Browse Articles

Turbulence in the tropical stratosphere, equatorial Kelvin waves, and the quasi-biennial oscillation

The tropical stratosphere is the gateway to the global stratosphere and a commonly proposed location for solar geoengineering. The dynamics of this remote and difficult to observe region are poorly understood, particularly at turbulent length scales. Existing observational estimates of turbulence frequency and strength vary widely. Furthermore, the sources of turbulence and the relationship between turbulence and the mean flow are largely unknown. We assembled a 21-y database of high vertical resolution (10 m) radiosonde data from four equatorial sites in two ocean basins to study tropical stratospheric turbulence frequency, variability, and sources. Turbulent layers thicker than 200 m are identified using subcritical Richardson number as a proxy for turbulence. We show that the turbulent fraction of the tropical stratosphere is strongly modulated by the quasi-biennial oscillation (QBO). Turbulence is enhanced during the QBO phase shifts, and the atmosphere is most turbulent right before the QBO phase switches from negative to positive, where turbulent instabilities typically occur within specific phases of Kelvin waves. Turbulence is less common when the QBO phase is well established, and the atmosphere is least turbulent during the negative phase of the QBO. The turbulent fraction of the equatorial lower stratosphere varies over a factor of ten depending on QBO phase. This relationship provides a robust observational constraint on the multiscale dynamics within this region, which is useful for evaluating atmospheric models, studying wave-mean flow interactions in the context of the QBO, and informing the operation of stratospheric aircraft and the injection of aerosol for geoengineering.

Progress in understanding the infrared spectrum of the H2O–O2 dimer

Spectra of the weakly bound H2O–O2 dimer are studied in the region of the H2O ν2 band using a tunable quantum cascade laser to probe a pulsed supersonic slit jet expansion. These are the first gas-phase infrared spectra of H2O–O2 and among only a few such results for O2-containing complexes. Almost 100 infrared lines are assigned based on the ground state combination differences from the microwave spectrum of H2O–O2. These lines belong to a main fundamental band, plus four combination bands lying 2 to 5 cm−1 above the fundamental. All correspond to the ortho-H2O (I = 1) nuclear spin species. Interpretation of the observed rotational levels is discussed. The original microwave analysis conflicts with the infrared results but can be corrected by changing the sign of a term or, better still, by using a published theory for weakly bound open shell complexes. The combination bands suggest that analogous ground state bands should be observable in the millimeter wave range. Many infrared transitions remain unassigned, including another extensive band apparently centered at 1603 cm−1, and some of these are probably due to the para-H2O spin species (I = 0). Splittings due to the unpaired O2 electron spin (S = 1), due to large amplitude tunneling motions, and due to a-axis rotational motion all have similar magnitudes for H2O–O2, so the resulting energy levels will be heavily mixed and not amenable to simple modeling. Accurate theoretical predictions of these effects should be possible for obtaining an enhanced understanding of the observed spectra.

Microbes could convert industrial wastewater into ecofriendly products

Newton’s algorithm for discrete classical dynamics

A recent article in J. Chem. Phys. argues that the two algorithms, the velocity-Verlet and position-Verlet integrators, commonly used in Molecular Dynamics (MD) simulations, are different [L. Ni and Z. Hu, J. Chem. Phys. 161, 226101 (2024)]. However, not only are the two algorithms just different formulations of the same discrete algorithm, but also are other simple discrete algorithms used in MD simulations in the natural sciences. They are all reformulations of the discrete algorithm derived by Newton in 1687 in Proposition I in the very first part of his book Principia. The different reformulations of Newton’s algorithm for discrete dynamics lead to identical discrete dynamics with the same invariances, momentum, angular momentum, and energy as Newton’s analytical dynamics. Hundreds of thousands of MD simulations with Newton’s discrete dynamics have appeared but unfortunately with many recorded errors for energies, potential energies, temperatures, and heat capacities. The public software for MD should be corrected.

BK channels mediate a presynaptic form of mGluR-LTD in the neonatal hippocampus

BK channels can control neuronal function, but their functional relevance in activity-dependent changes of synaptic function remains elusive. Here, we report that repetitive low-frequency stimulation activates BK channels through 12(S)HPETE, an arachidonic acid metabolite, produced downstream of postsynaptic metabotropic glutamate receptors (mGluRs) to trigger long-term depression (LTD) at CA3–CA1 synapses in hippocampal slices from P7–P10 mice. Activation of BK channels is subunit specific, as paxilline but not iberiotoxin blocked mGluR-LTD. Also, 12(S)HPETE does not change the electrophysiological properties of the BK channel when the BKα subunit is expressed alone but increases the channel open probability when the BKα is coexpressed with the β4-subunit. Our findings reveal an interaction between 12(S)HPETE and BK channels to regulate synaptic strength at central synapses and increase our understanding of the mechanisms underlying mGluR-LTD in the neonatal hippocampus that likely contribute to circuit maturation necessary for learning.

Thermostat-induced artificial lane formation in non-equilibrium molecular dynamics

While most thermostats in molecular dynamics are designed for equilibrium systems, their extension to non-equilibrium simulations has little theoretical justification. In the literature, an artifact referred to as “lane formation” was discovered; however, its cause remained unclear and was simply attributed to a constraint on velocity fluctuations or non-ergodicity in thermostats. In addition, global deterministic thermostatted dynamics was found to exhibit unceasing phase-space compression in steady states, incompatible with their expected stationary distributions and Gibbs entropy, which was mistakenly perceived as inescapable. In this work, we pinpoint that the dynamical cause of artificial lane formation is a stable fixed point in the momentum space induced by improper velocity rescaling, which produces effective repulsion between different species in a color flow, drains transverse kinetic energy and generates the unceasing compression. This artifact is deeply rooted in global deterministic thermostats, such as the Nosé–Hoover dynamics and configurational thermostat. With proper rescaling, the Langevin thermostat completely eliminates artificial lane formation and exemplifies how incompressible phase space and stationary distributions can be retained for non-equilibrium steady states.

Superconducting critical temperature elevated by intense magnetic fields

Below a critical temperature T c , superconductors transport electrical charge without dissipative energy losses. The application of a magnetic field B generally acts to suppress T c , up to some critical field strength at which T c → 0 K. Here, we investigate magnetic field–induced superconductivity in high-quality specimens of the triplet superconductor candidate UTe 2 in pulsed magnetic fields up to B = 70 T. Strikingly, we find that this material has a higher T c when B > 40 T ( T c ≈ 2.4 K) than it does for B = 0 T ( T c = 2.1 K). This observation points to a fundamentally distinct mechanism for the formation of superconductivity at high B in UTe 2 compared to the case of B = 0 T.

Biodegradable Tenebrio molitor antifreeze protein modified kinetic hydrate inhibitor: Insights into molecular interactions and structural flexibility

The formation of natural gas hydrates presents significant economic and safety challenges to the petroleum and gas industry, necessitating the development of effective prevention strategies. This study investigates an environmentally sustainable Tenebrio molitor antifreeze protein (TmAFP) modified to be a potential kinetic hydrate inhibitor. The aim of this study was to enhance the inhibitory activity of TmAFP by systematically substituting threonine (Thr) residues with glycine (Gly), alanine (Ala), or serine (Ser) at positions 29, 39, and 53. The Ala mutant demonstrated superior inhibition of hydrate formation, attributed to its optimized spatial conformation and enhanced hydrophobic interactions, followed by the Gly and Ser mutants. The wild-type TmAFP showed limited efficacy. The radial distribution function (RDF) analysis indicated that the mutations facilitated a better accommodation of adjacent residues within the hydrate crystal structure by adjusting the distance between Thri and Thri+2 to closely match the second peak in the RDF of methane molecules at 6.4 Å. The potential of mean force (PMF) calculations revealed that the Ala and Ser mutants exhibited enhanced interactions with hydrate cages, with PMF values of −0.73 and −0.71 kJ/mol, respectively, compared to the Gly mutant, which had a PMF value of 1.46 kJ/mol. By identifying the optimal mutation combination (T29 39 53A) to significantly increase the potency of TmAFP, this study provides a fundamental basis for the further development of hydrate inhibition strategies.

An organic electrochemical neuron for a neuromorphic perception system

Human perception systems are highly refined, relying on an adaptive, plastic, and event-driven network of sensory neurons. Drawing inspiration from Nature, neuromorphic perception systems hold tremendous potential for efficient multisensory signal processing in the physical world; however, the development of an efficient artificial neuron with a widely calibratable spiking range and reduced footprint remains challenging. Here, we report an efficient organic electrochemical neuron (OECN) with reduced footprint (<37 mm 2 ) based on high-performance vertical OECT (vOECT) complementary circuitry enabled by an advanced n-type polymer for balanced p-/n-type vOECT performance. The OECN exhibits outstanding neuronal characteristics, capable of producing spikes with a widely calibratable state-of-the art firing frequency range of 0.130 to 147.1 Hz. Leveraging this capability, we develop a neuromorphic perception system that integrates mechanical sensors with the OECN and integrates them with an artificial synapse for tactile perception. The system successfully encodes tactile stimulations into frequency-dependent spikes, which are further converted into postsynaptic responses. This bioinspired design demonstrates significant potential to advance cyborg and neuromorphic systems, providing them with perceptual capabilities.

Restoring rotational symmetry of multicomponent wavefunctions with nuclear orbitals

In this work, we present a non-orthogonal configuration interaction (NOCI) approach to address the rotational corrections in multicomponent quantum chemistry calculations where hydrogen nuclei and electrons are described with orbitals under Hartree–Fock (HF) and density functional theory (DFT) frameworks. The rotational corrections are required in systems such as diatomic (HX) and nonlinear triatomic molecules (HXY), where localized broken-symmetry nuclear orbitals have a lower energy than delocalized orbitals with the correct symmetry. By restoring rotational symmetry with the proposed NOCI approach, we demonstrate significant improvements in proton binding energy predictions at the HF level, with average rotational corrections of 0.46 eV for HX and 0.23 eV for HXY molecules. For computing rotational excitation energies, our results indicate that HF kinetic energy corrections are consistently accurate, while discrepancies arise in total energy predictions, primarily from an incomplete treatment of dynamical correlation effects. Rotational energy corrections in multicomponent DFT calculations, using the epc17-2 proton–electron correlation functional, lead to an overestimation of proton binding energies. This is as a result of double-counting of proton–electron correlation effects in the off-diagonal NOCI terms. As a correction, we propose a scaling scheme that effectively adjusts the proton–electron correlation contributions, bringing our results into close agreement with reference CCSD(T) data. The scaled rotational corrections, on average, increase the epc17-2 proton binding energy predictions by 0.055 eV for HX and 0.025 eV for HXY and yield average deviations of 1.0 cm−1 for rotational transitions.

The single-stranded DNA–binding factor SUB1/PC4 alleviates replication stress at telomeres and is a vulnerability of ALT cancer cells

To achieve replicative immortality, cancer cells must activate telomere maintenance mechanisms. In 10 to 15% of cancers, this is enabled by recombination-based alternative lengthening of telomeres pathways (ALT). ALT cells display several hallmarks including heterogeneous telomere length, extrachromosomal telomeric repeats, and ALT-associated PML bodies. ALT cells also have high telomeric replication stress (RS) enhanced by fork-stalling structures (R-loops and G4s) and altered chromatin states. In ALT cells, telomeric RS promotes telomere elongation but above a certain threshold becomes detrimental to cell survival. Manipulating RS at telomeres has thus been proposed as a therapeutic strategy against ALT cancers. Through analysis of genome-wide CRISPR fitness screens, we identified ALT-specific vulnerabilities and describe here our characterization of the roles of SUB1, a ssDNA-binding protein, in telomere stability. SUB1 depletion increases RS at ALT telomeres, profoundly impairing ALT cell growth without impacting telomerase-positive cells. During RS, SUB1 is recruited to stalled forks and ALT telomeres via its ssDNA-binding domain. This recruitment is potentiated by RPA depletion, suggesting that these factors may compete for ssDNA. The viability of ALT cells and their resilience toward RS also requires ssDNA binding by SUB1. SUB1 depletion accelerates cell death induced by FANCM depletion, triggering unsustainable levels of telomeric damage in ALT cells. Finally, combining SUB1 depletion with RS-inducing drugs rapidly induces replication catastrophe in ALT cells. Altogether, our work identifies SUB1 as an ALT susceptibility with roles in the mitigation of RS at ALT telomeres and suggests advanced therapeutic strategies for a host of still poorly managed cancers.

Work-biased path-sampling calculations of chemical potentials: Principles and applications to uranium oxide

We present the work-biased path-sampling scheme to calculate chemical potentials in atomic scale simulations. This scheme is based on a series of chained insertion and deletion paths from N to N + 1 to N atom systems, the sampling being performed on the paths themselves rather than on the final configurations. Equations for parallel path generations as well as geometrically biased insertions or deletions are presented. We then present two applications of our approach for the uranium dioxide crystal. The first is a test case validation of our approach for the insertion of a Xe atom in UO2. The second explores the relationship between cluster structure stability and oxygen chemical potential in overstoichiometric UO2+x oxide as a function of temperature from 800 to 2000 K and composition, from UO2 to UO2.16, using two different empirical potentials. We find that the evolution of the oxygen chemical potential is irregular, with dips for specific numbers of added oxygen atoms. Five oxygen clusters are stable at 800 K and are associated with strong dips in the chemical potential values. At intermediate temperatures, clusters of four and five oxygen atoms compete in stability. They become unstable at the highest temperatures, and the evolution of the chemical potential is then monotonous with composition.

The cGAS–STING, p38 MAPK, and p53 pathways link genome instability to accelerated cellular senescence in ATM-deficient murine lung fibroblasts

Ataxia–telangiectasia (A-T) is a pleiotropic genome instability syndrome resulting from the loss of the homeostatic protein kinase ATM. The complex phenotype of A-T includes progressive cerebellar degeneration, immunodeficiency, gonadal atrophy, interstitial lung disease, cancer predisposition, endocrine abnormalities, chromosomal instability, radiosensitivity, and segmental premature aging. Cultured skin fibroblasts from A-T patients exhibit premature senescence, highlighting the association between genome instability, cellular senescence, and aging. We found that lung fibroblasts derived from ATM-deficient mice provide a versatile experimental system to explore the mechanisms driving the premature senescence of primary fibroblasts lacking ATM. Atm −/− fibroblasts failed to proliferate under ambient oxygen conditions (21%). Although they initially proliferated under physiological oxygen levels (3%), they rapidly entered senescence. In contrast, wild-type (WT) lung fibroblasts did not senesce under 3% oxygen and eventually underwent immortalization and neoplastic transformation. However, rapid senescence could be induced in WT cells either by Atm gene ablation or persistent chemical inhibition of ATM kinase activity, with senescence induced by ATM inhibition being reversible upon inhibitor removal. Moreover, the concomitant loss of ATM and p53 led to senescence evasion, vigorous growth, rampant genome instability, and subsequent immortalization and transformation. Our findings reveal that the rapid senescence of Atm −/− lung fibroblasts is driven by the collaborative action of the cGAS–STING, p38 MAPK, and p53 pathways in response to persistent DNA damage, ultimately leading to the induction of interferon-α1 and downstream interferon-stimulated genes. We propose that accelerated cellular senescence may exacerbate specific A-T symptoms, particularly contributing to the progressive, life-threatening interstitial lung disease often observed in A-T patients during adulthood.

Dynamical properties of hydrogen fluid at high pressures

The properties of the hydrogen fluid at high pressures are still of interest to the scientific community. The experimentally unreachable dynamical properties could provide new insights into this field. In 2020 [Cheng et al., Nature 585, 217–220 (2020)], the machine-learned approach allows the calculation of the self-diffusion coefficient in the warm dense hydrogen with higher precision. After that, the work [van de Bund et al., Phys. Rev. Lett. 126(22), 225701 (2021)] reports the ab initio treatment of isotopic effects on diffusion in H2/D2 and a significant increase in its value in the region of the phase transition. Both works indicate the anomalous growth of diffusion, but the reasons for this phenomenon are unclear. In the present work, we reveal the plasma-like behavior of the diffusion growth. We apply the classical molecular dynamics method using a machine learning potential developed on the ab initio modeling for the prediction of diffusion and shear viscosity coefficients. We consider dependencies of the vibrational spectrum, molecule lifetime, diffusion, and shear viscosity coefficients on density along the isotherms in the temperature range from 600 to 1100 K.

Evolutionary adaptation under climate change: <i>Aedes</i> sp. demonstrates potential to adapt to warming

Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, promoting expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their warm edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis , a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and its genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in mosquito heat tolerance, and phenotypic trade-offs in tolerance to prolonged versus acute heat exposure. Further, we found genomic variation associated with prolonged heat tolerance was clustered in several regions of the genome, suggesting the presence of larger structural variants such as chromosomal inversions. A simple evolutionary model based on our data estimates that the maximum rate of evolutionary adaptation in mosquito heat tolerance will exceed the projected rate of climate warming, implying the potential for mosquitoes to track warming via genetic adaptation.

Monofluorinated acetal electrolyte for high-performance lithium metal batteries

High degree of fluorination for ether electrolytes has resulted in improved cycling stability of lithium metal batteries due to stable solid electrolyte interphase (SEI) formation and good oxidative stability. However, the sluggish ion transport and environmental concerns of high fluorination degree drive the need to develop less fluorinated structures. Here, we depart from the traditional ether backbone and introduce bis(2-fluoroethoxy)methane (F2DEM), featuring monofluorination of the acetal backbone. High coulombic efficiency and stable long-term cycling in Li||Cu half cells can be achieved with F2DEM even under fast Li metal plating conditions. The performance of F2DEM is further compared with diethoxymethane (DEM) and 2-[2-(2,2-difluoroethoxy)ethoxy]-1,1,1-trifluoroethane (F5DEE). A significantly lower overpotential is observed with F2DEM, which improves energy efficiency and enables its application in high-rate conditions. Comparative studies of F2DEM with DEM and F5DEE in anode-free lithium iron phosphate (LiFePO 4 ) LFP pouch cells and high-loading LFP coin cells further show improved capacity retention of F2DEM electrolyte, demonstrating its practical applicability. More importantly, we also extensively investigate the underlying mechanism for the superior performance of F2DEM through various techniques, including X-ray photoelectron spectroscopy, scanning electron microscopy, cryogenic electron microscopy, focused ion beam, electrochemical impedance spectroscopy, and titration gas chromatography. Overall, F2DEM facilitates improved Li deposition morphology with reduced amount of dead Li. This enables F2DEM to show superior performance, especially under higher charging and slower discharging rate conditions.

APOBEC3A deaminates CTG hairpin loops to promote fragility and instability of expanded CAG/CTG repeats

CAG/CTG repeats are prone to expansion, causing several inherited human diseases. The initiating sources of DNA damage which lead to inaccurate repair of the repeat tract to cause expansions are not fully understood. Expansion-prone CAG/CTG repeats are actively transcribed and prone to forming stable R-loops with hairpin structures forming on the displaced single-stranded DNA (S-loops). We previously determined that damage by the Saccharomyces cerevisiae cytosine deaminase, Fcy1, was required for both fragility and instability of CAG/CTG tracts engaged in R-loops. To determine whether this mechanism is more universal, we expressed human cytidine deaminases APOBEC3A (A3A), APOBEC3B (A3B), or activation-induced cytidine deaminase (AID) in our yeast system. We show that mutagenic activity of Apolipoprotein B messenger RNA-editing enzyme, catalytic polypeptides causes CAG/CTG fragility and instability, with A3A having the greatest effect followed by A3B and least from AID. A3A-induced repeat fragility was exacerbated by enrichment of R-loops at the repeat site. A3A and A3B-induced instability was dependent on the MutLγ nuclease and to a lesser extent, base excision repair factors. Deaminase activity assays on hairpin substrates containing CTG and GTC triplet sequences revealed that A3A prefers cytidines within the hairpin loop, and bulges in the hairpin stem alter preferred locations. Analysis of RNA expression levels in human cortex samples revealed that A3A is expressed in brain tissue that exhibits CAG/CTG repeat expansions and its expression is elevated in Huntington’s disease (HD) patient samples. These results implicate cytidine deamination by A3A as a potential source of repeat expansions in HD and other CAG/CTG repeat expansion disorders.

Synthesis of ethane from CO ₂ by a methyl transferase–inspired molecular catalyst

Molecular catalysts with a single metal center are reported to reduce CO 2 to a wide range of valuable single-carbon products like CO, HCOOH, CH 3 OH, etc. However, these catalysts cannot reduce CO 2 to two carbon products like ethane or ethylene and the ability to form C–C from CO 2 remains mostly limited to heterogeneous material-based catalysts. We report a set of simple iron porphyrins with pendant thiol group can catalyze the reduction of CO 2 to ethane (C 2 H 6 ) with H 2 O as the proton source with a Faradaic yield &gt;40% the rest being CO. The mechanism involves a CO 2 -derived methyl group transfer to the pendant thiol akin to the proposal forwarded for methyl transferases and a follow-up C–C bond formation of the thioether thus formed and a Fe(II)–CH 3 species generated by the reduction of a second molecule of CO 2 . The availability of a “parking space” in the molecular framework for the first reduced C 1 product from CO 2 reduction allows C–C bond formation resulting in a unique case where a component of natural gas can be generated from direct electrochemical reduction of CO 2 .

Mechanically Robust Bismuth-Embedded Carbon Microspheres for Ultrafast Charging and Ultrastable Sodium-Ion Batteries

Exome sequencing identifies genes for socioeconomic status in 350,770 individuals

Socioeconomic status (SES) is a critical factor in determining health outcomes and is influenced by genetic and environmental factors. However, our understanding of the genetic structure of SES remains incomplete. Here, we conducted a large-scale exome study of SES markers (household income, occupational status, educational attainment, and social deprivation) in 350,770 individuals. For rare coding variants, we identified 56 significant associations by gene-based collapsing tests, unveiling 7 additional SES-associated genes ( NRN1 , CCDC36 , RHOB , EP400 , NCAM1, TPTEP2-CSNK1E , and LINC02881 ). Exome-wide single common variant analysis revealed nine lead single-nucleotide polymorphisms (SNPs) associated with household income and 34 lead SNPs associated with EduYears, replicating previous GWAS findings. The gene–environment correlations had a substantial impact on the genetic associations with SES, as indicated by the significantly increased P values in several associations after controlling for geographic regions. Furthermore, we observed the pleiotropic effects of SES-associated genetic factors on a wide range of health outcomes, such as cognitive function, psychosocial status, and diabetes. This study highlights the contribution of coding variants to SES and their associations with health phenotypes.