Browse Articles

Potentially causal associations between placental DNA methylation and schizophrenia and other neuropsychiatric disorders

Accelerating polymer self-consistent field simulation and inverse DSA-lithography with deep neural networks

Self-consistent field theory (SCFT) is a powerful polymer field-theoretic simulation tool that plays a crucial role in the study of block copolymer (BCP) self-assembly. However, the computational cost of implementing SCFT simulations is comparatively high, particularly in computationally demanding applications where repeated forward simulations are needed. Herein, we propose a deep learning-based method to accelerate the SCFT simulations. By directly mapping early SCFT results to equilibrium structures using a deep neural network (DNN), this method bypasses most of the time-consuming SCFT iterations, significantly reducing the simulation time. We first applied this method to two- and three-dimensional large-cell bulk system simulations. Both results demonstrate that a DNN can be trained to predict equilibrium states based on early iteration outputs accurately. The number of early SCFT iterations can be tailored to optimize the trade-off between computational speed and predictive accuracy. The effect of training set size on DNN performance was also examined, offering guidance on minimizing dataset generation costs. Furthermore, we applied this method to the more computationally demanding inverse directed self-assembly-lithography problem. A covariance matrix adaptation evolution strategy-based inverse design method was proposed. By replacing the forward simulation model in this method with a trained DNN, we were able to determine the guiding template shapes that direct the BCP to self-assemble into the target structure with certain constraints, eliminating the need for any SCFT simulations. This improved the inverse design efficiency by a factor of 100, and the computational cost for training the network can be easily averaged out over repeated tasks.

Author Correction: A single-photon emitter coupled to a phononic-crystal resonator in the resolved-sideband regime

Structural, electronic, and ferroelectric transitions in van der Waals ferroelectric CuInP2Se6 under high temperature and high pressure

In this work, the high-temperature and high-pressure ferroelectric, structural, and electrical transport properties for CuInP2Se6 upon compression and decompression under different hydrostatic environments were comprehensively studied via Raman spectroscopy, electrical conductivity, and high-resolution transmission electron microscopy observations. Upon non-hydrostatic pressurization, CuInP2Se6 experienced two successive phase transitions at 5.4 and 14.1 GPa originating from the rapid compression of van der Waals gaps and the local structure variation of Se–P–Se bonds, followed by a metallization at 25.1 GPa. Furthermore, a ∼2.0 GPa pressure hysteresis was detected for the emergence of electronic transformation in CuInP2Se6 under hydrostatic conditions owing to the influence of hydrostaticity. Upon decompression, the phase transition of CuInP2Se6 was demonstrated to be reversible with considerable pressure hysteresis under different hydrostatic environments. In addition, the positive sinusoidal voltage-dependent electrical current relations with the nonlinearity factors of ∼1.0 manifested the Ohmic response of CuInP2Se6 under high pressure conditions. Meantime, the disappearance of the P1 Raman peak and the discontinuities in Raman shifts and full width at half-maximums offered robust evidence on the occurrence of ferroelectric crossover in CuInP2Se6. It is the first time that the phase boundary from the mixed antiferroelectric and ferroelectric (FE) orderings into the FE state of CuInP2Se6 is well established [i.e., TC (K) = 165.5 P (GPa) + 292.1] under the conditions of 298–873 K and 0.4–40.3 GPa. Our findings shed light on the ferroelectricity, crystalline structure, and electrical configuration of CuInP2Se6 under extreme conditions, which is of paramount significance to the fundamental research and potential applications for other metallic thio(seleno)phosphates.

Anion-mediated approach to overcome oxidation in ether electrolytes for high-voltage sodium-ion batteries

Dye–quencher pair screening for efficient photo-CIDNP: The role of molecular diffusion

Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging are well-established techniques to acquire diverse molecular information, while their potential applications remain limited due to low sensitivity. Photochemically induced dynamic nuclear polarization (photo-CIDNP) is one of the promising methods to solve this issue, and numerous studies have been conducted to understand its physical mechanism using a particular combination of a dye and a quencher of interest. However, the research across multiple dye–quencher combinations remains largely unexplored. Here, we explore plenty of dye–quencher combinations and reveal that not only the electron transfer process but also the optimal value of the g-value difference (Δg), considerably affected by the escape process of a radical pair, plays a key role in maximizing the enhancement of the NMR signal by photo-CIDNP. The combinations of 115 quenchers with several dyes were experimentally investigated, and 36 photo-CIDNP active quenchers were revealed. Exploration of many different dye–quencher combinations with four dyes revealed that molecular diffusion significantly affects the Δg dependence of photo-CIDNP enhancement of each dye. These findings provide important insights into pioneering new dye–quencher combinations suitable for biological and medical applications.

Long read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases

Effect of intermolecular interactions and elastic frustration on the dynamical properties of the isothermal relaxation of 1D spin crossover chains

We consider an open one-dimensional spin-crossover chain, in which each site can be in either a low spin (LS) or a high spin (HS) state. The sites interact elastically through nearest neighbor (nn) and next-nearest neighbor (nnn) springs with local equilibrium distances depending on the spin states. The system’s Hamiltonian is solved numerically using the Monte Carlo method, applied on both spin states and atomic displacements. This study focuses on the investigations of the isothermal relaxation of a photoinduced HS metastable chain, by analyzing the interplay between the electronic and structural properties along this process. The obtained results indicate that the nucleation and growth mechanisms of LS domains during relaxation are significantly influenced by the amplitude of the intermolecular interactions. Thus, increasing the latter reduces the number of HS/LS clusters due to the high cost of stored elastic energy at HS/LS interfaces. In the second part, we inject an elastic frustration between the equilibrium nn and nnn bond lengths, resulting in the emergence of two distinct relaxation regimes, which depend on the frustration rate, ξ. A detailed analysis of the effect of ξ on the isothermal HS to LS relaxation reveals the stabilization of rich intermediate self-organized electronic structures with long lifetime along this process. Thus, these results clearly demonstrate that the shape of the relaxation curves transforms from a continuous to a two-step behavior, which is reminiscent of the thermal dependence of the order parameters of such models in equilibrium thermodynamics.

FoxO3 controls cardiomyocyte proliferation and heart regeneration by regulating Sfrp2 expression in postnatal mice

Action-based two-dimensional infrared spectroscopy on the horizon

Time domain two-dimensional infrared (2DIR) spectroscopy extends the capabilities of traditional infrared spectroscopy by revealing information on vibrational modes’ anharmonicities, couplings, and energy transfer processes, making it a powerful tool for studying fast dynamic processes. Recent advancements in mid-IR laser technology and detection methods have significantly improved the resolution and acquisition rate of 2DIR spectroscopy. Despite these exciting developments, 2DIR spectroscopy remains limited by Abbe’s diffraction limit, which restricts its spatial resolution. Aimed to address this challenge, the integration of action-based detection methods, notably the atomic force microscope (AFM)-based photothermal detection, offers a promising solution. AFM-2DIR spectroscopy combines the high spatial resolution of AFM with the richness of molecular insights of 2DIR, allowing nanoscale analysis of heterogeneous samples. This new type of technique would open avenues for investigating complex molecular systems, surface phenomena, and nanostructures with unprecedented spatial precision, offering potential for research in chemistry, materials science, bio-macromolecules, and nanotechnology for the chemical physics community.

Active phase discovery in heterogeneous catalysis via topology-guided sampling and machine learning

Fluid flow inside slit-shaped nanopores: The role of surface morphology at the molecular scale

Non-equilibrium molecular dynamics (NEMD) simulations of fluid flow have highlighted the peculiarities of nanoscale flows compared to classical fluid mechanics; in particular, boundary conditions can deviate from the no-slip behavior at macroscopic scales. For fluid flow in slit-shaped nanopores, we demonstrate that surface morphology provides an efficient control on the slip length, which approaches zero when matching the molecular structures of the pore wall and the fluid. Using boundary-driven, energy-conserving NEMD simulations with a pump-like driving mechanism, we examine two types of pore walls—mimicking a crystalline and an amorphous material—that exhibit markedly different surface resistances to flow. The resulting flow velocity profiles are consistent with Poiseuille theory for incompressible, Newtonian fluids when adjusted for surface slip. For the two pores, we observe partial slip and no-slip behavior, respectively. The hydrodynamic permeability corroborates that the simulated flows are in the Darcy regime. However, the confinement of the fluid gives rise to an effective viscosity below its bulk value; wide pores exhibit a crossover between boundary and bulk-like flows. In addition, the thermal isolation of the flow causes a linear increase in fluid temperature along the flow, which we relate to strong viscous dissipation and heat convection, utilizing conservation laws of fluid mechanics. Noting that the investigated fluid model does not form droplets, our findings challenge the universality of previously reported correlations between slippage, solvophobicity, and a depletion zone. Furthermore, they underscore the need for molecular-scale modeling to accurately capture the fluid dynamics near boundaries and in nanoporous materials, where macroscopic models may not be applicable.

Expression of ENL YEATS domain tumor mutations in nephrogenic or stromal lineage impairs kidney development

Abstract Recurrent gain-of-function mutations in the histone reader protein ENL have been identified in Wilms tumor, the most prevalent pediatric kidney cancer. However, their pathological significance in kidney development and tumorigenesis in vivo remains elusive. Here, we generate mouse models mimicking ENL tumor (ENLT) mutations and show that heterozygous mutant expression in Six2 + nephrogenic or Foxd1 + stromal lineages leads to severe, lineage-specific kidney defects, both resulting in neonatal lethality. Six2-ENLT mutant kidneys display compromised cap mesenchyme, scant nephron tubules, and cystic glomeruli, indicative of premature progenitor commitment and blocked differentiation. Bulk and spatial transcriptomic analyses reveal aberrant activation of Hox and Wnt signaling genes in mutant nephrogenic cells. In contrast, Foxd1-ENLT mutant kidneys exhibit expansion in renal capsule and cap mesenchyme, with dysregulated stromal gene expression affecting stroma-epithelium crosstalk. Our findings uncover distinct pathways through which ENL mutations disrupt nephrogenesis, providing a foundation for further investigations into their role in tumorigenesis.

Method-independent cusps for atomic orbitals in quantum Monte Carlo

We present an approach for augmenting Gaussian atomic orbitals with correct nuclear cusps. Like the atomic orbital basis set itself and unlike previous cusp corrections, this approach is independent of the many-body method used to prepare wave functions for quantum Monte Carlo. Once the basis set and molecular geometry are specified, the cusp-corrected atomic orbitals are uniquely specified, regardless of which density functionals, quantum chemistry methods, or subsequent variational Monte Carlo optimizations are employed. We analyze the statistical improvement offered by these cusps in a number of molecules and find them to offer similar advantages as molecular-orbital-based approaches while remaining independent of the choice of many-body method.

Three-dimensional flexible thermoelectric fabrics for smart wearables

The OH + CH3SH process: Potential energy surface and theoretical dynamics study

In the present work, an analytical full-dimensional potential energy surface, PES-2024, was developed for the first time, describing the polyatomic OH + CH3SH gas-phase reaction. This reaction presents some intrinsic difficulties, such as 18 degrees of freedom; two possible reactive channels; methyl- and thiol-H abstraction reactions, (R1) and (R2), respectively; and the presence of intermediate complexes in the entrance and exit channels. In the valence bond-molecular mechanics, VB-MM, framework, we have developed this potential based on a reduced number of high-level ab initio calculations, the input data. The new PES has been subjected to a series of stringent tests. PES-2024 simultaneously describes both (R1) and (R2) reaction paths, forming the water molecule and describing reasonably the topology of the reaction: high exothermicities, low barriers, and the presence of intermediate complexes. Based on this surface, quasi-classical trajectory calculations were performed at room temperature for both paths, with special emphasis on the H2O(v1, v2, v3) product stretching (v1 and v3 modes) and bending (v2 mode) vibrational excitations, comparing the results with the recent experimental evidence. The available energy was mostly deposited as water vibrational energy, 44% and 47%, respectively, simulating the experimental evidence. These detailed state-to-state results lend confidence to the new surface.

Author Correction: Biophysical neural adaptation mechanisms enable artificial neural networks to capture dynamic retinal computation

Stepwise microsolvation of HCl revisited: Infrared investigation of selectively deuterated (HCl)m(H2O)n (m + n ≤ 4) cluster molecules

In a recent theoretical investigation of DCl–H2O, HCl–D2O, and DCl–D2O [Felker et al., J. Phys. Chem. A, 125(29), 6437 (2021)] employing an accurate 9D permutation invariant polynomial-neural network potential energy surface and a highly efficient bound-state methodology, all the intramolecular vibrational eigenstates and dimerization spectral shifts of the three isotopic binary 1:1 complexes have been predicted. By means of dedicated annealing procedures, relative concentration dependencies, and a specialized dual inlet deposition procedure enabling complexation between specific isotopically substituted subunits, the present work identifies the intramolecular vibrational transitions experimentally for these three isotopologues of the binary complex and the most stable cyclic conformations of selectively deuterated mixed (HCl)m(H2O)n (m + n ≤ 4) cluster molecules embedded in inert neon “quantum matrices” at 4 K. The vibrational assignments up to mixed ternary cluster molecules are supported by harmonic CCSD(T)-F12b/cc-pVTZ-F12 frequency predictions in conjunction with anharmonic corrections employing second-order vibrational perturbation theory (VPT2) at the MP2/aug-cc-pVTZ level of theory. While the assigned O–H and O–D stretching transitions in neon are systematically spectrally redshifted by 0.2%–0.5% relative to previously reported observations in supersonic jets, the assigned H–Cl and D–Cl stretching transitions all reveal anomalous excessive spectral redshifts in neon increasing with the size of the cluster molecules. These cluster-size dependent excessive H–Cl/D–Cl spectral redshifts in neon indicate that the extent of charge transfer is enhanced strongly with the complexation of an increasing number of H2O molecules as predicted by quantum chemical models for more than a decade.

Cholecystokinin neurons in the spinal trigeminal nucleus interpolaris regulate mechanically evoked predatory hunting in male mice

Structures and properties of Ca–Xe compounds at extreme pressure and temperature

Calcium, one of the most abundant elements in the Earth’s mantle, does not react easily with noble gases (e.g., He and Xe) under ambient conditions. However, high pressure can alter electron configurations in atoms, leading to the formation of unconventional compounds. In this study, we systematically investigate Ca–Xe compounds across pressures of 0–150 GPa using calypso structure prediction methods combined with first-principles calculations. We identify four novel Ca–Xe compounds Pm3̄m-CaXe, P4/mmm-CaXe2, I4/m-Ca3Xe, and P4/mmm-Ca2Xe3 that demonstrate stability over a wide pressure range from 37.5 to 150 GPa. All these compounds exhibit metallic properties and are dynamically stable, as indicated by the absence of imaginary frequencies in their phonon dispersion spectra. Ionic bonding between Ca and Xe is observed due to electron transfer from Ca to Xe. Ab initio molecular dynamics simulations show that Pm3̄m-CaXe, P4/mmm-CaXe2, and P4/mmm-Ca2Xe3 remain solid up to pressures of 135 GPa and temperatures of 4000 K. In contrast, I4/m-Ca3Xe undergoes a transition from solid to liquid at temperatures above 3500 K due to weakened Ca–Xe bonds. The findings suggest that these Ca–Xe compounds could potentially be synthesized experimentally under high-pressure conditions. The results offer theoretical guidance for discovering new high-pressure Xe compounds and provide valuable insights into Xe chemistry.