Transient Structures Research Articles

Energetic particle acceleration and transport with the novel Icarus+PARADISE model

With the rise of satellites and mankind's growing dependence on technology, there is an increasing awareness of space weather phenomena related to high-energy particles. Shock waves driven by coronal mass ejections (CMEs) and corotating interaction regions (CIRs) occasionally act as potent particle accelerators, generating hazardous solar energetic particles (SEPs) that pose risks to satellite electronics and astronauts. Numerical simulation tools capable of modelling and predicting large SEP events are thus highly demanded. We introduce the new Icarus+PARADISE model as an advancement of the previous EUHFORIA+PARADISE model. Icarus, based on the MPI-AMRVAC framework, is a three-dimensional magnetohydrodynamic code that models solar wind configurations from 0.1 au onwards, encompassing transient structures like CMEs or CIRs. Differing from EUHFORIA's uniform-only grid, Icarus incorporates solution adaptive mesh refinement (AMR) and grid stretching. The particle transport code PARADISE propagates energetic particles as test particles through these solar wind configurations by solving the focused transport equation in a stochastic manner. We validate our new model by reproducing EUHFORIA+PARADISE results. This is done by modelling the acceleration and transport of energetic particles in a synthetic solar wind configuration containing an embedded CIR.  Subsequently, we illustrate how the simulation results vary with grid resolution by employing different levels of AMR.. The resulting intensity profiles illustrate increased particle acceleration with higher levels of AMR in the shock region, better capturing the effects of the shock.

Dynamic three-dimensional structures of a metal-organic framework captured with femtosecond serial crystallography.

Crystalline systems consisting of small-molecule building blocks have emerged as promising materials with diverse applications. It is of great importance to characterize not only their static structures but also the conversion of their structures in response to external stimuli. Femtosecond time-resolved crystallography has the potential to probe the real-time dynamics of structural transitions, but, thus far, this has not been realized for chemical reactions in non-biological crystals. In this study, we applied time-resolved serial femtosecond crystallography (TR-SFX), a powerful technique for visualizing protein structural dynamics, to a metal-organic framework, consisting of Fe porphyrins and hexazirconium nodes, and elucidated its structural dynamics. The time-resolved electron density maps derived from the TR-SFX data unveil trifurcating structural pathways: coherent oscillatory movements of Zr and Fe atoms, a transient structure with the Fe porphyrins and Zr6 nodes undergoing doming and disordering movements, respectively, and a vibrationally hot structure with isotropic structural disorder. These findings demonstrate the feasibility of using TR-SFX to study chemical systems.

Producing Conventional and Transient Amino(mercapto)methyl Radicals by Addition of Muonium to a Crystalline Thioformamide (Mes*NHCH=S).

Muonium (Mu = µ+e-) is composed of a muon of light isotope of proton (µ+) and electron (e-) and can be used as a light surrogate for a hydrogen atom. In this paper, we investigated addition of muonium to a newly synthesized Mes*-substituted thioformamide (Mes*NHCH=S, Mes* = 2,4,6-tBu3C6H2). Transverse-field muon spin rotation (TF-µSR) of a solution sample of the thioformamide confirmed addition of muonium to the sulfur atom leading to the corresponding C-centered radical [Mes*NHC(H)·-SMu]. Density functional theory (DFT) calculations assigned a conventional amino(mercapto)methyl radical, in which both nitrogen and carbon were slightly pyramidalized, and the calculated muon hyperfine coupling constant (hfcc) including the muon isotope effect was compatible with the experimentally determined parameter. However, the muon level-crossing resonance (µLCR) spectrum of an anisotropic crystalline sample indicated two paramagnetic species, and the major product showed the considerably larger muon hfcc compared with the conventional structure of the amino(mercapto)methyl radical. The unusual transient muoniated thioformamide with the larger muon hfcc that showed rapid relaxation could be only explained by a transient structure including planarization of the nitrogen and carbon atoms in Mes*NHC(H)·-SMu.

The Reversible Transformation of a Vesicular Aggregate in Response to a pH Oscillation

The transformation of amphiphilic molecular assemblies in response to chemical oscillations is fundamental in biological systems. The reversible transformation of a vesicular aggregate (VA) in response to a pH oscillation is presented in this study. A VA composed of the cationic surfactant didodecyldimethylammonium bromide is transformed using a pH oscillation ranging between 3 and 7. When the VA attains a stable structure at extreme pH values, the transformation reaches the irreversible stage. However, the addition of a phosphate buffer to the VA suspension changes the pH oscillation pattern from being rectangular to triangular and decreases the oscillation amplitude, successfully achieving the reversible transformation of the VA. Maintaining the non-equilibrium (transient) structures throughout the transformation and not falling into the equilibrium state with a varying pH are essential for the reversible transformation. This may be common and essential for dynamics in biological cells.

Bending of a lipid membrane edge by annexin A5 trimers

Plasma membrane damage occurs in healthy cells and more frequently in cancer cells where high growth rates and metastasis result in frequent membrane damage. The annexin family of proteins plays a key role in membrane repair. Annexins are recruited at the membrane injury site by Ca+2 and repair the damaged membrane in concert with several other proteins. Annexin A4 (ANXA4) and ANXA5 form trimers at the bilayer surface, and previous simulations show that the trimers induce high local negative membrane curvature on a flat bilayer. The membrane-curvature-inducing property of ANXA5 is presumed to be vital to the membrane repair mechanism. A previously proposed descriptive model hypothesizes that ANXA5-mediated curvature force is utilized at the free edge of the membrane at a wound site to pull the wound edges together, resulting in the formation of a “neck”-shaped structure, which, when combined with a constriction force exerted by ANXA6, leads to membrane repair. The molecular details and mechanisms of repair remain unknown, in part because the membrane edge is a transient structure that is difficult to investigate both experimentally and computationally. For the first time, we investigate the impact of ANXA5 near a membrane edge, which is modeled by a bicelle under periodic boundary conditions. ANXA5 trimers induce both local curvature on the membrane leading to global bending of the bicelle. The global curvature depends on the density of annexins on the bicelle, and the curvature increases with the ANXA5 concentration until it reaches a plateau. The simulations suggest that not only do annexins induce local membrane curvature, but they can change the overall shape of a free-standing membrane. We also demonstrate that ANXA5 trimers reduce the rate of phosphatidylserine lipid diffusion from the cytoplasmic to the exoplasmic leaflet along the edge of the bicelle. In this way, membrane-bound annexins can potentially delay the apoptotic signal triggered by the presence of phosphatidylserine lipids in the outer leaflet, thus biding time for repair of the membrane hole. Our findings provide new insights into the role of ANXA5 at the edges of the membrane (the injury site) and support the curvature-constriction model of membrane repair.

Shine-Dalgarno Accessibility Governs Ribosome Binding to the Adenine Riboswitch.

Translational riboswitches located in the 5' UTR of the messenger RNA (mRNA) regulate translation through variation of the accessibility of the ribosome binding site (RBS). These are the result of conformational changes in the riboswitch RNA governed by ligand binding. Here, we use a combination of single-molecule colocalization techniques (Single-Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) and Single-Molecule Kinetic Analysis of Ribosome Binding (SiM-KARB)) and microscale thermophoresis (MST) to investigate the adenine-sensing riboswitch in Vibrio vulnificus, focusing on the changes of accessibility between the ligand-free and ligand-bound states. We show that both methods faithfully report on the accessibility of the RBS within the riboswitch and that both methods identify an increase in accessibility upon adenine binding. Expanding on the regulatory context, we show the impact of the ribosomal protein S1 on the unwinding of the RNA secondary structure, thereby favoring ribosome binding even for the apo state. The determined rate constants suggest that binding of the ribosome is faster than the time required to change from the ON state to the OFF state, a prerequisite for efficient regulation decision.

Skeleton coupling: a novel interlayer mapping of community evolution in temporal networks

Abstract Dynamic community detection (DCD) in temporal networks is a complicated task that involves the selection of a method and its associated hyperparameters. How to choose the most appropriate method generally depends on the type of network being analysed and the specific properties of the data that define the network. In functional temporal networks derived from neuronal spike train data, communities are expected to be transient, and it is common for the network to contain multiple singleton communities. Here, we compare the performance of different DCD methods on functional temporal networks built from synthetic neuronal time series data with known community structure. We find that, for these networks, DCD methods that utilize interlayer links to perform community carry over between layers outperform other methods. However, we also observe that DCD performance is highly dependent on the topology of interlayer links, especially in the presence of singleton and transient communities. We therefore define a novel way of defining interlayer links in temporal networks called skeleton coupling that is specifically designed to enhance the linkage of communities in the network throughout time based on the topological properties of the community history. We show that integrating skeleton coupling with current DCD methods improves the method’s performance in synthetic data with planted singleton and transient communities. The use of skeleton coupling to perform DCD will therefore allow for more accurate and interpretable results of community evolution in real-world neuronal data or in other systems with transient structure and singleton communities.

Endosperm cell death: roles and regulation in angiosperms.

Double fertilization in angiosperms results in the formation of a second zygote, the fertilized endosperm. Unlike its embryo sibling, the endosperm is a transient structure that eventually undergoes developmentally controlled programmed cell death (PCD) at specific time points of seed development or germination. The nature of endosperm PCD exhibits a considerable diversity, both across different angiosperm taxa and within distinct endosperm tissues. In endosperm-less species, PCD might cause central cell degeneration as a mechanism preventing the formation of a fertilized endosperm. In most other angiosperms, embryo growth necessitates the elimination of surrounding endosperm cells. Nevertheless, complete elimination of the endosperm is rare, and in most cases, specific endosperm tissues persist. In mature seeds, these persisting cells may be dead, such as the starchy endosperm in cereals, or remain alive to die only during germination, like the cereal aleurone or the endosperm of castor beans. In this review, we explore the current knowledge surrounding the cellular, molecular, and genetic aspects of endosperm PCD, and the influence environmental stresses have on PCD processes. Overall, this review provides an exhaustive overview of endosperm PCD processes in angiosperms, shedding light on its diverse mechanisms and its significance in seed development and seedling establishment.

Theoretical predictions and experimental measurements of novel aerostatic bearing with multi-inclined-orifice restrictors for the improvement of stability

This paper introduces a novel design featuring a multiple-inclined-orifice restrictor (MIOR) to address the challenge of turbulent vortices and the reduction of nano-vibrations in aerostatic bearings. This design optimizes the angle configuration to alter the dynamic airflow patterns within the chamber, suppress turbulent vortices, and mitigate nano-vibrations. Three-dimensional transient vortical structures, pressure fluctuation, and dynamic load-carrying capacity of aerostatic bearings with varying orifice angles were investigated through large eddy simulations. Additionally, load-carrying capacity and vibration tests were conducted on aerostatic bearings equipped with MIORs to validate the proposed model's accuracy and assess the effectiveness of MIOR. Remarkably, the experimental results were consistent with the simulation results, highlighting the exceptional stability and reduced vibration amplitude exhibited by MIORs with an angle of 110° while maintaining static performance.

Probing Laser‐Driven Structure Formation at Extreme Scales in Space and Time

AbstractIrradiation of solid surfaces with high intensity, ultrashort laser pulses triggers a variety of secondary processes that can lead to the formation of transient and permanent structures over a large range of length scales from mm down to the nano‐range. One of the most prominent examples are LIPSS – Laser‐Induced Periodic Surface Structures. While LIPSS have been a scientific evergreen for of almost 60 years, experimental methods that combine ultrafast temporal with the required nm spatial resolution have become available only recently with the advent of short pulse, short wavelength free electron lasers. Here, the current status and future perspectives in this field are discussed by exploiting the unique possibilities of these 4th‐generation light sources to address by time‐domain experimental techniques the fundamental LIPSS‐question, namely why and how laser irradiation can initiate the transition of a “chaotic” (rough) surface from an aperiodic into a periodic structure.

Coupled Electron-Nuclear Dynamics Induced and Monitored with Femtosecond Soft X-ray Pulses in the Amino Acid Glycine.

The coupling of electronic and nuclear motion in polyatomic molecules is at the heart of attochemistry. The molecular properties, transient structures, and reaction mechanism of these many-body quantum objects are defined on the level of electrons and ions by molecular wave functions and their coherent superposition, respectively. In the present contribution, we monitor nonadiabatic quantum wave packet dynamics during molecular charge motion by reconstructing both the oscillatory charge density distribution and the characteristic time-dependent nuclear configuration coordinate from time-resolved Auger electron spectroscopic data recorded in previous studies on glycine molecules [Schwickert et al. Sci. Adv. 2022, 8, eabn6848]. The electronic and nuclear motion on the femtosecond time scale was induced and probed in kinematically complete soft X-ray experiments at the FLASH free-electron laser facility. The detailed analysis of amplitude, instantaneous phase, and instantaneous frequency of the propagating many-body wave packet during its lifecycle provides unprecedented insight into dynamical processes beyond the Born-Oppenheimer approximation. We are confident that the refined experimental data evaluation helps to develop new theoretical tools to describe time-dependent molecular wave functions in complicated but ubiquitous non-Born-Oppenheimer photochemical conditions.

The Glucocorticoid Receptor’s tau1c Activation Domain 35 Years on—Making Order out of Disorder

Almost exactly 35 years after starting to work with the human glucocorticoid receptor (hGR), it is interesting for me to re-evaluate the data and results obtained in the 1980s–1990s with the benefit of current knowledge. What was understood then and how can modern perspectives increase that understanding? The hGR’s tau1c activation domain that we delineated was an enigmatic protein domain. It was apparently devoid of secondary and tertiary protein structures but nonetheless maintained gene activation activity in the absence of other hGR domains, not only in human cells but also in yeast, which is evolutionarily very divergent from humans and which does not contain hGR or other nuclear receptors. We now know that the basic machinery of cells is much more conserved across evolution than was previously thought, so the hGR’s tau1c domain was able to utilise transcription machinery components that were conserved between humans and yeast. Further, we can now see that structure–function aspects of the tau1c domain conform to a general mechanistic framework, such as the acidic exposure model, that has been proposed for many activation domains. As for many transcription factor activation domains, it is now clear that tau1c activity requires regions of transient secondary structure. We now know that there is a tendency for positive Darwinian selection to target intrinsically disordered protein domains. It will be interesting to study the distribution and nature of the many single nucleotide variants of the hGR in this respect.

Emerging insights into cephalic neural crest disorders: A single center experience.

Neural crest cells (NCCs) are transient structures in the fetal life in vertebrates, which develop at the junctional site of the non-neural and neural ectoderm, sharing a common developmental origin for diverse diseases. After Epithelio-mesenchymal (EMT) of the NCCs within the neural tube, delamination of NCCs occurs. After delamination, the transformation of these cells into various cell lineages produces melanocytes, bones, and cartilage of the skull, cells of the enteric and peripheral nervous system. After the conversion, these cells migrate into various locations of the entire body according to the cell lineage. Abnormalities in neural crest (NC) formation and migration result in various malformations and tumors, known as neurocristopathy. Herein, this case series describes a single-center experience in cephalic NC disorders over the past 3 years, including 17 cases of varying composition (i.e., vascular, dysgenetic, mixed, and neoplastic forms) involving the brain and occasionally skin, eyes, and face of the patients. In our study of 17 patients with cephalic NC disease, 6 (35.3%) patients had vascular form, 5 (29.4%) had dysgenetic form, 4 (23.5%) had mixed form, and 2 (11.7%) had neoplastic form. Brain involvement in the form of vascular or parenchyma or both vascular and parenchymal was seen in all of our patients (100%), skin in 6 (35.3%) patients, eye in 2 (11.7%), and face in 1 (5.9%) patient. Treatment was planned according to the various manifestations of the disease. Neural crest diseases (NCDs) are a rare and under-recognized group of disorders in the literature and may have been under-reported due to a lack of awareness regarding the same. More such reporting may increase the repertoire of these rare disorders such that clinicians can have a high degree of suspicion leading to early detection and timely counseling and also improve preventive strategies and help in developing new drugs for these disorders or prevent them.

Relativistic Electron Precipitation Driven by Mesoscale Transients, Inferred From Ground and Multi‐Spacecraft Platforms

AbstractPrecipitation of relativistic electrons into the Earth's atmosphere regulates the outer radiation belt fluxes and contributes to magnetosphere‐atmosphere coupling. One of the main drivers of such precipitation is electron scattering by whistler‐mode waves. Such waves typically originate at the equator, where they can resonate with and scatter sub‐relativistic (tens to a few hundred keV) electrons. However, they can occasionally propagate far away from the equator along field lines, reaching middle latitudes, where they can resonate with and scatter relativistic (>500 keV) electrons. Such a propagation is typical for the dayside, but statistically has not been found on the nightside where the waves are quickly damped along their propagation due to Landau damping. Here we explore two events of relativistic electron precipitation from low‐altitude observations on the nightside. Combining measurements of whistler‐mode waves from ground observatories, relativistic electron precipitation from low‐altitude satellites, total electron content maps from GPS receivers, and magnetic field and electron flux from equatorial satellites, we show wave ducting by plasma density gradients is the possible channel that allows the waves to reach middle latitudes and scatter relativistic electrons. We suggest that both whistler‐mode wave generation and ducting can be driven by equatorial mesoscale (with spatial scales of about one Earth radius) transient structures during nightside injections. We also compare these nightside events with observations of ducted waves and relativistic electron precipitation at the dayside, where wave generation and ducting are driven by ultra‐low‐frequency waves. This study demonstrates the potential importance of mesoscale transients in relativistic electron precipitation, but does not however unequivocally establish that ducted whistler‐mode waves are the primary cause of the observed electron precipitation.

THEMIS Observations of Magnetosheath‐Origin Foreshock Ions

AbstractThe ion foreshock, filled with backstreaming foreshock ions, is very dynamic with many transient structures that disturb the bow shock and the magnetosphere‐ionosphere system. It has been shown that foreshock ions can be generated through either solar wind reflection at the bow shock or leakage from the magnetosheath. While solar wind reflection is widely believed to be the dominant generation process, our investigation using Time History of Events and Macroscale Interactions during Substorms mission observations reveals that the relative importance of magnetosheath leakage has been underestimated. We show from case studies that when the magnetosheath ions exhibit field‐aligned anisotropy, a large fraction of them attains sufficient field‐aligned speed to escape upstream, resulting in very high foreshock ion density. The observed foreshock ion density, velocity, phase space density, and distribution function shape are consistent with such an escape or leakage process. Our results suggest that magnetosheath leakage could be a significant contributor to the formation of the ion foreshock. Further characterization of the magnetosheath leakage process is a critical step toward building predictive models of the ion foreshock, a necessary step to better forecast foreshock‐driven space weather effects.

Structure and interactions of prion-like domains in transcription factor Efg1 phase separation

Candida albicans, a prominent member of the human microbiome, can make an opportunistic switch from commensal coexistence to pathogenicity accompanied by an epigenetic shift between the white and opaque cell states. This transcriptional switch is under precise regulation by a set of transcription factors (TFs), with Enhanced Filamentous Growth Protein 1 (Efg1) playing a central role. Previous research has emphasized the importance of Efg1’s prion-like domain (PrLD) and the protein’s ability to undergo phase separation for the white-to-opaque transition of C. albicans. However, the underlying molecular mechanisms of Efg1 phase separation have remained underexplored. In this study, we delved into the biophysical basis of Efg1 phase separation, revealing the significant contribution of both N-terminal (N) and C-terminal (C) PrLDs. Through NMR structural analysis, we found that Efg1 N-PrLD and C-PrLD are mostly disordered but have prominent partial α-helical secondary structures in both domains. NMR titration experiments suggest that the partially helical structures in N-PrLD act as hubs for self-interaction as well as Efg1 interaction with RNA. Using condensed-phase NMR spectroscopy, we uncovered diverse amino acid interactions underlying Efg1 phase separation. Particularly, we highlight the indispensable role of tyrosine residues within the transient α-helical structures of PrLDs particularly in the N-PrLD compared to the C-PrLD in stabilizing phase separation. Our study provides evidence that the transient α-helical structure is present in the phase-separated state and highlights the particular importance of aromatic residues within these structures for phase separation. Together, these results enhance the understanding of C. albicans transcription factor interactions that lead to virulence and provide a crucial foundation for potential antifungal therapies targeting the transcriptional switch.

3D atomic structure from a single X-ray free electron laser pulse

X-ray Free Electron Lasers (XFEL) are cutting-edge pulsed x-ray sources, whose extraordinary pulse parameters promise to unlock unique applications. Several new methods have been developed at XFELs; however, no methods are known, which allow ab initio atomic level structure determination using only a single XFEL pulse. Here, we present experimental results, demonstrating the determination of the 3D atomic structure from data obtained during a single 25 fs XFEL pulse. Parallel measurement of hundreds of Bragg reflections was done by collecting Kossel line patterns of GaAs and GaP. To the best of our knowledge with these measurements, we reached the ultimate temporal limit of the x-ray structure solution possible today. These measurements open the way for obtaining crystalline structures during non-repeatable fast processes, such as structural transformations. For example, the atomic structure of matter at extremely non-ambient conditions or transient structures formed in irreversible physical, chemical, or biological processes may be captured in a single shot measurement during the transformation. It would also facilitate time resolved pump-probe structural studies making them significantly shorter than traditional serial crystallography.

Divergent growth of the transient brain compartments in fetuses with nonsyndromic isolated clefts involving the primary and secondary palate.

Cleft lip/palate is a common orofacial malformation that often leads to speech/language difficulties as well as developmental delays in affected children, despite surgical repair. Our understanding of brain development in these children is limited. This study aimed to analyze prenatal brain development in fetuses with cleft lip/palate and controls. We examined in utero MRIs of 30 controls and 42 cleft lip/palate fetal cases and measured regional brain volumes. Cleft lip/palate was categorized into groups A (cleft lip or alveolus) and B (any combination of clefts involving the primary and secondary palates). Using a repeated-measures regression model with relative brain hemisphere volumes (%), and after adjusting for multiple comparisons, we did not identify significant differences in regional brain growth between group A and controls. Group B clefts had significantly slower weekly cerebellar growth compared with controls. We also observed divergent brain growth in transient brain structures (cortical plate, subplate, ganglionic eminence) within group B clefts, depending on severity (unilateral or bilateral) and defect location (hemisphere ipsilateral or contralateral to the defect). Further research is needed to explore the association between regional fetal brain growth and cleft lip/palate severity, with the potential to inform early neurodevelopmental biomarkers and personalized diagnostics.

Anisotropic carrier dynamics and laser-fabricated luminescent patterns on oriented single-crystal perovskite wafers

Perovskite materials and their applications in optoelectronics have attracted intensive attentions in recent years. However, in-depth understanding about their anisotropic behavior in ultrafast carrier dynamics is still lacking. Here we explore the ultrafast dynamical evolution of photo-excited carriers and photoluminescence based on differently-oriented MAPbBr3 wafers. The distinct in-plane polarization of carrier relaxation dynamics of the (100), (110) and (111) wafers and their out-of-plane anisotropy in a picosecond time scale were found by femtosecond time- and polarization-resolved transient transmission measurements, indicating the relaxation process dominated by optical/acoustic phonon interaction is related to photoinduced transient structure rearrangements. Femtosecond laser two-photon fabricated patterns exhibit three orders of magnitude enhancement of emission due to the formation of tentacle-like microstructures. Such a ultrafast dynamic study carried on differently-oriented crystal wafers is believed to provide a deep insight about the photophysical process of perovskites and to be helpful for developing polarization-sensitive and ultrafast-response optoelectronic devices.

Persisting carotid duct and proximal external carotid artery agenesis in an adult.

The carotid duct (CD) is a transient embryological structure connecting the 3rd and 4th aortic arches. We found a persisting CD in an adult female case, by studying the computed tomography angiogram. On the left side, the proximal external carotid artery (ECA) agenesis was noted. The CD was inserted into the left subclavian artery and continued upwards to reach the level of the atlas, and then it descended to connect to a normally configured segment of that ECA. It could be speculated that the CD-to-ECA connection was possible via unregressed 1st and/or 2nd aortic arches. The segmental ECA agenesis is extremely rare, while its supply via a persisting patent CD was not reported previously to the authors' knowledge. The variants are extremely important during neck surgery because damaging the CD could determine hemorrhage, as well as ischemia in the ECA territory.