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Tensorial spin-phonon relaxation reveals mode-selective relaxation pathways in a single-molecule qubit
Understanding and controlling spin relaxation in molecular qubits is essential for developing chemically tunable quantum information platforms. We present a first-principles-parametrized analytical framework for evaluating spin relaxation dynamics in vanadyl phthalocyanine (VOPc) and its oxygenated derivative, VOPc(OH)8. By expanding the spin Hamiltonian in vibrational normal modes and computing both linear and quadratic spin–phonon coupling tensors via finite differences of the g-tensor, we construct a relaxation tensor that enters a Lindblad-type master equation, capturing both direct (one-phonon) and Raman (two-phonon) processes. A mode-resolved analysis reveals that relaxation is funneled through only a handful of low-frequency vibrations: in VOPc, three out-of-plane distortions of the phthalocyanine ring and V–O unit dominate, whereas in VOPc(OH)8, the additional oxygens shift these modes downward and suppress two of them, leaving a single strongly coupled mode as the main decoherence pathway. Both longitudinal (T1) and transverse (T2) relaxation are governed by this same set of vibrational modes, indicating that coherence loss is controlled by a common microscopic mechanism. This mode-selective picture offers a design strategy for engineering longer-lived molecular qubits.
In silico docking yields small molecule negative allosteric modulators targeting the core of Frizzled 7
Abstract Targeting the Frizzled family (FZD 1-10 ) of WNT receptors pharmacologically has, despite substantial therapeutic potential, proven difficult. Given an almost complete lack of validated, effective small molecules targeting FZDs, no putative ligand binding site has so far been identified. In order to target FZD 7 , a potential target for the treatment of intestinal tumors, we combine an approach of adapted docking setups and large molecular library docking screens, identifying compound C407. Applying pharmacological assays, genetically-encoded biosensors, site-directed mutagenesis, cryo-electron microscopy and molecular dynamics simulations, the compound binding site in the core of the seven transmembrane bundle is validated and C407 is confirmed as a negative allosteric modulator of WNT-induced and FZD-mediated WNT/ β -catenin signaling. In summary, we provide here the proof-of-principle that targeting FZDs with small molecule compounds is possible and effective. Future hit optimization and functional validation in disease-relevant in vitro and in vivo models will pave the way towards clinical exploration.
Resonances in inelastic collisions of Ne + D2 in the cold energy regime
Scattering resonances are quantum phenomena arising from the decay of metastable collision complexes trapped by a centrifugal barrier or supported by a closed channel that is coupled to a scattering state. As such, resonances can provide significant insights into the scattering process and serve as a sensitive probe of the interaction potential. In this article, we present a detailed analysis of a cluster of shape resonances associated with the orbital angular momentum L = 5 in the j = 2 → j′ = 0 rotational transition in Ne + D2 collisions for vibrational levels v = 0, 1, and 4. The energies and lifetimes of the resonances arising from different values of the total angular momentum quantum number J were analyzed through numerical fitting of the scattering matrix and employing a one-dimensional model based on an effective potential. We further investigated the sensitivity of the resonances to changes in the alignment of the D2 internuclear axis with respect to the initial relative velocity. Our results show that resonances can be exquisitely controlled by carefully selecting the initial alignment of the D2 molecule. In particular, not only the intensity of the resonance can be modulated but also the shape of the overall resonance profile can be altered, depending on the stereodynamical preferences of the individual resonances that contribute to the cluster.
Thermally driven surface phase separation in intermetallic alloys
THz insight into Debye relaxation in liquid water: Link to self-diffusion and viscosity
A non-standard analysis of the dielectric loss spectrum of liquid water in the Debye relaxation region (108–1013 Hz) is carried out in terms of dynamic conductivity σ(ν), with the Debye dielectric loss dome represented as the spectral trapezoid of an overdamped Lorentzian oscillator. Debye relaxation, in this framework, reflects the low-frequency tail of a strongly overdamped molecular oscillatory process with a characteristic frequency around 0.3 THz. The effectiveness of the σ-approach for identifying the relationship between the dielectric response and the self-diffusion D and viscosity η coefficients of liquid water is shown. Analytical expressions that link the dielectric and transport parameters of liquid water over a wide temperature range, from the triple point to the critical point (273–647 K), are derived.
Localized dissipation in linear moiré heat transport
Topology and spectral entanglement in cavity-mediated photon scattering
We develop a microscopic diagrammatic theory for cavity-mediated photon scattering in a topological one-dimensional insulator described by the Su–Schrieffer–Heeger model. Within the velocity-gauge formulation, we derive the photon self-energy and vertex corrections arising from virtual electron–hole excitations coupled to a quantized cavity mode, and we evaluate the resulting polariton dispersion and two-photon correlation spectra. Our analysis shows that vacuum fluctuations of the cavity field induce a momentum-resolved self-energy that mixes conduction and valence bands through virtual photon exchange, producing interband hybridization and avoided crossings in the electronic dispersion. This “cavity dressing” is symmetry-dependent, vanishing at the Brillouin-zone edge where the dipole matrix element is zero, and its strength is controlled by the spatial coherence range ζ≈(lc/a)2 of virtual excitations. We further examine how the cavity modifies nonlinear optical observables, including the Kerr nonlinearity and biphoton spectral entanglement, and identify the regimes where these effects become sensitive to the underlying topological phase. The theoretical framework established here provides a unified description of light–matter coupling in topological and polaritonic systems, bridging solid-state cavity QED with the emerging field of cavity-modified quantum materials. Our results suggest that engineered photonic environments can coherently reshape the electronic landscape of topological insulators, offering new routes to control collective electronic and optical phenomena through vacuum-field fluctuations.
APOBEC3 promotes squamous differentiation via IL-1A/AP-1 signaling
Abstract The APOBEC3 family of RNA and single stranded DNA cytidine deaminases contribute prominently to the mutagenesis of certain cancers including urothelial carcinoma of the bladder (UC). Remarkably, up to 70% of mutations in UC are attributable to the mutagenic activity of the APOBEC3 deaminases. Despite this strong association, few functional studies have investigated APOBEC3’s role in bladder cancer. We report a genetically engineered murine model with conditional knock out of Pten and Trp53 in addition to overexpression of mouse Apobec3 (UPPA). Analysis of bladder tumors from UPPA mice demonstrates that mA3 promotes tumor progression and squamous trans-differentiation. We establish that APOBEC3 promotes squamous differentiation through IL-1α and downstream activation of the AP-1 transcription factor. Bulk RNA-sequencing from human UC shows APOBEC3A as the only human APOBEC3 family member to correlate with squamous differentiation. Furthermore, single cell and spatial transcriptomics reinforces the role of APOBEC3A in fostering squamous trans-differentiation and promoting the emergence of a subpopulation of highly squamous epithelial cells. Our results demonstrate that mouse Apobec3 and human APOBEC3A promote squamous differentiation in urothelial carcinoma and that this trans-differentiation phenotype is mediated through IL-1α signaling, a target of FDA approved therapies for rheumatologic disease.
Random-phase approximation vs Møller–Plesset perturbation theory for many-body energy contributions of hydrogen-bonded molecular solids
The fragment-based approach is a promising strategy for applying correlated-wavefunction methods to lattice energies of molecular solids. A key requirement is the efficient inclusion of the long-distance and nonadditive contributions to the many-body expansion (MBE) of the lattice energy. This is especially important in crystals of polar molecules, where MBE converges slowly with distance. In this context, we compare the simplest coupled-cluster approach—the random-phase approximation (RPA)—against the well-established methodology of Møller–Plesset (MP) perturbation theory. Using the examples of solid ammonia, methanol, and formic acid, we show that the RPA with singles corrections based on the Kohn–Sham (KS) Perdew–Burke–Ernzerhof (PBE) orbitals yields near-benchmark accuracy for the two-body contributions. However, for any PBE-based variant of RPA, the three- and four-body contributions suffer from artifacts. For the nonadditive terms, the Hartree–Fock (HF) orbitals appear necessary. In fact, we find that the HF-based RPA with additional corrections recovers the nonadditive interactions about as accurately as the more expensive MP2.5 method. This is a departure from the typical KS-based RPA and an indication that the HF-based RPA can serve as an alternative to the usual MP methods in accurate approximations of the crystal lattice energy.
Flexible robotic hand harnesses large deformations for full-coverage human-like multimodal haptic perception
Isomer effects on neutral-loss dissociation channels of nitrogen-substituted PAH dications
We investigate two nitrogen-containing isomers of polycyclic aromatic hydrocarbons, quinoline and isoquinoline, of composition C9H7N in collisions with 7 keV O+ and 48 keV O6+ projectile ions. By employing ion–ion coincidence mass spectrometry, we determine branching ratios for H-loss, C2H2-loss, and HCN-loss dissociation channels of Q2+ and IQ2+. The overall contribution of HCN loss is found to be the dominant decay channel. A comparison with the results of a parallel experiment on naphthalene, the simplest PAH, reveals that HCN loss in both isomers has a higher propensity than the analogous C2H2 loss of naphthalene. The positional identity of the nitrogen atom in the two isomers mainly manifests in many-body fragmentation of their dications. Potential energy surfaces of Q2+ and IQ2+ are further computed to explore complete fragmentation mechanisms. Parent dications (Q2+ and IQ2+) are identified to isomerize via seven-membered ring structures before elimination of C2H2 and HCN. While prompt dissociation is the primary pathway, the dominant channel of each neutral-loss class also exhibits delayed fragmentation.
A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity
Pressure-induced phase transition of 3,4-dinitropyrazole by 2D hydrogen bonded networks
As a kind of energetic material, explosives would face an environment of high-pressure during initiation to detonation or under shock waves. Under such conditions, explosives would experience a phase transition and even directly decompose. Therefore, there is a need to achieve the high-pressure evolution of explosives. 3,4-dinitropyrazole (DNP), which has excellent energy and sensibility, can be used as a potential carrier of melt cast explosive to replace TNT. However, the structural evolution of DNP with the increase in pressure remains elusive. With the help of diamond anvil cell technology, in situ high-pressure angle-dispersive x-ray diffraction (ADXRD) and Raman spectra were performed to investigate the structural variations of DNP. Both ADXRD and Raman experiments indicated that the DNP experienced a phase transition in the pressure range between 6.1 and 9.2 GPa. After carefully analyzing the Hirshfeld surface, first-principles calculations, and Raman spectra, we suggested that the newly generated N–H⋯N hydrogen bonds should be responsible for these high-pressure changes. The DNP crystal packing patterns have been changed from 1D molecular tapes to 2D hydrogen bonded networks. This research systemically investigated the high-pressure structural changes of DNP and studied the evolution of weak intermolecular interactions, so it built the relationship between phase transition and weak intermolecular interactions.
Identification of a deep-branching lineage of algae using environmental plastid genomes
Abstract Marine algae underpin entire ocean ecosystems. Yet algae in culture poorly represent their large environmental diversity, and we have a limited understanding of their convoluted evolution by endosymbiosis. Here, we perform a phylogeny-guided plastid genome-resolved metagenomic survey of Tara Oceans expeditions. We present a curated resource of 660 new non-redundant plastid genomes of environmental marine algae, vastly expanding plastid genome diversity within major algal groups, including many without closely related reference genomes. Notably, we recover four plastid genomes, including one near-complete, forming a deep-branching plastid lineage of nano-size algae that we informally name leptophytes. This group is globally distributed and generally rare, although it can reach relatively high abundance in the Arctic. A near-complete mitochondrial genome showing strong co-occurrence with leptophyte plastids is also recovered and assigned to this group. Leptophytes encompass the enigmatic plastid group DPL2, one of the very few known plastid groups not clearly belonging to major algal groups and previously known only from 16S rDNA sequences. Comparative organellar genomics and phylogenomics indicate that leptophytes are sister to haptophytes, and raise the intriguing possibility that cryptophytes acquired their plastids from haptophytes. Collectively, our study demonstrates that metagenomics can reveal hidden organellar diversity, and improve models of plastid evolution.
Efficient 13C–13C correlations obtained by AL FRESCO mixing schemes under any arbitrary MAS spinning rates
An efficient chirp pulse-based mixing technique, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), is introduced for establishing broadband two-dimensional (2D) 13C–13C dipolar correlations in uniformly 13C-labeled protein samples. AL FRESCO utilizes a single or a series of frequency-swept (chirped) pulses applied to homonuclear spin pairs (e.g., 13Cs, 15Ns, or 1Hs) to mediate homonuclear correlations under magic-angle spinning (MAS). Originally developed for ultrafast MAS, we demonstrate that AL FRESCO performs robustly across a wide range of MAS rates. The AL FRESCO method exhibits strong immunity to dipolar truncation, allowing efficient recoupling of long-range interactions even in the presence of dominant short-range dipolar couplings and regardless of the chemical shift difference between the recoupled sites. A distinctive feature of AL FRESCO is its use of weak radiofrequency (rf) fields (5–20 kHz), independent of the MAS rate, significantly reducing sample heating and enabling extended mixing times (>1 s). This facilitates the observation of long-range correlations that are often inaccessible using conventional recoupling techniques under ultrafast MAS rates. The effectiveness of the method is governed by key parameters such as rf amplitude and envelope shape, dwell time (Δt), and sweep bandwidth. Numerical simulations and average Hamiltonian theory offer insight into the recoupling mechanism. Experimental validation was carried out via 2D 13C–13C correlation spectroscopy at fast, moderate, and slow MAS rates using three different protein systems: uniformly 13C,15N-labeled transthyretin, selectively 13C-[T,W]-labeled CrgA, and uniformly 13C,15N-labeled GB1.
Activation of the RSAD2-YTHDF1 axis in smooth muscle causes inflammatory bowel disease via intercellular mitochondrial transfer
Shaping the aggregates of discotic particles with directional pair interactions
Aggregation processes in systems of planar macromolecules and colloids drive a broad range of phenomena in natural systems and soft materials. Depending on the chemical architecture, intermolecular interactions in these systems may favor different relative pair orientations, such as stacking face–face or percolating edge–edge arrangements. In this work, we employ a versatile coarse-grained interaction model for disk-like particles to provide a general framework to rationalize the thermotropic formation of aggregates and predict the topology of the resulting suprastructures. Monte Carlo and Brownian dynamics simulations show that, with appropriate tuning of the interactions, discotics spontaneously nucleate into clusters with globular, planar, or stacked geometries, leading to materials with specific internal order and associated physicochemical properties.
The soil microbiome as an indicator of ecosystem multifunctionality in European soils
Simulating decoherence of two coupled spins using the generalized cluster correlation expansion
We simulate the coherence of two coupled electron spins interacting with a bath of nuclei using the generalized cluster correlation expansion method. An exchange interaction between the electrons facilitates a family of entangling gates that can be spoiled by nuclear-induced dephasing. Consequently, we study the dephasing of the coherent two-electron system by characterizing the T2 and T2* of the two-electron reduced density matrix for various system parameters in the range mimicking magnetic molecules, including magnetic field strength and orientation, exchange interaction strength, distance between the two spins, minimum distance between electron and nuclei and between nuclei, and nuclei density. We find the optimal regime for each parameter in which the coherence time is maximized and provide a physical understanding of it.