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At least 127 records · Page 7

Stochastic journeys of cell progenies through compartments and the role of self-renewal, symmetric and asymmetric division

Abstract Division and differentiation events by which cell populations with specific functions are generated often take place as part of a developmental programme, which can be represented by a sequence of compartments. A compartment is the set of cells with common characteristics; sharing, for instance, a spatial location or a phenotype. Differentiation events are transitions from one compartment to the next. Cells may also die or divide. We consider three different types of division events: (i) where both daughter cells inherit the mother’s phenotype (self-renewal), (ii) where only one of the daughters changes phenotype (asymmetric division), and (iii) where both daughters change phenotype (symmetric division). The self-renewal probability in each compartment determines whether the progeny of a single cell, moving through the sequence of compartments, is finite or grows without bound. We analyse the progeny stochastic dynamics with probability generating functions. In the case of self-renewal, by following one of the daughters after any division event, we may construct lifelines containing only one cell at any time. We analyse the number of divisions along such lines, and the compartment where lines terminate with a death event. Analysis and numerical simulations are applied to a five-compartment model of the gradual differentiation of hematopoietic stem cells and to a model of thymocyte development: from pre-double positive to single positive (SP) cells with a bifurcation to either SP4 or SP8 in the last compartment of the sequence.

Science & Technology - Other Topics↗

Universal time-dependent Ginzburg-Landau theory

We study the hydrodynamics of superconductors within the framework of Schwinger-Keldysh effective field theory (EFT). We show that in the vicinity of the superconducting phase transition the most general leading-order EFT satisfying the local Kubo-Martin-Schwinger condition is described by a version of the time-dependent Ginzburg-Landau (TDGL) equations augmented with stochastic terms. This version of TDGL is applicable in the gapless regime independent of any microscopic details. Within this approach, it is possible to include systematically the effects of nonuniform temperature and heat conductivity, as well as explicit or spontaneous breaking of time reversal. Here, we also introduce a thermal version of the Josephson relation and use it to construct an exotic hydrodynamics describing a phase of matter where heat can flow without dissipation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Generative AI models for learning flow maps of stochastic dynamical systems in bounded domains

Simulating stochastic differential equations (SDEs) in bounded domains, presents significant computational challenges due to particle exit phenomena, which requires accurate modeling of interior stochastic dynamics and boundary interactions. Despite the success of machine learning-based methods in learning SDEs, existing learning methods are not applicable to SDEs in bounded domains because they cannot accurately capture the particle exit dynamics. We present a unified hybrid data-driven approach that combines a conditional diffusion model with an exit prediction neural network to capture both interior stochastic dynamics and boundary exit phenomena. Our ML model consists of two major components: a neural network that learns exit probabilities using binary cross-entropy loss with rigorous convergence guarantees, and a training-free diffusion model that generates state transitions for non-exiting particles using closed-form score functions. The two components are integrated through a probabilistic sampling algorithm that determines particle exit at each time step and generates appropriate state transitions. Here, the performance of the proposed approach is demonstrated via three test cases: a one-dimensional simplified problem for theoretical verification, a two-dimensional advection-diffusion problem in a bounded domain, and a three-dimensional problem of interest to magnetically confined fusion plasmas.

Bounded domains↗

Dynamic scaling of order parameter fluctuations in model B

Brookhaven National Laboratory has performed a dedicated set of experiments, called the Beam Energy Scan (BES), with the goal of location a possible critical point in the phase diagram of nuclear matter, This point is analogous to the endpoint of the liquid-gas phase transition in water, where the liquid phase corresponds to a phase of hadrons, and the gas phase to a plasma of quarks and gluons. In order to describe the data generated by these experiments we have studied numerical simulations of the stochastic diffusion equation with a conserved charge. Here, we focus on the dynamics in the vicinity of a critical point in the Ising universality class. The model we consider is expected to describe the critical dynamics near a possible QCD critical point if the coupling of the order parameter to the momentum density of the fluid can be neglected. The simulations are performed on a spatial lattice, and the time evolution is performed using a Metropolis algorithm. We determine the dynamical critical exponent z ≃ 3.972(2), which agrees with predictions of the epsilon expansion. We also study non-equilibrium sweeps of the reduced temperature and observe approximate Kibble-Zurek scaling.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Unprecedented generation of 3D heterostructures by mechanochemical disassembly and re-ordering of incommensurate metal chalcogenides

Three-dimensional heterostructures are usually created either by assembling two-dimensional building blocks into hierarchical architectures or using stepwise chemical processes that sequentially deposit individual monolayers. Both approaches suffer from a number of issues, including lack of suitable precursors, limited reproducibility, and poor scalability of the preparation protocols. Therefore, development of alternative methods that enable preparation of heterostructured materials is desired. We create heterostructures with incommensurate arrangements of well-defined building blocks using a synthetic approach that comprises mechanical disassembly and simultaneous reordering of layered transition-metal dichalcogenides, MX 2 , and non-layered monochalcogenides, REX, where M = Ta, Nb, RE = Sm, La, and X = S, Se. We show that the discovered solid-state processes are rooted in stochastic mechanochemical transformations directed by electronic interaction between chemically and structurally dissimilar solids toward atomic-scale ordering, and offer an alternative to conventional heterostructuring. Details of composition–structure–properties relationships in the studied materials are also highlighted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum membrane phases in synthetic lattices of cold molecules or Rydberg atoms

Here, we calculate properties of dipolar interacting ultracold molecules or Rydberg atoms in a semisynthetic three-dimensional configuration—one synthetic dimension plus a two-dimensional real-space optical lattice or periodic microtrap array—using the stochastic Green's function quantum Monte Carlo method. Through a calculation of thermodynamic quantities and appropriate correlation functions, along with their finite-size scalings, we show that there is a second-order transition to a low-temperature phase in which two-dimensional “sheets” form in the synthetic dimension of internal rotational or electronic states of the molecules or Rydberg atoms, respectively. Simulations for different values of the interaction V, which acts between atoms or molecules that are adjacent both in real and synthetic space, allow us to compute a phase diagram. We find a finite-temperature transition at sufficiently large V as well as a quantum phase transition—a critical value V c below which the transition temperature vanishes.

74 ATOMIC AND MOLECULAR PHYSICS↗

Magnetism and magnetotransport in the kagome antiferromagnet Mn 3 Ge

We perform classical Monte Carlo and stochastic Landau-Lifshitz-Gilbert simulations to study the temperature-dependent magnetism of the kagome antiferromagnet Weyl metal Mn3Ge, and we find that a long-range chiral order sets in at a transition temperature well below the Neel temperature (T N ). Based on the crystalline symmetries imposed by the chiral magnetic order, we argue for the presence of multiple isoenergetic Weyl nodes (nodes that are at the same energy and with a congruent Fermi surface around them) near the chemical potential. Using the semiclassical Boltzmann equations, we show that the combined contribution to the net longitudinal magnetoconductance (LMC) and the planar Hall conductance (PHC) from tilted Weyl nodes can lead to signatures that are qualitatively distinct from that of a single pair of Weyl nodes. In particular, we show that magnetic orders with different chiralities can give rise to different periods in LMC and PHC as a function of the in-plane magnetic field direction. As a result, this is ultimately related to differences in the symmetry-imposed constraints on the Weyl nodes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

From Coherence to Function: Exploring the Connection in Chemical Systems

The role of quantum mechanical coherences or coherent superposition states in excited state processes has received considerable attention in the last two decades largely due to advancements in ultrafast laser spectroscopy. These coherence effects hold promise for enhancing the efficiency and robustness of functionally relevant processes, even when confronted with energy disorder and environmental fluctuations. Understanding coherence deeply drives us to unravel mechanisms and dynamics controlled by order and synchronization at a quantum mechanical level, envisioning optical control of coherence to enhance functions or create new ones in molecular and material systems. In this frontier, the interplay between electronic and vibrational dynamics, specifically the influence of vibrations in directing electronic dynamics, has emerged as the leading principle. Here, two energetically disparate quantum degrees of freedom work in-sync to dictate the trajectory of an excited state reaction. Moreover, with the vibrational degree being directly related to the structural composition of molecular or material systems, new molecular designs could be inspired by tailoring certain structural elements. In the realm of chemical kinetics, our understanding of the dynamics of chemical transformations is underpinned by fundamental theories, such as transition state theory, activated rate theory, and Marcus theory. These theories elucidate reaction rates by considering the energy barriers that must be overcome for reactants to transform into products. Those barriers are surmounted by the stochastic nature of energy gap fluctuations within reacting systems, emphasizing that the reaction coordinate, the pathway from reactants to products, is not rigidly defined by a specific vibrational motion but encompasses a diverse array of molecular motions. While less is known about the involvement of specific intramolecular vibrational modes, their significance in certain cases cannot be overlooked. In this Account, we summarize key experimental findings that offer deeper insights into the complex electronic–vibrational trajectories encompassing excited states afforded from state-of-the-art ultrafast laser spectroscopy in three exemplary processes: photoinduced electron transfer, singlet–triplet intersystem crossing, and intramolecular vibrational energy flow in molecular systems. We delve into the rapid decoherence, or loss of phase and amplitude correlations, of vibrational coherences along promoter vibrations during subpicosecond intersystem crossing dynamics in a series of binuclear platinum complexes. This rapid decoherence illustrates the vibration-driven reactive pathways from the Franck–Condon state to the curve crossing region. We also explore the generation of new vibrational coherences induced by impulsive reaction dynamics rather than by the laser pulse in these systems, which sheds light on specific energy dissipation pathways and thereby on the progression of the reaction trajectory in the vicinity of the curve crossing on the product side. Another property of vibrational coherences, amplitude, reveals how energy can flow from one vibration to another in the electronic excited state of a terpyridine–molybdenum complex hosting a nonreactive dinitrogen substrate. In conclusion, a slight change in vibrational energy triggers a quasi-resonant interaction, leading to constructive wavepacket interference and ultimately intramolecular vibrational redistribution from a Franck–Condon active terpyridine vibration to a dinitrogen stretching vibration, energizing the dinitrogen bond.

Electrical energy↗

A tail of eternal inflation

Non-trivial inflaton self-interactions can yield calculable signatures of primordial non-Gaussianity that are measurable in cosmic surveys. We calculate the non-Gaussian corrections to Stochastic Inflation within the framework of Soft de Sitter Effective Theory, from which we derive the associated probability distribution for the scalar fluctuations. As a consequence of this new result, we show that the phase transition to slow-roll eternal inflation is often incalculable in these models. Instead, this transition is sensitive to the non-Gaussian tail of the distribution of scalar fluctuations, which probes physics inside the horizon, potentially beyond the cutoff scale of the Effective Field Theory of Inflation. We delineate the parameter space consistent with current observations and weak coupling at horizon crossing in which the large fluctuations relevant for eternal inflation can only be determined by appealing to a UV completion. We also argue that this breakdown of the perturbative description is required for the de Sitter entropy to reflect the number of de Sitter microstates.

79 ASTRONOMY AND ASTROPHYSICS↗

Hierarchical Multi-agent Large Language Model Reasoning for Autonomous Heterogeneous Catalyst Discovery

Artificial intelligence is reshaping scientific exploration, but most methods automate procedural tasks without engaging in scientific reasoning, limiting autonomy in discovery. We demonstrate that hierarchical agentic large language model reasoning can efficiently drive simulation and scientific exploration. Across two chemical applications, CO adsorption on Cu surface transition metal adatoms and on M–N–C catalysts, reasoning-guided exploration reduces required atomistic simulations by up to 90% relative to heuristic or random selection. Comparisons across single-agent, multi-agent, and stochastic baselines show that hierarchical strategies yield more coherent and information-efficient search trajectories. Reasoning traces reveal chemically grounded decisions that cannot be explained by semantic bias or stochastic sampling. We realize these agentic reasoning strategies in Materials Agents for Simulation and Theory in Electronic-structure Reasoning (MASTER), a multimodal system that translates natural language into density functional theory workflows. Altogether, multi-agent collaboration accelerates heterogeneous catalyst discovery and marks a step toward more autonomous, reasoning-guided scientific exploration.

30 DIRECT ENERGY CONVERSION↗

A Logarithmic Bayesian Approach to Quantum Error Detection

We consider the problem of continuous quantum error correction from a Bayesian perspective, proposing a pair of digital filters using logarithmic probabilities that are able to achieve near-optimal performance on a three-qubit bit-flip code, while still being reasonable to implement on low-latency hardware. These practical filters are approximations of an optimal filter that we derive explicitly for finite time steps, in contrast with previous work that has relied on stochastic differential equations such as the Wonham filter. By utilizing logarithmic probabilities, we are able to eliminate the need for explicit normalization and can reduce the Gaussian noise distribution to a simple quadratic expression. The state transitions induced by the bit-flip errors are modeled using a Markov chain, which for log-probabilities must be evaluated using a LogSumExp function. We develop the two versions of our filter by constraining this LogSumExp to have either one or two inputs, which favors either simplicity or accuracy, respectively. Using simulated data, we demonstrate that the single-term and two-term filters are able to significantly outperform both a double threshold scheme and a linearized version of the Wonham filter in tests of error detection under a wide variety of error rates and time steps.

97 MATHEMATICS AND COMPUTING↗

A Novel Deep Reinforcement Learning Approach to Traffic Signal Control with Connected Vehicles

The advent of connected vehicle (CV) technology offers new possibilities for a revolution in future transportation systems. With the availability of real-time traffic data from CVs, it is possible to more effectively optimize traffic signals to reduce congestion, increase fuel efficiency, and enhance road safety. The success of CV-based signal control depends on an accurate and computationally efficient model that accounts for the stochastic and nonlinear nature of the traffic flow. Without the necessity of prior knowledge of the traffic system’s model architecture, reinforcement learning (RL) is a promising tool to acquire the control policy through observing the transition of the traffic states. In this paper, we propose a novel data-driven traffic signal control method that leverages the latest in deep learning and reinforcement learning techniques. By incorporating a compressed representation of the traffic states, the proposed method overcomes the limitations of the existing methods in defining the action space to include more practical and flexible signal phases. The simulation results demonstrate the convergence and robust performance of the proposed method against several existing benchmark methods in terms of average vehicle speeds, queue length, wait time, and traffic density.

42 ENGINEERING↗

Improved filters for angular filter refractometry

Angular filter refractometry is an optical diagnostic that measures the absolute contours of a line-integrated density gradient by placing a filter with alternating opaque and transparent zones in the focal plane of a probe beam, which produce corresponding alternating light and dark regions in the image plane. Identifying transitions between these regions with specific zones on the angular filter (AF) allows the line-integrated density to be determined, but the sign of the density gradient at each transition is degenerate and must be broken using other information about the object plasma. Additional features from diffraction in the filter plane often complicate data analysis. Here, in this paper, we present an improved AF design that uses a stochastic pixel pattern with a sinusoidal radial profile to minimize unwanted diffraction effects in the image caused by the sharp edges of the filter bands. We also present a technique in which a pair of AFs with different patterns on two branches of the same probe beam can be used to break the density gradient degeneracy. Both techniques are demonstrated using a synthetic diagnostic and data collected on the OMEGA EP (extended performance) laser.

47 OTHER INSTRUMENTATION↗

Critical fluid dynamics in two and three dimensions

We describe a numerical method for simulating stochastic fluid dynamics near a critical point in the Ising universality class. This theory is known as model H, and is expected to govern the nonequilibrium dynamics of quantum chromodynamics (QCD) near a possible critical endpoint of the phase transition between a hadron liquid and the quark-gluon plasma. The numerical algorithm is based on a Metropolis scheme, and automatically ensures that the distribution function of the hydrodynamic variables in equilibrium is independent of the transport coefficients and only governed by the microscopic free energy. We verify dynamic scaling near the critical point of a two and three-dimensional fluid and extract the associated critical exponent z. Here, we find z≃3 in three dimensions, and z≃2 for a two-dimensional fluid. In a finite system, we observe a crossover between the mean field value z=4 and the true critical exponent z≃3 (z≃2 in d=2). This crossover is governed by the values of the correlation length and the renormalized shear viscosity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Exploring the early Universe with Gaia and Theia

It has recently been pointed out that Gaia is capable of detecting a stochastic gravitational wave background in the sensitivity band between the frequency of pulsar timing arrays and LISA. Here, we argue that Gaia and Theia have great potential for early universe cosmology, since such a frequency range is ideal for probing phase transitions in asymmetric dark matter, SIMP and the cosmological QCD transition. Furthermore, there is the potential for detecting primordial black holes in the solar mass range produced during such an early universe transition and distinguish them from those expected from the QCD epoch. Finally, we discuss the potential for Gaia and Theia to probe topological defects and the ability of Gaia to potentially shed light on the recent NANOGrav results.

79 ASTRONOMY AND ASTROPHYSICS↗

IHE Material and IHE Subassembly Qualification Test Description and Criteria (v. 14.7)

The purpose of the deflagration-to-detonation test is to demonstrate that an IHE material will not undergo deflagration-to-detonation transition (DDT) under stockpile relevant conditions of scale, confinement, and material condition. Inherent in this test design is the assumption that ignition does occur, with onset of deflagration. The test design will incorporate large margins and replicates to account for the stochastic nature of DDT events.

36 MATERIALS SCIENCE↗

Astrophysical Insights into Radial Velocity Jitter from an Analysis of 600 Planet-search Stars

Radial velocity (RV) detection of planets is hampered by astrophysical processes on the surfaces of stars that induce a stochastic signal, or “jitter,” which can drown out or even mimic planetary signals. Here, we empirically and carefully measure the RV jitter of more than 600 stars from the California Planet Search sample on a star by star basis. As part of this process, we explore the activity–RV correlation of stellar cycles and include appendices listing every ostensibly companion-induced signal we removed and every activity cycle we noted. We then use precise stellar properties from Brewer et al. to separate the sample into bins of stellar mass and examine trends with activity and with evolutionary state. We find that RV jitter tracks stellar evolution and that in general, stars evolve through different stages of RV jitter: the jitter in younger stars is driven by magnetic activity, while the jitter in older stars is convectively driven and dominated by granulation and oscillations. We identify the “jitter minimum”—where activity-driven and convectively driven jitter have similar amplitudes—for stars between 0.7 and 1.7 M {sub ⊙} and find that more-massive stars reach this jitter minimum later in their lifetime, in the subgiant or even giant phases. Finally, we comment on how these results can inform future RV efforts, from prioritization of follow-up targets from transit surveys like TESS to target selection of future RV surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Monitored Fluctuating Hydrodynamics

We introduce a hydrodynamic framework for describing monitored classical stochastic processes. We study the conditional ensembles for these monitored processes—i.e., we compute spacetime correlation functions conditioned on a fixed, typical measurement record. In the presence of global symmetries we show that these conditional ensembles can undergo measurement-induced “sharpening” phase transitions as a function of the monitoring rate; moreover, even weak monitoring can give rise to novel critical phases, derived entirely from a classical perspective. We give a simple hydrodynamic derivation of the known “charge-fuzzy phase” for weakly monitored diffusive many-body quantum systems. We show that although the unmonitored symmetric and asymmetric exclusion processes are in different universality classes of transport, the fluctuations in their conditional ensembles flow to the same fixed point with emergent relativistic invariance under monitoring. On the other hand, weakly monitored systems with non-Abelian symmetries enter a novel strongly coupled fixed point with nontrivial dynamical exponent, which we characterize. Our formalism naturally accounts for monitoring general observables, such as currents or density gradients, and allows for a direct calculation of information-theoretic diagnostics of sharpening transitions, including the Shannon entropy of the measurement record.

classical statistical mechanics↗