Browse Articles

Phase formation and phase stability for the homogenous and heterogeneous amorphous metals versus the crystalline phase

From molecular dynamics (MD) simulations of melt-quenching and thermal aging procedures in pure Ag, Cu, Ag–Cu binary alloys, and Cu–Zr binary alloys, we have identified two distinct amorphous phases for a metastable undercooled liquid: the homogeneous L-phase with low shear rigidity and the heterogenous G-phase with much higher shear rigidity and a heterogeneity length scale Λ. Here, we examine two-phase equilibration studies showing that the G-phase melts to form the L-phase above ~1,000 K, which then transforms to form the crystal (X) phase; however, below the melting point of the G-Phase (~990 K), the X- and G-phases do not transform into each other. We suggest the presence of a G-phase is likely responsible for embrittlement often observed in metallic glasses. We also consider how mechanical milling or irradiation-induced defect accumulation in the crystalline metallic alloy triggers a crystal-to-glass transition. We use the Cu 2 Zr system as a model to investigate random interchange of Zr and Cu atoms at room temperature leading to a transition from a crystalline Laves-phase to an L-glass through formation and growth of amorphous regions and destabilization of the crystal. During relaxation of the nonequilibrium structures by annealing, the configurations either reverted to the crystalline phase or evolve to a heterogeneous G-phase equivalent to the G-phase formed during thermal quenching and aging of the melt. Athermal defect accumulation in the G-phase at low temperature led to a transition back to the L-phase. Our findings show how athermal disordering drives transitions among the X-, L-, and G-phases.

Molecular dynamics simulations of functionalized hBN nanopores in water: <i>Ab initio</i> force field and implications for water desalination

Heteropolar two-dimensional materials, including hexagonal boron nitride (hBN), are promising candidates for seawater desalination and osmotic power harvesting, but previous simulation studies have considered bare, unterminated nanopores in molecular dynamics (MD) simulations. There is presently a lack of force fields to describe functionalized nanoporous hBN in aqueous media. To address this gap, we conduct density functional theory (DFT)-based ab initio MD simulations of hBN nanopores surrounded by water molecules. The results reveal a high propensity for hydrogen (H) and hydroxyl (OH) functionalization at boron edges, while nitrogen edges are functionalized with H and occasionally with oxygen (O), highlighting a route to tune membranes. We demonstrate the role of the Grotthuss mechanism during the functionalization of hBN edges in water. We develop high-fidelity force fields for H- and OH-functionalized hBN nanopores using potential energy surface fitting based on DFT calculations. The nonbonded parameters for H functionalization are obtained by training a force field for borazine (B3N3H6). We find that the proposed force field enables stable MD simulations of water/ion transport through B- and N-terminated hBN nanopores. Our results also indicate that previous studies that considered bare nanopores without functional groups overestimated the water flux and underestimated the ionic rejection of nanoporous hBN. Overall, our work is expected to enable the realistic modeling of edge-functionalized hBN in aqueous media for various application areas.

Valuing the benefits of reducing firearm violence in the United States

Justifying a proposed government regulation intended to reduce firearm violence requires a conceptually sound estimate of the monetized value of that impact and how that value is distributed across the population. Some previous estimates do not serve as a valid basis for policy evaluation or are out of date. A nationally representative survey was conducted by the AP-NORC Center for Public Affairs Research in August 2022 (n = 660). The authors designed and added a series of contingent-valuation items to the questionnaire. Double-bounded estimates of willingness-to-pay (WTP) were derived from a regression analysis of responses regarding voting on a hypothetical referendum on a state-wide package of measures designed to reduce gun violence at specified cost to taxpayers. Average WTP for a reduction of 20% in the state rate of gun violence was $744 per household (IQR:$668–$928), implying a national total of $97.6 billion. Household WTP was positively associated with household income, the respondent’s assessment of the seriousness of gun violence in their community and the subjective likelihood that they would become a victim of gun violence. A variety of tests support the claim that this application of the contingent-valuation method provided valid results. WTP is the recognized basis for assessing the value of proposed federal regulations. The estimated WTP for reducing gun violence is about twice as high as a recent cost-of-injury estimate and provides a much different picture of the incidence of costs by income and demographic characteristics.

Interstellar spectroscopic detection of HC(S)NC and DC(S)NC

The detection of HC(S)CN in TMC-1 suggests that HC(S)NC may also exist. To aid in its possible detection, HC(S)NC and its deuterated isotopologue DC(S)NC were investigated via high-level ab initio methods, specifically CCSD(T) and CCSD(T)-F12. By utilizing multidimensional potential energy surfaces derived from explicitly correlated coupled-cluster calculations, we analyzed their geometrical parameters, vibrational frequencies, rotational constants, and a comprehensive set of spectroscopic constants generated via the vibrational second-order perturbation theory, vibrational self-consistent field, and vibrational configuration interaction theory(VCI) approaches. HC(S)NC is thermodynamically stable relative to the HCS + NC dissociation limit, with a predicted bond dissociation energy of 4.1 eV. The calculated vibrational frequencies are characterized by two bright modes that correspond to CN stretching. Finally, HC(S)NC shows a significant dipole moment, predicted to be 1.9 D, making its detection via rotational spectroscopy plausible.

Dispersal of influenza virus populations within the respiratory tract shapes their evolutionary potential

Viral infections are characterized by dispersal from an initial site to secondary locations within the host. How the resultant spatial heterogeneity shapes within-host genetic diversity and viral evolutionary pathways is poorly understood. Here, we show that virus dispersal within and between the nasal cavity and trachea maintains diversity and is therefore conducive to adaptive evolution, whereas dispersal to the lungs gives rise to population heterogeneity. We infected ferrets either intranasally or by aerosol with a barcoded influenza A/California/07/2009 (H1N1) virus. At 1, 2, or 4 days postinfection, dispersal was assessed by collecting 52 samples from throughout the respiratory tract of each animal. Irrespective of inoculation route, barcode compositions across the nasal turbinates and trachea were similar and highly diverse, revealing little constraint on the establishment of infection in the nasal cavity and descent through the trachea. Conversely, infection of the lungs produced genetically distinct viral populations. Lung populations were pauci-clonal, suggesting that each seeded location received relatively few viral genotypes. While aerosol inoculation gave distinct populations at every lung site sampled, within-host dispersal after intranasal inoculation produced larger patches, indicative of local expansion following seeding of the lungs. Throughout the respiratory tract, barcode diversity declined over time, but new diversity was generated through mutation. De novo variants were often unique to a given location, indicating that localized replication following dispersal resulted in population divergence. In summary, dispersal within the respiratory tract operates differently between regions and contributes to the potential for viral evolution to proceed independently in multiple within-host subpopulations.

How well do empirical molecular mechanics force fields model the cholesterol condensing effect?

Membrane properties are determined in part by lipid composition, and cholesterol plays a large role in determining these properties. Cellular membranes show a diverse range of cholesterol compositions, the effects of which include alterations to cellular biomechanics, lipid raft formation, membrane fusion, signaling pathways, metabolism, pharmaceutical therapeutic efficacy, and disease onset. In addition, cholesterol plays an important role in non-cellular membranes, with its concentration in the skin lipid matrix being implicated in several skin diseases. In phospholipid membranes, cholesterol increases the tail ordering of neighboring lipids, decreasing the membrane lateral area and increasing the thickness. This reduction in the lateral area, known as the cholesterol condensing effect, results from cholesterol–lipid mixtures deviating from ideal mixing. Capturing the cholesterol condensing effect is crucial for molecular dynamics simulations as it directly affects the accuracy of predicted membrane properties, which are essential for understanding membrane function. We present a comparative analysis of cholesterol models across several popular force fields: CHARMM36, Slipids, Lipid17, GROMOS 53A6L, GROMOS-CKP, MARTINI 2, MARTINI 3, and ELBA. The simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membranes with varying cholesterol concentrations were conducted to calculate the partial-molecular areas of cholesterol and other condensing parameters, which are compared to the experimental data for validation. While all tested force fields predict small negative deviations from ideal mixing in cholesterol–DOPC membranes, only all-atom force fields capture the larger deviations expected in DMPC membranes. United-atom and coarse-grained models under-predict this effect, condensing fewer neighboring lipids by smaller magnitudes, resulting in too small deviations from ideal mixing. These results suggest that all-atom force fields, particularly CHARMM36 or Slipids, should be used for accurate simulations of cholesterol-containing membranes.

Reply to Boomsma: The evidence that eusociality evolved from monogamous ancestors is inconclusive

Extending Badger's rule. I. The relationship between energy and structure in hydrogen bonds

We derive a new expression for the strength of a hydrogen bond (VHB) in terms of the elongation of the covalent bond of the donor fragment participating in the hydrogen bond (ΔrHB) and the intermolecular coordinates R (separation between the heavy atoms) and θ (deviation of the hydrogen bond from linearity). The expression includes components describing the covalent D–H bond of the hydrogen bond donor via a Morse potential, the Pauli repulsion, and electrostatic interactions between the constituent fragments using a linear expansion of their dipole moment and a quadratic expansion of their polarizability tensor. We fitted the parameters of the model using ab initio electronic structure results for six hydrogen bonded dimers, namely, NH3–NH3, H2O–H2O, HF–HF, H2O–NH3, HF–H2O, and HF–NH3, and validated its performance for extended parts of their potential energy surfaces, resulting in a mean absolute error ranging from 0.07 to 0.31 kcal/mol. The derived expression describes the energy–structure relationship in terms of a single structural parameter, namely, the elongation of the donor’s covalent bond (ΔrHB), and suggests the novel relationship of 8.0 kcal/mol pm−1 (or 0.8 kcal/mol per 0.001 Å elongation). This structural parameter is easily obtained from theory and can serve as the single descriptor of the strength of individual hydrogen bonds.

Global urban greening and its implication for urban heat mitigation

Urban vegetation provides essential ecosystem services and benefits to support biodiversity and human well-being in urban areas. However, the dynamic trends, driving factors, and their implications to urban heat mitigation at the global scale remain largely unclear. Here, we used a high-resolution enhanced vegetation index (EVI) dataset to examine the vegetation dynamics in 11,235 urban areas worldwide, identify the driving factors behind its changes, and estimate the potential urban heat mitigation benefits of these changes. We found that 40.75% urban areas (1.51 Mha) evidenced a greening trend (showing increasing EVI), in contrast to 49.60% urban areas showing browning (decreasing EVI). Notably, urban centers in both developed and developing countries contribute to this greening trend. We, nevertheless, found significant spatial disparities in this greening trend, with cities in the Global North showing higher greening ratios than those in the Global South. The driving factors of urban vegetation change trend lead to significant differentiation in and around urban areas. The rapid increase in urbanization intensity and the negative effects of nitrogen deposition are the dominant factors leading to vegetation browning in urban peripheries. However, nitrogen deposition and urbanization intensity have shown positive effects on vegetation greening within urban centers. Crucially, compared to areas with vegetation browning or no significant change, vegetation greening areas have a more significant cooling effect, potentially mitigating the urban heat island effect, especially during summer daytime. Our findings highlight the importance of enhancing urban vegetation greening to promote equitable urban development and ensure effective climate change mitigation.

Nature and stability of the chemical bond in H3C–XHn (XHn = CH3, NH2, OH, F, Cl, Br, I)

We have quantum chemically analyzed the trends in bond dissociation enthalpy (BDE) of H3C–XHn single bonds (XHn = CH3, NH2, OH, F, Cl, Br, I) along three different dissociation pathways at ZORA-BLYP-D3(BJ)/TZ2P: (i) homolytic dissociation into H3C∙ + ∙XHn, (ii) heterolytic dissociation into H3C+ + −XHn, and (iii) heterolytic dissociation into H3C− + +XHn. The associated BDEs for the three pathways differ not only quantitatively but, in some cases, also in terms of opposite trends along the C–X series. Based on activation strain analyses and quantitative molecular orbital theory, we explain how these differences are caused by the profoundly different electronic structures of, and thus bonding mechanisms between, the resulting fragments in the three different dissociation pathways. We demonstrate that the nature and strength of a chemical bond are only fully defined when considering both (i) the molecule in which the bond exists and (ii) the fragments from which it forms or into which it dissociates.

The importance of IP6 for ADAR RNA-editing enzymes and antiviral defense

Rationalizing protein–ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics

The Effective Fragment Potential (EFP) method, a polarizable quantum mechanics-based force field for describing non-covalent interactions, is utilized to calculate protein–ligand interactions in seven inactive cyclin-dependent kinase 2–ligand complexes, employing structural data from molecular dynamics simulations to assess dynamic and solvent effects. Our results reveal high correlations between experimental binding affinities and EFP interaction energies across all the structural data considered. Using representative structures found by clustering analysis and excluding water molecules yields the highest correlation (R2 of 0.95). In addition, the EFP pairwise interaction energy decomposition analysis identifies critical interactions between the ligands and protein residues and provides insight into their nature. Overall, this study indicates the potential applications of the EFP method in structure-based drug design.

The evolution of signaling and monitoring in plant–fungal networks

Experiments have shown that when one plant is attacked by a pathogen or herbivore, this can lead to other plants connected to the same mycorrhizal network up-regulating their defense mechanisms. It has been hypothesized that this represents signaling, with attacked plants producing a signal to warn other plants of impending harm. We examined the evolutionary plausibility of this and other hypotheses theoretically. We found that the evolution of plant signaling about an attack requires restrictive conditions, and so will rarely be evolutionarily stable. The problem is that signaling about an attack provides a benefit to competing neighbors, even if they are kin, and so reduces the relative fitness of signaling plants. Indeed, selection is often more likely to push plant behavior in the opposite direction—with plants signaling dishonestly about an attack that has not occurred, or suppressing a cue that they have been attacked. Instead, we show that there are two viable alternatives that could explain the empirical data: 1) the process of being attacked leads to a cue (information about the attack) which is too costly for the attacked plant to fully suppress; 2) mycorrhizal fungi monitor their host plants, detect when they are attacked, and then the fungi signal this information to warn other plants in their network. Our results suggest the empirical work that would be required to distinguish between these possibilities.

Molecular dynamics investigation of structural, thermal, and dynamic properties of maghemite through thermal cycling

We analyzed the thermal, structural, and dynamic properties of maghemite using classical molecular dynamics, focusing on bulk and nanoparticle systems. We explored their behavior when heated to high temperatures (above the melting point) and during cooling, as well as under thermal cycles ending at intermediate temperatures. Our findings show that in the bulk system, both the tetrahedral and octahedral iron sub-lattices undergo a phase transition prior to melting. Cooling the system from above this transition, or from above the melting point, leads to the formation of different metastable maghemite structures. In contrast, this sub-lattice transition is absent in nanoparticles, where melting occurs through an interface-mediated process. At temperatures just above the transition, nanoparticles adopt an ellipsoidal shape, which is retained during cooling. In addition, the specific heat of both bulk and nanoparticle systems at temperatures above the Debye temperature is evaluated and compared with the available experimental data. Overall, our results highlight the complex thermal behavior of maghemite across a range of temperatures, which remains insufficiently explored experimentally. Further experimental investigations could also provide valuable feedback for model refinements.

Identification of <i>ARHGEF11</i> (PDZ-RhoGEF) as an in vivo regulator of synapses and cognition

Given the influence of cognitive abilities on life outcomes, there is inherent value in identifying genes involved in controlling learning and memory. Further, cognitive dysfunction is a core feature of many neuropsychiatric disorders. Here, we use a combinatory in silico approach to identify human gene targets that will have an especially high likelihood of individually and directly impacting cognition. This broad and unbiased screen led to the specific identification of ARHGEF11 , which encodes PDZ-RhoGEF. PDZ-RhoGEF is a largely RhoA-specific activator that is highly enriched in dendritic spines, and recent work identified hyperexpression of PDZ-RhoGEF in the prefrontal cortex of bipolar disorder subjects, a disease characterized by an early emergence and persistence of broad scope cognitive dysfunction. Here, we characterize the effects of PDZ-RhoGEF on synaptic and behavioral phenotypes, and we identify molecular and biochemical mechanisms that control PDZ-RhoGEF’s expression, synaptic spatial localization, and enzymatic activity. Importantly, our identified direct regulators of PDZ-RhoGEF (miR-132 and DISC1) have themselves been repeatedly implicated in controlling cognitive phenotypes in humans, including those caused by several neuropsychiatric disorders. Taken together, our findings indicate that PDZ-RhoGEF is a key convergence point among multiple synaptic and cognition-relevant signaling cascades with potential translational significance.

Isovalent substitution-induced pseudodoping in ZrxTi1−xSe2 transition metal dichalcogenides

The crystal and electronic structure of ZrxTi1−xSe2 (0 &amp;lt; x &amp;lt; 1) compounds and their electrical resistivity have been studied in detail for the first time. A combination of soft x-ray spectroscopic methods (XPS, XAS, and ResPES) was used to investigate the electronic structure. The lattice parameters as a function of the metal concentration x obey Vegard’s law. It was shown that the substitution of Ti by Zr results in an increase in the Fermi energy, attributed to the lower binding energy of Zr 4d compared to Ti 3d in the ZrxTi1−xSe2 valence band. Given that the oxidation states of both Ti and Zr are +4, and the concentration of free charge carriers remains unchanged upon substitution, the observed effect is explained by a reduced density of electronic states near the Fermi level. The influence of temperature on the Ti 2p–3d and Zr 3p–4d ResPES spectra is interpreted in terms of pseudodoping occurring with the substitution of Ti by Zr.

Adenosine diphosphate stimulates VEGF-independent choroidal endothelial cell proliferation: A potential escape from anti-VEGF therapy

We hypothesized that a strategy employing tissue-specific endothelial cells (EC) might facilitate the identification of tissue- or organ-specific vascular functions of ubiquitous metabolites. An unbiased approach was employed to identify water-soluble small molecules with mitogenic activity on choroidal EC. We identified adenosine diphosphate (ADP) as a candidate, following biochemical purification from mouse EL4 lymphoma extracts. ADP stimulated the growth of bovine choroidal EC (BCEC) and other bovine or human eye-derived EC. ADP induced rapid phosphorylation of extracellular signal-regulated kinase in a dose- and time-dependent manner. ADP-induced BCEC proliferation could be blocked by pretreatment with specific antagonists of the purinergic receptor P2Y1 but not with a vascular endothelial growth factor (VEGF) inhibitor, indicating that the EC mitogenic effects of ADP are not mediated by stimulation of the VEGF pathway. Intravitreal administration of ADP expanded the neovascular area in a mouse model of choroidal neovascularization. Single-cell transcriptomics from human choroidal datasets show the expression of P2RY1, but not other ADP receptors, in EC with a pattern similar to VEGFR2. Although ADP has been reported to be a growth inhibitor for vascular EC, here we describe its growth-stimulating effects for BCEC and other eye-derived EC.

Preliminary evidence of immune infiltration and neutrophil degranulation in peripheral blood of non-obese OSA patients related to cognitive decline

Erratum: “Exciton and biexciton transient absorption spectra of CdSe quantum dots with varying diameters” [J. Chem. Phys. 160, 014708 (2024)]

Effective doses received by the gastrointestinal tract compartments of adults due to food intake in Egypt

Abstract 226Ra, 232Th, and 40K levels in various foods frequently consumed by Egyptians were determined using a gamma-ray spectrometer based on the germanium detector (HPGe). Activity concentrations of 226Ra, 232Th, and 40K were in the range of &lt; 0.10 to 0.79 ± 0.07, &lt; 0.09 to 0.42 ± 0.04, and &lt; 1.96 to 89.73 ± 2.96 Bq/kg, respectively. The gastrointestinal tract (GIT) model was employed to estimate the effective doses received by the different parts of the adult’s gastrointestinal tract, i.e., stomach (ST), small intestine (SI), upper large intestine (ULI), and lower large intestine (LLI), due to the ingestion of the analyzed foods. This estimation was based on mathematical calculations of the energy absorbed by organs due to transformations of ingested radionuclides. The effective doses (μSv/y) received by each compartment were 8.86 (ST), 8.76 (SI), 66.90 (ULI), and 176.76 (LLI). The results do not exceed the safe thresholds set by global organizations UNSCEAR and WHO, 290 and 250–400 μSv/y, respectively. Therefore, radionuclide intakes due to investigated food consumption do not pose any significant radiological impact.