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Cutting-edge X-ray sources have enabled the structural dynamics of proteins to be tracked during biochemical processes, but the findings have been questioned. Two experts discuss the implications of a study that digs into this issue.Absorption of multiple photons alters structural dynamics of proteins. [ABSTRACT FROM AUTHOR]

We employ two-dimensional electronic-vibrational (2DEV) spectroscopy to study the coherent dynamics of coupled vibrational modes in an excitonically-coupled dimer model. The advantage of separating excitation and detection in different frequency regimes allows us to directly probe the electronic and vibrational coherences in the time-evolved 2DEV spectra. The complexity of vibrational coherence of two coupled modes is directly revealed by cross peaks in the 2DEV spectra. With the help of the ensuing time traces, we can follow how the vibrational coherence changes over time in the monomer model and, subsequently, in the dimer model. We show that the complexity of two coupled vibrational modes and the interaction between electronic and vibrational coherences in molecular systems can be effectively disentangled using the 2DEV spectroscopy technique. [ABSTRACT FROM AUTHOR]

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer 1,2 . However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore 3-17 . As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern 18,19 whether this experimental approach 20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions 18,19 . Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics 21 ) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments 20 such that mechanistically relevant insight emerges., (© 2024. The Author(s).)

Objective: Rhodopsin from the eubacterium Exiguobacterium sibiricum (ESR) performs the lightdependent proton pumping function. The operation of ESR is based on the ultrafast photochemical reaction of isomerization of the retinal chromophore, which triggers dark processes closed in a photocycle. Many parameters of the photocycle are determined by the presence of a hydrogen bond between the primary counterion Asp85 and the chromophore. ESR in detergent micelles pumps protons most efficiently at pH > 9, when such a bond is most probable. Methods: In the present study, the photochemical reaction of ESR at pH 9.5 was investigated by femtosecond laser absorption spectroscopy. Results and Discussion: It was shown that photoisomerization of the chromophore group occurs in 0.51 ps, with the contribution from the reactive excited state being ca. 80%. A comparison with the earlier obtained data for pH 7.4 showed that, at pH 9.5, the reaction proceeds much faster and more efficiently. Conclusions: The present results confirm the important role of the chromophore group counterion in the photoactivated processes of rhodopsins. [ABSTRACT FROM AUTHOR]

Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution. [ABSTRACT FROM AUTHOR]

Within the kinetic-atomistic approach, a new approach is proposed for constructing the temperature dependence of the stationary velocity of propagation of the solid–liquid interface (SLI) in metals: aluminum, copper, and iron with different crystallographic orientations. The considered temperature range includes the range of maximum allowable overheating/overcooling values for each of the metals. A significant modification to the well-known kinetic model with the Wilson–Frenkel (WF) diffusion constraint, which is used to construct the response function, is made. An atomistic simulation of the processes of melting/crystallization of metals aluminum, copper, and iron is carried out over the entire temperature range using three interaction potentials of the "embedded atom" family. By comparing the simulation results with the data of the modified kinetic model, the response function of the interface velocity in the range of maximum allowable overheating/overcooling values in metals is constructed using the least squares criterion. The use of the modified WF kinetic model in calculations significantly improves the accuracy of the response function over the considered temperature range. The resulting temperature dependence of the interface velocity is diffusion-limited and is described by the same equation for each metal over the considered temperature range. [ABSTRACT FROM AUTHOR]

Directly resolving structural changes in material on the atomic scales of time and space is desired in studies of many disciplines. Ultrafast electron diffraction (UED), which combines the temporal resolution of femtosecond-pulse laser and the spatial sensitivity of electron diffraction, is an advancing methodology serving such a goal. Here we present the design of a UED apparatus with multiple operation modes for observation of collective atomic motions in solid material of various morphologies. This multi-mode UED employs a pulsed electron beam with propagation trajectory of parallel and convergent incidences, and diffraction configurations of transmission and reflection, as well utilities of preparation and characterization of cleaned surface and adsorbates. We recorded the process of electron–phonon coupling in single crystal molybdenum ditelluride following excitation of femtosecond laser pulses, and diffraction patterns of polycrystalline graphite thin film under different settings of electron optics, to demonstrate the temporal characteristics and tunable probe spot of the built UED apparatus, respectively. [ABSTRACT FROM AUTHOR]

Colloidal crystals are used to understand fundamentals of atomic rearrangements in condensed matter and build complex metamaterials with unique functionalities. Simulations predict a multitude of self-assembled crystal structures from anisotropic colloids, but these shapes have been challenging to fabricate. Here, we use two-photon lithography to fabricate Archimedean truncated tetrahedrons and self-assemble them under quasi-2D confinement. These particles self-assemble into a hexagonal phase under an in-plane gravitational potential. Under additional gravitational potential, the hexagonal phase transitions into a quasi-diamond two-unit basis. In-situ imaging reveal this phase transition is initiated by an out-of-plane rotation of a particle at a crystalline defect and causes a chain reaction of neighboring particle rotations. Our results provide a framework of studying different structures from hard-particle self-assembly and demonstrates the ability to use confinement to induce unusual phases. [ABSTRACT FROM AUTHOR]

X-ray and electron scattering from free gas-phase molecules is examined using the independent atom model (IAM) and ab initio electronic structure calculations. The IAM describes the effect of the molecular geometry on the scattering, but does not account for the redistribution of valence electrons due to, for instance, chemical bonding. By examining the total, i.e. energy-integrated, scattering from three molecules, fluoroform (CHF3), 1,3-cyclohexadiene (C6H8) and naphthalene (C10H8), the effect of electron redistribution is found to predominantly reside at small-to-medium values of the momentum transfer (q ≤ 8 Å-1) in the scattering signal, with a maximum percent difference contribution at 2 ≤ q ≤ 3 Å-1. A procedure to determine the molecular geometry from the large-q scattering is demonstrated, making it possible to more clearly identify the deviation of the scattering from the IAM approximation at small and intermediate q and to provide a measure of the effect of valence electronic structure on the scattering signal. [ABSTRACT FROM AUTHOR]

During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ 70 -RNAP and the λP R promoter. Cryo-EM snapshots revealed that the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As the nt-strand 'read-out' extends, the RNAP clamp closes, expelling an inhibitory σ 70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating that yet unknown conformational changes complete RPo formation in subsequent steps. Given that these events likely describe DNA opening at many bacterial promoters, this study provides insights into how DNA sequence regulates steps of RPo formation., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

We report results of theoretical studies, showing that in a BBO crystal there are directions with temperature-noncritical interactions for three-wave processes over the entire transparency range. All phase-matching processes for frequency conversion (generation of harmonics, sum and difference frequency generation, and parametric generation) are temperature-critical, but can be implemented with a record-breaking temperature phase-matching width (up to 150°C cm). [ABSTRACT FROM AUTHOR]

We study the threshold characteristics of SRS generation at a wavelength of 2.84 μm in a hollow-core revolver fiber filled with methane depending on the duration of positively chirped broadband pump pulses at a wavelength of 1.56 μm. It is experimentally proven that the average effective SRS gain increases from 0.2 × 10–2 cm/GW to 3.3 × 10–2 cm/GW while the threshold pump intensity decreases from 36 GW/cm2 to 1.4 GW/cm2 as the effective pump pulse duration increases in the range of 10 to 321 ps (and with a corresponding dimensionless linear chirp of ~10 to 300). An analysis of threshold characteristics showed that SRS conversion exhibits high nonstationarity even at the maximum width of the pump pulse envelope. According to the results of numerical simulation, the effect of dispersion and SPM in a hollow-core fiber contributes to a significant increase in the SRS threshold in pump pulse energy, especially for positively chirped pulses lasting less than 100 ps. [ABSTRACT FROM AUTHOR]

The widespread use of plastics has raised concerns about their persistence in aquatic and terrestrial environments. Tiny plastic particles, microplastics, and nanoplastics generated due to degradation lead to real environmental problems. Rapid identification of potential hotspots of nanoplastics contamination has been challenging due to a lack of field-based detection methods. This study aimed to develop a single-step portable method to detect nanoplastics in water samples. Using a customdesigned fluorometer, an optimized Nile Red-based method has been successfully extended to detect nanoplastics within 10 minutes from wastewater samples with a limit of detection of 35 µg/mL. This method can be broadly used to monitor nanoplastic load during wastewater treatment and in different surface water streams which drain into urban watersheds. [ABSTRACT FROM AUTHOR]

Technical advances paired with developments in methodology have enabled electron microscopy to reach atomic resolution. Further improving the information limit in microscopic imaging requires further improvements in methodology. Here we report a ptychographic method that describes the object as the sum of discrete atomic-orbital-like functions (for example, Gaussian functions) and the probe in terms of aberration functions. Using this method, we realize an improved information limit of microscopic imaging, reaching down to 14 pm. High-quality probes and objects contribute to superior signal-to-noise ratios at low electron doses, allowing for relaxation of the sample thickness restriction to 50 nm for dense materials. Additionally, our method has the capability to decompose the total phase into element components, revealing that the information limit is element dependent. With enhanced spatial resolution, signal-to-noise ratio and thickness threshold compared with conventional ptychography methods, our local-orbital ptychography may find applications in atomic-resolution imaging of metals, ceramics, electronic devices or beam-sensitive material., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible. Cryogenic electron ptychography (Cryo-EPty) is an emerging method for imaging the structure of biomacromolecules. Here, authors develop single particle analysis based on cryo-EPty phase for high contrast, wide spatial frequency-band 3D imaging. [ABSTRACT FROM AUTHOR]

Photocathodes—materials that convert photons into electrons through a phenomenon known as the photoelectric effect—are important for many modern technologies that rely on light detection or electron-beam generation1–3. However, current photocathodes are based on conventional metals and semiconductors that were mostly discovered six decades ago with sound theoretical underpinnings4,5. Progress in this field has been limited to refinements in photocathode performance based on sophisticated materials engineering1,6. Here we report unusual photoemission properties of the reconstructed surface of single crystals of the perovskite oxide SrTiO3(100), which were prepared by simple vacuum annealing. These properties are different from the existing theoretical descriptions4,7–10. In contrast to other photocathodes with a positive electron affinity, our SrTiO3 surface produces, at room temperature, discrete secondary photoemission spectra, which are characteristic of efficient photocathode materials with a negative electron affinity11,12. At low temperatures, the photoemission peak intensity is enhanced substantially and the electron beam obtained from non-threshold excitations shows longitudinal and transverse coherence that differs from previous results by at least an order of magnitude6,13,14. The observed emergence of coherence in secondary photoemission points to the development of a previously undescribed underlying process in addition to those of the current theoretical photoemission framework. SrTiO3 is an example of a fundamentally new class of photocathode quantum materials that could be used for applications that require intense coherent electron beams, without the need for monochromatic excitations.The reconstructed surface of single crystals of SrTiO3(100), prepared by simple vacuum annealing, produces discrete secondary photoemission spectra at room temperature and has increased peak intensities at low temperatures. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: Singlet fission (SF) has potential applications in high‐efficiency photo‐energy harvesting applications, but its practical application is hindered by the limited number of materials. In this work, we explored the bay aromatic substitution strategy for the design of new perylenediimide (PDI) based SF materials. A series of PDI derivatives with biphenyl or naphthalene units substituted at the bay positions were designed and synthesized to investigate the effects of aromatic substitutes on their photodynamic behaviours. The bay substitutions do not shift the energy level of the PDI core significantly but give rise to different intermolecular coupling strengths in the thin films and affect the intermolecular SF efficiency. Femtosecond transient absorption (fsTA) spectroscopy reveals that appropriate spacing configuration from the bay aromatic substitution groups enhances the SF yields by promoting the interaction of neighbouring PDI cores. Triplet exciton yields of up to 183% have been obtained from these new PDI derivatives, making them potential candidates in future SF‐based optoelectronics. [ABSTRACT FROM AUTHOR]

Recent advances in automation have fostered the development of unattended data collection services at a handful of synchrotron facilities worldwide. At the Swiss Light Source, the installation of new high-throughput sample changers at all three macromolecular crystallography beamlines and the commissioning of the Fast Fragment and Compound Screening pipeline created a unique opportunity to automate data acquisition. Here, the DA+ microservice software stack upgrades, implementation of an automatic loop-centering service and deployment of the Smart Digital User (SDU) software for unattended data collection are reported. The SDU software is the decision-making software responsible for communications between services, sample and device safety, sample centering, sample alignment with grid based X-ray diffraction and, finally, data collection. [ABSTRACT FROM AUTHOR]

Aging proteins in the lens become increasingly aggregated and insoluble, contributing to presbyopia. In this study, we investigated the ability of aggrelyte‐2 (N,S‐diacetyl‐L‐cysteine methyl ester) to reverse the water insolubility of aged human lens proteins and to decrease stiffness in cultured human and mouse lenses. Water‐insoluble proteins (WI) of aged human lenses (65–75 years) were incubated with aggrelyte‐2 (500 μM) for 24 or 48 h. A control compound that lacked the S‐acetyl group (aggrelyte‐2C) was also tested. We observed 19%–30% solubility of WI upon treatment with aggrelyte‐2. Aggrelyte‐2C also increased protein solubility, but its effect was approximately 1.4‐fold lower than that of aggrelyte‐2. The protein thiol contents were 1.9‐ to 4.9‐fold higher in the aggrelyte‐2‐ and aggrelyte‐2C‐treated samples than in the untreated samples. The LC–MS/MS results showed Nε‐acetyllysine (AcK) levels of 1.5 to 2.1 nmol/mg protein and 0.6 to 0.9 nmol/mg protein in the aggrelyte‐2‐ and aggrelyte‐2C‐treated samples. Mouse (C57BL/6J) lenses (incubated for 24 h) and human lenses (incubated for 72 h) with 1.0 mM aggrelyte‐2 showed significant decreases in stiffness with simultaneous increases in soluble proteins (human lenses) and protein‐AcK levels, and such changes were not observed in aggrelyte‐2C‐treated lenses. Mass spectrometry of the solubilized protein revealed AcK in all crystallins, but more was observed in α‐crystallins. These results suggest that aggrelyte‐2 increases protein solubility and decreases lens stiffness through acetylation and disulfide reduction. Aggrelyte‐2 might be useful in treating presbyopia in humans. [ABSTRACT FROM AUTHOR]

There is an increasing demand for simple and efficient sample delivery technology to match the rapid development of serial crystallography and its wide application in analyzing the structural dynamics of biological macromolecules. Here, a microfluidic rotating-target device is presented, capable of three-degrees-of-freedom motion, including two rotational degrees of freedom and one translational degree of freedom, for sample delivery. Lysozyme crystals were used as a test model with this device to collect serial synchrotron crystallography data and the device was found to be convenient and useful. This device enables in situ diffraction from crystals in a microfluidic channel without the need for crystal harvesting. The circular motion ensures that the delivery speed can be adjusted over a wide range, showing its good compatibility with different light sources. Moreover, the three-degrees-of-freedom motion guarantees the full utilization of crystals. Hence, sample consumption is greatly reduced, and only 0.1 mg of protein is consumed in collecting a complete dataset. [ABSTRACT FROM AUTHOR]

Aqueous zinc battery has been regarded as one of the most promising energy storage systems due to its low cost and environmental benignity. However, the safety concern on Zn anodes caused by uncontrolled Zn dendrite growth in aqueous electrolyte hinders their application. Herein, sucrose with multi-hydroxyl groups has been introduced into aqueous electrolyte to modify Zn2+ solvation environment and create a protection layer on Zn anode, thus effectively retarding the growth of zinc dendrites. Atomistic simulations and experiments confirm that sucrose molecules can enter into the solvation sheath of Zn2+, and the as-formed unique solvation structure enhances the mobility of Zn2+. Such fast Zn2+ kinetics in sucrose-modified electrolyte can successfully suppress the dendrite growth. With this sucrose-modified aqueous electrolyte, Zn/Zn symmetric cells present more stable cycle performance than those using pure aqueous electrolyte; Zn/C cells also deliver an impressive higher energy density of 129.7 Wh·kg−1 and improved stability, suggesting a great potential application of sucrose-modified electrolytes for future Zn batteries. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Electron diffraction has been a powerful tool to investigate atomistic structures of molecules, liquids, and solids. Time-resolved diffraction with pulsed electron beams is capable of visualizing transient structural changes with the combined fast temporal and atomic-scale spatial resolutions. Considerable effort has been devoted to producing ultrashort electron pulses for the imaging of atomic and electronic motions occurring on the time scale of femtoseconds and attoseconds, respectively. This account briefly describes technologies for producing ultrashort electron pulses including our recent works where we produced and detected attosecond electron pulses by manipulating electron beams with laser light. A qualitative discussion is given on the modulation of a diffraction pattern due to a change of electron density distribution in a molecule. Electron diffraction with attosecond pulses will allow to visualize how electron clouds in a molecule or material evolve in space and time during a reaction. [ABSTRACT FROM AUTHOR]

The Raman generation parameters at a wavelength of 2.84 μm in a hollow-core revolver fiber filled with methane are studied, dependent on the gas pressure and on the energy and duration of chirped pulses of erbium fiber-optic pumping source with a wavelength of 1.56 μm. It is shown that the threshold energy of pumping pulses decreases as the methane pressure increases, and the growth in their duration promotes more efficient Raman conversion 1.56 μm → 2.84 μm. The maximum pulse energy at a wavelength of 2.84 and the quantum conversion efficiency are 1.6 μJ and 12%, respectively. It is numerically demonstrated that the quantum conversion efficiency can be increased up to the value above 50% at single-mode pumping radiation with pulse energy up to 100 μJ. The calculations show that the main process limiting the Raman conversion efficiency in the studied parameter range is the coherent four-wave interaction. [ABSTRACT FROM AUTHOR]

Nanomedicine is among the most fascinating areas of research. Most of the newly discovered pharmaceutical polymorphs, as well as many new synthesized or isolated natural products, appear only in form of nanocrystals. The development of techniques that allow investigating the atomic structure of nanocrystalline materials is therefore one of the most important frontiers of crystallography. Some unique features of electrons, like their non‐neutral charge and their strong interaction with matter, make this radiation suitable for imaging and detecting individual atoms, molecules, or nanoscale objects down to sub‐angstrom resolution. In the recent years the development of three‐dimensional (3D) electron diffraction (3D ED) has shown that electron diffraction can be successfully used to solve the crystal structure of nanocrystals and most of its limiting factors like dynamical scattering or limited completeness can be easily overcome. This article is a review of the state of the art of this method with a specific focus on how it can be applied to beam sensitive samples like small‐molecule organic nanocrystals. This article is categorized under:Therapeutic Approaches and Drug Discovery > Emerging Technologies [ABSTRACT FROM AUTHOR]

In recent years, molecular alignment echoes induced by a pair of time-delayed femtosecond laser pulses have been proposed and have aroused wide research interest. However, we demonstrate that an alignment echo can be alternatively produced by a shaped femtosecond laser pulse with a V-style spectral phase modulation. The full, fractional, and imaginary alignment echoes are formed by the excitation of the tailored two time-delayed sub-pulses. Both the delay time and the ratio of intensity between the two sub-pulses can be easily manipulated by designing the modulation parameters to induce various types of echoes. We further show that the optimal ratio of intensity between the two sub-pulses, which results in the maximal alignment degrees of the full echo, closely correlates with the energy of the sub-pulse. When the pulse energy is relatively low, the maximal alignment degree of the full echo is obtained when the two sub-pulses have equal intensity. The optimal ratio of intensity increases with the excitation energy of the first pump pulse. [ABSTRACT FROM AUTHOR]

The potential therapeutic uses of electromagnetic fields (EMF), part of the nonionizing radiation spectrum, increase with time. Among them, those considering the potential antitumor effects exerted by the Magnetic Fields (MFs), part of the EMF entity, have gained more and more interest. A recent review on this subject reports the MFs' effect on apoptosis of tumor cells as one of the most important breakthroughs. Apoptosis is considered a key mechanism regulating the genetic stability of cells and as such is considered of fundamental importance in cancer initiation and development. According to an atomic/sub-atomic analysis, based on quantum physics, of the complexity of biological life and the role played by oxygen and its radicals in cancer biology, a possible biophysical mechanism is described. The mechanism considers the influence of MFs on apoptosis through an effect on electron spin that is able to increase reactive oxygen species (ROS) concentration. Impacting on the delicate balance between ROS production and ROS elimination in tumor cells is considered a promising cancer therapy, affecting different biological processes, such as apoptosis and metastasis. An analysis in the literature, which allows correlation between MFs exposure characteristics and their influence on apoptosis and ROS concentration, supports the validity of the mechanism. [ABSTRACT FROM AUTHOR]

Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities., (© 2023 The Authors. Yeast published by John Wiley & Sons Ltd.)

We propose a scheme to inverse engineer the Hamiltonian of any general driven three-level system by employing a SU(3) transformation. For special cases, the scheme is then introduced to explore nonadiabatic dynamic evolution of systems with two-photon resonance. We demonstrate that, by selecting the control parameters with explicit function forms, both the ideal process and the practical evolution driving with the truncation of pulses, systematic error and decaying can implement fast population transfer with high fidelity. Moreover, the nonadiabatic passages are not reconstructed by the superadiabatic approach. [ABSTRACT FROM AUTHOR]

Carbon-based materials have been studied for their antimicrobial properties. Previously, most antimicrobial studies are investigated with suspended nanoparticles in a liquid medium. Most works are often carried out with highly ordered pyrolytic graphite. These materials are expensive and are not viable for mass use on high-touch surfaces. Additionally, highly antimicrobial silver nanoparticles are often incorporated onto substrates by chemical reduction. At times, harmful chemicals are used. In this work, low-cost graphite pencils are mechanically exfoliated and transferred onto Si substrates. The sparsely-covered graphite flakes are treated by either plasma O2 or UV irradiation. Subsequently, Ag is photo reduced in the presence of UV onto selected graphite flake samples. It is found that graphite flake surface topography and defects are dependent on the treatment process. High surface roughness and (defects density, I D/ I G) are induced by plasma O2 follows by UV and pristine graphite flake as follows: 6.45 nm (0.62), 4.96 nm (0.5), 3.79 nm (0.47). Antimicrobial tests with E. coli reveal high killing efficiency by photoreduced Ag-on-graphite flake. The reversible effect of Ag leaching can be compensated by repeating the photoreduction process. This work proposes that UV treatment is a promising technique over that of plasma O2 in view that the latter treated surface could repel bacteria resulting in lower bacteria-killing efficiency. [ABSTRACT FROM AUTHOR]

A novel approach to the remote-control system for the compact multi-crystal energy-dispersive spectrometer for X-ray emission spectroscopy (XES) applications has been developed. This new approach is based on asynchronous communication between software components and on reactive design principles. In this paper, the challenges faced, their solutions, as well as the implementation and future development prospects are identified. The main motivation of this work was the development of a new holistic communication protocol that can be implemented to control various hardware components allowing both independent operation and easy integration into different SCADA systems. [ABSTRACT FROM AUTHOR]

This perspective review describes emerging techniques and future opportunities for time-resolved serial femtosecond crystallography (TR-SFX) experiments using high repetition rate XFEL sources. High repetition rate sources are becoming more available with the European XFEL in operation and the recently upgraded LCLS-II will be available in the near future. One efficient use of these facilities for TR-SFX relies on pump–probe experiments using a laser to trigger a reaction of light-responsive proteins or mix-and-inject experiments for light-unresponsive proteins. With the view to widen the application of TR-SFX, the promising field of photocaged compounds is under development, which allows the very fast laser triggering of reactions that is no longer limited to naturally light-responsive samples. In addition to reaction triggering, a key concern when performing an SFX experiment is efficient sample usage, which is a main focus of new high repetition rate-compatible sample delivery methods. [ABSTRACT FROM AUTHOR]

Climate change is causing decreases in pH and dissolved oxygen (DO) in coastal ecosystems. Canopy‐forming giant kelp can locally increase DO and pH through photosynthesis, with the most pronounced effect expected in surface waters where the bulk of kelp biomass resides. However, limited observations are available from waters in canopies and measurements at depth show limited potential of giant kelp to ameliorate chemical conditions. We quantified spatiotemporal variability of surface biogeochemistry and assessed the role of biological and physical drivers in pH and DO modification at two locations differing in hydrodynamics inside and outside of two kelp forests in Monterey Bay, California in summer 2019. pH, DO, dissolved inorganic carbon (DIC), and temperature were measured at and near the surface, in conjunction with physical parameters (currents and pressure), nutrients, and metrics of phytoplankton and kelp biological processes. DO and pH were highest, with lower DIC, at the surface inside kelp forests. However, differences inside vs. outside of kelp forests were small (DO 6–8%, pH 0.05 higher in kelp). The kelp forest with lower significant wave height and slower currents had greater modification of surface biogeochemistry as indicated by larger diel variation and slightly higher mean DO and pH, despite lower kelp growth rates. Differences between kelp forests and offshore areas were not driven by nutrients or phytoplankton. Although kelp had clear effects on biogeochemistry, which were modulated by hydrodynamics, the small magnitude and spatial extent of the effect limits the potential of kelp forests to mitigate acidification and hypoxia. [ABSTRACT FROM AUTHOR]

Biology systems harvest solar energy to regulate ions and molecules precisely across cell membrane that is essential to maintain their life sustainability. Recently, artificial light-driven directional ion transport through graphene oxide membranes has been established, where the membrane converts light power into a transmembrane motive force. Herein, we report a silver nanoparticles decorated graphene oxide membranes for enhanced photo-driven ionic transport. Asymmetric light stimulated charge carrier dynamics, such as advanced light absorption efficiency, extended lifetime and efficient separation of photo-excited charge carriers, are account for the ion-driven force enhancement. Based on metal nanoparticles decoration, the concept of the guest-interactions of plasmon-enhanced photo-driven ion transport in two-dimentional layered membranes will stimulate broad researches in sensing, energy storage and conversion and water treatment. [ABSTRACT FROM AUTHOR]

The healing of cutaneous wounds is a dynamic process including overlapping phases of inflammation, proliferation, reepithelialization and remodeling. Proper wound healing is essential for the reestablishment of structural and functional integrity of the damaged tissue. Rodents are valuable biological tools for understanding tissue repair process and for developing effective treatment strategies, despite anatomical and physiological differences between human and animal skin. The purpose of the study is to evaluate the cutaneous wound healing assessment for an excisional wound model in rats, for further testing with innovative medical devices loaded with biological active compounds. CD-SD female rats were surgically operated to excise one full‐thickness circular skin patch, 20 mm diameter, in the dorsal region. Patches applied were changed every other day and samples of wounds/scars were collected on the 7th and 14th postoperative days. Macroscopic monitoring and histopathological examination assessed the wound healing process over time. Results showed that rats provide an optimal animal model for cutaneous wound healing, as data obtained can provide valuable translational information and can contribute in optimizing treatment protocols. [ABSTRACT FROM AUTHOR]

An actively Q-switched quasi-three-level Nd:YLF laser emitting at 908 nm, for the first time to our knowledge, was demonstrated. A RTP double-crystal scheme was used to realize electro-optical Q-switcher, and a L-shaped cavity structure was designed to suppress parasitic oscillation at 1047 nm. An 806 nm laser diode was used as the pump source with about 480 ÎĽ s pulse width. With 46.4 mJ pump pulse energy input at repetition rate of 100 Hz, maximum output pulse energies of 0.84 mJ and 0.73 mJ were obtained with output transmissions of 6.5% and 11%, respectively. The corresponding peak pulse powers were up to 14.3 kW and 12.1 kW, and the output pulse widths were 58.6 ns and 60.3 ns. The central laser wavelengths were both at 908.3 nm with spectral bandwidth of over 0.7 nm. [ABSTRACT FROM AUTHOR]

Low-loss dielectric modes are important features and functional bases of fundamental optical components in on-chip optical devices. However, dielectric near-field modes are challenging to reveal with high spatiotemporal resolution and fast direct imaging. Herein, we present a method to address this issue by applying time-resolved photoemission electron microscopy to a low-dimensional wide-bandgap semiconductor, hexagonal boron nitride (hBN). Taking a low-loss dielectric planar waveguide as a fundamental structure, static vector near-field vortices with different topological charges and the spatiotemporal evolution of waveguide modes are directly revealed. With the lowest-order vortex structure, strong nanofocusing in real space is realized, while near-vertical photoemission in momentum space and narrow spread in energy space are simultaneously observed due to the atomically flat surface of hBN and the small photoemission horizon set by the limited photon energies. Our approach provides a strategy for the realization of flat photoemission emitters., (© 2023. Springer Nature Limited.)

Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms., (© 2023. Springer Nature Limited.)

The primary step of almost any interaction between light and materials is the electrodynamic response of the electrons to the optical cycles of the impinging light wave on sub-wavelength and sub-cycle dimensions 1 . Understanding and controlling the electromagnetic responses of a material 2-11 is therefore essential for modern optics and nanophotonics 12-19 . Although the small de Broglie wavelength of electron beams should allow access to attosecond and ångström dimensions 20 , the time resolution of ultrafast electron microscopy 21 and diffraction 22 has so far been limited to the femtosecond domain 16-18 , which is insufficient for recording fundamental material responses on the scale of the cycles of light 1,2,10 . Here we advance transmission electron microscopy to attosecond time resolution of optical responses within one cycle of excitation light 23 . We apply a continuous-wave laser 24 to modulate the electron wave function into a rapid sequence of electron pulses, and use an energy filter to resolve electromagnetic near-fields in and around a material as a movie in space and time. Experiments on nanostructured needle tips, dielectric resonators and metamaterial antennas reveal a directional launch of chiral surface waves, a delay between dipole and quadrupole dynamics, a subluminal buried waveguide field and a symmetry-broken multi-antenna response. These results signify the value of combining electron microscopy and attosecond laser science to understand light-matter interactions in terms of their fundamental dimensions in space and time., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halobacterium salinarum, 95 years later. Although these findings were made by physiological observation of pigmented tissue and cell bodies, recent progress in genomic and metagenomic analyses has revealed that there are more than 10,000 microbial rhodopsins and 9000 animal rhodopsins with large diversity and tremendous new functionality. In this Cell Science at a Glance article and accompanying poster, we provide an overview of the diversity of functions, structures, color discrimination mechanisms and optogenetic applications of these two rhodopsin families, and will also highlight the third distinctive rhodopsin family, heliorhodopsin. [ABSTRACT FROM AUTHOR]

The coherent lattice dynamics in thin crystalline Sb and Bi films has been investigated using ultrafast electron diffraction. The samples were exposed to Ti:sapphire femtosecond laser radiation and probed by ultrashort electron pulses. The registered generation of coherent optical phonons in the crystals corresponded to the A1g and Eg modes and their combinations in Sb, as well as to the manifestation of the A1g mode and its first and second overtones in Bi. Detection of optical phonons with frequencies of up to 9 THz indicated that a temporal resolution at a level of ~100 fs was obtained. An ultrafast electron diffractometer for studying nonlinear laser-induced processes in molecular and cluster beams has been developed based on a femtosecond electron source. [ABSTRACT FROM AUTHOR]

Primary photoisomerization reactions of the retinal protonated Schiff base (RPSB) inside type I and type II rhodopsins are ultrafast and exhibit high quantum yields. Specific protein environments are thought to facilitate photoisomerization of RPSB; however, the detailed mechanisms of tuning the reaction timescales and specificity are far from being understood. Here, by using molecular dynamics simulations and large-scale XMCQDPT2-based QM/MM modeling, we gain insight into the role played by the protein environment in specific photoisomerization of RPSB from all-trans to 13-cis in microbial rhodopsin KR2 and from 11-cis to all-trans in bovine visual rhodopsin. By analyzing the calculated vibronic band shapes, we explore the early-time excited-state dynamics of RPSB in both types of rhodopsins. We show that the protein environment changes vibrational modes, which become excited following the S0–S1 transition, by pre-twisting the chromophore about a certain double bond in the ground electronic state. This reduces a barrier that hinders intramolecular rotation in the excited state, thus facilitating photoisomerization across the specific double bond. Moreover, pre-twisting of RPSB also provides conditions for initial in-phase excitation of the fundamental vibrational modes involved in the reaction coordinate, enabling vibrationally coherent barrierless excited-state decay in the photochemistry of vision. [ABSTRACT FROM AUTHOR]

Chlorophylls (Chl)s exist in a variety of flavors and are ubiquitous in both the energy and electron transfer processes of photosynthesis. The functions they perform often occur on the ultrafast (fs–ns) time scale and until recently, these have been difficult to measure in real time. Further, the complexity of the binding pockets and the resulting protein-matrix effects that alter the respective electronic properties have rendered theoretical modeling of these states difficult. Recent advances in experimental methodology, computational modeling, and emergence of new reaction center (RC) structures have renewed interest in these processes and allowed researchers to elucidate previously ambiguous functions of Chls and related pheophytins. This is complemented by a wealth of experimental data obtained from decades of prior research. Studying the electronic properties of Chl molecules has advanced our understanding of both the nature of the primary charge separation and subsequent electron transfer processes of RCs. In this review, we examine the structures of primary electron donors in Type I and Type II RCs in relation to the vast body of spectroscopic research that has been performed on them to date. Further, we present density functional theory calculations on each oxidized primary donor to study both their electronic properties and our ability to model experimental spectroscopic data. This allows us to directly compare the electronic properties of hetero- and homodimeric RCs. [ABSTRACT FROM AUTHOR]

A new scheme is proposed to improve the electron beam quality of ionization-induced injection by tailoring gas profile in laser wakefield acceleration. Two-dimensional particle-in-cell simulations show that the ionization-induced injection mainly occurs in high-density stage and automatically truncates in low-density stage due to the decrease of the wakefield potential difference. The beam loading can be compensated by the elongated beam resulting from the density transition stage. The beam quality can be improved by shorter injection distance and beam loading effect. A quasi-monoenergetic electron beam with a central energy of 258 MeV and an energy spread of 5.1% is obtained under certain laserâ€"plasma conditions. [ABSTRACT FROM AUTHOR]