Browse Articles

Nanoscale greenhouse effect for promoting solar-driven CO2 reduction with water to CH4

Direct visualization of the existence of surface local chemical order in a high-entropy CoCrFeMnNi alloy

Human narcolepsy is linked to degeneration of both locus coeruleus and hypocretin neurons

Abstract Earlier studies led to the conclusion that human narcolepsy with cataplexy was correlated with the loss of hypocretin (Hcrt = orexin) neurons in the hypothalamus. We now report that individuals having narcolepsy with cataplexy also have an average 46% loss in the number and an 18% increase in the size of brainstem norepinephrine neurons in the locus coeruleus (LC), based on our analysis of 11 brains of individuals having narcolepsy with cataplexy. Microglial clustering around Hcrt neurons in the hypothalamus and around noradrenergic neurons in the locus coeruleus of individuals having narcolepsy with cataplexy indicates microglial involvement in the degeneration of both of these neuronal groups.

Critical spin fluctuations across the superconducting dome in La2−xSrxCuO4

Abstract Overdoped cuprate superconductors are strange metals above their superconducting transition temperature. In such materials, the electrical resistivity has a strong linear dependence on temperature ( T ) and electrical current is not carried by electron quasiparticles as in conventional metals. Here we demonstrate that the strange metal behaviour co-exists with strongly temperature-dependent critical spin fluctuations showing dynamical scaling across the cuprate phase diagram. Our neutron scattering observations and the strange metal behaviour are consistent with a spin density wave quantum phase transition in a metal with spatial disorder in the tuning parameter. Numerical computations using a theory of spin density waves in a disordered metal yield an extended ‘Griffiths phase’ with scaling properties in agreement with experimental observations. Thus we establish that low-energy spin excitations and spatial disorder are central to the strange metal behaviour.

Determinants of chromosome-specific telomere lengths among 2573 All of Us participants

Abstract Telomere length is a biomarker of aging and disease risk. Most human studies have assessed average telomere length, limiting our understanding of variability across chromosome arms. Using long-read sequencing data from >2500 All of Us participants, we estimate chromosome-specific telomere lengths and characterize sources of biological and technical variation. Telomere length varies by chromosome arm, accounting for 9.1% of total variance. Substantial variance (8.9%) in chromosome-specific telomere lengths is attributable to individual, independent of age, suggesting that inter-individual differences in length are established at birth and maintained through life. Age is inversely associated with length for all arms, but longer arms show stronger association. We demonstrate that chromosome-specific telomere estimates enable analysis of disease associations for individual telomeres and for individuals’ shortest telomere. Overall, this work highlights the utility of long-read sequencing for population-scale analysis of chromosome-specific telomere lengths and provides a framework to guide future studies.

Expanding the targeted protein degradation approach with small molecule chimeras directed to the 26S proteasome

4f-5d orbital tag-team catalysis empowers high-loading zinc–iodine batteries

Tryptophanol enhances nitrogen assimilation in marine diatoms

Cartilage targeting hydrogel nanoplatform degrades BRD4 to alleviate osteoarthritis via Nav1.7 axis

Predictive patterning via solid-state dewetting of transferred single-crystal films

Abstract Designing and exploiting the dewetting of single-crystal films to create specific patterns for fabricating functional structures requires improved predictability and extensibility. In this study, we demonstrate that templated solid-state dewetting of single-crystal films can be guided to form regular patterns on arbitrary surfaces. This is achieved by adopting multiscale calculation schemes and implementing the dewetting results of single-crystal Pd(100) films transferred onto amorphous SiO 2 substrates. The anisotropies of Pd surface energy and gas adsorption strength lead to <001> and <011> in-plane facets, favoring the latter as oxygen adsorption increases or the hydrogen flow rate is sufficiently high. This leads to anisotropic dewetting patterns whose geometric characteristics depend significantly on initial crystallographic alignment and annealing ambient. A combination of computational and experimental methods is used to design and guide dewetting to create electrode patterns with submicron channels for thin-film transistors, demonstrating their feasibility for fabricating functional structures on various substrates.

A controllable human spinal cord model with full dorsoventral patterning

Activity-driven swelling and dynamics in segmentally active Rouse chains

We study a segmentally active Rouse chain in which activity is confined to a single contiguous segment of tunable length and position along the contour. Employing analytical normal-mode theory together with Brownian-dynamics simulations, we quantify how localized activity governs conformation and dynamics. Using global conformational measures such as the mean square radius of gyration and end-to-end distance, we observe an unusual swelling pattern: for a fixed length of the active segment, placing the segment near a chain end results in enhanced swelling than positioning the same segment at midchain, reflecting efficient coupling to long-wavelength modes when activity is end-driven. In contrast, fluctuations within a prescribed observation window depend not only on the location and size of the active segment but also on how much the window overlaps the active region. We further examine the dynamics of a tagged point on the chain, which exhibits distinct signatures in the form of a characteristic sequence of diffusive–subdiffusive–superdiffusive crossovers when the tag lies within the active region, while the response is progressively attenuated as the tag is moved away from it. Our results present a minimal, analytically tractable framework for heterogeneous activity in block polymers, providing a basis for extending and interpreting experimental measurements on active biopolymers.

Full-dimensional quantum scattering calculations of rovibrationally excited HD+HD collisions

Full-dimensional quantum scattering calculations are reported for rovibrational transitions in HD+HD collisions using a highly accurate interaction potential for the H2–H2 system. Several near-resonant rovibrational transitions are identified that conserve the overall rotational angular momentum and nearly conserve the internal energy of the collision partners. Key anisotropic terms that drive the rotational transitions and angular momentum partial waves that contribute to low-energy resonant features in the energy dependence of the cross-sections are identified. The computed results agree with total cross-sections reported in previous experimental results, including resonant features in the energy dependence of the cross-section. In particular, low-energy cross-sections show a strong resonant feature associated with an l = 3 partial wave in the incident channel. Rate coefficients for several inelastic rotational and rovibrational transitions are reported for temperatures ranging from 0.1 to 200 K, and they display a maximum between 1 and 10 K, reflecting the important contributions from the l = 3 shape resonance that occurs around 2.5 K.

Vibrational energy relaxation of excited free OH stretching mode at the surface of ice: An <i>ab initio</i> molecular dynamics simulation study

The vibrational energy relaxation dynamics of the excited free OH bond on the ice surface are investigated using ab initio molecular dynamics (AIMD) simulations. The present AIMD study reproduces experimental results obtained via pump–probe sum-frequency generation spectroscopy. Simulations were conducted at 100 and 200 K for ice surfaces and compared with previous results at 300 K for water surfaces. The relaxation mechanisms were analyzed by selectively constraining specific vibrational modes, revealing distinct pathways: intramolecular stretch coupling, bend coupling, and intermolecular stretch coupling via reorientation or dipole–dipole interactions. At higher temperatures, intramolecular stretch coupling dominates, while at lower temperatures, the reorientation of the free OH is restricted; alternatively, intermolecular dipole–dipole coupling becomes more significant due to the vibrational delocalization of ice. For isotopically diluted systems (HOD in D2O), relaxation occurs primarily through stretch–bend combination coupling.

Characterization of diarylethene-based photoswitches with core and valence photoabsorption and photoemission spectroscopies

We investigate the electronic structure of two dithienylethene (DTE) molecular photoswitches, BTF6 and PTF6, in the gas phase by combining valence photoelectron spectroscopy (PES), x-ray photoelectron spectroscopy, and the near-edge x-ray absorption fine structure. DTEs have attracted significant attention due to their high photoisomerization quantum yield, fatigue resistance, and thermal irreversibility, which underpin applications ranging from molecular machines to photoswitchable biomolecules. Supported by first-principles simulations, our analysis elucidates how the different extent of π-conjugation, arising from the distinct thiophene/benzothiophene subunits, manifests across the various spectroscopic observables. By comparing the calculated signatures of the open- and closed-ring isomers, we further assess the sensitivity of each probe to the structural changes associated with photoinduced cyclization. Overall, these results deliver a detailed picture of the intrinsic electronic properties of DTEs in the gas phase and provide a robust basis for future time-resolved studies of their ultrafast photoisomerization dynamics.

Equation-of-motion coupled-cluster methods for doubly ionized and doubly electron-attached states with single, double, and triple substitutions: Theory, implementation, and benchmarks

We present new and computationally efficient implementation of the equation-of-motion (EOM) coupled-cluster methods for doubly ionized (DIP) and doubly electron-attached (DEA) states including single, double, and triple substitutions. In particular, EOM operators include up to 4-hole-2-particle substitutions in EOM-DIP-CCSDT and up to 4-particle-2-holes substitutions in EOM-DEA-CCSDT; both treatments include up to 3-hole-3-particle substitutions in the CC part. These methods have been implemented in the Q-CHEM package using effective and open-mp parallel libtensor and libxm backends. The implementation takes advantage of permutational and point-group symmetries (Abelian subgroups only) and is partially spin-adapted in the case of closed-shell references; it enables both the conventional double-precision and single-precision execution. This paper reports the programmable expressions and details of the implementation. The capabilities of the full EOM-DIP/DEA-CCSDT are demonstrated by application to methylene diradical (CH2), water (H2O), ammonia (NH3), cyclobutadiene (C4H4), acetylene (C2H2), ethylene (C2H4), and formaldehyde (CH2O), highlighting the utility of these methods for treating diradicals, excited states, and Auger decay.

Efficient implementation of analytical Raman intensities

In this study, we report an analytical derivative implementation of static polarizability gradients, needed for the prediction of Raman spectra, in the ORCA program. Our implementation is capable of handling density functionals up to the meta-GGA level and makes use of RIJ and COSX integral approximations to improve the scaling of calculations using both pure and hybrid functionals. Solvent effects can be included with CPCM. We examine the errors in RIJ and COSX Raman activities and find both approximations safe to use in routine calculations. In an effort to further systematically reduce errors resulting from RIJ, we introduce an automatic procedure to minimally augment auxiliary basis sets with diffuse functions if these are detected in the orbital basis set. Compared with numerical derivatives previously available in ORCA, we achieve speedups of up to 1–2 orders of magnitude. Finally, we demonstrate that these developments allow us to calculate fully analytical harmonic Raman spectra of systems containing more than 100 atoms, with the polarizability gradient only introducing a moderate overhead (lower than 10%) to the Hessian calculation.

Ring-polymer instanton theory for tunneling between asymmetric wells

Instanton theory has arisen as a practical tool for calculating tunneling splittings in molecular systems. Unfortunately, the original formulation of instanton theory fundamentally breaks down when trying to calculate the level splitting in asymmetric double wells, as there is no imaginary-time periodic orbit connecting the two non-degenerate minima. We have, therefore, developed a new formulation of instanton theory based on a projected flux correlation function that is applicable to these asymmetric systems. Comparison with exact quantum-mechanical results in one- and two-dimensional models demonstrates that it has a reasonably high accuracy, similar to that reported for instanton theory in the symmetric case. The theory is then applied to study tunneling between non-degenerate minima in the biomolecule α-fenchol, for which we find good agreement with experiment. Finally, we use the connection to instanton rate theory, which is also derived from flux correlation functions, to discuss the often misunderstood relationship between tunneling splittings and reaction rate constants.

Fast evaluation of unbiased atomic forces in <i>ab initio</i> variational Monte Carlo via the Lagrangian technique

Ab initio quantum Monte Carlo (QMC) methods are state-of-the-art electronic structure calculations based on highly parallelizable stochastic frameworks for accurate solutions of the many-body Schrödinger equation, suitable for modern many-core supercomputer architectures. Despite its potential, one of the major drawbacks that still hinders QMC applications, especially when targeting dynamical properties of large systems or extensive datasets, is the lack of an affordable method to compute atomic forces that are consistent with the corresponding potential energy surfaces (PESs), also known as unbiased atomic forces. Recently, one of the authors in the present paper proposed a way to obtain unbiased forces with the Jastrow-correlated Slater determinant Ansatz, where the determinant part is frozen to the values obtained by a mean-field method, such as density functional theory [K. Nakano, M. Casula, and G. Tenti, Phys. Rev. B 109, 205151 (2024)]. However, the proposed method has a significant drawback for its applications: for a system with N nuclei, one requires 6N additional density functional theory (DFT) calculations to get unbiased forces, which is not negligible as the system size increases. This paper presents a way to replace the 6N DFT calculations with a single coupled-perturbed Kohn–Sham calculation, following the so-called Lagrangian technique established in quantum chemistry. This improves the computational cost and scalability of the method. We also demonstrate that the developed unbiased variational Monte Carlo (VMC) force calculation improves not only the consistency with PESs but also its accuracy, by investigating three molecules from the rMD17 benchmark set, and comparing the unbiased VMC forces with those obtained by the coupled-cluster singles and doubles with perturbative triples [CCSD(T)] calculations. We found that the bare VMC forces are biased from the CCSD(T) ones, while the unbiased ones give values closer to those of the CCSD(T) ones. Our benchmark test also reveals that the unbiased VMC forces yield very consistent values with hybrid and meta generalized gradient approximations (e.g., ωB97X-D3BJ and ωB97M-D3BJ), but do not necessarily yield values that are very close to those of CCSD(T). Our finding paves the way to generate machine learning interatomic potentials based on VMC forces more efficiently and accurately.

IEPDYN: Integral-equation formalism of population dynamics

We propose the integral-equation formalism of population dynamics (IEPDYN) to describe the population dynamics of distinct configurational states. According to classical reaction dynamics theory, the probability density associated with a given state obeys the Liouville equation, including influx from and efflux to neighboring states. By introducing a Markov approximation for the crossing of boundaries separating the states, tractable integral equations governing the state populations are derived. Once the time-dependent quantities appearing in these equations are evaluated, the population dynamics on long timescales can be obtained. Because these quantities depend only on a few states in the local neighborhood of a given state, they can be computed using a set of short-timescale molecular dynamics (MD) simulations. The IEPDYN method is formulated in continuous time and therefore does not rely on a coarse-grained timescale (lag time). Consequently, kinetic quantities obtained from IEPDYN are free from lag-time dependence, which has been discussed as a limitation in other approaches. We apply the IEPDYN method to the binding and unbinding kinetics of CH4/CH4, Na+/Cl−, and 18-crown-6-ether (crown ether)/K+ in water. For both kinetics, the time constants estimated from the IEPDYN method are comparable to those obtained from brute-force MD simulations. The required timescale of each MD trajectory in the IEPDYN method is approximately two orders of magnitude shorter than that in the brute-force MD approach in the crown ether/K+ system. This reduction in the trajectory timescale enables applications to complex binding and unbinding systems whose characteristic timescales are far beyond those directly accessible by brute-force MD simulations.