important for further development of femtosecond time-resolved XES methods and, we believe, generally necessary for

In this work, second-generation Car–Parrinello-based mixed quantum-classical mechanics molecular dynamics simulations of small nanoparticles of NbP, NbAs, TaAs, and 1T-TaS2 in water are presented. The first three materials are topological Weyl semimetals, which were recently discovered to be active catalysts in photocatalytic water splitting. The aim of this research was to correlate potential differences

Resolving gas phase molecular motions with simultaneous spatial and temporal resolution is rapidly coming within the reach of x-ray Free Electron Lasers (XFELs) and Mega-electron-Volt (MeV) electron beams. These two methods enable scattering experiments that have yielded fascinating new results, and while both are important methods for determining transient molecular structures in photochemical reactions

The experimental observation of femtosecond dynamics in atoms and molecules by stroboscopic technologies utilizing x ray or electron flashes has attracted much attention and has rapidly developed. We propose a feasible ultrafast electron diffraction (UED) technology with high brightness and a sub-10 fs temporal resolution. We previously demonstrated a UED system with an overall temporal resolution

Structural details of thermoresponsive, cationically poly(N-iso-propylacrylamide-co-methacrylamido propyl trimethyl ammonium chloride) microgels and the influence of the anionic electrolyte polystyrene sulfonate (PSS) on the internal structure and dynamics of the cationic microgels have been studied with a combination of small angle neutron scattering (SANS) and neutron spin echo (NSE) spectroscopy

We have recorded the diffraction patterns from individual xenon clusters irradiated with intense extreme ultraviolet pulses to investigate the influence of light-induced electronic changes on the scattering response. The clusters were irradiated with short wavelength pulses in the wavelength regime of different 4d inner-shell resonances of neutral and ionic xenon, resulting in distinctly different

We study the non-equilibrium structural dynamics of the incommensurate and nearly commensurate charge-density wave (CDW) phases in 1T- TaS 2. Employing ultrafast low-energy electron diffraction with 1 ps temporal resolution, we investigate the ultrafast quench and recovery of the CDW-coupled periodic lattice distortion (PLD). Sequential structural relaxation processes are observed by tracking the intensities

Understanding guest exchange processes in metal–organic frameworks is an important step toward the rational design of functional materials with tailor-made properties. The dehydration of the flexible metal-organic framework [Co(AIP)(bpy)0.5(H2O)]•2H2O was studied by novel in situ dynamic x-ray diffraction techniques. The complex mechanism of dehydration, along with the as-yet unreported metastable

Ultrafast x-ray and electron scattering techniques have proven to be useful for probing the transient elastic lattice deformations associated with photoexcited coherent acoustic phonons. Indeed, femtosecond electron imaging using an ultrafast electron microscope (UEM) has been used to directly image the influence of nanoscale structural and morphological discontinuities on the emergence, propagation

X-ray free-electron lasers promise diffractive imaging of single molecules and nanoparticles with atomic spatial resolution. This relies on the averaging of millions of diffraction patterns of identical particles, which should ideally be isolated in the gas phase and preserved in their native structure. Here, we demonstrated that polystyrene nanospheres and Cydia pomonella granulovirus can be transferred

Time-resolved serial femtosecond crystallography (TR-SFX) at an x-ray free electron laser enables protein structural changes to be imaged on time-scales from femtoseconds to seconds. It can, however, be difficult to grasp the nature and timescale of global protein motions when structural changes are not isolated near a single active site. New tools are, therefore, needed to represent the global nature

The performance of optoelectronic devices strongly depends on charge carrier dynamics on top of surfaces of the absorber layers. Unfortunately, this information cannot be selectively probed using conventional ultrafast laser spectroscopic methods, due to the large penetration depth (tens of nm to μm) of the photon pulses in the pump-probe configurations. Therefore, ultrafast time-resolved approaches

Optical excitation of spin-ordered rare earth metals triggers a complex response of the crystal lattice since expansive stresses from electron and phonon excitations compete with a contractive stress induced by spin disorder. Using ultrafast x-ray diffraction experiments, we study the layer specific strain response of a dysprosium film within a metallic heterostructure upon femtosecond laser-excitation

X-ray free-electron lasers (XFELs) open the possibility of obtaining diffraction information from a single biological macromolecule. This is because XFELs can generate extremely intense x-ray pulses that are so short that diffraction data can be collected before the sample is destroyed. By collecting a sufficient number of single-particle diffraction patterns, the three-dimensional electron density

Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S 2 ( π , π * ) state is found to promptly relax to S 1 ( n ,   π *) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both

A pump–probe approach was designed to determine the internal proton transfer (PT) rate in a series of poly-peptide radical cations containing both histidine and tryptophan. The proton transfer is driven by the gas-phase basicity difference between residues. The fragmentation scheme indicates that the gas-phase basicity of histidine is lower than that of radical tryptophan so that histidine is always

We studied the thermal transport across a GaAs/AlGaAs interface using time-resolved Reflection High Energy Electron Diffraction. The lattice temperature change of the GaAs nanofilm was directly monitored and numerically simulated using diffusive heat equations based on Fourier's Law. The extracted thermal boundary resistances (TBRs) were found to decrease with increasing lattice temperature imbalance

The conversion of light into usable chemical and mechanical energy is pivotal to several biological and chemical processes, many of which occur in solution. To understand the structure–function relationships mediating these processes, a technique with high spatial and temporal resolutions is required. Here, we report on the design and commissioning of a liquid-phase mega-electron-volt (MeV) ultrafast

Methylation occurs in a myriad of systems with protective and regulatory functions. 8-methoxypyrene-1,3,6-trisulfonate (MPTS), a methoxy derivative of a photoacid, serves as a model system to study effects of methylation on the excited state potential energy landscape. A suite of spectroscopic techniques including transient absorption, wavelength-tunable femtosecond stimulated Raman spectroscopy (FSRS)

In this paper, we present a data workflow developed to operate the adJUstiNg Gain detector FoR the Aramis User station (JUNGFRAU) adaptive gain charge integrating pixel-array detectors at macromolecular crystallography beamlines. We summarize current achievements for operating at 9 GB/s data-rate a JUNGFRAU with 4 Mpixel at 1.1 kHz frame-rate and preparations to operate at 46 GB/s data-rate a JUNGFRAU

Numerous studies have suggested a significant role that protein dynamics play in optimizing enzyme catalysis, and changes in conformational sampling offer a window to explore this role. Thermolysin from Bacillus thermoproteolyticus rokko, which is a heat-stable zinc metalloproteinase, serves here as a model system to study changes of protein function and conformational sampling across a temperature

Microcrystal electron diffraction, or MicroED, is a method that is capable of determining structure from very small and thin 3D crystals using a transmission electron microscope. MicroED has been successfully used on microcrystalline samples, including proteins, peptides, and small organic molecules, in many cases to very high resolutions. In this work, the MicroED workflow will be briefly described

Here, we report on a novel narrowband High Harmonic Generation (HHG) light source designed for ultrafast photoelectron spectroscopy (PES) on solids. Notably, at 16.9 eV photon energy, the harmonics bandwidth equals 19 meV. This result has been obtained by seeding the HHG process with 230 fs pulses at 515 nm. The ultimate energy resolution achieved on a polycrystalline Au sample at 40 K is ∼22 meV at

Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration

The manipulation of liquids at nanoscale dimensions is a central goal of the emergent nanofluidics field. Such endeavors extend to nanodroplets, which are ubiquitous objects involved in many technological applications. Here, we employ time-resolved electron microscopy to elucidate the formation of so-called jumping nanodroplets on a graphene surface. We flash-melt a thin gold nanostructure with a laser

In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations