Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis.

Dynamin 1 mediates fission of endocytic synaptic vesicles in the brain and has two major splice variants, Dyn1xA and Dyn1xB, which are nearly identical apart from the extended C-terminal region of Dyn1xA. Despite a similar set of binding partners, only Dyn1xA is enriched at endocytic zones and accelerates vesicle fission during ultrafast endocytosis. Here, we report that Dyn1xA achieves this localization by preferentially binding to Endophilin A1 through a newly defined binding site within its long C-terminal tail extension. Endophilin A1 binds this site at higher affinity than the previously reported site, and the affinity is determined by amino acids within the Dyn1xA tail but outside the binding site. This interaction is regulated by the phosphorylation state of two serine residues specific to the Dyn1xA variant. Dyn1xA and Endophilin A1 colocalize in patches near the active zone, and mutations disrupting Endophilin A binding to the long tail cause Dyn1xA mislocalization and stalled endocytic pits on the plasma membrane during ultrafast endocytosis. Together, these data suggest that the specificity for ultrafast endocytosis is defined by the phosphorylation-regulated interaction of Endophilin A1 with the C-terminal extension of Dyn1xA.

Unraveling dynamic protein structures by two-dimensional infrared spectra with a pretrained machine learning model.

Dynamic protein structures are crucial for deciphering their diverse biological functions. Two-dimensional infrared (2DIR) spectroscopy stands as an ideal tool for tracing rapid conformational evolutions in proteins. However, linking spectral characteristics to dynamic structures poses a formidable challenge. Here, we present a pretrained machine learning model based on 2DIR spectra analysis. This model has learned signal features from approximately 204,300 spectra to establish a "spectrum-structure" correlation, thereby tracing the dynamic conformations of proteins. It excels in accurately predicting the dynamic content changes of various secondary structures and demonstrates universal transferability on real folding trajectories spanning timescales from microseconds to milliseconds. Beyond exceptional predictive performance, the model offers attention-based spectral explanations of dynamic conformational changes. Our 2DIR-based pretrained model is anticipated to provide unique insights into the dynamic structural information of proteins in their native environments.

Chemical bond reorganization in intramolecular proton transfer revealed by ultrafast X-ray photoelectron spectroscopy.

Time-resolved X-ray photoelectron spectroscopy (TR-XPS) is used in a simulation study to monitor the excited state intramolecular proton transfer between oxygen and nitrogen atoms in 2-(iminomethyl)phenol. Real-time monitoring of the chemical bond breaking and forming processes is obtained through the time evolution of excited-state chemical shifts. By employing individual atomic probes of the proton donor and acceptor atoms, we predict distinct signals with opposite chemical shifts of the donor and acceptor groups during proton transfer. Details of the ultrafast bond breaking and forming dynamics are revealed by extending the classical electron spectroscopy chemical analysis to real time. Through a comparison with simulated time-resolved photoelectron spectroscopy at the valence level, the distinct advantage of TR-XPS is demonstrated thanks to its atom specificity.

Ultrafast universal fabrication of configurable porous silicone-based elastomers by Joule heating chemistry.

Silicone-based elastomers (SEs) have been extensively applied in numerous cutting-edge areas, including flexible electronics, biomedicine, 5G smart devices, mechanics, optics, soft robotics, etc. However, traditional strategies for the synthesis of polymer elastomers, such as bulk polymerization, suspension polymerization, solution polymerization, and emulsion polymerization, are inevitably restricted by long-time usage, organic solvent additives, high energy consumption, and environmental pollution. Here, we propose a Joule heating chemistry method for ultrafast universal fabrication of SEs with configurable porous structures and tunable components (e.g., graphene, Ag, graphene oxide, TiO2, ZnO, Fe3O4, V2O5, MoS2, BN, g-C3N4, BaCO3, CuI, BaTiO3, polyvinylidene fluoride, cellulose, styrene-butadiene rubber, montmorillonite, and EuDySrAlSiOx) within seconds by only employing H2O as the solvent. The intrinsic dynamics of the in situ polymerization and porosity creation of these SEs have been widely investigated. Notably, a flexible capacitive sensor made from as-fabricated silicone-based elastomers exhibits a wide pressure range, fast responses, long-term durability, extreme operating temperatures, and outstanding applicability in various media, and a wireless human-machine interaction system used for rescue activities in extreme conditions is established, which paves the way for more polymer-based material synthesis and wider applications.

Ultrafast generation of hidden phases via energy-tuned electronic photoexcitation in magnetite.

Phase transitions occurring in nonequilibrium conditions can evolve through high-energy intermediate states inaccessible via equilibrium adiabatic conditions. Because of the subtle nature of such hidden phases, their direct observation is extremely challenging and requires simultaneous visualization of matter at subpicoseconds and subpicometer scales. Here, we show that a magnetite crystal in the vicinity of its metal-to-insulator transition evolves through different hidden states when controlled via energy-tuned ultrashort laser pulses. By directly monitoring magnetite's crystal structure with ultrafast electron diffraction, we found that upon near-infrared (800 nm) excitation, the trimeron charge/orbital ordering pattern is destroyed in favor of a phase-separated state made of cubic-metallic and monoclinic-insulating regions. On the contrary, visible light (400 nm) activates a photodoping charge transfer process that further promotes the long-range order of the trimerons by stabilizing the charge density wave fluctuations, leading to the reinforcement of the monoclinic insulating phase. Our results demonstrate that magnetite's structure can evolve through completely different metastable hidden phases that can be reached long after the initial excitation has relaxed, breaking ground for a protocol to control emergent properties of matter.

Ultrafast terahertz Stark spectroscopy reveals the excited-state dipole moments of retinal in bacteriorhodopsin.

The photoinduced all-trans to 13-cis isomerization of the retinal Schiff base represents the ultrafast first step in the reaction cycle of bacteriorhodopsin (BR). Extensive experimental and theoretical work has addressed excited-state dynamics and isomerization via a conical intersection with the ground state. In conflicting molecular pictures, the excited state potential energy surface has been modeled as a pure S[Formula: see text] state that intersects with the ground state, or in a 3-state picture involving the S[Formula: see text] and S[Formula: see text] states. Here, the photoexcited system passes two crossing regions to return to the ground state. The electric dipole moment of the Schiff base in the S[Formula: see text] and S[Formula: see text] state differs strongly and, thus, its measurement allows for assessing the character of the excited-state potential. We apply the method of ultrafast terahertz (THz) Stark spectroscopy to measure electric dipole changes of wild-type BR and a BR D85T mutant upon electronic excitation. A fully reversible transient broadening and spectral shift of electronic absorption is induced by a picosecond THz field of several megavolts/cm and mapped by a 120-fs optical probe pulse. For both BR variants, we derive a moderate electric dipole change of 5 [Formula: see text] 1 Debye, which is markedly smaller than predicted for a neat S[Formula: see text]-character of the excited state. In contrast, S[Formula: see text]-admixture and temporal averaging of excited-state dynamics over the probe pulse duration gives a dipole change in line with experiment. Our results support a picture of electronic and nuclear dynamics governed by the interaction of S[Formula: see text] and S[Formula: see text] states in a 3-state model.

PanDepth, an ultrafast and efficient genomic tool for coverage calculation.

Coverage quantification is required in many sequencing datasets within the field of genomics research. However, most existing tools fail to provide comprehensive statistical results and exhibit limited performance gains from multithreading. Here, we present PanDepth, an ultra-fast and efficient tool for calculating coverage and depth from sequencing alignments. PanDepth outperforms other tools in computation time and memory efficiency for both BAM and CRAM-format alignment files from sequencing data, regardless of read length. It employs chromosome parallel computation and optimized data structures, resulting in ultrafast computation speeds and memory efficiency. It accepts sorted or unsorted BAM and CRAM-format alignment files as well as GTF, GFF and BED-formatted interval files or a specific window size. When provided with a reference genome sequence and the option to enable GC content calculation, PanDepth includes GC content statistics, enhancing the accuracy and reliability of copy number variation analysis. Overall, PanDepth is a powerful tool that accelerates scientific discovery in genomics research.

SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition.

Protein sequence design can provide valuable insights into biopharmaceuticals and disease treatments. Currently, most protein sequence design methods based on deep learning focus on network architecture optimization, while ignoring protein-specific physicochemical features. Inspired by the successful application of structure templates and pre-trained models in the protein structure prediction, we explored whether the representation of structural sequence profile can be used for protein sequence design. In this work, we propose SPDesign, a method for protein sequence design based on structural sequence profile using ultrafast shape recognition. Given an input backbone structure, SPDesign utilizes ultrafast shape recognition vectors to accelerate the search for similar protein structures in our in-house PAcluster80 structure database and then extracts the sequence profile through structure alignment. Combined with structural pre-trained knowledge and geometric features, they are further fed into an enhanced graph neural network for sequence prediction. The results show that SPDesign significantly outperforms the state-of-the-art methods, such as ProteinMPNN, Pifold and LM-Design, leading to 21.89%, 15.54% and 11.4% accuracy gains in sequence recovery rate on CATH 4.2 benchmark, respectively. Encouraging results also have been achieved on orphan and de novo (designed) benchmarks with few homologous sequences. Furthermore, analysis conducted by the PDBench tool suggests that SPDesign performs well in subdivided structures. More interestingly, we found that SPDesign can well reconstruct the sequences of some proteins that have similar structures but different sequences. Finally, the structural modeling verification experiment indicates that the sequences designed by SPDesign can fold into the native structures more accurately.

Specific and Nonuniform Brain States during Cold Perception in Mice.

The quest to decode the complex supraspinal mechanisms that integrate cutaneous thermal information in the central system is still ongoing. The dorsal horn of the spinal cord is the first hub that encodes thermal input which is then transmitted to brain regions via the spinothalamic and thalamocortical pathways. So far, our knowledge about the strength of the interplay between the brain regions during thermal processing is limited. To address this question, we imaged the brains of adult awake male mice in resting state using functional ultrasound imaging during plantar exposure to constant and varying temperatures. Our study reveals for the first time the following: (1) a dichotomy in the response of the somatomotor-cingulate cortices and the hypothalamus, which was never described before, due to the lack of appropriate tools to study such regions with both good spatial and temporal resolutions. (2) We infer that cingulate areas may be involved in the affective responses to temperature changes. (3) Colder temperatures (ramped down) reinforce the disconnection between the somatomotor-cingulate and hypothalamus networks. (4) Finally, we also confirm the existence in the mouse brain of a brain mode characterized by low cognitive strength present more frequently at resting neutral temperature. The present study points toward the existence of a common hub between somatomotor and cingulate regions, whereas hypothalamus functions are related to a secondary network.

Dynamics of Anions: From Bound to Unbound States and Everything In Between.

Gas-phase anions present an ideal playground for the exploration of excited-state dynamics. They offer control in terms of the mass, extent of solvation, internal temperature, and conformation. The application of a range of ion sources has opened the field to a vast array of anionic systems whose dynamics are important in areas ranging from biology to star formation. Here, we review recent experimental developments in the field of anion photodynamics, demonstrating the detailed insight into photodynamical and electron-capture processes that can be uncovered. We consider the electronic and nuclear ultrafast dynamics of electronically bound excited states along entire reaction coordinates; electronically unbound states showing that photochemical concepts, such as chromophores and Kasha's rule, are transferable to electron-driven chemistry; and nonvalence states that straddle the interface between bound and unbound states. Finally, we consider likely developments that are sure to keep the field of anion dynamics buoyant and impactful.

Lipid Landscapes: Vibrational Spectroscopy for Decoding Membrane Complexity.

Cell membranes are incredibly complex environments containing hundreds of components. Despite substantial advances in the past decade, fundamental questions related to lipid-lipid interactions and heterogeneity persist. This review explores the complexity of lipid membranes, showcasing recent advances in vibrational spectroscopy to characterize the structure, dynamics, and interactions at the membrane interface. We include an overview of modern techniques such as surface-enhanced infrared spectroscopy as a steady-state technique with single-bilayer sensitivity, two-dimensional sum-frequency generation spectroscopy, and two-dimensional infrared spectroscopy to measure time-evolving structures and dynamics with femtosecond time resolution. Furthermore, we discuss the potential of multiscale molecular dynamics (MD) simulations, focusing on recently developed simulation algorithms, which have emerged as a powerful approach to interpret complex spectra. We highlight the ongoing challenges in studying heterogeneous environments in multicomponent membranes via current vibrational spectroscopic techniques and MD simulations. Overall, this review provides an up-to-date comprehensive overview of the powerful combination of vibrational spectroscopy and simulations, which has great potential to illuminate lipid-lipid, lipid-protein, and lipid-water interactions in the intricate conformational landscape of cell membranes.

Few-Cycle Surface Plasmon Polaritons.

Surface plasmon polaritons (SPPs) can confine and guide light in nanometer volumes and are ideal tools for achieving electric field enhancement and the construction of nanophotonic circuitry. The realization of the highest field strengths and fastest switching requires confinement also in the temporal domain. Here, we demonstrate a tapered plasmonic waveguide with an optimized grating structure that supports few-cycle surface plasmon polaritons with >70 THz bandwidth while achieving >50% light-field-to-plasmon coupling efficiency. This enables us to observe the─to our knowledge─shortest reported SPP wavepackets. Using time-resolved photoelectron microscopy with suboptical-wavelength spatial and sub-10 fs temporal resolution, we provide full spatiotemporal imaging of co- and counter-propagating few-cycle SPP wavepackets along tapered plasmonic waveguides. By comparing their propagation, we track the evolution of the laser-plasmon phase, which can be controlled via the coupling conditions.

Direct Visualization of Dark Interlayer Exciton Transport in Moiré Superlattices.

Moiré superlattices have emerged as an unprecedented manipulation tool for engineering correlated quantum phenomena in van der Waals heterostructures. With moiré potentials as a naturally configurable solid-state that sustains high exciton density, interlayer excitons in transition metal dichalcogenide heterostructures are expected to achieve high-temperature exciton condensation. However, the exciton degeneracy state is usually optically inactive due to the finite momentum of interlayer excitons. Experimental observation of dark interlayer excitons in moiré potentials remains challenging. Here we directly visualize the dark interlayer exciton transport in WS2/h-BN/WSe2 heterostructures using femtosecond transient absorption microscopy. We observe a transition from classical free exciton gas to quantum degeneracy by imaging temperature-dependent exciton transport. Below a critical degeneracy temperature, exciton diffusion rates exhibit an accelerating downward trend, which can be explained well by a nonlinear quantum diffusion model. These results open the door to quantum information processing and high-precision metrology in moiré superlattices.

Momentum-Space Observation of Optically Excited Nonthermal Electrons in Graphene with Persistent Pseudospin Polarization.

The unique optical properties of graphene, with broadband absorption and ultrafast response, make it a critical component of optoelectronic and spintronic devices. Using time-resolved momentum microscopy with high data rate and high dynamic range, we report momentum-space measurements of electrons promoted to the graphene conduction band with visible light and their subsequent relaxation. We observe a pronounced nonthermal distribution of nascent photoexcited electrons with lattice pseudospin polarization in remarkable agreement with results of simple tight-binding theory. By varying the excitation fluence, we vary the relative importance of electron-electron vs electron-phonon scattering in the relaxation of the initial distribution. Increasing the excitation fluence results in increased noncollinear electron-electron scattering and reduced pseudospin polarization, although up-scattered electrons retain a degree of polarization. These detailed momentum-resolved electron dynamics in graphene demonstrate the capabilities of high-performance time-resolved momentum microscopy in the study of 2D materials and can inform the design of graphene devices.

Giant Terahertz Birefringence in an Ultrathin Anisotropic Semimetal.

Manipulating the polarization of light at the nanoscale is key to the development of next-generation optoelectronic devices. This is typically done via waveplates using optically anisotropic crystals, with thicknesses on the order of the wavelength. Here, using a novel ultrafast electron-beam-based technique sensitive to transient near fields at THz frequencies, we observe a giant anisotropy in the linear optical response in the semimetal WTe2 and demonstrate that one can tune the THz polarization using a 50 nm thick film, acting as a broadband wave plate with thickness 3 orders of magnitude smaller than the wavelength. The observed circular deflections of the electron beam are consistent with simulations tracking the trajectory of the electron beam in the near field of the THz pulse. This finding offers a promising approach to enable atomically thin THz polarization control using anisotropic semimetals and defines new approaches for characterizing THz near-field optical response at far-subwavelength length scales.

Direct Nanosecond Multiframe Imaging of Irreversible Dynamics in 4D Electron Microscopy.

Irreversible ultrafast events are prevalent in nature, yet their capture in real time poses significant challenges. Traditional single-shot imaging technologies, which utilize a single optical pump and single delayed electron probe, offer high spatiotemporal resolution but fail to capture the entire dynamic evolutions. Here, we introduce a novel imaging method employing a single optical pump and delayed multiple electron probes. This approach, facilitated by an innovative deflector in ultrafast electron microscopy, enables the acquisition of nine frames per exposure, paving the way for statistical and quantitative analyses. We have developed an algorithm that corrects frame-by-frame distortions, realizing a cross-correlation enhancement of ∼26%. Achieving ∼12 nm and 20 ns resolution, our method allows for the comprehensive visualization of laser-induced behaviors in Au nanoparticles, including merging, jumping, and collision processes. Our results demonstrate the capability of this multiframe imaging technique to document irreversible processes across materials science and biology with unprecedented nanometer-nanosecond precision.

Exciton-Phonon Coupling Induces a New Pathway for Ultrafast Intralayer-to-Interlayer Exciton Transition and Interlayer Charge Transfer in WS2-MoS2 Heterostructure: A First-Principles Study.

Despite the weak, van der Waals interlayer coupling, photoinduced charge transfer vertically across atomically thin interfaces can occur within surprisingly fast, sub-50 fs time scales. An early theoretical understanding of charge transfer is based on a noninteracting picture, neglecting excitonic effects that dominate optical properties of such materials. We employ an ab initio many-body perturbation theory approach, which explicitly accounts for the excitons and phonons in the heterostructure. Our large-scale first-principles calculations directly probe the role of exciton-phonon coupling in the charge dynamics of the WS2/MoS2 heterobilayer. We find that the exciton-phonon interaction induced relaxation time of photoexcited excitons at the K valley of MoS2 and WS2 is 67 and 15 fs at 300 K, respectively, which sets a lower bound to the intralayer-to-interlayer exciton transfer time and is consistent with experiment reports. We further show that electron-hole correlations facilitate novel transfer pathways that are otherwise inaccessible to noninteracting electrons and holes.

Ultrafast Coherent Exciton Couplings and Many-Body Interactions in Monolayer WS2.

Transition metal dichalcogenides (TMDs) are quantum confined systems with interesting optoelectronic properties, governed by Coulomb interactions in the monolayer (1L) limit, where strongly bound excitons provide a sensitive probe for many-body interactions. Here, we use two-dimensional electronic spectroscopy (2DES) to investigate many-body interactions and their dynamics in 1L-WS2 at room temperature and with sub-10 fs time resolution. Our data reveal coherent interactions between the strongly detuned A and B exciton states in 1L-WS2. Pronounced ultrafast oscillations of the transient optical response of the B exciton are the signature of a coherent 50 meV coupling and coherent population oscillations between the two exciton states. Supported by microscopic semiconductor Bloch equation simulations, these coherent dynamics are rationalized in terms of Dexter-like interactions. Our work sheds light on the role of coherent exciton couplings and many-body interactions in the ultrafast temporal evolution of spin and valley states in TMDs.

Electron Imaging of Nanoscale Charge Distributions Induced by Femtosecond Light Pulses.

Surface charging is ubiquitously observable during in situ transmission electron microscopy of nonconducting specimens as a result of electron beam/sample interactions or optical stimuli and often limits the achievable image stability and spatial or spectral resolution. Here, we report on the electron-optical imaging of surface charging on a nanostructured surface following femtosecond multiphoton photoemission. By quantitatively extracting the light-induced electrostatic potential and studying the charging dynamics on relevant time scales, we gain insights into the details of the multiphoton photoemission process in the presence of an electrostatic background field. We study the interaction of the charge distribution with the high-energy electron beam and secondary electrons and propose a simple model to describe the interplay of electron- and light-induced processes. In addition, we demonstrate how to mitigate sample charging by simultaneously optically illuminating the sample.

Exploring the Fundamental Spatial Limits of Magnetic All-Optical Switching.

All-optical switching (AOS) results in ultrafast and deterministic magnetization reversal upon single laser pulse excitation, potentially supporting faster and more energy-efficient data storage. To explore the fundamental limits of achievable bit densities in AOS, we have used soft X-ray transient grating spectroscopy to study the ultrafast magnetic response of a GdFe alloy after a spatially structured excitation with a periodicity of 17 nm. The ultrafast spatial evolution of the magnetization in combination with atomistic spin dynamics and microscopic temperature model calculations allows us to derive a detailed phase diagram of AOS as a function of both the absorbed energy density and the nanoscale excitation period. Our results suggest that the minimum size for AOS in GdFe alloys, induced by a nanoscale periodic excitation, is around 25 nm and that this limit is governed by ultrafast lateral electron diffusion and by the threshold for optical damage.