Browse Articles

Hidden domain boundary dynamics toward crystalline perfection

A central paradigm of nonequilibrium physics concerns the dynamics of heterogeneity and disorder, impacting processes ranging from the behavior of glasses to the emergent functionality of active matter. Understanding these complex mesoscopic systems requires probing the microscopic trajectories associated with irreversible processes, the role of fluctuations and entropy growth, and the timescales on which nonequilibrium responses are ultimately maintained. Approaches that illuminate these processes in model systems may enable a more general understanding of other heterogeneous nonequilibrium phenomena, and potentially define ultimate speed and energy cost limits for information processing technologies. Here, we apply ultrafast single-shot X-ray photon correlation spectroscopy to resolve the nonequilibrium, heterogeneous, and irreversible mesoscale dynamics during a light-induced phase transition in a (PbTiO 3 ) 16 /(SrTiO 3 ) 16 superlattice. Such ferroelectric superlattice systems are a useful platform to study phase transitions and topological dynamics due to their high degree of tunability. This provides an approach for capturing the nucleation of the light-induced phase, the formation of transient mesoscale defects at the boundaries of the nuclei, and the eventual annihilation of these defects, even in systems with complex polarization topologies. We identify a nonequilibrium correlation response spanning >10 orders of magnitude in timescales, with multistep behavior similar to the plateaus observed in supercooled liquids and glasses. We further show how the observed time-dependent long-time correlations can be understood in terms of stochastic and non-Markovian dynamics of domain walls, encoded in waiting-time distributions with power-law tails. This work defines possibilities for probing the nonequilibrium and correlated dynamics of disordered and heterogeneous media.

Supercarbon assembly inspired two-dimensional hourglass fermion

By using a tight-binding model, first-principles calculations, and ab initio molecular dynamics simulations, we theoretically demonstrate that the C76-Td-assembled two-dimensional (2D) honeycomb lattice is stable at room temperature and is resistant to mechanical deformation. We disclose that each C76-Td mimics a single carbon atom (geometrically and electronically); hence, it plays the role of one supercarbon. This inspires that the 2D material exhibits an exotic hourglass-like fermion at the Fermi level. Furthermore, we suggest that biaxial strains could modify the hourglass shape, including the electronic Fermi velocity, and induce magnetization. Hexagonal boron nitride can be employed as a protective layer without affecting the electronic structure of this material. This hourglass fermion has the potential to serve as a promising material for high-speed electronic devices and to bridge the gap between zero-dimensional spherical carbon clusters and two-dimensional graphene.

PKM2 controls cochlear development through lactate-dependent transcriptional regulation

Understanding the role of metabolic processes during inner ear development is essential for identifying targets for hair cell (HC) regeneration, as metabolic choices play a crucial role in cell proliferation and differentiation. Among the metabolic processes, growing evidence shows that glucose metabolism is closely related to organ development. However, the role of glucose metabolism in mammalian inner ear development and HC regeneration remains unclear. In this study, we found that glycolytic metabolism is highly active during mouse and human cochlear prosensory epithelium expansion. Using mouse cochlear organoids, we revealed that glycolytic activity in cochlear nonsensory epithelial cells was predominantly dominated by pyruvate kinase M2 (PKM2). Deletion of PKM2 induced a metabolic switch from glycolysis to oxidative phosphorylation, impairing cochlear organoid formation. Furthermore, conditional loss of PKM2 in cochlear progenitors hindered sensory epithelium morphogenesis, as demonstrated in PKM2 knockout mice. Mechanistically, pyruvate is generated by PKM2 catalysis and then converted into lactate, which then lactylates histone H3, regulating the transcription of key genes for cochlear development. Specifically, accumulated lactate causes histone H3 lactylation at lysine 9 (H3K9la), upregulating the expression of Sox family transcription factors through epigenetic modification. Moreover, overexpression of PKM2 in supporting cells (SCs) triggered metabolism reprogramming and enhanced HC generation in cultured mouse and human cochlear explants. Our findings uncover a molecular mechanism of sensory epithelium formation driven by glycolysis-lactate flow and suggest unique approaches for mammalian HC regeneration.

Dielectric profile at the Pt(111)/water interface

The dielectric constant, although a simplified concept when considering atomic scales, enters many mean-field, electrochemical interface models and constant potential models as an important parameter. Here, we use ab initio and machine-learned molecular dynamics to scrutinize the behavior of the electronic contribution to ɛr(z) as a function of distance z from a Pt(111) surface. We show that the resulting dielectric profile can largely be explained as a sum of the metallic response and the density-scaled water response at the interface. A slight enhancement of the dielectric response close to the surface can be explained by elongated, strongly polarizable orbitals induced by metal/water bonding. In spite of this enhancement, our results suggest the presence of a region with a very low dielectric constant close to the surface (where the orientational dielectric response does not kick in yet), even for water in contact with hydrophilic metallic interfaces. This region will restrict the double layer capacitance to relatively low values even at potentials where dielectric saturation does not play a role yet. This finding has implications on possible interpretations of double layer capacitances, the dependence of surface electric fields on the ion size, and on electrochemical kinetics.

Analogue-Sensitive Inhibition of Histone Demethylases Uncovers Member-Specific Function in Ribosomal Protein Synthesis

Engaging dystonia networks with subthalamic stimulation

Deep brain stimulation is an efficacious treatment for dystonia. While the internal pallidum serves as the primary target, recently, stimulation of the subthalamic nucleus (STN) has been investigated. However, optimal targeting within this structure and its surroundings have not been studied in depth. Indeed, historical targets that have been used for surgical treatment of dystonia are directly adjacent to the STN. Further, multiple types of dystonia exist, and outcomes are variable, suggesting that not all types would profit maximally from the same target. Therefore, a thorough investigation of neural substrates underlying stimulation effects on dystonia signs and symptoms is warranted. Here, we analyze a multicenter cohort of isolated dystonia patients with subthalamic implantations ( N = 58) and relate their stimulation sites to improvements of appendicular and cervical symptoms as well as blepharospasm. Stimulation of the ventral oral posterior nucleus of thalamus and surrounding regions were associated with improvements in cervical dystonia, while stimulation of the dorsolateral STN was associated with improvements in limb dystonia and blepharospasm. This dissociation was matched by structural connectivity analysis, where the cerebellothalamic, corticospinal, and pallidosubthalamic tracts were associated with improvements of cervical dystonia, while hyperdirect and subthalamopallidal pathways with alleviation of limb dystonia and blepharospasm. On the level of functional networks, improvements of limb dystonia were associated with connectivity to the corresponding somatotopic regions in the primary motor cortex, while alleviation of cervical dystonia to the cingulo-opercular network. These findings shed light on the pathophysiology of dystonia and may guide DBS targeting and programming in the future.

Exceptionally large fluctuations in orientational order: The lessons of large-deviation theory for liquid crystalline systems

How condensed-matter simulations depend on the number of molecules being simulated (N) is sometimes itself a valuable piece of information. Liquid crystals provide a case in point. Light scattering and 2d-IR experiments on isotropic-phase samples display increasingly large orientational fluctuations (“pseudo-nematic domains”) as the samples approach their nematic phase. The growing length scale of those locally ordered domains is readily seen in simulation as an ever-slower convergence of the distribution of orientational order parameters with N. But the rare-event character and exceptionally slow time scales of the largest fluctuations make them difficult to sample accurately. We show in this paper how taking a large-deviation-theory perspective enables us to leverage simulation-derived information more effectively. A key insight of the theory is that finding quantities such as orientational order parameters (extensive variables) is completely equivalent to deducing the conjugate (intensive) thermodynamic field required to equilibrate that amount of order—and that knowing the relationship between the two (the “equation of state”) can easily be turned into knowing the relative free energy of that degree of order. A variety of well-known thermodynamic integration strategies are already founded on this idea, but instead of applying an artificially imposed external field, we use a priori statistical mechanical insights into the small and large-field limits to construct a simulation-guided, interpolated, equation of state. The free energies that result mostly need information from the most probable configurations, making the simulation process far more efficient than waiting for (or artificially generating) large fluctuations.

Molecular H₂ as the Reducing Agent in Low-Temperature Oxide Reduction Using Calcium Hydride

Turbulence in the tropical stratosphere, equatorial Kelvin waves, and the quasi-biennial oscillation

The tropical stratosphere is the gateway to the global stratosphere and a commonly proposed location for solar geoengineering. The dynamics of this remote and difficult to observe region are poorly understood, particularly at turbulent length scales. Existing observational estimates of turbulence frequency and strength vary widely. Furthermore, the sources of turbulence and the relationship between turbulence and the mean flow are largely unknown. We assembled a 21-y database of high vertical resolution (10 m) radiosonde data from four equatorial sites in two ocean basins to study tropical stratospheric turbulence frequency, variability, and sources. Turbulent layers thicker than 200 m are identified using subcritical Richardson number as a proxy for turbulence. We show that the turbulent fraction of the tropical stratosphere is strongly modulated by the quasi-biennial oscillation (QBO). Turbulence is enhanced during the QBO phase shifts, and the atmosphere is most turbulent right before the QBO phase switches from negative to positive, where turbulent instabilities typically occur within specific phases of Kelvin waves. Turbulence is less common when the QBO phase is well established, and the atmosphere is least turbulent during the negative phase of the QBO. The turbulent fraction of the equatorial lower stratosphere varies over a factor of ten depending on QBO phase. This relationship provides a robust observational constraint on the multiscale dynamics within this region, which is useful for evaluating atmospheric models, studying wave-mean flow interactions in the context of the QBO, and informing the operation of stratospheric aircraft and the injection of aerosol for geoengineering.

Progress in understanding the infrared spectrum of the H2O–O2 dimer

Spectra of the weakly bound H2O–O2 dimer are studied in the region of the H2O ν2 band using a tunable quantum cascade laser to probe a pulsed supersonic slit jet expansion. These are the first gas-phase infrared spectra of H2O–O2 and among only a few such results for O2-containing complexes. Almost 100 infrared lines are assigned based on the ground state combination differences from the microwave spectrum of H2O–O2. These lines belong to a main fundamental band, plus four combination bands lying 2 to 5 cm−1 above the fundamental. All correspond to the ortho-H2O (I = 1) nuclear spin species. Interpretation of the observed rotational levels is discussed. The original microwave analysis conflicts with the infrared results but can be corrected by changing the sign of a term or, better still, by using a published theory for weakly bound open shell complexes. The combination bands suggest that analogous ground state bands should be observable in the millimeter wave range. Many infrared transitions remain unassigned, including another extensive band apparently centered at 1603 cm−1, and some of these are probably due to the para-H2O spin species (I = 0). Splittings due to the unpaired O2 electron spin (S = 1), due to large amplitude tunneling motions, and due to a-axis rotational motion all have similar magnitudes for H2O–O2, so the resulting energy levels will be heavily mixed and not amenable to simple modeling. Accurate theoretical predictions of these effects should be possible for obtaining an enhanced understanding of the observed spectra.

Microbes could convert industrial wastewater into ecofriendly products

Newton’s algorithm for discrete classical dynamics

A recent article in J. Chem. Phys. argues that the two algorithms, the velocity-Verlet and position-Verlet integrators, commonly used in Molecular Dynamics (MD) simulations, are different [L. Ni and Z. Hu, J. Chem. Phys. 161, 226101 (2024)]. However, not only are the two algorithms just different formulations of the same discrete algorithm, but also are other simple discrete algorithms used in MD simulations in the natural sciences. They are all reformulations of the discrete algorithm derived by Newton in 1687 in Proposition I in the very first part of his book Principia. The different reformulations of Newton’s algorithm for discrete dynamics lead to identical discrete dynamics with the same invariances, momentum, angular momentum, and energy as Newton’s analytical dynamics. Hundreds of thousands of MD simulations with Newton’s discrete dynamics have appeared but unfortunately with many recorded errors for energies, potential energies, temperatures, and heat capacities. The public software for MD should be corrected.

BK channels mediate a presynaptic form of mGluR-LTD in the neonatal hippocampus

BK channels can control neuronal function, but their functional relevance in activity-dependent changes of synaptic function remains elusive. Here, we report that repetitive low-frequency stimulation activates BK channels through 12(S)HPETE, an arachidonic acid metabolite, produced downstream of postsynaptic metabotropic glutamate receptors (mGluRs) to trigger long-term depression (LTD) at CA3–CA1 synapses in hippocampal slices from P7–P10 mice. Activation of BK channels is subunit specific, as paxilline but not iberiotoxin blocked mGluR-LTD. Also, 12(S)HPETE does not change the electrophysiological properties of the BK channel when the BKα subunit is expressed alone but increases the channel open probability when the BKα is coexpressed with the β4-subunit. Our findings reveal an interaction between 12(S)HPETE and BK channels to regulate synaptic strength at central synapses and increase our understanding of the mechanisms underlying mGluR-LTD in the neonatal hippocampus that likely contribute to circuit maturation necessary for learning.

Thermostat-induced artificial lane formation in non-equilibrium molecular dynamics

While most thermostats in molecular dynamics are designed for equilibrium systems, their extension to non-equilibrium simulations has little theoretical justification. In the literature, an artifact referred to as “lane formation” was discovered; however, its cause remained unclear and was simply attributed to a constraint on velocity fluctuations or non-ergodicity in thermostats. In addition, global deterministic thermostatted dynamics was found to exhibit unceasing phase-space compression in steady states, incompatible with their expected stationary distributions and Gibbs entropy, which was mistakenly perceived as inescapable. In this work, we pinpoint that the dynamical cause of artificial lane formation is a stable fixed point in the momentum space induced by improper velocity rescaling, which produces effective repulsion between different species in a color flow, drains transverse kinetic energy and generates the unceasing compression. This artifact is deeply rooted in global deterministic thermostats, such as the Nosé–Hoover dynamics and configurational thermostat. With proper rescaling, the Langevin thermostat completely eliminates artificial lane formation and exemplifies how incompressible phase space and stationary distributions can be retained for non-equilibrium steady states.

Superconducting critical temperature elevated by intense magnetic fields

Below a critical temperature T c , superconductors transport electrical charge without dissipative energy losses. The application of a magnetic field B generally acts to suppress T c , up to some critical field strength at which T c → 0 K. Here, we investigate magnetic field–induced superconductivity in high-quality specimens of the triplet superconductor candidate UTe 2 in pulsed magnetic fields up to B = 70 T. Strikingly, we find that this material has a higher T c when B > 40 T ( T c ≈ 2.4 K) than it does for B = 0 T ( T c = 2.1 K). This observation points to a fundamentally distinct mechanism for the formation of superconductivity at high B in UTe 2 compared to the case of B = 0 T.

Biodegradable Tenebrio molitor antifreeze protein modified kinetic hydrate inhibitor: Insights into molecular interactions and structural flexibility

The formation of natural gas hydrates presents significant economic and safety challenges to the petroleum and gas industry, necessitating the development of effective prevention strategies. This study investigates an environmentally sustainable Tenebrio molitor antifreeze protein (TmAFP) modified to be a potential kinetic hydrate inhibitor. The aim of this study was to enhance the inhibitory activity of TmAFP by systematically substituting threonine (Thr) residues with glycine (Gly), alanine (Ala), or serine (Ser) at positions 29, 39, and 53. The Ala mutant demonstrated superior inhibition of hydrate formation, attributed to its optimized spatial conformation and enhanced hydrophobic interactions, followed by the Gly and Ser mutants. The wild-type TmAFP showed limited efficacy. The radial distribution function (RDF) analysis indicated that the mutations facilitated a better accommodation of adjacent residues within the hydrate crystal structure by adjusting the distance between Thri and Thri+2 to closely match the second peak in the RDF of methane molecules at 6.4 Å. The potential of mean force (PMF) calculations revealed that the Ala and Ser mutants exhibited enhanced interactions with hydrate cages, with PMF values of −0.73 and −0.71 kJ/mol, respectively, compared to the Gly mutant, which had a PMF value of 1.46 kJ/mol. By identifying the optimal mutation combination (T29 39 53A) to significantly increase the potency of TmAFP, this study provides a fundamental basis for the further development of hydrate inhibition strategies.

An organic electrochemical neuron for a neuromorphic perception system

Human perception systems are highly refined, relying on an adaptive, plastic, and event-driven network of sensory neurons. Drawing inspiration from Nature, neuromorphic perception systems hold tremendous potential for efficient multisensory signal processing in the physical world; however, the development of an efficient artificial neuron with a widely calibratable spiking range and reduced footprint remains challenging. Here, we report an efficient organic electrochemical neuron (OECN) with reduced footprint (<37 mm 2 ) based on high-performance vertical OECT (vOECT) complementary circuitry enabled by an advanced n-type polymer for balanced p-/n-type vOECT performance. The OECN exhibits outstanding neuronal characteristics, capable of producing spikes with a widely calibratable state-of-the art firing frequency range of 0.130 to 147.1 Hz. Leveraging this capability, we develop a neuromorphic perception system that integrates mechanical sensors with the OECN and integrates them with an artificial synapse for tactile perception. The system successfully encodes tactile stimulations into frequency-dependent spikes, which are further converted into postsynaptic responses. This bioinspired design demonstrates significant potential to advance cyborg and neuromorphic systems, providing them with perceptual capabilities.

Restoring rotational symmetry of multicomponent wavefunctions with nuclear orbitals

In this work, we present a non-orthogonal configuration interaction (NOCI) approach to address the rotational corrections in multicomponent quantum chemistry calculations where hydrogen nuclei and electrons are described with orbitals under Hartree–Fock (HF) and density functional theory (DFT) frameworks. The rotational corrections are required in systems such as diatomic (HX) and nonlinear triatomic molecules (HXY), where localized broken-symmetry nuclear orbitals have a lower energy than delocalized orbitals with the correct symmetry. By restoring rotational symmetry with the proposed NOCI approach, we demonstrate significant improvements in proton binding energy predictions at the HF level, with average rotational corrections of 0.46 eV for HX and 0.23 eV for HXY molecules. For computing rotational excitation energies, our results indicate that HF kinetic energy corrections are consistently accurate, while discrepancies arise in total energy predictions, primarily from an incomplete treatment of dynamical correlation effects. Rotational energy corrections in multicomponent DFT calculations, using the epc17-2 proton–electron correlation functional, lead to an overestimation of proton binding energies. This is as a result of double-counting of proton–electron correlation effects in the off-diagonal NOCI terms. As a correction, we propose a scaling scheme that effectively adjusts the proton–electron correlation contributions, bringing our results into close agreement with reference CCSD(T) data. The scaled rotational corrections, on average, increase the epc17-2 proton binding energy predictions by 0.055 eV for HX and 0.025 eV for HXY and yield average deviations of 1.0 cm−1 for rotational transitions.

The single-stranded DNA–binding factor SUB1/PC4 alleviates replication stress at telomeres and is a vulnerability of ALT cancer cells

To achieve replicative immortality, cancer cells must activate telomere maintenance mechanisms. In 10 to 15% of cancers, this is enabled by recombination-based alternative lengthening of telomeres pathways (ALT). ALT cells display several hallmarks including heterogeneous telomere length, extrachromosomal telomeric repeats, and ALT-associated PML bodies. ALT cells also have high telomeric replication stress (RS) enhanced by fork-stalling structures (R-loops and G4s) and altered chromatin states. In ALT cells, telomeric RS promotes telomere elongation but above a certain threshold becomes detrimental to cell survival. Manipulating RS at telomeres has thus been proposed as a therapeutic strategy against ALT cancers. Through analysis of genome-wide CRISPR fitness screens, we identified ALT-specific vulnerabilities and describe here our characterization of the roles of SUB1, a ssDNA-binding protein, in telomere stability. SUB1 depletion increases RS at ALT telomeres, profoundly impairing ALT cell growth without impacting telomerase-positive cells. During RS, SUB1 is recruited to stalled forks and ALT telomeres via its ssDNA-binding domain. This recruitment is potentiated by RPA depletion, suggesting that these factors may compete for ssDNA. The viability of ALT cells and their resilience toward RS also requires ssDNA binding by SUB1. SUB1 depletion accelerates cell death induced by FANCM depletion, triggering unsustainable levels of telomeric damage in ALT cells. Finally, combining SUB1 depletion with RS-inducing drugs rapidly induces replication catastrophe in ALT cells. Altogether, our work identifies SUB1 as an ALT susceptibility with roles in the mitigation of RS at ALT telomeres and suggests advanced therapeutic strategies for a host of still poorly managed cancers.

Work-biased path-sampling calculations of chemical potentials: Principles and applications to uranium oxide

We present the work-biased path-sampling scheme to calculate chemical potentials in atomic scale simulations. This scheme is based on a series of chained insertion and deletion paths from N to N + 1 to N atom systems, the sampling being performed on the paths themselves rather than on the final configurations. Equations for parallel path generations as well as geometrically biased insertions or deletions are presented. We then present two applications of our approach for the uranium dioxide crystal. The first is a test case validation of our approach for the insertion of a Xe atom in UO2. The second explores the relationship between cluster structure stability and oxygen chemical potential in overstoichiometric UO2+x oxide as a function of temperature from 800 to 2000 K and composition, from UO2 to UO2.16, using two different empirical potentials. We find that the evolution of the oxygen chemical potential is irregular, with dips for specific numbers of added oxygen atoms. Five oxygen clusters are stable at 800 K and are associated with strong dips in the chemical potential values. At intermediate temperatures, clusters of four and five oxygen atoms compete in stability. They become unstable at the highest temperatures, and the evolution of the chemical potential is then monotonous with composition.