Steady-state Population Research Articles

Isomeric Population Transfer of the ^{229}Th Nucleus via Hyperfine Electronic Bridge.

The electronic bridge (EB) excitation of nuclei has been found as a versatile approach to efficiently excite the ^{229}Th isomers. Previous studies on EB excitation have typically disregarded the hyperfine structure as well as the decay of the excited atoms and ions by just treating the nucleus-electron coupling perturbatively. In the present work, we apply a quantum-optical approach to nonperturbatively investigate EB excitation of ^{229}Th^{3+} ions. This approach considers both the hyperfine structure and atomic decay through dressed hyperfine state and quantum master equation techniques. Numerical results show that the isomeric steady-state population of the time-independent scheme is constrained by atomic decay to a maximum of only 27.9%. By leveraging the dark state, however, the (time-dependent) stimulated Raman adiabatic passage method theoretically reaches a remarkable 99.7% isomeric population transfer and demonstrates a potential nuclear-laser scheme via the EB mechanism. Our quantum-optical approach exhibits a large flexibility and paves a promising avenue for utilizing advanced quantum-control technologies to design and optimize experimental schemes of EB excitation.

Raman-phonon-polariton condensation in a transversely pumped cavity

Phonon polaritons are hybrid states of light and matter that are typically realised when optically active phonons couple strongly to photons. We suggest a new approach to realising phonon polaritons, by employing a transverse-pumping Raman scheme, as used in experiments on cold atoms in optical cavities. This approach allows hybridisation between an optical cavity mode and any Raman-active phonon mode. Moreover, this approach enables one to tune the effective phonon–photon coupling by changing the strength of the transverse pumping light. We show that such a system may realise a phonon-polariton condensate. To do this, we find the stationary states and use Floquet theory to determine their stability. We thus identify distinct superradiant and lasing states in which the polariton modes are macroscopically populated. We map out the phase diagram of these states as a function of pump frequencies and strengths. Using parameters for transition metal dichalcogenides, we show that realisation of these phases may be practicably obtainable. The ability to manipulate phonon mode frequencies and attain steady-state populations of selected phonon modes provides a new tool for engineering correlated states of electrons.

Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency.

Growing evidence suggests that activity-dependent gene expression is crucial for neuronal plasticity and behavioral experience. Enhancer RNAs (eRNAs), a class of long noncoding RNAs, play a key role in these processes. However, eRNAs are highly dynamic and are often present at lower levels than their corresponding mRNAs, making them difficult to detect using total RNA-seq techniques. Nascent RNA sequencing, which separates nascent RNAs from the steady-state RNA population, has been shown to increase the ability to detect activity-induced eRNAs with a higher signal-to-noise ratio. However, there is a lack of bioinformatic tools or pipelines for detecting eRNAs utilizing nascent RNA-seq and other multiomics data sets. In this study, we addressed this gap by developing a novel bioinformatic framework, e-finder, for finding eRNAs and have made it available to the scientific community. Additionally, we reanalyzed our previous nascent RNA sequencing data and compared them with total RNA-seq data to identify activity-regulated RNAs in neuronal cell populations. Using H3K27 acetylome data, we characterized activity-dependent eRNAs that drive the transcriptional activity of the target genes. Our analysis identified a subset of eRNAs involved in mediating synapse organization, which showed increased activity-dependent transcription after the potassium chloride stimulation. Notably, our data suggest that nascent RNA-seq with an enriched H3K27ac signal exhibits high resolution to identify potential eRNAs in response to membrane depolarization. Our findings uncover the role of the eRNA-mediated gene activation network in neuronal systems, providing new insights into the molecular processes characterizing neurological diseases.

Quantum Spin Probe of Single Charge Dynamics.

Electronic defects in semiconductors form the basis for emerging quantum technologies, but many defect centers are difficult to access at the single-particle level. A method for probing optically inactive spin defects would reveal semiconductor physics at the atomic scale and advance the study of new quantum systems. We exploit the intrinsic correlation between the charge and spin states of defect centers to measure the charge populations and dynamics of single substitutional nitrogen spin defects in diamond. By probing their steady-state spin population, read out at the single-defect level with a nearby nitrogen vacancy center, we directly measure the defect ionization-corroborated by first-principles calculations-an effect we do not have access to with traditional coherence-based quantum sensing.

Telomerase RNA structural heterogeneity in living human cells detected by DMS-MaPseq.

Telomerase is a specialized reverse transcriptase that uses an intrinsic RNA subunit as the template for telomeric DNA synthesis. Biogenesis of human telomerase requires its RNA subunit (hTR) to fold into a multi-domain architecture that includes the template-containing pseudoknot (t/PK) and the three-way junction (CR4/5). These two hTR domains bind the telomerase reverse transcriptase (hTERT) protein and are thus essential for telomerase catalytic activity. Here, we probe the structure of hTR in living cells using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and ensemble deconvolution analysis. Unexpectedly, approximately 15% of the steady state population of hTR has a CR4/5 conformation lacking features thought to be required for hTERT binding. The proportion of hTR CR4/5 that is folded into the primary functional conformation does not require hTERT expression and the fraction of hTR that assumes a misfolded CR4/5 domain is not refolded by overexpression of its hTERT binding partner. This result suggests a functional role for an RNA folding cofactor other than hTERT during telomerase biogenesis. Mutagenesis demonstrates that stabilization of the alternative CR4/5 conformation is detrimental to telomerase assembly and activity. Moreover, the alternative CR4/5 conformation is not found in telomerase RNP complexes purified from cells via an epitope tag on hTERT, supporting the hypothesis that only the major CR4/5 conformer is active. We propose that this misfolded portion of the cellular hTR pool is either slowly refolded or degraded. Thus, kinetic traps for RNA folding that have been so well-studied in vitro may also present barriers for assembly of ribonucleoprotein complexes in vivo.

Small-area population forecasting in a segregated city using density-functional fluctuation theory

Policy decisions concerning housing, transportation, and resource allocation would all benefit from accurate small-area population forecasts. However, despite the success of regional-scale migration models, developing neighborhood-scale forecasts remains a challenge due to the complex nature of residential choice. Here, we introduce an innovative approach to this challenge by extending density-functional fluctuation theory (DFFT), a proven approach for modeling group spatial behavior in biological systems, to predict small-area population shifts over time. The DFFT method uses observed fluctuations in small-area populations to disentangle and extract effective social and spatial drivers of segregation, and then uses this information to forecast intra-regional migration. To demonstrate the efficacy of our approach in a controlled setting, we consider a simulated city constructed from a Schelling-type model. Our findings indicate that even without direct access to the underlying agent preferences, DFFT accurately predicts how broader demographic changes at the city scale percolate to small-area populations. In particular, our results demonstrate the ability of DFFT to incorporate the impacts of segregation into small-area population forecasting using interactions inferred solely from steady-state population count data.

[formula omitted]-symmetry induced bi-stability in non-Hermitian cavity magnomechanics

We study the steady-state non-Hermitian magnomechanical system driven by a transverse magnetic field directly interacting with YIG sphere yielding in magnons excitation, which later interacts with cavity microwave photons. To make the system non-Hermitian, we use a traveling field directly interacting with magnons generating gain to the system. We start by illustrating PT-configuration of the system containing two PT broken regions around exceptional point and PT protected region along the axis of exceptional point. We discover that the steady-state population of cavity photons and magnons show bistable behavior depending upon the PT configuration, which becomes more significant as the values of the magnon–photon coupling and traveling field strength increases. We illustrate that steady-state photon only shows bistable behavior when the system in lossy PT broken configuration, means strength of traveling field is less than the magnon–photon coupling. Otherwise, it will just contain a single stable state because of bistability suppression with gain in the system, which is unlike with any other investigation in this direction. Further, a larger magnon–photon coupling increases photon intensity and decreases magnon intensity, because of photon and magnon energy exchange, leading to enhanced photon bistablity and decreased magnon bistability. However, in case of increasing strength of traveling field, both photon as well as magnon bistability is appeared to be decreasing. We also study the steady-state effective potential of the system and illustrate the occurrence of bistability with nonlinear interactions between contour trajectories, which similarly depends on the PT broken configuration of the system.

Emergence of Boltzmann Subspaces in Open Quantum Systems Far from Equilibrium.

Single molecule junctions are important examples of complex out-of-equilibrium many-body quantum systems. We identify a nontrivial clustering of steady state populations into distinctive subspaces with Boltzmann-like statistics, which persist far from equilibrium. Such Boltzmann subspaces significantly reduce the information needed to describe the steady state, enabling modeling of high-dimensional systems that are otherwise beyond the reach of current computations. The emergence of Boltzmann subspaces is demonstrated analytically and numerically for fermionic transport systems of increasing complexity.

Manipulation and enhancement of the performance of Otto cycle in the presence of nonthermal reservoirs

In this work, we investigate the impact of energetic coherence in nonthermal reservoirs on the performance of the Otto cycle. We first focus on the situation where the working substance is a qubit. Due to the existence of coherence of nonthermal reservoir, various anomalous operating regimes such as the engine and refrigerator with efficiencies exceeding Carnot limits, as well as the hybrid refrigerator that can simultaneously achieve cooling and supplying work to an external agent, can occur. We demonstrate that the energetic coherence of the system’s steady state plays a significant role in determining the cycle’s functions by adding an additional stroke implementing dephasing and phase modulation operations in the cycle. The energetic coherence of the system is necessary to trigger the reservoir’s coherence to exert influences on the cycle. We decompose the thermodynamic quantities to the components arising from the populations and coherence of the system, and find that the reservoir’s coherence impacts the cycle from two aspects: one is the modification of the system’s steady-state populations or temperatures, and the other is the direct contributions to the heat in the interaction between the system and reservoirs. We then explore the scenario where the working substance is two identical qubits, and the reservoirs are common to them. We show that the degenerate coherence of the system in the steady state can enhance the performances of the cycle as different machines. Additionally, the energetic coherence of the reservoir modifies the functions of the cycle still through the energetic coherence of the system rather than their degenerate coherence.

Modelling the Dynamics of Outbreak Species: The Case of Ditrupa arietina (O.F. Müller), Gulf of Lions, NW Mediterranean Sea

An outbreak species exhibits extreme, rapid population fluctuations that can be qualified as discrete events within a continuous dynamic. When outbreaks occur they may appear novel and disconcerting because the limiting factors of their dynamics are not readily identifiable. We present the first population hybrid dynamic model that combines continuous and discrete processes, designed to simulate marine species outbreaks. The deterministic framework was tested using the case of an unexploited benthic invertebrate species: the small, serpulid polychaete Ditrupa arietina. This species is distributed throughout the northeast Atlantic Ocean and Mediterranean Sea; it has a life cycle characterised by a pelagic dispersive larval stage, while juveniles and adults are sedentary. Sporadic reports of extremely high, variable densities (from <10 to >10,000 ind.m−2) have attracted attention from marine ecologists for a century. However, except for one decade-long field study from the Bay of Banyuls (France, Gulf of Lions, Mediterranean Sea), observations are sparse. Minimal formulations quantified the processes governing the population dynamics. Local population continuous dynamics were simulated from a size-structured model with a null immigration–emigration flux balance. The mathematical properties, based on the derived hybrid model, demonstrated the possibilities of reaching an equilibrium for the population using a single number of recruits per reproducer. Two extrapolations were made: (1) local population dynamics were simulated over 180 years using North Atlantic Oscillation indices to force recruitment variability and (2) steady-state population densities over the Gulf of Lions were calculated from a connectivity matrix in a metapopulation. The dynamics reach a macroscopic stability in both extrapolations, despite the absence of density regulating mechanisms. This ensures the persistence of D. arietina, even when strong, irregular oscillations characteristic of an outbreak species are observed. The hybrid model suggests that a macroscopic equilibrium for a population with variable recruitment conditions can only be characterised for time periods which contain several outbreak occurrences distributed over a regional scale.

Exploring cooperative evolution with tunable payoff’s loners using reinforcement learning

Imitation and replication have emerged as a paradigm in numerous studies that explore the evolution of cooperative behavior. Since they embrace the essence of natural selection, it is widely recognized in exploring the evolution of biological behaviors. However, it is not easy to express the way individuals select and optimize in these simple and elegant ways in the complex and variable interactive environments. Currently, reinforcement learning is widely used in the study of strategy updating dynamics and agent learning processes in game theory. Therefore, we introduce the Q-learning algorithms into the voluntary public goods game to explore the impact of cooperative evolution. Simulation results demonstrate that when the synergy factor is large and the adjust loner payoff’s multiply factor is smaller, the number of cooperators becomes gradually consistent. As the synergy factor increases, the evolution of the proportion of defectors become nonlinear. Furthermore, we further explore the Q-table and strategy updating processes of agents in the steady state under a smaller multiply factor that adjusts the loner’s payoff. The results find inconsistency between the average Q-values and the steady state population strategy distribution. Subsequently, we explain the reason for the inconsistency by analyzing strategy sequence, namely that there are a number of agents who constantly change strategies in the population, and the Q-values of these agents have an impact on the overall Q-values. In addition, evolutionary snapshots of agent strategy sequences are observed. The results find that the agent’s strategic selection shows greater instability when the proportions of cooperators, defectors, and loners in the population are relatively balanced. Finally, the effect of parameters in the Q-learning algorithm on cooperative behavior is analyzed. This study hopes to provide valuable insights into understanding the dynamics of cooperation in complex social interactions.

The 5P3/2→6PJ(J=1/2,3/2) Electric Dipole Forbidden Transitions in Rubidium

This paper presents a general review of the results of the experimental and theoretical work carried out by our research group to study the 5P3/2→6PJ electric quadrupole transition in atomic rubidium. The experiments were carried out with room-temperature atoms in an absorption cell. A steady-state population of atoms in the 5P3/2 excited state is produced by a a narrow-bandwidth preparation laser locked to the D2 transition. A second CW laser is used to produce the forbidden transition with resolution of the 6PJ hyperfine states of both rubidium isotopes. The process is detected by recording the 420(422) nm fluorescence that occurs when the atoms in the 6PJ state decay directly into the 5S ground state. The fluorescence spectra show a strong dependence on the relative polarization directions of the preparation laser and the beam producing the forbidden transition. This dependence is directly related to a strong anisotropy in the populations of the 5P3/2 intermediate magnetic substates, and also to the electric quadrupole selection rules over magnetic quantum numbers. A calculation based on the rate equations that includes velocity and detuning dependent transition rates is adequate to reproduce these results. The forbidden transition is also shown to be an ideal probe to measure the Autler–Townes splitting generated in the preparation of the 5P3/2 state. Examples of spectra obtained with cold atoms in a magneto-optical trap (MOT) are also presented. These spectra show the expected Autler–Townes doublet structure with asymmetric line profiles that result as a consequence of the red-detuning of the trapping laser in the MOT.

Floquet-tailored Rydberg interactions

The Rydberg blockade is a key ingredient for entangling atoms in arrays. However, it requires atoms to be spaced well within the blockade radius, which limits the range of local quantum gates. Here we break this constraint using Floquet frequency modulation, with which we demonstrate Rydberg-blockade entanglement beyond the traditional blockade radius and show how the enlarged entanglement range improves qubit connectivity in a neutral atom array. Further, we find that the coherence of entangled states can be extended under Floquet frequency modulation. Finally, we realize Rydberg anti-blockade states for two sodium Rydberg atoms within the blockade radius. Such Rydberg anti-blockade states for atoms at close range enables the robust preparation of strongly-interacting, long-lived Rydberg states, yet their steady-state population cannot be achieved with only the conventional static drive. Our work transforms between the paradigmatic regimes of Rydberg blockade versus anti-blockade and paves the way for realizing more connected, coherent, and tunable neutral atom quantum processors with a single approach.

A model for the infrared-radio correlation of main sequence galaxies at gigahertz frequencies and its variation with redshift and stellar mass

Context. The infrared-radio correlation (IRRC) of star-forming galaxies can be used to estimate their star formation rate (SFR) based on the radio continuum luminosity at MHz–GHz frequencies. For its practical application in future deep radio surveys, it is crucial to know whether the IRRC persists at high redshift z. Aims. Previous works have reported that the 1.4 GHz IRRC correlation of star-forming galaxies is nearly z-invariant up to z ≈ 4, but depends strongly on the stellar mass M⋆. This should be taken into account for SFR calibrations based on radio luminosity. Methods. To understand the physical cause behind the M⋆ dependence of the IRRC and its properties at higher z, we constructed a phenomenological model for galactic radio emission. Our model is based on a dynamo-generated magnetic field and a steady-state cosmic ray population. It includes a number of free parameters that determine the galaxy properties. To reduce the overall number of model parameters, we also employed observed scaling relations. Results. We find that the resulting spread of the infrared-to-radio luminosity ratio, q(z, M⋆), with respect to M⋆ is mostly determined by the scaling of the galactic radius with M⋆, while the absolute value of the q(z, M⋆) curves decreases with more efficient conversion of supernova energy to magnetic fields and cosmic rays. Additionally, decreasing the slope of the cosmic ray injection spectrum, αCR, results in higher radio luminosity, decreasing the absolute values of the q(z, M⋆) curves. Within the uncertainty range of our model, the observed dependence of the IRRC on M⋆ and z can be reproduced when the efficiency of supernova-driven turbulence is 5%, 10% of the kinetic energy is converted into magnetic energy, and αCR ≈ 3.0. Conclusions. For galaxies with intermediate to high (M⋆ ≈ 109.5 − 1011 M⊙) stellar masses, our model results in an IRRC that is nearly independent of z. For galaxies with lower masses (M⋆ ≈ 108.5 M⊙), we find that the IR-to-radio flux ratio increases with increasing redshift. This matches the observational data in that mass bin which, however, only extends to z ≈ 1.5. The increase in the IR-to-radio flux ratio for low-mass galaxies at z ≳ 1.5 that is predicted by our model could be tested with future deep radio observations.

Stochastic model for cell population dynamics quantifies homeostasis in colonic crypts and its disruption in early tumorigenesis.

The questions of how healthy colonic crypts maintain their size, and how homeostasis is disrupted by driver mutations, are central to understanding colorectal tumorigenesis. We propose a three-type stochastic branching process, which accounts for stem, transit-amplifying (TA) and fully differentiated (FD) cells, to model the dynamics of cell populations residing in colonic crypts. Our model is simple in its formulation, allowing us to estimate all but one of the model parameters from the literature. Fitting the single remaining parameter, we find that model results agree well with data from healthy human colonic crypts, capturing the considerable variance in population sizes observed experimentally. Importantly, our model predicts a steady-state population in healthy colonic crypts for relevant parameter values. We show that APC and KRAS mutations, the most significant early alterations leading to colorectal cancer, result in increased steady-state populations in mutated crypts, in agreement with experimental results. Finally, our model predicts a simple condition for unbounded growth of cells in a crypt, corresponding to colorectal malignancy. This is predicted to occur when the division rate of TA cells exceeds their differentiation rate, with implications for therapeutic cancer prevention strategies.

Overcoming leakage in quantum error correction

The leakage of quantum information out of the two computational states of a qubit into other energy states represents a major challenge for quantum error correction. During the operation of an error-corrected algorithm, leakage builds over time and spreads through multi-qubit interactions. This leads to correlated errors that degrade the exponential suppression of the logical error with scale, thus challenging the feasibility of quantum error correction as a path towards fault-tolerant quantum computation. Here, we demonstrate a distance-3 surface code and distance-21 bit-flip code on a quantum processor for which leakage is removed from all qubits in each cycle. This shortens the lifetime of leakage and curtails its ability to spread and induce correlated errors. We report a tenfold reduction in the steady-state leakage population of the data qubits encoding the logical state and an average leakage population of less than 1 × 10−3 throughout the entire device. Our leakage removal process efficiently returns the system back to the computational basis. Adding it to a code circuit would prevent leakage from inducing correlated error across cycles. With this demonstration that leakage can be contained, we have resolved a key challenge for practical quantum error correction at scale.

Single-cell mass distributions reveal simple rules for achieving steady-state growth.

Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates from optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells. Here, we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for individual cell mass accumulation and cell number increase via cell division to balance out. Steady-state growth is important for reliable cell mass distributions and experimental reproducibility. We discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.

Strong coupling dynamics of driven quantum systems with permanent dipoles

Many optically active systems possess spatially asymmetric electron orbitals. These generate permanent dipole moments, which can be stronger than the corresponding transition dipole moments, significantly affecting the system dynamics and creating polarized Fock states of light. We derive a master equation for these systems with an externally applied driving field by employing an optical polaron transformation that captures the photon mode polarization induced by the permanent dipoles. This provides an intuitive framework to explore their influence on the system dynamics and emission spectrum. We find that permanent dipoles introduce multiple-photon processes and a photon sideband, which causes substantial modifications to single-photon transition dipole processes. In the presence of an external drive, permanent dipoles lead to an additional process that we show can be exploited to control the decoherence and transition rates. We derive the emission spectrum of the system, highlighting experimentally detectable signatures of optical polarons, and measurements that can identify the parameters in the system Hamiltonian, the magnitude of the differences in the permanent dipoles, and the steady-state populations of the system.

Intense γ -Photon and High-Energy Electron Production by Neutron Irradiation: Effects of Nuclear Excitations on Reactor Materials

The effects of neutron irradiation on materials are often interpreted in terms of atomic recoils, initiated by neutron impacts and producing crystal lattice defects. In addition, there is a remarkable two-step process, strongly pronounced in the medium-weight and heavy elements. This process involves the generation of energetic {\gamma} photons in nonelastic collisions of neutrons with atomic nuclei, achieved via capture and inelastic reactions. Subsequently, high-energy electrons are excited through the scattering of {\gamma} photons by the atomic electrons. We derive and validate equations enabling a fast and robust evaluation of photon and electron fluxes produced by the neutrons in the bulk of materials. The two-step n-{\gamma}-e scattering creates a nonequilibrium dynamically fluctuating steady-state population of high-energy electrons, with the spectra of photon and electron energies extending well into the mega-electron-volt range. This stimulates vacancy diffusion through electron-triggered atomic recoils, primarily involving vacancy-impurity dissociation, even if thermal activation is ineffective. Tungsten converts the energy of fusion or fission neutrons into a flux of {\gamma} radiation at the conversion efficiency approaching 99%, with implications for structural materials, superconductors, and insulators, as well as phenomena like corrosion, and helium and hydrogen isotope retention.

Steady state population balance modelling of precipitation processes: Nucleation, growth and size-dependent agglomeration

In this work a numerical methodology to solve the steady state Population Balance Equation (PBE) is developed. Three crystallisation mechanisms are included, namely: nucleation, size-independent growth and size-dependent loose agglomeration. The numerical method is based on the discretisation of the crystal size as distributed variable. In order to describe the loose agglomeration, the numerical methodology solves two PBE: one including the nucleation and growth mechanisms and one accounting for the agglomeration process. From the first PBE, liquid phase composition, supersaturation, developed crystal surface and Crystallite Size Distribution (CSD) are obtained. Similarly, the second PBE leads to the Agglomerate Size Distribution (ASD). The study of the size-dependant agglomeration kernel induces an additional numerical difficulty due to the dependency of both PBE and agglomeration kernel on the particle size. An accelerated fixed point algorithm based on the crossed secant method is adapted to overcome the difficulty and accurately solve the agglomeration PBE. The oxalic precipitation of uranium is simulated using this numerical methodology. First, the experimental results of a reference case are compared with the numerical predictions in terms of particle size distribution, mean size, mass fraction and moments. Then, the operating conditions are varied in order to test the algorithm robustness and performances. In all cases, the crossed secant method ensures the size-dependent agglomeration PBE solution and properly predicts the ASD. The developed numerical methodology predicts the mean particle size under the experimental uncertainty in a reasonable computation time and number of iterations.