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How accurate are DFT forces? Unexpectedly large uncertainties in molecular datasets
Training of general-purpose machine learning interatomic potentials (MLIPs) relies on large datasets with properties usually computed with density functional theory (DFT). A prerequisite for accurate MLIPs is that the DFT data are well converged to minimize numerical errors. A possible symptom of errors in DFT force components is nonzero net force. Here, we consider net forces in datasets including SPICE, Transition1x, ANI-1x, ANI-1xbb, AIMNet2, QCML, and OMol25. Several of these datasets suffer from significant nonzero DFT net forces. We also quantify individual force component errors by comparison to recomputed forces using more reliable DFT settings at the same level of theory, and we find significant discrepancies in force components averaging from 1.7 meV/Å in the SPICE dataset to 33.2 meV/Å in the ANI-1x dataset. These findings underscore the importance of well converged DFT data as increasingly accurate MLIP architectures become available.
Feeding Drosophila highly radioresistant fungi improves survival and gut morphology following acute gamma radiation exposure
Abstract Diverse fungi have been historically vital reservoirs of drug discovery, providing life-saving pharmaceuticals. Many species of fungi, yeasts in particular, are highly resistant to radiation, with their cellular contents potentially conferring dietary radioresistance. We developed a Drosophila model to test whether feeding two highly radioresistant fungi, Aureobasidium pullulans and Rhodotorula taiwanensis, could improve fly lifespan and gut morphology after acute irradiation. We constructed a dosimetry curve for the lifespan response of males and females to irradiation and found dose-dependent and sex-specific effects on lifespan. We also determined that the sex-specific response to irradiation correlated with nuclear morphology defects in the gut, with the more radiosensitive males displaying increased midgut cellular holes and aberrant nuclear morphology. To determine if feeding Aureobasidium pullulans and Rhodotorula taiwanensis before irradiation could improve survival and gut morphology, we first exclusively fed males and females each fungus and observed that they tolerated the diet well. Using these methods, we found that only two days of pre-feeding Aureobasidium pullulans increased male lifespan, but not female, after irradiation, and improved nuclear morphology in the gut. However, dietary Rhodotorula taiwanensis was not protective. Overall, this study identified a highly radioresistant dietary fungus, Aureobasidium pullulans , as effective for extending male Drosophila lifespan and improving gut morphology following irradiation. Since the gut is particularly sensitive to the effects of irradiation, this fungus indicates a potential therapeutic for patients undergoing radiotherapy. Furthermore, this method could identify additional radioresistant fungi that protect the gut from radiation injury.
Electron transfer controlled by hydrogen bond donor/acceptor exchange in [H2O]6−
We present results from Path Integral Molecular Dynamics simulations that describe the characteristics of the exchange between the hydrogen-bond donor/acceptor roles of two key water molecules in the most stable isomer of the H2O6−, at cryogenic conditions. We investigated a reactive path described in terms of geared rotations of the water pair, which leads to a substantial reorganization of the localization of the excess negative charge. In the reactant and product states, the electron exhibits a surface solvation structure, lying in the vicinity of the acceptor partner of the pair involved in the HB exchange and spanning a spatial domain on the order of 10 Å, away from the cluster boundaries. In contrast, at transition states, the excess charge extends along a spatial realm that encompasses the locations of both partners in the dimer unit, which participate in the electron solvation on an equal footing. The introduction of quantum fluctuations in the treatment of the nuclear coordinates promotes important modifications in the otherwise classical double-well free-energy profile associated with the exchange. The most relevant changes manifest in the appearance of a plateau-like transition-state regime, which is clearly associated with the onset of proton tunneling. Differences in the activation energies between the isolated neutral dimer case and the anionic water hexamer are discussed. The quantum description of the nuclei also promotes a reduction in the predicted vertical detachment energies at reactant/product states; this result contrasts with the increment observed at transition states. In addition, tunneling effects are also manifested in the modifications operative in the electron delocalization at transition states.
Glycopolymer binds pathogenic IgM autoantibodies and pulls them into the mononuclear phagocyte system for degradation
Visualization of hydrogen isotope exchange in single molecule by tip-enhanced Raman images
Intramolecular hydrogen isotope exchange (HIE) plays a pivotal role in regulating molecular photoelectric properties, reaction pathways, and kinetic control. However, due to intrinsic limitations of conventional techniques, direct real-space observation of the atom-by-atom HIE process at the single-molecule level remains challenging, as does the difficulty of accurately counting and locating intramolecular isotope-substituted atoms. Herein, taking the experimentally accessible coronene as a model system, we theoretically demonstrate the capability of tip-enhanced Raman scattering (TERS), modulated by vibrational interference between atomic motions in a given normal mode, to distinguish and identify various hydrogen-to-deuterium isotope substitution configurations. By overlaying mode-specific TERS images at characteristic vibrational frequencies, our approach allows precise determination of the number, spatial positions, and isotopic categories (deuterium/tritium) of exchanged atoms in an individual molecule. These findings establish TERS imaging as a powerful technique to directly visualize intramolecular isotopic transformations, providing new insights into quantum vibrational dynamics and interference-mediated reaction pathways at the nanoscale.
Sleep disorders in renal patients: a comparative analysis of dialysis and post-renal transplant outcomes
Surface hopping with nuclear quantum effects through path-integral coarse graining
Incorporating nuclear quantum effects (NQEs), such as tunneling and zero-point energy, in nonadiabatic dynamics is of fundamental importance. We propose a simple and robust scheme based on introducing an effective quantum potential for the nuclei in mixed quantum-classical trajectory approaches. The most straightforward method is to combine the fewest-switches surface hopping (FSSH) method with centroid molecular dynamics, which we name as centroid-surface surface hopping. Furthermore, the unfavorable computational overhead of path-integral simulations can be mitigated via the recently developed path-integral coarse-graining scheme, achieving efficiency comparable to FSSH with classical nuclei. The method is benchmarked against exact quantum mechanical calculations on two one-dimensional two-state model systems, each with three sets of parameters covering both the golden-rule and near-adiabatic regimes. Results show that our method predicts quantitatively accurate reaction rates and correlation functions, even in the deep tunneling regime, on both model systems for all the parameter sets tested. This development paves the way for efficient and accurate modeling of NQEs in nonadiabatic reactions/processes in the future.
Pemetrexed negatively impacts embryonic development by inducing oxidative stress in mouse oocytes
<i>Ab initio</i> simulations of dynamics of EMI-BF4 ionic liquid propellant used in electrospray thrusters for nanosatellite applications
Detailed quantum-chemistry calculations of field-induced fragmentation reactions of ionic liquids are presented. The simulations identified the most likely channels for hard (breaking covalent bonds) fragmentation. The computed energetics for hard and soft (breaking clusters into moieties) fragmentation can be incorporated in multiscale models of thrusters’ operation. The simulations determined that soft fragmentation occurs on a picosecond timescale, revealing that these large and flexible ions can be heated when accelerated by the electric field. Although the acquired internal kinetic energy is not sufficient to break covalent bonds in cold molecules, it can result in the fragmentation of hotter molecules. The results contribute to a better understanding of processes occurring in thrusters that use ionic liquids as propellants and suggest that deviations from the idealized behavior of the propellant (as charged point-mass particles) in the acceleration region might be important. The results of this study provide a foundation for further improvement of multi-scale models of thrusters’ operation.
A rank ordering and analysis of nine resilience competencies demonstrates the special importance of thought management in maintaining resilience
Inverse design of drying-induced assembly of multicomponent colloidal-particle films using surrogate models
The properties of films assembled by drying colloidal-particle suspensions depend sensitively on both the particles and the processing conditions, making them challenging to engineer. In this work, we develop and test an inverse-design strategy based on surrogate modeling to identify conditions that yield a target film structure. We consider a two-component hard-sphere colloidal suspension whose designable parameters are the particle sizes, the initial composition of particles, and the drying rate. Film drying is simulated approximately using Brownian dynamics. Surrogate models based on Gaussian process regression (GPR) and Chebyshev polynomial interpolation are trained on a loss function, computed from the simulated film structures, that guides the design process. We find the surrogate models to be effective for both approximation and optimization using only a small number of samples of the loss function. The GPR models are typically slightly more accurate than polynomial interpolants trained using comparable amounts of data, but the polynomial interpolants are more computationally convenient. This work has important implications not only for designing colloidal materials but also more broadly as a strategy for engineering nonequilibrium assembly processes.
Development and preliminary validation of a predictive model for IgA nephropathy progression
Nitrile infrared intensity is more sensitive to local electric field change than its frequency: Application to probe protein hydration dynamics
The stretching vibration of a nitrile (C≡N) group gives rise to a sharp and strong infrared (IR) absorption band. Because the frequency (νCN) and molar extinction coefficient at νCN (εCN) of this vibrotational mode depend not only on the parent molecule but also on interactions that can affect the electronic distribution of the C≡N triple bond, it has found broad utility as an IR probe of the local environment of various chemical and biological systems. However, most previous studies only used the νCN to extract the information of interest. Herein, we show that the integrated molar extinction coefficient [∫ενdν] of the C≡N band has a stronger dependence on local electric field than its frequency and, hence, can be used to probe smaller environmental changes, as demonstrated in a proof-of-principle application. In addition, we find that for a series of C≡N IR bands that are measured with different aromatic nitriles or in different solvents, the νCN exhibits a linear correlation with the square root of the frequency normalized ∫ενdν, indicating that the underlying IR transition dipole moment is linearly dependent on the electronic interaction between the C≡N triple bond and the parent aromatic molecule.
Superior transplant recipient outcome prediction and pathology assessment using rapid deep learning applied to procurement kidney biopsies
A systematic methodology to develop bottom-up coarse-grained models for sequence-specific polypeptoids
Current developments in the precise synthesis of sequence-controlled polymers allow for new opportunities in designing materials with finely tunable properties. In particular, polypeptoids offer a robust platform for sequence-specific polymers that can be produced at gram scale and offer a range of sidechain chemistries that far exceed those of polypeptides and natural protein-based biopolymers. However, the vast chemical design space of polypeptoids demands high-throughput screening, which is not yet synthetically feasible. Moreover, the lack of large structural and property databases limits the development of AI-based predictive models. These challenges highlight the need for systematic, physics-based computational methods to understand and predict how sequence impacts the polypeptoid structure and material properties. Here, we create a multiscale simulation workflow to develop bottom-up coarse-grained (CG) peptoid models using the relative entropy approach, to create a library of peptoid monomers suitable for studying the CG models of a wide range of sequences in both long-chain and multi-chain simulations. Using a representative subset of peptoid chemistries, we validate the resulting CG models by comparison with all-atom simulations and experimental end-to-end distance measurements measured through double electron–electron resonance spectroscopy. This approach is encouraging for polymer platforms that lack large databases as it offers a bottom-up framework to navigate the vast sequence and chemistry space of sequence-defined polymers, enabling molecular-level insight and in silico screening of peptoid-based materials.
Development and validation of identification models for aortic dissection and non-ST-segment elevation acute coronary syndrome in the emergency department
Abstract Aortic dissection (AD) and non-ST-segment elevation acute coronary syndrome (NSTE-ACS) are critical illnesses whose prompt identification within the emergency department is challenging. This study aimed to establish rapid discrimination models to differentiate between these conditions. Patients of the training set and validation set were collected from January 2020 to June 2023. All patients used their final diagnosis. Discriminant models were constructed via univariate and multivariate logistic regression analyses. Based on the results of the two models, two web calculators were developed. A total of 1314 patients were included in the study, with 997 patients (399 AD patients and 598 NSTE-ACS patients) and 317 patients (132 AD patients and 185 NSTE-ACS patients) in the training and validation sets, respectively. The semi-model consisted of six clinical characteristics (age, heart rate, pulse pressure, temperature, hypertension, diabetes), with an area under the ROC curve (AUC) of 0.792 and 0.823 in the training and validation sets. The whole-model included five clinical characteristics (age, pulse pressure, hypertension, diabetes) and two point-of-care test data (high sensitivity troponin I, D-dimer). It had a higher predictive value compared to the semi-model, with AUCs of 0.973 and 0.980 in the training and validation sets, respectively. Given the optimal cutoff point, the semi-model demonstrated a sensitivity of 0.716 and a specificity of 0.734, whereas the whole-model displayed a sensitivity of 0.930 and a specificity of 0.946. Both identification models can be used as reliable tools for rapidly identifying AD and NSTE-ACS.
Terahertz and dielectric spectral calculations of aqueous CaCl2 solutions using polarizable models: Intra- and inter-species contributions involving permanent and induced dipoles and ion current
Intermolecular interactions, structure, and dynamics of aqueous CaCl2 solutions are investigated through calculations of the terahertz (THz) and dielectric spectra from molecular dynamics simulations using explicit polarizable models for both water and the ions. Calculations are performed for three different concentrations of CaCl2 in water at room temperature. For each system, the difference absorption spectrum shows several features in the THz region. We dissected the difference absorption spectrum further into ion–ion, water–water, and ion–water components. The ion–ion contribution is further dissected into cation–cation, anion–anion, and cation–anion self and cross correlation contributions. The ion–water terms are further separated into cation–water and anion–water correlations. These dissections provide detailed insights into ion–ion and ion–water correlations and dynamical behavior of the hydrated ions. We further separated the cation–water and anion–water contributions into permanent dipole–permanent dipole, permanent dipole–induced dipole, and induced dipole–induced dipole correlation components, which reveal the nature and magnitude of these interactions contributing to the ion–water THz spectrum. Our calculations of the anisotropy of induced dipole moments reveal that the presence of Ca2+ ions in the vicinity of Cl− ions increases the anisotropy of the induced dipole moments of the anions. The present study also reveals a significant presence of contact ion pairs in the CaCl2 solutions, especially at higher concentrations. We also explored the influence of heterogeneity of water hydrogen bonds around Ca2+ ions on THz spectral features of hydration shell water. We also calculated the low-frequency dielectric spectrum, including the static dielectric constant of each solution, which accounts for both dipole–dipole and current–dipole contributions.
Hollow polyaniline/pyrrole-chitosan supported Pt-Cu0.5Zn0.5Fe2O4 nanoparticles as an efficient electrocatalyst for enhancement of the methanol oxidation reaction
Nonvolatile switchable electromagnetically induced transparency in terahertz range
The terahertz frequency range has attracted significant interest for its potential in applications such as high-speed communication, sensing, and imaging. However, the dynamic control of terahertz waves remains a challenge. Here, we present a switchable metasurface incorporating the Ge–Sb–Te (GST) phase-change material, designed to achieve switchable electromagnetically induced transparency (EIT) in the terahertz frequency range. The metasurface features an array of gold stripes on a thin GST sublayer, with the quasi-BIC-related EIT mode arising from a hybrid symmetry-protected Friedrich–Wintgen supercavity mode. By carefully adjusting the geometric parameters of the gold stripes, the EIT bandwidth can be precisely tuned through the controlled asymmetry. The phase transition of GST induces a significant change in the metasurface electrical properties, enabling robust nonvolatile switching between transparent and opaque states of the device. Both theoretical analysis and experimental validation confirm the efficacy of this design for dynamic modulation in the terahertz regime, demonstrating its potential for advanced terahertz photonic applications.