Browse Articles

Repeatability of protein structural evolution following convergent gene fusions

Abstract Convergent evolution of proteins provides insights into repeatability of genetic adaptation. While local convergence of proteins at residue or domain level has been characterized, global structural convergence by inter-domain/molecular interactions remains largely unknown. Here we present structural convergent evolution on fusion enzymes of aldehyde dehydrogenases (ALDHs) and alcohol dehydrogenases (ADHs). We discover BdhE (bifunctional dehydrogenase E), an enzyme clade that emerged independently from the previously known AdhE family through distinct gene fusion events. AdhE and BdhE show shared enzymatic activities and non-overlapping phylogenetic distribution, suggesting common functions in different species. Cryo-electron microscopy reveals BdhEs form donut-like homotetramers, contrasting AdhE’s helical homopolymers. Intriguingly, despite distinct quaternary structures and < 30% amino acid sequence identity, both enzymes forms resemble dimeric structure units by ALDH-ADH interactions via convergently elongated loop structures. These findings suggest convergent gene fusions recurrently led to substrate channeling evolution to enhance two-step reaction efficiency. Our study unveils structural convergence at inter-domain/molecular level, expanding our knowledges on patterns behind molecular evolution exploring protein structural universe.

Author Correction: A noninvasive model for chronic kidney disease screening and common pathological type identification from retinal images

Author Correction: VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data

Macrophage ferroptosis potentiates GCN2 deficiency induced pulmonary venous arterialization

Multiple independent acquisitions of a metallophore-synthesis gene by plants through horizontal microbial gene transfer

Abstract The evolution of land plants is marked by major innovations enhancing their vegetative and reproductive fitness. Despite their extensive adaptations to terrestrial habitats, plants rely on ecological interactions with microbes for various physiological processes. Beyond their role as critical partners in the conquest of, and diversification on land, fungi and bacteria also serve as sources of genetic tools. Analyses of the gene space of land plant model organisms suggest that such transfers are unique and ancient. However here, using genomic data spanning the diversity of mosses, we demonstrate that a metallophore-synthesis gene was acquired independently from distinct microbial donors by at least five plant lineages. Furthermore we find that the first NAS gene acquired by mosses was later replaced by another fungal copy, transferred to another major moss lineage. Such a complex history of acquisition of a gene may reflect a more general pattern of highly dynamic gene exchange across the tree of life.

Gestational diabetes linked to autism in study: what scientists say

Daily briefing: World’s first AI-designed viruses attack antibiotic-resistant bacteria

A binary (e, 2e) spectroscopy investigation and detailed analysis of the 4d5/2 and 4d3/2 inner shell ionization of Xe

We report the momentum profiles for the binary (e, 2e) reaction of the Xe 4d5/2 and 4d3/2 inner shell ionization transitions. The experiment has been performed at an incident electron energy of 1270 eV, using a highly sensitive multichannel electron momentum spectrometer with a coverable momentum range up to 9 a.u. The experimental results were compared with the associated theoretical profiles calculated by the plane wave impulse approximation (PWIA), the distorted wave impulse approximation (DWIA), and the distorted wave Born approximation (DWBA) models, using the relativistic and non-relativistic Kohn–Sham orbitals as the target electron orbitals. The superiority of the DWBA model over not only the PWIA but also the DWIA was found for the whole momentum range up to 9 a.u., demonstrating that the interaction between the projectile and target electrons, as well as the distorted wave effect, plays an important role in explaining the momentum profile of inner-shell ionization. Furthermore, it was experimentally revealed that the branching ratio of the 4d5/2 and 4d3/2 ionizations slightly deviates from the value of the non-relativistic ratio and is only weakly dependent upon the momentum over the momenta investigated, indicating that the relativistic effect on the Xe 4d wavefunction is fairly small, as predicted by the theory. These results would provide detailed insight into the relativistic effect on electron distributions and (e, 2e) reaction dynamics for the inner-shell ionization.

Photoinduced selective electrons transfer and secondary orbital splitting in CeO2 bulk

As a typical wide bandgap semiconductor and a ubiquitous constituent in catalytic systems for a variety of applications, the dynamical processes of photoinduced electrons transfer (PET) in CeO2 are crucial for advancing the understanding of semiconductor physics and photocatalysis. In this study, we analyze orbital-resolved PET in CeO2 using real-time time-dependent density functional theory simulations. We discovered remarkable selectivity in the interatomic PET in CeO2. In particular, the photogenerated electrons maintain a consistent transport pathway from the O-2p orbital to the Ce-4f and Ce-5d orbitals, irrespective of the polarization state (linear and circular) of the external optical field. We further observed a secondary splitting found upon the crystal field splitting in Ce-5d and Ce-4f orbitals due to the symmetry breaking of the original coordination field of Ce atom. The secondary splitting is manipulated by the polarization state of the external optical field and the detailed dependency is deciphered, which provides us guidance for manipulating the orbital splitting by optical. Comparative analysis with the electrons transfer characteristics induced by hole doping reveals that the selectivity of interatomic electron transfer and the secondary splitting are unique to the photoexcitation process. Our results and findings shed new light on the microscopic mechanisms and dynamical processes underlying PET in CeO2 and may be generalized to other oxide semiconductors. These new insights may be beneficial for deciphering the ultrafast time-resolved spectroscopy experiments and for understanding the photocatalysis mechanisms in ceria-based photocatalysis materials.

Coupling to rotational manifolds to improve gas-phase pump–probe spectroscopic models

The physical picture of gas-phase optical transitions is normally presented as an isolated two-level system balanced by upward and downward processes. Isolated models assume a phenomenological treatment of collisional dephasing but do not strictly account for collisional population exchange with the rotational baths. While this assumption is valid under low-intensity conditions, where excitation is rate-limiting, isolated models can deviate from Beer’s Law at sufficient pressures and monochromatic intensities when both collisional broadening and power broadening are comparable to (or greater than) lifetime broadening, which are not uncommon conditions for cavity enhanced spectroscopies in the mid-IR spectral range. Although this problem has been addressed by rate-equation models for linear absorption measurements, a general treatment for multi-level quantum mechanical models suitable for non-linear absorption measurements (two-photon/two-color/pump–probe) is lacking. Isolated models require physical parameter inputs that disagree with expected values by at least an order of magnitude. These non-physical models undermine the ability to predict non-linear signal strengths under untested conditions and thereby limit the potential to optimize the sensitivity of non-linear spectroscopies and to expand their analytical applications (e.g., new analytes and/or buffer gases, changes in cavity free-spectral-range, changes in intracavity powers or wavelengths, and accurate investigation of physical phenomena). In this study, we derive bath-coupled models for gaseous pump–probe spectroscopy by application of the quantum Lindblad equation and detailed balance. Bath-coupled models are shown to fit data consistently across variations in intensity and agree with all physically expected values.

Mixed quantum-classical methods for polaron spectral functions

In this work, using two distinct semiclassical approaches—namely, the mean-field Ehrenfest method and the mapping approach to surface hopping—we investigate the spectral function of a single charge interacting with phonons on a lattice. This quantity is relevant for the description of angle-resolved photoemission experiments. Focusing on the one-dimensional Holstein model, we compare the performance of these approaches across a range of coupling strengths and lattice sizes, exposing the relative strengths and weaknesses of each. We demonstrate that these approaches can be efficiently applied with reasonable accuracy to ab initio polaron models. Our work provides a route to the calculation of spectral properties in realistic electron–phonon-coupled systems in a computationally inexpensive manner with encouraging accuracy.

Non-equilibrium dynamics of disordered bead-spring networks with active forces

We investigate, using Langevin dynamics simulations, the Rouse-type dynamics of active harmonic bead-spring percolation clusters of square and triangular lattices. Two types of active stochastic forces, modeled as a random telegraph process with correlation time τ, are considered: force monopoles, acting on individual nodes in random directions, and force dipoles, where extensile or contractile forces act between pairs of nodes. For force monopoles, a dynamical steady state is reached where the network is dynamically swollen and the mean square displacement (MSD) shows sub-diffusive behavior at t > τ, MSD ∼ tν, with ν=1−ds2 where ds is the spectral dimension, in accord with a previously advanced general analytic theory. In contrast, dipolar forces require diverging times to reach steady state and lead to network shrinkage. Within a quasi-steady-state approximation, the MSD is found to saturate at the same temporal regime t > τ, which is followed by ballistic-like and/or diffusive behaviors. We further extend our study of dipolar forces to dilution regimes above the isostatic threshold, also known as “rigidity percolation”. Here, weak dipolar forces effectively do not shrink the network in steady state. Instead, they induce “rotational swimming” of the network. Yet, for the triangular lattice, an incipient discontinuous collapse transition occurs above a critical force amplitude value. Conversely, we find a continuous crossover to a collapsed state for the non-diluted square lattice, resulting from its marginal stability. We suggest that disordered solids be poised above the isostatic point to be stable against active dipolar forces, provided that the dynamical persistent length remains lower than the spring rest length.

Approaching the scaling limit of transport through lattices with dephasing

We examine the stationary-state equations for lattices with generalized Markovian dephasing and relaxation. When the Hamiltonian is quadratic, the single-particle correlation matrix has a closed system of equations even in the presence of these two processes. The resulting equations have a vectorized form related to, but distinct from, Lyapunov’s equation. We present an efficient solution that helps to achieve the scaling limit, e.g., of the current decay with lattice length. As an example, we study the super-diffusive-to-diffusive transition in a lattice with long-range hopping and dephasing. The approach enables calculations with up to 104 sites, representing an increase of 10 to 40 times over prior studies. This enables a more precise extraction of the diffusion exponent, enhances agreement with theoretical results, and supports the presence of a phase transition. There is a wide range of problems that have Markovian relaxation, noise, and driving. They include quantum networks for machine-learning-based classification and extended reservoir approaches for transport. The results here will be useful for these classes of problems.

Vibrationally state-resolved rotational relaxation time

In high-temperature non-equilibrium flows, the traditional Parker rotational relaxation model based on the rigid rotor assumption fails to accurately describe the effects of internal molecular structure on the energy transfer processes, creating a critical bottleneck for precise modeling. This study aims to establish an improved computational framework for rotational relaxation times that incorporates vibrational state-resolved calculations and rovibrational coupling effects to overcome fundamental limitations of existing simplified models. Based on the variable soft sphere molecular model and statistical inelastic cross section theory, an exponential correlation function was introduced to accurately describe transition probabilities between rotational energy levels, establishing a complete state-to-state rotational relaxation time computational model. Through systematic parameter sensitivity analysis, a strict linear relationship between the averaged rotational relaxation time and the model parameter θ′ was discovered, significantly streamlining the parameter fitting procedure. For N2–N2, N2–N, O2–O2, and O2–O systems, optimal θ′ values were determined with average relative errors below 0.7% when validated against recent theoretical data. Important computational guidelines were established. The improved model provides theoretically accurate and computationally efficient tools for transport coefficient calculations in hypersonic flow numerical simulations, with significant implications for engineering applications such as atmospheric reentry and interplanetary exploration.

Haven ratio for correlated ion hopping in oxide glasses from NMR spin–lattice relaxation

The ionic transport in glasses and supercooled liquids exhibits complex dynamical behavior characterized by non-exponential correlation functions, often described by stretched exponential decay. This study investigates the connection between the Haven ratio HR, which measures the deviation of diffusivity of modifier alkali cations from random walk due to their backward-correlated hopping, and the stretching exponent β of the orientational correlation function associated with the nuclear magnetic resonance spin–lattice relaxation (NMR SLR) of these alkali nuclides. By analyzing the temperature-dependent NMR SLR rate data of alkali ions in a wide range of supercooled oxide network liquids, this study reveals a hitherto unknown approximate equality between HR and β. This relationship is shown to be consistent with a model of backward-correlated hopping of mobile modifier ions in a temporally frozen oxide network. Estimation of NMR SLR β for individual alkali ions in mixed-alkali systems offers a pathway to estimate species-specific HR values that are otherwise experimentally inaccessible. These findings, when taken together, suggest that β can serve as a proxy for HR and offer new insight into the microscopic nature of glassy ion transport.

Kinetic pathways of coesite densification from metadynamics

We study compression of coesite to pressures above 35 GPa, substantially beyond the equilibrium transition pressure to octahedral phases (8 GPa to stishovite). Experiments at room temperature showed that up to 30 GPa the metastable coesite structure develops only minor displacive changes (coesite-II and coesite-III) while the Si atoms remain 4-coordinated. Beyond 30 GPa, reconstructive transformations start, following different pathways from the complex structure of coesite. In addition to amorphization, two different crystalline outcomes were observed. One is the formation of defective high-pressure octahedral phases [Hu et al., Nat. Commun. 6, 6630 (2015)], and another one is the formation of unusual and complex dense phases coesite-IV and coesite-V with Si atoms in 4-fold, 5-fold, and 6-fold coordination [Bykova et al., Nat. Commun. 9, 4789 (2018)]. Capturing these structural transformations computationally represents a challenge. Here, we show that employing metadynamics with Si–O coordination number and volume as generic collective variables in combination with a machine-learning based ACE potential [Erhard et al., Nat. Commun. 15, 1927 (2024)], one naturally observes all three mentioned pathways, resulting in the phases observed experimentally. We describe the atomistic mechanisms along the transformation pathways. While the pathway to coesite-IV is simpler, the transformation to octahedral phases involves two steps: first, a hcp sublattice of O atoms is formed where Si atoms occupy octahedral positions, but the octahedron chains do not form a regular pattern. In the second step, the Si atoms order and the chains develop a more regular arrangement. We predict that the pathway to coesite-IV is preferred at room temperature while, at 600 K, the formation of octahedral phases is more likely.

Classical density functional theory for nanoparticle-laden droplets

Droplets of a pure fluid, such as water, in an open container surrounded by gas, are thermodynamically unstable and evaporate quickly. In a recent paper [Archer et al., J. Chem. Phys. 159, 194503 (2023)], we employed lattice density functional theory (DFT) to demonstrate that nanoparticles or solutes dissolved in a liquid droplet can make it thermodynamically stable against evaporation. In this study, we extend our model by using continuum DFT, which allows for a more accurate description of the fluid and nanoparticle density distributions within the droplet and enables us to consider size ratios between nanoparticles and solvent particles up to 10:1. While the results of the continuum DFT agree well with those of our earlier lattice DFT findings, our approach here allows us to refine our understanding of the stability and structure of nanoparticle-laden droplets. This is particularly relevant in light of the recent global COVID-19 pandemic, which has underscored the critical role of aerosol particles in virus transmission. Understanding the stability and lifetime of these virion-laden aerosols is crucial for assessing their impact on airborne disease spread.

Quantifying water hydrogen bonding from the surface electrostatic potential at varying iso-density contours

The electrostatic potential plotted on varying contours (VS) of the electron density guides us in the understanding of how water interactions exactly take place. Water—H2O—is extremely well balanced, having a hydrogen VS,max and an oxygen VS,min of similar magnitude. As such, it has the capacity to donate and accept hydrogen bonds equally well. This has implications for the interactions that water molecules form, which are reviewed here, first in water–small molecule models and then in complex sites as lactose and its crystals and in protein–protein interfaces. Favorable and unfavorable interactions are evaluated from the electrostatic potential plotted on varying contours of the electronic density, allowing these interactions to be readily visualized. As such, with one calculation, all interactions can be analyzed by gradually looking deeper into the electron density envelope and finding the nearly touching contour. Its relation with interaction strength has the electrostatic potential to be used in scoring functions. When properly implemented, we expect this approach to be valuable in modeling and structure validation, avoiding tedious interaction strength calculations. Here, applied to water interactions in a variety of systems, we conclude that all water interactions take the same general form, with water behaving as a “neutral” agent, allowing its interaction partner to determine if it donates or accepts a hydrogen bond, or both, as determined by the highest possible interaction strength(s).

Hydrogen activation on Fe3O4(110): From molecular H2 to atomic H under reducing conditions

Hydrogen reduction of Fe3O4 plays a pivotal role in sustainable steelmaking, offering a low-carbon alternative to traditional carbothermic processes. In this study, we employ density functional theory to investigate the dissociative adsorption of molecular H2 and the subsequent adsorption behavior of atomic H on Fe3O4 (110) surfaces, considering both stoichiometric and O-deficient configurations. Our results reveal that the type and location of O vacancies critically influence both the thermodynamics and kinetics of H2 activation. Compared to the perfect surface, the presence of O vacancies increases the activation barrier for H2 dissociation. Twofold coordinated O sites, which are thermodynamically more favorable to form, reduce the reaction exothermicity. Conversely, threefold coordinated O vacancies, though less readily formed, stabilize the dissociated state more strongly but incur the highest activation barrier. For atomic H adsorption, adsorption is strongly favored at O sites over Fe, particularly at hollow sites adjacent to twofold O ions. While O vacancies themselves are not favorable adsorption sites, they alter the local electronic environment and change the H binding strength. Bonding strength, quantified via the integrated crystal orbital Hamiltonian population, shows a strong linear correlation with H adsorption energies across all surface types. This correlation underscores the critical role of H–O orbital hybridization in stabilizing adsorbed H species and provides a quantitative link between adsorption strength and the underlying surface–adsorbate bonding characteristics. Our results offer atomic-level insights into defect-mediated H2 activation and H adsorption on Fe3O4, with implications for advancing hydrogen-based processes in steel production, hydrogen storage, and heterogeneous catalysis.

Aqueous sol-gel synthesis of epitaxial Bi2212 thin films enabled by OP-10 surfactant modification

This study employed metal nitrates as precursors, glycine as a complexing agent, and deionized water as the solvent to synthesize Bi2Sr2CaCu2O8+x (Bi2212) thin films on SrTiO3(100) single-crystal substrates using the sol-gel method. Dodecylphenol polyoxyethylene ether (OP-10) was introduced as a surfactant to enhance the wettability of the Bi2212 sol on the single-crystal substrate, leveraging its excellent miscibility with the sol. The influence of OP-10 modification was examined on both the substrate wettability and the key properties of Bi2212 films, including crystallinity, texture, surface morphology, and superconducting performance. The results demonstrate that OP-10 modification significantly improves the wettability of the Bi2212 sol on SrTiO3(100) single-crystal substrates. Consequently, Bi2212 superconducting films with smooth, continuous surfaces and (00l) epitaxial growth were successfully achieved on SrTiO3(100) substrates. The in-plane orientation relationship was determined to be Bi2212[100](001)//SrTiO3[011](100). The surface roughness of these films remained around 15 nm. All prepared films displayed excellent superconducting properties. This work establishes a valuable research foundation for the preparation of multicomponent functional oxide thin films via the aqueous sol-gel route.