Browse Articles

Coherent phonon transport in 2D layered $$\mathrm{Cu_3BHT}$$ metal organic frameworks

Hypergraph-based models of random chemical reaction networks: Conservation laws, connectivity, and percolation

Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs, representing species and reactions as distinct nodes, or simpler derived graphs, which can obscure the relationship between the statistical properties of these representations and the physical characteristics of the CRN. We introduce a straightforward model for generating random CRNs that preserve their hypergraph structure and atomic composition, enabling the direct study of chemically relevant features. Notably, our approach distinguishes two notions of connectivity that are equivalent in graphs but differ fundamentally in hypergraphs. These notions exhibit percolation-like phase transitions, which we analyze in detail. The first type of connectivity has relevance to steady-state synthesis and transduction, determining the effective reactions an open CRN can perform at steady state. The second type is suitable to identify which species can be produced from a given initial set of species in a closed CRN. Our findings highlight the importance of hypergraph-based modeling for uncovering the complex behaviors of CRNs.

Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress

Graphene aerogel for supercapacitors: influence of hydrothermal reduction parameters on electrochemical performance

Non-resonant elastic and inelastic x-ray scattering study of nitrous oxide

The non-resonant elastic and inelastic x-ray scattering technique has been employed to study the molecular structure and the K-shell excitations of N atoms for nitrous oxide (NT-NC-O). The elastic squared form factor and the chemical shift and generalized oscillator strengths for the K-shell excitations of NT/NC: 3π ←1s of nitrous oxide have been determined from the x-ray scattering spectra, which were measured from 20° to 100° at an incident photon energy of about 10 keV and an energy resolution of about 1.3 eV. The obtained chemical shift is consistent with most of the previous data measured by electron scattering and x-ray absorption spectroscopy, while the present elastic squared form factor and generalized oscillator strengths are in good agreement with our calculations and previous results available in the literature. Based on the measured elastic squared form factor and the independent atom model, the bond lengths of NT-NC and NC-O, namely, rNTNC=1.14±0.09 Å and rNCO=1.17±0.09 Å, are derived, and the chemical binding effect is observed. Meanwhile, the effect of different chemical environments on the generalized oscillator strengths of NT: 3π ←1s and NC: 3π ←1s transitions has been demonstrated experimentally. Since the first Born approximation is valid in x-ray scattering, the present elastic squared form factor and generalized oscillator strengths can serve as a benchmark to test the theoretical methods and the ones measured by traditional electron energy loss spectroscopy.

Induction chemotherapy plus camrelizumab followed by concurrent chemoradiotherapy in unresectable locally advanced esophageal squamous cell carcinoma: a single-arm phase II trial

Abstract Concurrent chemoradiotherapy (CCRT) has remained the standard treatment for unresectable locally advanced esophageal squamous cell carcinoma (ESCC), yet survival remains poor. This single-arm, phase II trial aims to evaluate the efficacy and safety of two cycles of induction chemotherapy with camrelizumab followed by CCRT in previously untreated patients with unresectable locally advanced ESCC. The primary endpoint, the 1-year overall survival (OS) rate in the per-protocol population (N = 46), was 87.0% (95% confidence interval [CI]: 77.7%–97.3%), exceeding the pre-specified target. Secondary endpoints included OS in the intention-to-treat (ITT) population, progression-free survival (PFS), overall response rate (ORR), disease control rate (DCR), duration of response, safety, and health-related quality of life. In the ITT population (N = 49), the 1-year OS rate was 85.7% (95% CI: 76.5%–96.1%). The 1-year PFS rates in the per-protocol and ITT populations were 71.7% (95% CI: 59.8%–86.0%) and 71.4% (95% CI: 59.8%–85.3%), respectively. The median OS, PFS, and duration of response were not reached. Following CCRT, the ORR was 93.5%, with a DCR of 95.7%. Lymphopenia was the most frequent Grade ≥3 adverse event (100%). One patient died from treatment-related myelosuppression. Health-related quality of life generally improved after induction therapy, with significant improvements in global health status, emotional functioning, and some symptom relief, despite a slight decline in physical functioning. Here, we show that induction chemoimmunotherapy followed by CCRT exhibits promising efficacy and manageable safety in patients with unresectable locally advanced ESCC, thus warranting further randomized controlled trials. Trial number: ChiCTR2000034304.

Relationship between coffee concentration and bowel motility using bowel-sound-based stimulus-response plots in healthy individuals

Determination of binding free energy shifts in protein complexes induced by single and double amino acid mutations using molecular dynamics simulations

Binding free energy between protein molecules strongly influences protein functions. In particular, shifts in binding free energy caused by amino acid mutations alter the conformational stability of two protein complexes, potentially resulting in functional changes. Predicting these changes in binding free energy due to amino acid mutations remains a considerable challenge. In this study, we propose a simple procedure to calculate the binding free energy shifts in protein complexes resulting from amino acid mutations. We applied this method to the Barnase–Barstar complex, performing molecular dynamics simulations combined with alchemical free energy calculations. Our analysis included three single mutants of Barnase, seven single mutants of Barstar, and three double mutants. The predicted binding free energy shifts were generally consistent with the experimental results, with the exception of two cases. We showed that our method is effective for predicting binding free energy changes when the amino acid mutations do not induce large-scale conformational changes in the protein complex.

Benchmarking informatics workflows for data-independent acquisition single-cell proteomics

Abstract Recent years have seen a rise of single-cell proteomics by data-independent acquisition mass spectrometry (DIA MS). While diverse data analysis strategies have been reported in literature, their impact on the outcome of single-cell proteomic experiments has been rarely investigated. Here, we present a framework for benchmarking data analysis strategies for DIA-based single-cell proteomics. This framework provides a comprehensive comparison of popular DIA data analysis software tools and searching strategies, as well as a systematic evaluation of method combinations in subsequent informatic workflow, including sparsity reduction, missing value imputation, normalization, batch effect correction, and differential expression analysis. Benchmarking on simulated single-cell samples consisting of mixed proteomes and real single-cell samples with a spike-in scheme, recommendations are provided for the data analysis for DIA-based single-cell proteomics.

2-[18F]FDG PET identifies metabolic substrates of sudden cardiac death in hypertrophic cardiomyopathy

On the origin of hydrophilic interactions at alumina surfaces

Despite advances in understanding macroscopic wetting behavior, the atomistic mechanisms underlying hydrophilicity at solid–liquid interfaces remain only partially understood, particularly for chemically and structurally complex surfaces. Alumina, a widely used oxide in catalysis and surface coatings, exhibits such complexity due to the variability in surface termination and hydroxylation. In this study, we investigate the hydrophilicity of three crystallographic terminations of hydroxylated alumina—(0001), (1120), and (0112)–using molecular dynamics simulations based on neural network potential trained on density functional theory data. We quantify hydrophilicity through mean square displacement, density fluctuations, hydrogen bonding characteristics, vibrational density of states, the tetrahedral order parameter, and the contact angle. Our results reveal a clear hydrophilicity trend of (1120) < (0001) < (0112), with the relatively flat surface (1120) showing the least structured interfacial water and the corrugated surface (0112) showing the most pronounced confinement and hydrogen bonding. This trend is reflected in reduced water mobility, suppressed density fluctuations, stronger surface-to-water hydrogen bonds, and greater disruption of tetrahedral order near the (0112) interface. These findings demonstrate that atomic-scale surface roughness and the degree to which it can disrupt the structure of water are key to forming strong surface-to-water hydrogen bonds, thereby offering a microscopic rationale for hydrophilic behavior at oxide surfaces.

Multiscale red blood cell hitchhiking for targeted deep tissue gene delivery in lungs

Abstract The clinical impact of gene therapies is constrained by poor delivery to target tissues beyond the liver after intravenous administration. Current molecular targeting strategies, such as capsid engineering or gene-carrier surface modification, have achieved only limited success due to their inability to overcome the hierarchical barriers from injection to deep tissue transduction. Here, we introduce a Multiscale Approach using RBC-mediated hitchhiking and Vascular Endothelium Leakage (MARVEL), which integrates red blood cell hitchhiking with VEGF-induced vascular permeabilization to enhance accumulation and penetration of cargoes. Using adeno-associated viruses (AAVs) as a model, MARVEL markedly increases AAV localization in the lungs, improves endothelial transcytosis, and enables gene expression in deeper tissue layers while maintaining a favorable safety profile. We further demonstrate that MARVEL can be adopted into an in situ hitchhiking approach, bypassing the need for ex vivo formulation. MARVEL provides a scalable strategy to address long-standing delivery challenges in gene therapy.

Integrative transcriptomics and network analysis reveals core genes driving meningioma pathogenesis and clinical outcomes

ABACUS: An electronic structure analysis package for the AI era

ABACUS (Atomic-orbital Based Ab initio Computation at USTC) is an open-source software for first-principles electronic structure calculations and molecular dynamics simulations. It mainly features density functional theory (DFT) and molecular dynamics functions and is compatible with both plane wave basis sets and numerical atomic orbital basis sets. ABACUS serves as a platform that facilitates the integration of various electronic structure methods, such as Kohn–Sham DFT, stochastic DFT, orbital-free DFT, real-time time-dependent DFT, etc. In addition, with the aid of high-performance computing, ABACUS is designed to perform efficiently and provide massive amounts of first-principles data for generating general-purpose machine learning potentials, such as deep potential with attention models. Furthermore, ABACUS serves as an electronic structure platform that interfaces with several artificial intelligence-assisted algorithms and packages, such as DeePKS-kit, DeePMD, DP-GEN, DeepH, DeePTB, HamGNN, etc.

Chemical weathering of molecular single crystals to monoliths of quantum dots

Questionnaire development and validation for adolescent social media sports content production

Cation–DNA outer sphere coordination in DNA polymorphism

There are two approaches to describing DNA–ion interactions. The physical approach is an analysis of electrostatic interactions between ions and charges on the DNA molecule. The coordination chemistry approach is a search for modes of direct binding of ions to ionophores of DNA. We study both the inner- and outer sphere coordination of ions by ionophores of the A and C forms of DNA in molecular dynamics simulations in two low-polarity solvents: ethanol–water and methanol–water mixtures. We show that the counterion–DNA outer sphere coordination plays a key role in the experimentally observed conformational polymorphism of the DNA molecule: a transition to the A form in ethanol and to the C form in methanol. We identify the ionophores responsible for the existence of the A- and C-complexes. In both complexes, the ions’ inner sphere ligands are mostly water molecules; the ions reside in water clusters. In the ethanol–water mixture, the water clusters are large, the major groove of the A-DNA is filled with water, and all ionophores are accessible to ions. In the methanol–water mixture, the water clusters are small, and a large number of methanol clusters are present near the DNA surface. They interfere with the coordination of ions in one of the ionophores of the major groove and also with other ionophores near phosphates. Therefore, in methanol, the interaction energy of counterions with A-DNA cannot compensate for the repulsion between closely located phosphates. Consequently, the ions fill the more accessible ionophores of the C-complex, converting DNA into the C form.

A hindrance-plane-hindrance molecular engineering strategy towards self-assembled nanorods for enhanced photodynamic therapy

Heat fluxes and thermal stability in the mixolimnion of a tropical heliothermal meromictic crater lake

Abstract An 11-month high-resolution dataset from a rare, hypersaline crater lake on Mexico’s Isla Isabel reveals its intense heliothermal regime is not a permanent state but a distinct seasonal phenomenon. The development of a subsurface temperature maximum exceeding 47 °C is driven by ectogenic meromixis, where a massive influx of clear freshwater during the rainy season forms a low-density surface cap, suppressing vertical mixing and trapping solar radiation in the denser, saltier layers below. Salinity is therefore the fundamental control on the lake’s physical dynamics, creating the precondition for massive subsurface energy storage. This study provides the first definitive characterization of a complete annual cycle in a tropical heliothermal lake, establishing it as a critical model system for understanding the physical stability and response of these rare ecosystems to seasonal climatic forcing.

Ion transport in water film on silica and mica surfaces: Insights from microsecond molecular dynamics and logarithmic mean-force dynamics

Ion transport in water films on mineral surfaces is crucial for geophysical and engineering applications. However, probing these nanoscale phenomena is challenging for both experiments and conventional molecular dynamics (MD) simulations, which struggle to sample the rare ion transport events due to high computational cost. Consequently, the free energy barrier, which governs an ion's lateral entry into the film from the adjacent water-saturated region on the mineral surface, remained unevaluated. To address this, we employed microsecond MD and advanced free energy calculation methods (LogMFD/LogPD) to investigate ion energetics on silica and mica surfaces. Our results reveal a profound difference: a discernible free energy barrier of ∼3 kJ/mol for Cl− transport into the film on α-quartz, whereas the barrier is negligible on the muscovite mica. This difference is attributed to the local ionic environment; mica’s dense Na+ counterion layer stabilizes incoming Cl−, while its absence on α-quartz creates an unstable state. This mechanism was further confirmed in infinitely dilute systems, where the transport barrier on both mineral surfaces is strongly modulated by the presence and location of the counterion. These findings provide molecular-level insights into ion distributions and diffusivities in heterogeneous geological formations and highlight the utility of advanced sampling to resolve the complex energy landscapes governing nanoscale transport.