Daily Papers

Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from being proven. One challenge in engineering and understanding biochemical computation is the intrinsic noise due to chemical fluctuations. In this paper, we draw insights from machine learning theory, chemical reaction network theory, and statistical physics to show that the broad and biologically relevant class of detailed balanced chemical reaction networks is capable of representing and conditioning complex distributions. These results illustrate how a biochemical computer can use intrinsic chemical noise to perform complex computations. Furthermore, we use our explicit physical model to derive thermodynamic costs of inference.

We show how to extract from a sufficiently long time series of stationary fluctuations of chemical reactions an estimate of the entropy production. This method, which is based on recent work on fluctuation theorems, is direct, non-invasive, does not require any knowledge about the underlying dynamics, and is applicable even when only partial information is available. We apply it to simple stochastic models of chemical reactions involving a finite number of states, and for this case, we study how the estimate of dissipation is affected by the degree of coarse-graining present in the input data.

We study an autonomous model of a Maxwell demon that works by rectifying thermal fluctuations of chemical reactions. It constitutes the chemical analog of a recently studied electronic demon. We characterize its scaling behavior in the macroscopic limit, its performances, and the impact of potential internal delays. We obtain analytical expressions for all quantities of interest, namely, the generated reverse chemical current, the output power, the transduction efficiency, and the correlations between the numbers of molecules. Due to a bound on the nonequilibrium response of its chemical reaction network, we find that, contrary to the electronic case, there is no way for the Maxwell demon to generate a finite output in the macroscopic limit. Finally, we analyze the information thermodynamics of the Maxwell demon from a bipartite perspective. In the limit of a fast demon, the information flow is obtained, its pattern in the state space is discussed, and the behavior of the partial efficiencies related to the measurement and the feedback processes is examined.

This chapter provides a pedagogical introduction and overview of spatial and temporal correlation and fluctuation effects resulting from the fundamentally stochastic kinetics underlying chemical reactions and the dynamics of populations or epidemics. After reviewing the assumptions and mean-field type approximations involved in the construction of chemical rate equations for uniform reactant densities, we first discuss spatial clustering in birth-death systems, where non-linearities are introduced through either density-limiting pair reactions, or equivalently via local imposition of finite carrying capacities. The competition of offspring production, death, and non-linear inhibition induces a population extinction threshold, which represents a non-equilibrium phase transition that separates active from absorbing states. This continuous transition is characterized by the universal scaling exponents of critical directed percolation clusters. Next we focus on the emergence of depletion zones in single-species annihilation processes and spatial population segregation with the associated reaction fronts in two-species pair annihilation. These strong (anti-)correlation effects are dynamically generated by the underlying stochastic kinetics. Finally, we address noise-induced and fluctuation-stabilized spatio-temporal patterns in basic predator-prey systems, exemplified by spreading activity fronts in the two-species Lotka-Volterra model as well as spiral structures in the May-Leonard variant of cyclically competing three-species systems akin to rock-paper-scissors games.

We discuss the effect of a strong magnetic field on the chemical freezeout points in the ultrarelativistic heavy-ion collision. As a result of the inverse magnetic catalysis or the magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freezeout. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced especially at high baryon density. The charge conservation partially cancels the enhancement but our calculation shows that the electric charge fluctuation and the charge chemical potential could serve as a magnetometer. We find that the fluctuation exhibits a crossover behavior rapidly increased for eB >~ (0.4GeV)^2, while the charge chemical potential has better sensitivity to the magnetic field.

We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in better exploring the energy landscape of a small protein under chemical interference such as chemical denaturation. An excessive amount of water molecules in all-atomistic molecular dynamics simulations often negatively impacts the sampling efficiency of some advanced sampling techniques such as the replica exchange method and it makes the investigation of chemical interferences on protein dynamics difficult. Thus, there is a need to develop an effective strategy that focuses on sampling structural changes in protein conformations rather than solvent molecule fluctuations. In this work, we address this issue by devising a multiscale simulation scheme (MultiSCAAL) that bridges the gap between all-atomistic molecular dynamics simulation and coarse-grained molecular simulation. The two key features of this scheme are the Boltzmann inversion and a protein atomistic reconstruction method we previously developed (SCAAL). Using MultiSCAAL, we were able to enhance the sampling efficiency of proteins solvated by explicit water molecules. Our method has been tested on the folding energy landscape of a small protein Trp-cage with explicit solvent under 8M urea using both the all-atomistic replica exchange molecular dynamics (AA-REMD) and MultiSCAAL. We compared computational analyses on ensemble conformations of Trp-cage with its available experimental NOE distances. The analysis demonstrated that conformations explored by MultiSCAAL better agree with the ones probed in the experiments because it can effectively capture the changes in side chain orientations that can flip out of the hydrophobic pocket in the presence of urea and water molecules.

Approximations based on moment-closure (MA) are commonly used to obtain estimates of the mean molecule numbers and of the variance of fluctuations in the number of molecules of chemical systems. The advantage of this approach is that it can be far less computationally expensive than exact stochastic simulations of the chemical master equation. Here we numerically study the conditions under which the MA equations yield results reflecting the true stochastic dynamics of the system. We show that for bistable and oscillatory chemical systems with deterministic initial conditions, the solution of the MA equations can be interpreted as a valid approximation to the true moments of the CME, only when the steady-state mean molecule numbers obtained from the chemical master equation fall within a certain finite range. The same validity criterion for monostable systems implies that the steady-state mean molecule numbers obtained from the chemical master equation must be above a certain threshold. For mean molecule numbers outside of this range of validity, the MA equations lead to either qualitatively wrong oscillatory dynamics or to unphysical predictions such as negative variances in the molecule numbers or multiple steady-state moments of the stationary distribution as the initial conditions are varied. Our results clarify the range of validity of the MA approach and show that pitfalls in the interpretation of the results can only be overcome through the systematic comparison of the solutions of the MA equations of a certain order with those of higher orders.

The classical Coulomb gas model has served as one of the most versatile frameworks in statistical physics, connecting a vast range of phenomena across many different areas. Nonequilibrium generalisations of this model have so far been studied much more scarcely. With the abundance of contemporary research into active and driven systems, one would naturally expect that such generalisations of systems with long-ranged Coulomb-like interactions will form a fertile playground for interesting developments. Here, we present two examples of novel macroscopic behaviour that arise from nonequilibrium fluctuations in long-range interacting systems, namely (1) unscreened long-ranged correlations in strong electrolytes driven by an external electric field and the associated fluctuation-induced forces in the confined Casimir geometry, and (2) out-of-equilibrium critical behaviour in self-chemotactic models that incorporate the particle polarity in the chemotactic response of the cells. Both of these systems have nonlocal Coulomb-like interactions among their constituent particles, namely, the electrostatic interactions in the case of the driven electrolyte, and the chemotactic forces mediated by fast-diffusing signals in the case of self-chemotactic systems. The results presented here hint to the rich phenomenology of nonequilibrium effects that can arise from strong fluctuations in Coulomb interacting systems, and a rich variety of potential future directions, which are discussed.

All known up to now models of chemical oscillations are based exclusively on kinetic considerations. The chemical gross-process equation is split usually by elementary steps, each step is supplied by an arrow and a differential equation, joint solution to such a construction under certain, often ad hoc chosen conditions and with ad hoc numerical coefficients leads to chemical oscillations. Kinetic perception of chemical oscillations reigns without exclusions. However, as it was recently shown by the author for the laser and for the electrochemical systems, chemical oscillations follow also from solutions to the basic expressions of discrete thermodynamics of chemical equilibria. Graphically those solutions are various fork bifurcation diagrams, and, in certain types of chemical systems, oscillations are well pronounced in the bistable bifurcation areas. In this work we describe a general thermodynamic approach to chemical oscillations as opposite to kinetic models, and depict some of their new features like spontaneity and fractality. The paper doubts exclusivity of the kinetic approach to chemical oscillations, and its aim is to discuss and exemplify thermodynamically predicted chemical oscillations in closed chemical systems.

We consider N classical particles interacting via the Coulomb potential in spatial dimension d and in the presence of an external trap, at equilibrium at inverse temperature beta. In the large N limit, the particles are confined within a droplet of finite size. We study smooth linear statistics, i.e. the fluctuations of sums of the form {cal L}_N = sum_{i=1}^N f({bf x}_i), where {bf x}_i's are the positions of the particles and where f({bf x}_i) is a sufficiently regular function. There exists at present standard results for the first and second moments of {cal L}_N in the large N limit, as well as associated Central Limit Theorems in general dimension and for a wide class of confining potentials. Here we obtain explicit expressions for the higher order cumulants of {cal L}_N at large N, when the function f({bf x})=f(|{bf x}|) and the confining potential are both rotationnally invariant. A remarkable feature of our results is that these higher cumulants depend only on the value of f'(|{bf x}|) and its higher order derivatives evaluated exactly at the boundary of the droplet, which in this case is a d-dimensional sphere. In the particular two-dimensional case d=2 at the special value beta=2, a connection to the Ginibre ensemble allows us to derive these results in an alternative way using the tools of determinantal point processes. Finally we also obtain the large deviation form of the full probability distribution function of {cal L}_N.

We study the chemical distance of supercritical Bernoulli percolation on Z^d. Recently, Dembin [Dem22] showed that the chemical distance exhibits sublinear variance, a phenomenon now referred to as superconcentration. In this article, we establish an equivalence between this phenomenon and chaotic behavior of geodesics under small perturbations of the configuration, thereby confirming Chatterjee's general principle relating anomalous fluctuations to chaos in the context of Bernoulli percolation. Our methods rely on a dynamical version of the effective radius, refining the notion first proposed in [CN25], in order to measure the co-influence of a given edge whose weight may be infinite. Together with techniques from the theory of lattice animals, this approach allows us to quantify the total co-influence of edges in terms of the overlap between original and perturbed geodesics.

In a two-band superconductor, two qualitatively different fluctuation modes related to the gap modules contribute to free energy and heat capacity, in addition to the phase fluctuations. The first mode has divergent temperature behaviour since it accounts for the critical fluctuations around the phase transition point, Tc, along with pseudo-critical ones associated with former instability of the weaker-superconductivity component. The involvement of these two factors, competing under interband interaction, results in the Ginzburg number which increases with Tc non-monotonically, allowing the reduction up to 75%. This makes fluctuations effective for revealing additional superconducting component in the system. The second mode does not diverge, but has a jump at Tc, defined uniquely by the strength of interband interaction. This mode contributes fundamentally beyond critical domain.

Metallic alloys often form phases - known as solid solutions - in which chemical elements are spread out on the same crystal lattice in an almost random manner. The tendency of certain chemical motifs to be more common than others is known as chemical short-range order (SRO) and it has received substantial consideration in alloys with multiple chemical elements present in large concentrations due to their extreme configurational complexity (e.g., high-entropy alloys). Short-range order renders solid solutions "slightly less random than completely random", which is a physically intuitive picture, but not easily quantifiable due to the sheer number of possible chemical motifs and their subtle spatial distribution on the lattice. Here we present a multiscale method to predict and quantify the SRO state of an alloy with atomic resolution, incorporating machine learning techniques to bridge the gap between electronic-structure calculations and the characteristic length scale of SRO. The result is an approach capable of predicting SRO length scale in agreement with experimental measurements while comprehensively correlating SRO with fundamental quantities such as local lattice distortions. This work advances the quantitative understanding of solid-solution phases, paving the way for SRO rigorous incorporation into predictive mechanical and thermodynamic models.

The paper sets forth comprehensive basics of Discrete Thermodynamics of Chemical Equilibria (DTD), developed by the author during the last decade and spread over series of publications. Based on the linear equations of irreversible thermodynamics, De Donder's definition of the thermodynamic force, and the Le Chatelier principle, DTD brings forward a notion of chemical equilibrium as a balance of internal and external thermodynamic forces, acting against a chemical system. The basic expression of DTD is a logistic map that ties together energetic characteristics of the chemical transformation in the system, its deviation from true thermodynamic equilibrium, and the sum of thermodynamic forces, causing that deviation. System deviation from thermodynamic equilibrium is the major variable of the theory. Solutions to the basic map define the chemical system domain of states comprising bifurcation diagrams with four areas, from true thermodynamic equilibrium to chaos, having specific distinctive meaning for chemical systems. The theory is derived from the currently recognized ideas of chemical thermodynamics and binds classical and contemporary thermodynamics of chemical equilibria into a unique concept. DTD opens new opportunities in understanding and analysis of equilibria in chemical systems. Some new results, included in the paper, have never been published before.

The friction coefficient of a particle can depend on its position as it does when the particle is near a wall. We formulate the dynamics of particles with such state-dependent friction coefficients in terms of a general Langevin equation with multiplicative noise, whose evaluation requires the introduction of specific rules. Two common conventions, the Ito and the Stratonovich, provide alternative rules for evaluation of the noise, but other conventions are possible. We show the requirement that a particle's distribution function approach the Boltzmann distribution at long times dictates that a drift term must be added to the Langevin equation. This drift term is proportional to the derivative of the diffusion coefficient times a factor that depends on the convention used to define the multiplicative noise. We explore the consequences of this result in a number examples with spatially varying diffusion coefficients. We also derive path integral representations for arbitrary interpretation of the noise, and use it in a perturbative study of correlations in a simple system.

This paper develops a comprehensive theoretical framework that imports concepts from stochastic thermodynamics to model price impact and characterize the feasibility of round-trip arbitrage in financial markets. A trading cycle is treated as a non-equilibrium thermodynamic process, where price impact represents dissipative work and market noise plays the role of thermal fluctuations. The paper proves a Financial Second Law: under general convex impact functionals, any round-trip trading strategy yields non-positive expected profit. This structural constraint is complemented by a fluctuation theorem that bounds the probability of profitable cycles in terms of dissipated work and market volatility. The framework introduces a statistical ensemble of trading strategies governed by a Gibbs measure, leading to a free energy decomposition that connects expected cost, strategy entropy, and a market temperature parameter. The framework provides rigorous, testable inequalities linking microstructural impact to macroscopic no-arbitrage conditions, offering a novel physics-inspired perspective on market efficiency. The paper derives explicit analytical results for prototypical trading strategies and discusses empirical validation protocols.

The statistical mechanics of Gibbs is a juxtaposition of subjective, probabilistic ideas on the one hand and objective, mechanical ideas on the other. In this paper, we follow the path set out by Jaynes, including elements added subsequently to that original work, to explore the consequences of the purely statistical point of view. We show how standard methods in the equilibrium theory could have been derived simply from a description of the available problem information. In addition, our presentation leads to novel insights into questions associated with symmetry and non-equilibrium statistical mechanics. Two surprising consequences to be explored in further work are that (in)distinguishability factors are automatically predicted from the problem formulation and that a quantity related to the thermodynamic entropy production is found by considering information loss in non-equilibrium processes. Using the problem of ion channel thermodynamics as an example, we illustrate the idea of building up complexity by successively adding information to create progressively more complex descriptions of a physical system. Our result is that such statistical mechanical descriptions can be used to create transparent, computable, experimentally-relevant models that may be informed by more detailed atomistic simulations. We also derive a theory for the kinetic behavior of this system, identifying the nonequilibrium `process' free energy functional. The Gibbs relation for this functional is a fluctuation-dissipation theorem applicable arbitrarily far from equilibrium, that captures the effect of non-local and time-dependent behavior from transient driving forces. Based on this work, it is clear that statistical mechanics is a general tool for constructing the relationships between constraints on system information.

The solar wind is a medium characterized by strong turbulence and significant field fluctuations on various scales. Recent observations have revealed that magnetic turbulence exhibits a self-similar behavior. Similarly, high-resolution measurements of the proton density have shown comparable characteristics, prompting several studies into the multifractal properties of these density fluctuations. In this work, we show that low-resolution observations of the solar wind proton density over time, recorded by various spacecraft at Lagrange point L1, also exhibit non-linear and multifractal structures. The novelty of our study lies in the fact that this is the first systematic analysis of solar wind proton density using low-resolution (hourly) data collected by multiple spacecraft at the L1 Lagrange point over a span of 17 years. Furthermore, we interpret our results within the framework of non-extensive statistical mechanics, which appears to be consistent with the observed nonlinear behavior. Based on the data, we successfully validate the q-triplet predicted by non-extensive statistical theory. To the best of our knowledge, this represents the most rigorous and systematic validation to date of the q-triplet in the solar wind.

Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create inhomogeneities that can dramatically affect the reaction rate. The extreme case is that of a reaction coupled to a phase transformation, whose kinetics must depend on the order parameter -- and its gradients, at phase boundaries. This Account presents a general theory of chemical kinetics based on nonequilibrium thermodynamics. The reaction rate is a nonlinear function of the thermodynamic driving force (free energy of reaction) expressed in terms of variational chemical potentials. The Cahn-Hilliard and Allen-Cahn equations are unified and extended via a master equation for non-equilibrium chemical thermodynamics. For electrochemistry, both Marcus and Butler-Volmer kinetics are generalized for concentrated solutions and ionic solids. The theory is applied to intercalation dynamics in the phase separating Li-ion battery material Li_xFePO_4.

Recent JWST observations with NIRCam and MIRI of the ultra-short-period super-Earth 55 Cancri e indicate a possible volatile atmosphere surrounding the planet. Previous analysis of the NIRCam spectra suggested potential absorption features from CO2 or CO and significant sub-weekly variability. The MIRI low-resolution spectrum does not contain substantial features but was found to be consistent with effective heat redistribution models. In this work, we computed a grid of over 25000 self-consistent 1D forward models incorporating H-N-O-C-S-P-Si-Ti equilibrium chemistry and assessed plausible atmospheric compositions based on the current JWST data. Despite exhaustive analysis, the composition and properties of the atmosphere remain elusive. While our results statistically favour a global, hydrogen-free, nitrogen-dominated atmosphere enriched in PO and CO2, various alternative compositions, including H2O-,CO-, PH3-, or Si-bearing remain viable explanations. Unconstrained heat redistribution efficiency and absolute NIRCam flux are among the largest sources of uncertainty in our analysis. We also find that the heat redistribution factor and surface pressure are highly degenerate with atmospheric composition, and that these parameters cannot be independently constrained using current JWST observations. Furthermore, we show that the observed variability may arise from dynamic interactions between the atmosphere and an underlying magma ocean, driving rapid shifts in atmospheric chemistry and thermal emission. Our results highlight the importance of using self-consistent forward models when analysing novel JWST spectra with limited signal-to-noise ratios -- such as those of 55 Cancri e -- as it allows for a more comprehensive evaluation of potential atmospheric scenarios while also being less sensitive to subtle spectral differences than retrievals...

A stochastic gravitational wave background causes the apparent positions of distant sources to fluctuate, with angular deflections of order the characteristic strain amplitude of the gravitational waves. These fluctuations may be detectable with high precision astrometry, as first suggested by Braginsky et al. in 1990. Several researchers have made order of magnitude estimates of the upper limits obtainable on the gravitational wave spectrum \Omega_gw(f), at frequencies of order f ~ 1 yr^-1, both for the future space-based optical interferometry missions GAIA and SIM, and for VLBI interferometry in radio wavelengths with the SKA. For GAIA, tracking N ~ 10^6 quasars over a time of T ~ 1 yr with an angular accuracy of \Delta \theta ~ 10 \mu as would yield a sensitivity level of \Omega_gw ~ (\Delta \theta)^2/(N T^2 H_0^2) ~ 10^-6, which would be comparable with pulsar timing. In this paper we take a first step toward firming up these estimates by computing in detail the statistical properties of the angular deflections caused by a stochastic background. We compute analytically the two point correlation function of the deflections on the sphere, and the spectrum as a function of frequency and angular scale. The fluctuations are concentrated at low frequencies (for a scale invariant stochastic background), and at large angular scales, starting with the quadrupole. The magnetic-type and electric-type pieces of the fluctuations have equal amounts of power.

Initial states of dense matter with nonzero electron chiral imbalance could potentially give rise to strong magnetic fields through chiral plasma instability. Previous work indicated that unless chiral chemical potential is as large as the electron vector chemical potential, the growth of magnetic fields due to the instability is washed out by chirality flipping rate enabled by electron mass. We re-examine this claim in a broader range of parameters and find that at higher temperatures the hierarchy is reversed supporting a growing magnetic field for an initial electron chiral chemical potential much smaller than the electron vector chemical potential. Further, we identify a qualitatively new effect relevant for magnetized hot and dense medium where chiral magnetic effect (CME) sourced by density fluctuation acts as a powerful source of Joule heating. Remarkably, even modest chiral chemical potentials (keV) in such environment can deposit energy densities set by the QCD scale in a relatively short time of the order of a few milliseconds or seconds. We speculate how this mechanism makes CME-driven Joule heating a potentially critical ingredient in the dynamics of turbulent density fluctuation of supernovae and neutron star mergers.

We present a scheme to obtain an inexpensive and reliable estimate of the uncertainty associated with the predictions of a machine-learning model of atomic and molecular properties. The scheme is based on resampling, with multiple models being generated based on sub-sampling of the same training data. The accuracy of the uncertainty prediction can be benchmarked by maximum likelihood estimation, which can also be used to correct for correlations between resampled models, and to improve the performance of the uncertainty estimation by a cross-validation procedure. In the case of sparse Gaussian Process Regression models, this resampled estimator can be evaluated at negligible cost. We demonstrate the reliability of these estimates for the prediction of molecular energetics, and for the estimation of nuclear chemical shieldings in molecular crystals. Extension to estimate the uncertainty in energy differences, forces, or other correlated predictions is straightforward. This method can be easily applied to other machine learning schemes, and will be beneficial to make data-driven predictions more reliable, and to facilitate training-set optimization and active-learning strategies.

Synchronization in one dimension displays generic scale invariance with universal properties previously observed in surface kinetic roughening and the wider context of the Kardar-Parisi-Zhang (KPZ) universality class. This has been established for phase oscillators and also for some limit-cycle oscillators, both in the presence of columnar (quenched) disorder and of time-dependent noise, by extensive numerical simulations, and has been analytically motivated by continuum approximations in the strong oscillator coupling limit. The robustness and the precise boundaries in parameter space for such critical behavior remain unclear, however, which may preclude further developments, including the extension of these results to higher dimensions and the experimental observation of nonequilibrium criticality in synchronizing (e.g.~electronic or chemical) oscillators. We here present complete numerical phase diagrams of one-dimensional synchronization, including saturation times and values, but, most importantly, also dynamical features giving insight into the gradual emergence of synchronous dynamics, based on systems of phase oscillators with either type of randomness. In the absence of synchronization, the dynamics evolves as expected for random deposition (for time-dependent noise) or linear growth (for columnar disorder), while a crossover from Edwards-Wilkinson to Kardar-Parisi-Zhang behavior (with the corresponding type of randomness) is observed as the randomness strength, or the nonoddity of the coupling among oscillators, is increased in the synchronous region -- their combined effect being partially captured by the so-called KPZ coupling. The distortion of scaling due to phase slips near the desynchronization boundary, a feature that is likely to play a role in experimental contexts, is also discussed.

Multiplicative noise, also known as speckle or pepper noise, commonly affects images produced by synthetic aperture radar (SAR), lasers, or optical lenses. Unlike additive noise, which typically arises from thermal processes or external factors, multiplicative noise is inherent to the system, originating from the fluctuation in diffuse reflections. These fluctuations result in multiple copies of the same signal with varying magnitudes being combined. Consequently, despeckling, or removing multiplicative noise, necessitates different techniques compared to those used for additive noise removal. In this paper, we propose a novel approach using Stochastic Differential Equations based diffusion models to address multiplicative noise. We demonstrate that multiplicative noise can be effectively modeled as a Geometric Brownian Motion process in the logarithmic domain. Utilizing the Fokker-Planck equation, we derive the corresponding reverse process for image denoising. To validate our method, we conduct extensive experiments on two different datasets, comparing our approach to both classical signal processing techniques and contemporary CNN-based noise removal models. Our results indicate that the proposed method significantly outperforms existing methods on perception-based metrics such as FID and LPIPS, while maintaining competitive performance on traditional metrics like PSNR and SSIM.

Macroscopic entropy production σ^{(tot)} in the general nonlinear isothermal chemical reaction system with mass action kinetics is decomposed into a free energy dissipation and a house-keeping heat: σ^{(tot)}=σ^{(fd)}+σ^{(hk)}; σ^{(fd)}=-rd A/rd t, where A is a generalized free energy function. This yields a novel nonequilibrium free energy balance equation rd A/rd t=-σ^{(tot)}+σ^{(hk)}, which is on a par with celebrated entropy balance equation rd S/rd t=σ^{(tot)}+η^{(ex)} where η^{(ex)} is the rate of entropy exchange with the environment.For kinetic systems with complex balance, σ^{(fd)} and σ^{(hk)} are the macroscopic limits of stochastic free energy dissipation and house-keeping heat, which are both nonnegative, in the Delbrück-Gillespie description of the stochastic chemical kinetics.Therefore, we show that a full kinetic and thermodynamic theory of chemical reaction systems that transcends mesoscopic and macroscopic levels emerges.

In 2000, Gillespie rehabilitated the chemical Langevin equation (CLE) by describing two conditions that must be satisfied for it yield a valid approximation of the chemical master equation (CME). In this work, we construct an original path integral description of the CME, and show how applying Gillespie's two conditions to it directly leads to a path integral equivalent to the CLE. We compare this approach to the path integral equivalent of a large system size derivation, and show that they are qualitatively different. In particular, both approaches involve converting many sums into many integrals, and the difference between the two methods is essentially the difference between using the Euler-Maclaurin formula and using Riemann sums. Our results shed light on how path integrals can be used to conceptualize coarse-graining biochemical systems, and are readily generalizable.

In this note, we show that the Local Molecular Field theory of Weeks et. al. can be re-derived as an extremum problem for an approximate Helmholtz free energy. Using the resulting free energy as a classical, fluid density functional yields an implicit solvent method identical in form to the Molecular Density Functional theory of Borgis et. al., but with an explicit formula for the 'ideal' free energy term. This new expression for the ideal free energy term can be computed from all-atom molecular dynamics of a solvent with only short-range interactions. The key hypothesis required to make the theory valid is that all smooth (and hence long-range) energy functions obey Gaussian statistics. This is essentially a random phase approximation for perturbations from a short-range only, 'reference,' fluid. This single hypothesis is enough to prove that the self-consistent LMF procedure minimizes a novel density functional whose 'ideal' free energy is the molecular system under a specific, reference Hamiltonian, as opposed to the non-interacting gas of conventional density functionals. Implementation of this new functional into existing software should be straightforward and robust.

We numerically investigate some properties of unbalanced St\"{u}ckelberg holographic superconductors, by considering backreaction effects of fields on the background geometry. More precisely, we study the impacts of the chemical potential mismatch and St\"{u}ckelberg mechanism on the condensation and conductivity types (electrical, spin, mixed, thermo-electric, thermo-spin and thermal conductivity). Our results show that the St\"{u}ckelberg's model parameters C_{alpha} and alpha not only have significant impacts on the phase transition, but also affect the conductivity pseudo-gap and the strength of conductivity fluctuations. Moreover, the effects of these parameters on a system will be gradually reduced as the imbalance grows. We also find that the influence of alpha on the amplitude of conductivity fluctuations depends on the magnitude of the both C_{alpha} and deltamu/mu in the electric and thermal conductivity cases. This results in that increasing alpha can damp the conductivity fluctuations of an unbalanced system in contrast to balanced ones.

We derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains - parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource.

The Shannon entropy in the atomic, molecular and chemical physics context is presented by using as test cases the hydrogenic-like atoms H_c, {He_c}^+ and {Li_c}^{2+} confined by an impenetrable spherical box. Novel expressions for entropic uncertainty relation and Shannon entropies S_r and S_p are proposed to ensure their physical dimensionless characteristic. The electronic ground state energy and the quantities S_r, S_p and S_t are calculated for the hydrogenic-like atoms to different confinement radii by using a variational method. The global behavior of these quantities and different conjectures are analyzed. The results are compared, when available, with those previously published.

Ultralight dark matter is an interesting dark matter candidate describing the lightest end of the mass parameter space. This model produces an oscillating granular pattern in halo densities. These fluctuations have the potential to produce a time-varying density along the line of sight creating a small lensing signal for any stars observed through a dark matter halo which oscillates on the de Broglie timescale. In this work, we study this stochastic lensing signal taking into account the impact of density granules as well as the central soliton. We calculate the amplitude and temporal properties of this signal and estimate how stellar observations may be used to constrain the ultralight dark matter mass and abundance.

We present an escape rate theory for current-induced chemical reactions. We use Keldysh nonequilibrium Green's functions to derive a Langevin equation for the reaction coordinate. Due to the out of equilibrium electronic degrees of freedom, the friction, noise, and effective temperature in the Langevin equation depend locally on the reaction coordinate. As an example, we consider the dissociation of diatomic molecules induced by the electronic current from a scanning tunnelling microscope tip. In the resonant tunnelling regime, the molecular dissociation involves two processes which are intricately interconnected: a modification of the potential energy barrier and heating of the molecule. The decrease of the molecular barrier (i.e. the current induced catalytic reduction of the barrier) accompanied by the appearance of the effective, reaction-coordinate-dependent temperature is an alternative mechanism for current-induced chemical reactions, which is distinctly different from the usual paradigm of pumping vibrational degrees of freedom.

A theoretical approach to describing transport of an entire ensemble of clusters with different sizes as a single species in gas has been developed. The major assumption is an existence of local partial chemical equilibrium between the clusters. It is shown that thermal diffusion emerges in the collective description as a significant factor even if it is negligible when transport of the original molecular species is considered. Analytical expressions for the effective diffusion and thermal diffusion coefficients at temperature, pressure, and chemical composition gradients have been derived. The theory has been applied to a technology of H2S conversion in a centrifugal plasma-chemical reactor and has made it possible to account for sulfur clusters in numerical process modeling.

Large-amplitude molecular motions which occur during isomerization can cause significant changes in electronic structure. These variations in electronic properties can be used to identify vibrationally-excited eigenstates which are localized along the potential energy surface. This work demonstrates that nuclear quadrupole hyperfine interactions can be used as a diagnostic marker of progress along the isomerization path in both the HC14N/H14NC and DC15N/D15NC chemical systems. Ab initio calculations at the CCSD(T)/cc-pCVQZ level indicate that the hyperfine interaction is extremely sensitive to the chemical bonding of the quadrupolar 14N nucleus and can therefore be used to determine in which potential well the vibrational wavefunction is localized. A natural bonding orbital analysis along the isomerization path further demonstrates that hyperfine interactions arise from the asphericity of the electron density at the quadrupolar nucleus. Using the CCSD(T) potential surface, the quadrupole coupling constants of highly-excited vibrational states are computed from a one-dimensional internal coordinate path Hamiltonian. The excellent agreement between ab initio calculations and recent measurements demonstrates that nuclear quadrupole hyperfine structure can be used as a diagnostic tool for characterizing localized HCN and HNC vibrational states.

Most Galactic Globular Clusters (GCs) harbour multiple populations of stars (MPs), composed of at least two generations: the first characterized by a "standard" α-enhanced metal mixture, as observed in field halo stars of the Milky Way, and the second displaying anti-correlated CN--ONa chemical abundance pattern in combination with an enhanced helium fraction. Adequate collections of stellar spectra are needed to characterize the effect of such stellar abundance changes on the integrated light of GCs. We present a grid of synthetic stellar spectra covering the atmospheric parameters relevant to old stellar populations at four subsolar metallicities and two abundance patterns, representative of first- and second-generations of stars in GCs. Integrated spectra of populations were computed using our stellar grid and empirical stellar populations, namely, colour-magnitude diagrams from literature for Galactic GCs. The spectra range from 290 to 1000nm, where we measured the effect on several spectrophotometric indices due to the surface abundance variations attributed to MPs. We find non-negligible effects of the MPs on spectroscopic indices sensitive to C, N, Ca, or Na, and on Balmer indices; we also describe how MPs modify specific regions in the near-UV and near-IR that can be measured with narrow or medium photometric passbands. The effects vary with metallicity. A number of these changes remain detectable even when accounting for the stochastic fluctuations due to the finite nature of the stellar population cluster.

We investigate the time evolution of the Boltzmann entropy of a dilute gas of N particles, N>>1, as it undergoes a free expansion doubling its volume. The microstate of the system, a point in the 4N dimensional phase space, changes in time via Hamiltonian dynamics. Its entropy, at any time t, is given by the logarithm of the phase space volume of all the microstates giving rise to its macrostate at time t. The macrostates that we consider are defined by coarse graining the one-particle phase space into cells Δ_α. The initial and final macrostates of the system are equilibrium states in volumes V and 2V, with the same energy E and particle number N. Their entropy per particle is given, for sufficiently large systems, by the thermodynamic entropy as a function of the particle and energy density, whose leading term is independent of the size of the Δ_α. The intermediate (non-equilibrium) entropy does however depend on the size of the cells Δ_α. Its change with time is due to (i) dispersal in physical space from free motion and to (ii) the collisions between particles which change their velocities. The former depends strongly on the size of the velocity coarse graining Δv: it produces entropy at a rate proportional to Δv. This dependence is investigated numerically and analytically for a dilute two-dimensional gas of hard discs. It becomes significant when the mean free path between collisions is of the same order or larger than the length scale of the initial spatial inhomogeneity. In the opposite limit, the rate of entropy production is essentially independent of Δv and is given by the Boltzmann equation for the limit Δvrightarrow 0. We show that when both processes are active the time dependence of the entropy has a scaling form involving the ratio of the rates of its production by the two processes.

We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming the separation of time scales for electronic and nuclear dynamics we employ the Langevin equation for the reaction coordinate. The Langevin equation contains current-induced forces and is used to define nonequilibrium, effective potential energy surface for current-carrying molecular systems. The current-induced forces are computed via Keldysh nonequilibrium Green's functions. Once the nonequilibrium, current-depended potential energy surface is defined, the chemical reaction is modeled as an escape of a Brownian particle from the potential well. We demonstrate that the barrier between the reactant and the product states can be controlled by the bias voltage. When the molecule is asymmetrically coupled to the electrodes, the reaction can be catalyzed or stopped depending on the polarity of the tunneling current.

Chemical transport models (CTMs), which simulate air pollution transport, transformation, and removal, are computationally expensive, largely because of the computational intensity of the chemical mechanisms: systems of coupled differential equations representing atmospheric chemistry. Here we investigate the potential for machine learning to reproduce the behavior of a chemical mechanism, yet with reduced computational expense. We create a 17-layer residual multi-target regression neural network to emulate the Carbon Bond Mechanism Z (CBM-Z) gas-phase chemical mechanism. We train the network to match CBM-Z predictions of changes in concentrations of 77 chemical species after one hour, given a range of chemical and meteorological input conditions, which it is able to do with root-mean-square error (RMSE) of less than 1.97 ppb (median RMSE = 0.02 ppb), while achieving a 250x computational speedup. An additional 17x speedup (total 4250x speedup) is achieved by running the neural network on a graphics-processing unit (GPU). The neural network is able to reproduce the emergent behavior of the chemical system over diurnal cycles using Euler integration, but additional work is needed to constrain the propagation of errors as simulation time progresses.

Recent observations by the James Webb Space Telescope have revealed massive galaxies at very high redshift (zsimeq 7-15). The question of whether the existence of such galaxies is expected in the corresponding JWST surveys has received a lot of attention, though the answer straddles areas of cosmology and complex astrophysical details of high-redshift galaxy formation. The growth rate of density fluctuations determines the amplitude of overdensities that collapse to form galaxies. Late-time modifications of growth, combined with measurements at both zsim 1 from large-scale structure and zsim 1000 from the cosmic microwave background, affect the predictions for the abundance of first galaxies in the universe. In this paper, we point out that the late-time growth rate of structure affects the statistical significance of high-redshift, high-mass objects very weakly. Consequently, if the existence and abundance of these objects are confirmed to be unexpected, the variations in the late-time growth history are unlikely to explain these anomalies.

The independent atom ansatz of density functional theory yields an accurate analytical expression for dynamic correlation energy in the H_{2} molecule: E_{c} = 0.5(1 - 2)(ab|ba) for the atom-additive self-consistent density rho = |a|^{2} + |b|^{2}. Combined with exact atomic self-exchange, it recovers more than 99.5 % of nearly exact SCAN exchange-correlation energy at R > 0.5 A, differing by less than 0.12 eV. The total energy functional correctly dissociates the H-H bond and yields absolute errors of 0.002 A, 0.19 eV, and 13 cm^{-1} relative to experiment at the tight binding computational cost. The chemical bond formation is attributed to the asymptotic Heitler-London resonance of quasi-orthogonal atomic states (- (ab|ba)) with no contributions from kinetic energy or charge accumulation in the bond.

The local structure of V_{2}O_{3}, an archetypal strongly correlated electron system that displays a metal-insulator transition around 160 K, has been investigated via pair distribution function (PDF) analysis of neutron and x-ray total scattering data. The rhombohedral-to-monoclinic structural phase transition manifests as an abrupt change on all length scales in the observed PDF. No monoclinic distortions of the local structure are found above the transition, although coexisting regions of phase-separated rhombohedral and monoclinic symmetry are observed between 150 K and 160 K. This lack of structural fluctuations above the transition contrasts with the known presence of magnetic fluctuations in the high-temperature state, suggesting that the lattice degree of freedom plays a secondary role behind the spin degree of freedom in the transition mechanism.

Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to efficiently navigate chemical space. Scientific foundation models trained on large unlabeled datasets offer a path toward exploring chemical space across diverse application domains. Here we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenization scheme that comprehensively captures nuclear, electronic, and geometric information, MIST learns from a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure -- property relationships and match or exceed state-of-the-art performance across benchmarks spanning physiology, electrochemistry, and quantum chemistry. We demonstrate the ability of these models to solve real-world problems across chemical space, including multiobjective electrolyte solvent screening, olfactory perception mapping, isotope half-life prediction, stereochemical reasoning for chiral organometallic compounds, and binary and multi-component mixture property prediction. Probing MIST models using mechanistic interpretability methods reveals identifiable patterns and trends not explicitly present in the training data, suggesting that the models learn generalizable scientific concepts. We formulate hyperparameter-penalized Bayesian neural scaling laws and use them to reduce the computational cost of model development by an order of magnitude. The methods and findings presented here represent a significant step toward accelerating materials discovery, design, and optimization using foundation models and provide valuable guidance for training compute-optimal scientific foundation models.

The measured neutron flux from the Moons south polar region shows evidence of locally enhanced hydrogen concentrations, likely in the form of water ice, within most permanently shadowed regions (PSR), poleward of 77 deg S latitude. Results are consistent with the original findings of Watson et al, 1961, which found that the PSRs cryogenic surfaces create exclusive conditions for the sequestration of water ice, due to their extremely low sublimation rates. Widespread PSR hydrogenation is demonstrated in several studies by showing that the contrasting PSR area distribution is being instrumentally blurred. The PSRs expected hydrogen observations are correlated by their area fraction of the fixed 30 km diameter footprint area of the Collimated Sensor for Epithermal Neutrons (CSETN), which is part of the Lunar Exploration Neutron Detector (LEND) onboard the Lunar Reconnaissance Orbiter (LRO). The correlation indicates that the PSRs are similarly hydrogenated, with an expected concentration = 0.27 wt%, relative to that of the anhydrous reference terrain (lower bounds). Hydrogen concentrations are demonstrated to be correlated to maximum temperature distributions within the basins of Haworth, Shoemaker and Faustini PSRs. Cabeus-1 PSR shows an anomalously enhanced hydrogen concentration indicating a second process contributes to its hydrogen budget. Results are consistent with ongoing processes that introduce volatiles to the surface including outgassing, solar wind production with regolith silicates, and mixing from small scale meteor impacts and diurnal temperature variation. We validate the bandpass filter used to subtract CSETNs detection of uncollimated neutrons with profiles of several PSRs neutron suppression before and after processing. Keywords: Moon, Epithermal Neutron, Hydrogen, Water, Ice, Volatiles, LRO, LEND, Diviner, LOLA

We prove stability for a class of heterogeneous catalysis models in the L_p-setting. We consider a setting in a finite three-dimensional pore of cylinder-like geometry, with the lateral walls acting as a catalytic surface. Under a reasonable condition on the involved parameters, we show that given equilibria are normally stable, i.e. solutions are attracted at an exponential rate. The potential incidence of instability is discussed as well.

We present Symphony, an E(3)-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree E(3)-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

The gamma-ray burst (GRB) GRB 211211A and GRB 060614, believed to originate from the merger of compact objects, exhibit similarities to the jetted tidal disruption event (TDE) Sw J1644+57, by showing violent variabilities in the light-curve during the decay phase. Previous studies suggest that such fluctuations in TDE may arise from the fallback of tidal disrupted debris. In this paper, we introduce the fluctuations of the mass distribution {rm d}M/{rm d}E for the debris ejected during the tidal disruption (with energy E) and study their impact on jet power. Turbulence induced by tidal force and the self-gravity of the debris may imprint variabilities in {rm d}M/{rm d}E during fallback. We model these fluctuations with a power density spectrum propto f_{rm E}^{beta}, where f_{rm E} = 1/E and beta is the power-law index. We find that the resulting light curve can preserve the fluctuation characteristics from {rm d}M/{rm d}E. In addition, the observed fluctuations in the light-curves can be reproduced for a given suitable beta. Based on the observations, we find that the value of beta should be around -1.

EXAFS studies at the As K edge as a function of temperature have been carried out in SmFeAsO_{1-x}F_x (x = 0 and 0.2) compounds to understand the role of local structural distortions superconductivity observed in F doped compound. A significant correlation between thermal variation of local structural parameters like anion height and superconducting onset is found in the fluorinated compound. Such a variation in anion height is absent in non-superconducting compound. Increase in Fe-As bond distance just below superconducting onset temperature indicates a similarity in distortions observed in high T_C cuprates and these Fe based superconductors.

The progress in modelling time series and, more generally, sequences of structured data has recently revamped research in anomaly detection. The task stands for identifying abnormal behaviors in financial series, IT systems, aerospace measurements, and the medical domain, where anomaly detection may aid in isolating cases of depression and attend the elderly. Anomaly detection in time series is a complex task since anomalies are rare due to highly non-linear temporal correlations and since the definition of anomalous is sometimes subjective. Here we propose the novel use of Hyperbolic uncertainty for Anomaly Detection (HypAD). HypAD learns self-supervisedly to reconstruct the input signal. We adopt best practices from the state-of-the-art to encode the sequence by an LSTM, jointly learned with a decoder to reconstruct the signal, with the aid of GAN critics. Uncertainty is estimated end-to-end by means of a hyperbolic neural network. By using uncertainty, HypAD may assess whether it is certain about the input signal but it fails to reconstruct it because this is anomalous; or whether the reconstruction error does not necessarily imply anomaly, as the model is uncertain, e.g. a complex but regular input signal. The novel key idea is that a detectable anomaly is one where the model is certain but it predicts wrongly. HypAD outperforms the current state-of-the-art for univariate anomaly detection on established benchmarks based on data from NASA, Yahoo, Numenta, Amazon, and Twitter. It also yields state-of-the-art performance on a multivariate dataset of anomaly activities in elderly home residences, and it outperforms the baseline on SWaT. Overall, HypAD yields the lowest false alarms at the best performance rate, thanks to successfully identifying detectable anomalies.

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

The overwhelming majority of molecules remains unexplored. This is mostly due to the sheer number of them, which prohibits any enumeration of chemical space, the set of all such molecules. In practice, only subsets of chemical space are considered, but those subsets exhibit substantial bias, prohibiting data-driven characterization of chemical space itself. In this work, we provide a method produce unbiased representative random samples of chemical space without enumeration of constituent molecules and to estimate the number of molecules in any custom chemical space. The approach is applicable to molecules which can be represented as graph and runs efficiently even for molecules of 30 atoms. We use it to estimate the representativeness of current databases with respect to their underlying chemical space and to establish a necessary criterion for a lower bound of database sizes to be representative of an underlying chemical space.

This paper introduces a continuous-time stochastic dynamical framework for understanding how large language models (LLMs) may self-amplify latent biases or toxicity through their own chain-of-thought reasoning. The model posits an instantaneous "severity" variable x(t) in [0,1] evolving under a stochastic differential equation (SDE) with a drift term μ(x) and diffusion σ(x). Crucially, such a process can be consistently analyzed via the Fokker--Planck approach if each incremental step behaves nearly Markovian in severity space. The analysis investigates critical phenomena, showing that certain parameter regimes create phase transitions from subcritical (self-correcting) to supercritical (runaway severity). The paper derives stationary distributions, first-passage times to harmful thresholds, and scaling laws near critical points. Finally, it highlights implications for agents and extended LLM reasoning models: in principle, these equations might serve as a basis for formal verification of whether a model remains stable or propagates bias over repeated inferences.

The reionization of helium is thought to occur at 2.5lesssim zlesssim4, marking the last phase transition and final global heating event of the intergalactic medium (IGM). Since it is driven by rare quasars, helium reionization should give rise to strong temperature fluctuations in the IGM between neutral and recently-ionized regions of order sigma (ln T) sim Delta T/T = 20-50%. We introduce a novel method to search for reionization-induced temperature fluctuations in the IGM by using the effective optical depths of the Lyman-alpha forest towards a large number of background quasars. Higher IGM temperatures give rise to lower effective optical depths in the Lyman-alpha forest, implying that temperature fluctuations will broaden the observed optical depth distribution. We measured the distributions of effective Lyman-alpha forest optical depths across 71 X-Shooter spectra from the XQ-100 survey in four redshift bins from z=3.76 to z=4.19 and compared them to a large-volume cosmological hydrodynamical simulation. A good agreement is found between the observations and the simulation, which does not include temperature fluctuations; therefore, we do not detect a signature of helium reionization. We then post-process the simulations to include an increasing amount of temperature fluctuations until the model becomes inconsistent with the observations. We obtain tight constraints on sigma (ln T) < 0.29 (<0.40) at 2 sigma (3 sigma) at z=3.76 when averaging over scales of 100 comoving Mpc, and weaker constraints for higher redshifts and smaller scales. Our constraints are the tightest to date, and imply that either the IGM temperature contrast caused by helium reionization is less than sim30%, or that the process has not yet significantly started at z=3.76.

Astrochemical models of interstellar clouds, the sites of stars, and planet formation require information about spin-state chemistry to allow quantitative comparison with spectroscopic observations. In particular, it is important to know if full scrambling or H abstraction (also known as proton hopping) takes place in ion-neutral reactions. The reaction of Cl+ and HCl+ with H2 and isotopologues has been studied at cryogenic temperatures between 20 and 180 K using a 22 pole radio frequency ion trap. Isotopic exchange processes are used to probe the reaction mechanism of the HCl+ + H2 reaction. The results are compared with previous measurements and theoretical predictions. The rate coefficients for the Cl+ + H2 and HCl+ + H2 reactions are found to be constant in the range of temperatures studied, except for the DCl+ + D2 reaction, where a weak negative temperature dependence is observed, and reactions with D2 are found to be significantly slower than the Langevin rate. No isotopic exchange reactions are observed to occur for the H2Cl+ ion. The analysis of the products of the HCl+ + H2 isotopic system clearly indicates that the reaction proceeds via simple hydrogen atom abstraction.

We describe pre-perihelion optical observations of interstellar comet 3I/ATLAS taken during July - September 2025 using the Nordic Optical Telescope. Fixed aperture photometry of the comet is well described by a power law function of heliocentric distance, rH, with the exponent (``index") n = 3.8+/-0.3 across the 4.6 au to 1.8 au distance range (phase function 0.04+/-0.02 magnitude/degree assumed). This indicates that the dust production rates vary in proportion to rH**(-1.8+/-0.3). An rH**(-2) variation is expected of a strongly volatile material, and consistent with independent spectroscopic observations showing that carbon dioxide is the primary driver of activity. The measured heliocentric index is unremarkable in the context of solar system comets, for which n is widely dispersed, and provides no basis on which to describe 3I as either dynamically old (thermally processed) or new (pristine). The morphology of the comet changes from a Sun-facing dust fan in the early 2025 July observations, to one dominated by an antisolar dust tail at later dates. We attribute the delayed emergence of the tail to the large size (effective radius 0.1 mm) and slow ejection (5 m/s) of the optically dominant dust particles, and their consequently sluggish response to solar radiation pressure. Small (micron-sized) particles may be present but not in numbers sufficient to dominate the scattering cross-section. Their relative depletion possibly reflects interparticle cohesion, which binds small particles more effectively than large ones. A similar preponderance of 0.1 mm grains was reported in 2I/Borisov. However, 2I differed from 3I in having a much smaller (asteroid-like) heliocentric index, n = 1.9+/-0.1. Dust production rates in 3I are 180 kg/s at 2 au, compared with 70 kg/s in 2I/Borisov at the same distance.

In order to make accurate predictions of material properties, current machine-learning approaches generally require large amounts of data, which are often not available in practice. In this work, an all-round framework is presented which relies on a feedforward neural network, the selection of physically-meaningful features and, when applicable, joint-learning. Next to being faster in terms of training time, this approach is shown to outperform current graph-network models on small datasets. In particular, the vibrational entropy at 305 K of crystals is predicted with a mean absolute test error of 0.009 meV/K/atom (four times lower than previous studies). Furthermore, joint-learning reduces the test error compared to single-target learning and enables the prediction of multiple properties at once, such as temperature functions. Finally, the selection algorithm highlights the most important features and thus helps understanding the underlying physics.

Reciprocity is a fundamental symmetry present in many natural phenomena and engineered systems. Distinct situations where this symmetry is broken are typically grouped under the umbrella term "nonreciprocity", colloquially defined by: the action of A on B neq the action of B on A. In this review, we elucidate what nonreciprocity is by providing an introduction to its most salient classes: nonvariational dynamics, violations of Newton's third law, broken detailed balance, nonreciprocal responses and nonreciprocity of arbitrary linear operators. Next, we point out where to find these manifestations of non-reciprocity, from ensembles of particles with field mediated interactions to synthetic neural networks and open quantum systems. Given this breadth of contexts and the lack of an all-encompassing definition, it makes it all the more intriguing that some general conclusions can be gathered, when distinct definitions of nonreciprocity overlap. We explore what these universal consequences are with a special emphasis on collective phenomena that arise in nonreciprocal many-body systems. The topics covered include nonreciprocal phase transitions and non-normal amplification of noise and perturbations. We conclude with some open questions.

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems, particularly during the origins of life. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. These forces can be quantified using the Price equation, which is a standard tool used in evolutionary biology to quantify evolutionary change. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. We demonstrate this using the Graded Autocatalysis Replication Domain computer model, describing simple protocell composed out of molecules and its replication, which respectively analogue to the group and the individuals. In contrast to previous treatments of this model, we treat the lipid molecules themselves as replicating individuals and the protocells they form as groups of individuals. Our goal is to demonstrate how evolutionary biology tools and concepts can be applied in chemistry and we suggest that molecular cooperation may arise as a result of group selection. Further, the biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology.

In this work, we introduce a novel approach for predicting thermodynamic properties of binary mixtures, which we call the similarity-based method (SBM). The method is based on quantifying the pairwise similarity of components, which we achieve by comparing quantum-chemical descriptors of the components, namely σ-profiles. The basic idea behind the approach is that mixtures with similar pairs of components will have similar thermodynamic properties. The SBM is trained on a matrix that contains some data for a given property for different binary mixtures; the missing entries are then predicted by the SBM. As an example, we consider the prediction of isothermal activity coefficients at infinite dilution (γ^infty_{ij}) and show that the SBM outperforms the well-established physical methods modified UNIFAC (Dortmund) and COSMO-SAC-dsp. In this case, the matrix is only sparsely occupied, and it is shown that the SBM works also if only a limited number of data for similar mixtures is available. The SBM idea can be transferred to any mixture property and is a powerful tool for generating essential data for many applications.

The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculations are performed on full protein structures. Of the tested empirical and QM derived predictors, Procs14 reproduced the QM chemical shifts with the highest accuracy. A comparison with the QM derived predictor CheShift-2 on X-ray structures and NMR ensembles with experimental chemical shift data, showed that Procs14 predicted the chemical shifts with the best accuracy. The predictions on the NMR ensembles exhibited the best performance. This suggests that future work might benefit from using ensemble sampling when performing simulations of protein folding with chemical shifts. Procs14 is implemented in the markov chain monte carlo protein folding framework PHAISTOS. The computational efficient implementation of Procs14 allows for rapid predictions and therefore potential use in refinement and folding of protein structures.

Far-field chemical microscopy providing molecular electronic or vibrational fingerprint information opens a new window for the study of three-dimensional biological, material, and chemical systems. Chemical microscopy provides a nondestructive way of chemical identification without exterior labels. However, the diffraction limit of optics hindered it from discovering more details under the resolution limit. Recent development of super-resolution techniques gives enlightenment to open this door behind far-field chemical microscopy. Here, we review recent advances that have pushed the boundary of far-field chemical microscopy in terms of spatial resolution. We further highlight applications in biomedical research, material characterization, environmental study, cultural heritage conservation, and integrated chip inspection.

It is demonstrated that self-diffusion and shear viscosity data for the TIP4P/Ice water model reported recently [L. Baran, W. Rzysko and L. MacDowell, J. Chem. Phys. {\bf 158}, 064503 (2023)] obey the microscopic version of the Stokes-Einstein relation without the hydrodynamic diameter.

Central to our understanding of chemical reactivity is the principle of mass conservation, which is fundamental for ensuring physical consistency, balancing equations, and guiding reaction design. However, data-driven computational models for tasks such as reaction product prediction rarely abide by this most basic constraint. In this work, we recast the problem of reaction prediction as a problem of electron redistribution using the modern deep generative framework of flow matching. Our model, FlowER, overcomes limitations inherent in previous approaches by enforcing exact mass conservation, thereby resolving hallucinatory failure modes, recovering mechanistic reaction sequences for unseen substrate scaffolds, and generalizing effectively to out-of-domain reaction classes with extremely data-efficient fine-tuning. FlowER additionally enables estimation of thermodynamic or kinetic feasibility and manifests a degree of chemical intuition in reaction prediction tasks. This inherently interpretable framework represents a significant step in bridging the gap between predictive accuracy and mechanistic understanding in data-driven reaction outcome prediction.

The 100 MW cryogenic liquid oxygen/hydrogen multi-injector combustor BKD operated by the DLR Institute of Space Propulsion is a research platform that allows the study of thermoacoustic instabilities under realistic conditions, representative of small upper stage rocket engines. We use data from BKD experimental campaigns in which the static chamber pressure and fuel-oxidizer ratio are varied such that the first tangential mode of the combustor is excited under some conditions. We train an autoregressive Bayesian neural network model to forecast the amplitude of the dynamic pressure time series, inputting multiple sensor measurements (injector pressure/ temperature measurements, static chamber pressure, high-frequency dynamic pressure measurements, high-frequency OH* chemiluminescence measurements) and future flow rate control signals. The Bayesian nature of our algorithms allows us to work with a dataset whose size is restricted by the expense of each experimental run, without making overconfident extrapolations. We find that the networks are able to accurately forecast the evolution of the pressure amplitude and anticipate instability events on unseen experimental runs 500 milliseconds in advance. We compare the predictive accuracy of multiple models using different combinations of sensor inputs. We find that the high-frequency dynamic pressure signal is particularly informative. We also use the technique of integrated gradients to interpret the influence of different sensor inputs on the model prediction. The negative log-likelihood of data points in the test dataset indicates that predictive uncertainties are well-characterized by our Bayesian model and simulating a sensor failure event results as expected in a dramatic increase in the epistemic component of the uncertainty.

Knowledge of mixtures' phase equilibria is crucial in nature and technical chemistry. Phase equilibria calculations of mixtures require activity coefficients. However, experimental data on activity coefficients is often limited due to high cost of experiments. For an accurate and efficient prediction of activity coefficients, machine learning approaches have been recently developed. However, current machine learning approaches still extrapolate poorly for activity coefficients of unknown molecules. In this work, we introduce the SMILES-to-Properties-Transformer (SPT), a natural language processing network to predict binary limiting activity coefficients from SMILES codes. To overcome the limitations of available experimental data, we initially train our network on a large dataset of synthetic data sampled from COSMO-RS (10 Million data points) and then fine-tune the model on experimental data (20 870 data points). This training strategy enables SPT to accurately predict limiting activity coefficients even for unknown molecules, cutting the mean prediction error in half compared to state-of-the-art models for activity coefficient predictions such as COSMO-RS, UNIFAC, and improving on recent machine learning approaches.

Gaussian process (GP) regression provides a strategy for accelerating saddle point searches on high-dimensional energy surfaces by reducing the number of times the energy and its derivatives with respect to atomic coordinates need to be evaluated. The computational overhead in the hyperparameter optimization can, however, be large and make the approach inefficient. Failures can also occur if the search ventures too far into regions that are not represented well enough by the GP model. Here, these challenges are resolved by using geometry-aware optimal transport measures and an active pruning strategy using a summation over Wasserstein-1 distances for each atom-type in farthest-point sampling, selecting a fixed-size subset of geometrically diverse configurations to avoid rapidly increasing cost of GP updates as more observations are made. Stability is enhanced by permutation-invariant metric that provides a reliable trust radius for early-stopping and a logarithmic barrier penalty for the growth of the signal variance. These physically motivated algorithmic changes prove their efficacy by reducing to less than a half the mean computational time on a set of 238 challenging configurations from a previously published data set of chemical reactions. With these improvements, the GP approach is established as, a robust and scalable algorithm for accelerating saddle point searches when the evaluation of the energy and atomic forces requires significant computational effort.

We study in detail a one-dimensional lattice model of a continuum, conserved field (mass) that is transferred deterministically between neighbouring random sites. The model falls in a wider class of lattice models capturing the joint effect of random advection and diffusion and encompassing as specific cases, some models studied in the literature, like the Kang-Redner, Kipnis-Marchioro-Presutti, Takayasu-Taguchi, etc. The motivation for our setup comes from a straightforward interpretation as advection of particles in one-dimensional turbulence, but it is also related to a problem of synchronization of dynamical systems driven by common noise. For finite lattices, we study both the coalescence of an initially spread field (interpreted as roughening), and the statistical steady-state properties. We distinguish two main size-dependent regimes, depending on the strength of the diffusion term and on the lattice size. Using numerical simulations and mean-field approach, we study the statistics of the field. For weak diffusion, we unveil a characteristic hierarchical structure of the field. We also connect the model and the iterated function systems concept.

Three epochs in development of chemical dynamics are presented. We try to understand the modern research programs in the light of classical works. Three eras (or waves) of chemical dynamics can be revealed in the flux of research and publications. These waves may be associated with leaders: the first is the van't Hoof wave, the second may be called the Semenov--Hinshelwood wave and the third is definitely the Aris wave. Of course, the whole building was impossible without efforts of hundreds of other researchers. Some of of them are mentioned in our brief review.

A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It utilizes multiple kinetic cycles in time, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein. In the present paper, we thoroughly investigate both the deterministic (microscopic) and stochastic (mesoscopic) models, and focus on the identification of the source of temporal cooperativity via comparing with allosteric cooperativity. A thermodynamic analysis confirms again the claim that the chemical equilibrium state exists if and only if the phosphorylation potential triangle G=0, in which case the amplification of sensitivity is completely abolished. Then we provide comprehensive theoretical and numerical analysis with the first-order and zero-order assumptions in phosphorylation-dephosphorylation cycle respectively. Furthermore, it is interestingly found that the underlying mathematics of temporal cooperativity and allosteric cooperativity are equivalent, and both of them can be expressed by "dissociation constants", which also characterizes the essential differences between the simple and ultrasensitive PdPC switches. Nevertheless, the degree of allosteric cooperativity is restricted by the total number of sites in a single enzyme molecule which can not be freely regulated, while temporal cooperativity is only restricted by the total number of molecules of the target protein which can be regulated in a wide range and gives rise to the ultrasensitivity phenomenon.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

We explore the consequences of multi-trace deformations in applications of gauge-gravity duality to condensed matter physics. We find that they introduce a powerful new "knob" that can implement spontaneous symmetry breaking, and can be used to construct a new type of holographic superconductor. This knob can be tuned to drive the critical temperature to zero, leading to a new quantum critical point. We calculate nontrivial critical exponents, and show that fluctuations of the order parameter are `locally' quantum critical in the disordered phase. Most notably the dynamical critical exponent is determined by the dimension of an operator at the critical point. We argue that the results are robust against quantum corrections and discuss various generalizations.

From a viewpoint of stochastic thermodynamics, we derive equations that describe the collective dynamics near the order-disorder transition in the globally coupled XY model and near the synchronization-desynchronization transition in the Kuramoto model. A new way of thinking is to interpret the deterministic time evolution of a macroscopic variable as an external operation to a thermodynamic system. We then find that the irreversible work determines the equation for the collective dynamics. When analyzing the Kuramoto model, we employ a generalized concept of irreversible work which originates from a non-equilibrium identity associated with steady state thermodynamics.

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

We theoretically identify the noise-induced coherent contribution to the ergotropy of a four-level quantum heat engine coupled to a unimodal quantum cavity. We utilize a protocol where the passive state's quasiprobabilities can be analytically identified from the population-coherence coupled reduced density matrix. The reduced density matrix elements are evaluated using a microscopic quantum master equation formalism. Multiple ergotropies within the same coherence interval, each characterized by a positive and pronounced coherent contribution, are observed. These ergotropies are a result of population inversion as well as quasiprobability-population inversion, controllable through the coherence measure parameters. The optimal flux and power of the engine are found to be at moderate values of ergotropy with increasing values of noise-induced coherence. The optimal power at different coherences is found to possess a constant ergotropy.

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

The striking fractal geometry of strange attractors underscores the generative nature of chaos: like probability distributions, chaotic systems can be repeatedly measured to produce arbitrarily-detailed information about the underlying attractor. Chaotic systems thus pose a unique challenge to modern statistical learning techniques, while retaining quantifiable mathematical properties that make them controllable and interpretable as benchmarks. Here, we present a growing database currently comprising 131 known chaotic dynamical systems spanning fields such as astrophysics, climatology, and biochemistry. Each system is paired with precomputed multivariate and univariate time series. Our dataset has comparable scale to existing static time series databases; however, our systems can be re-integrated to produce additional datasets of arbitrary length and granularity. Our dataset is annotated with known mathematical properties of each system, and we perform feature analysis to broadly categorize the diverse dynamics present across the collection. Chaotic systems inherently challenge forecasting models, and across extensive benchmarks we correlate forecasting performance with the degree of chaos present. We also exploit the unique generative properties of our dataset in several proof-of-concept experiments: surrogate transfer learning to improve time series classification, importance sampling to accelerate model training, and benchmarking symbolic regression algorithms.

In this paper, we examine the thermodynamic behavior of a quantum harmonic oscillator with a position-dependent mass (PDM), where spatial inhomogeneity is modeled through a deformation parameter α. Based on the exact energy spectrum, we explore the resulting thermodynamic quantities and superstatistics. Our findings reveal that increasing α leads to a decrease in entropy and specific heat, reflecting a confinement-induced reduction in the number of accessible states. The partition function and free energy exhibit smooth behavior across all parameter regimes, indicating the absence of critical phase transitions. This study underscores the influence of mass deformation on quantum thermal responses and demonstrates that, while the overall thermodynamic trends are consistent with those reported in the literature, certain distinctive features emerge due to the specific form of the deformation.

A physically motivated equation that determines the number of electrons of a molecule is proposed based on chemical common sense. It shows that all molecules are entangled in the number of electrons and results in the fundamental assumption of molecular energy convexity that underpins molecular quantum mechanics. The proposed physical principle includes the molecular size consistency principle as a special case. Application of wavefunction theory to the principle shows that an individual molecule with a noninteger number of electrons is locally physical albeit locally unreal. The energy of a molecule is piecewise linear with respect to its continuous number of electrons. The continuity of the number of electrons allows the definition of an electronic chemical potential of a single molecule. A state function equivalent to the energy of a molecule can be defined using the chemical potential as a variable. The aforementioned physical principle can alternatively be expressed as a simple additivity with the new state function. The latter also shows that the quantum entanglement in the number of electrons can be viewed as all molecules sharing the same chemical potential.

In contrast to entropy, which increases monotonically, the "complexity" or "interestingness" of closed systems seems intuitively to increase at first and then decrease as equilibrium is approached. For example, our universe lacked complex structures at the Big Bang and will also lack them after black holes evaporate and particles are dispersed. This paper makes an initial attempt to quantify this pattern. As a model system, we use a simple, two-dimensional cellular automaton that simulates the mixing of two liquids ("coffee" and "cream"). A plausible complexity measure is then the Kolmogorov complexity of a coarse-grained approximation of the automaton's state, which we dub the "apparent complexity." We study this complexity measure, and show analytically that it never becomes large when the liquid particles are non-interacting. By contrast, when the particles do interact, we give numerical evidence that the complexity reaches a maximum comparable to the "coffee cup's" horizontal dimension. We raise the problem of proving this behavior analytically.

The Eigenstate Thermalization Hypothesis (ETH) has been established as a cornerstone for understanding thermalization in quantum many-body systems. Recently, there has been growing interest in the full ETH, which extends the framework of the conventional ETH and postulates a smooth function to describe the multi-point correlations among matrix elements. Within this framework, free cumulants play a central role, and most previous studies have primarily focused on closed systems. In this paper, we extend the analysis to a system-bath setup, considering both an idealized case with a random-matrix bath and a more realistic scenario where the bath is modeled as a defect Ising chain. In both cases, we uncover a universal scaling of microcanonical free cumulants of system observables with respect to the interaction strength. Furthermore we establish a connection between this scaling behavior and the thermalization dynamics of the thermal free cumulants of corresponding observables.

Uncovering the rules governing the nonequilibrium dynamics of the membranes that define biological cells is of central importance to understanding the physics of living systems. We theoretically and computationally investigate the behavior of flexible quasispherical vesicles that exchange membrane constituents, internal volume, and heat with an external reservoir. The excess chemical potential and osmotic pressure difference imposed by the reservoir act as generalized thermodynamic driving forces that modulate vesicle morphology. We show that the renormalization of membrane mechanical properties by nonequilibrium driving gives rise to a morphological transition between a weakly driven regime, in which growing vesicles remain quasispherical, and a strongly driven regime, in which vesicles accommodate rapid membrane uptake by developing surface wrinkles. Additionally, we propose a minimal vesicle growth-shape law, derived using insights from stochastic thermodynamics, that robustly describes vesicle growth dynamics even in strongly driven, far-from-equilibrium regimes.

Many chemical concepts can be well defined in the context of quantum chemical theories. Examples are the electronegativity scale of Mulliken and Jaffe and the hard and soft acids and bases concept of Pearson. The sound theoretical basis allows for a systematic definition of such concepts. However, while they are often used to describe and compare chemical processes in terms of reactivity, their predictive power remains unclear. In this work, we elaborate on the predictive potential of chemical reactivity concepts, which can be crucial for autonomous reaction exploration protocols to guide them by first-principles heuristics that expoit these concepts.

Light-matter interactions that lead to nonthermal changes in size of the sample constitute a photostrictive effect in many compounds. The photostriction phenomenon was observed in four main groups of materials, ferroelectrics, polar, and non-polar semiconductors, as well as in organic-based materials that are reviewed here. The key mechanisms of photostriction and its dependence on several parameters and perturbations are assessed. The major literature of the photostriction is surveyed, and the review ends with a summary of the proposed technical applications.

This topical review article gives an overview of the interplay between quantum information theory and thermodynamics of quantum systems. We focus on several trending topics including the foundations of statistical mechanics, resource theories, entanglement in thermodynamic settings, fluctuation theorems and thermal machines. This is not a comprehensive review of the diverse field of quantum thermodynamics; rather, it is a convenient entry point for the thermo-curious information theorist. Furthermore this review should facilitate the unification and understanding of different interdisciplinary approaches emerging in research groups around the world.

The two-body problem of variational electrodynamics possesses differential-delay equations of motion with state-dependent delays of neutral type and solutions that can have velocity discontinuities on countable sets. From a periodic orbit possessing some mild properties at breaking points, we define a synchronization function in R x R3, which is further used to construct two bounded oscillatory functions vanishing at breaking points and whose first derivatives are continuous and defined everywhere but at breaking points. The oscillatory functions are associated with a PDE identity in H2(R3), and we postulate ordering conditions for the PDE identity to define a Fredholm-Schroedinger operator with an O(1/r2) spin-orbit forcing term belonging to L2(R3). As an application, we introduce the Chemical Principle criterion to select orbits with asymptotically vanishing far-fields and estimate the Bohr radius parameter of the Fredholm-Schroedinger PDE using the boundary-layer of orbits chosen according to the Chemical Principle criterion. Last, working backward, we derive a Chemical Principle-like condition from the ordering conditions.

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian. A surrogate energy surface is constructed and updated after each electronic structure calculation. The method is applied to a test set of 500 molecular reactions previously generated by Hermez and coworkers [J. Chem. Theory Comput. 18, 6974 (2022)]. An order of magnitude reduction in the number of electronic structure calculations needed to reach the saddle point configurations is obtained by using the GPR compared to the dimer method. Despite the wide range in stiffness of the molecular degrees of freedom, the calculations are carried out using Cartesian coordinates and are found to require similar number of electronic structure calculations as an elaborate internal coordinate method implemented in the Sella software package. The present implementation of the GPR surrogate model in C++ is efficient enough for the wall time of the saddle point searches to be reduced in 3 out of 4 cases even though the calculations are carried out at a low Hartree-Fock level.

The gradual insertion method for direct calculation of the chemical potential by molecular simulation is applied in the NpT ensemble to different quadrupolar two-centre Lennard-Jones fluids at high density state points. The results agree well with Widom's test particle insertion but show at very high densities significantly smaller statistical uncertainties. The gradual insertion method, which is coupled here with preferential sampling, extends the density range where reliable information on the chemical potential can be obtained. Application details are reported.

The Sherrington-Kirkpatrick spin-glass model used the replica symmetry method to find the phase transition of the system. In 1979-1980, Parisi proposed a solution based on replica symmetry breaking (RSB), which allowed him to identify the underlying phases of complex systems such as spin-glasses. Regardless of the method used for detection, the intrinsic phase of a system exists whether or not replicas are considered. We introduce a single replica method of spin-glass phase detection using the field's variation experienced by each spin in a system configuration. This method focuses on a single replica with quenched random couplings. Each spin inevitably observes a different field from the others. Our results show that the mean and variance of fields named "Spontaneous Configurational Field" experienced by spins are suitable indicators to explore different ferromagnetic, paramagnetic, and mixed phases. To classify different phases of the system with defined indicators we have developed an algorithm based on machine learning to analyze the desired samples.

It has been suggested previously that an ultra-soft fermionic excitation develops, albeit with a small spectral weight, in a system of massless fermions and scalar bosons with Yukawa interaction at high temperature (T). In this paper we study how this excitation is modified at finite chemical potential (μ). We relate the existence of the ultra-soft mode to symmetries, in particular charge conjugation, and a supersymmetry of the free system which is spontaneously broken by finite temperature and finite density effects, as argued earlier by Lebedev and Smilga. A non vanishing chemical potential breaks both symmetries explicitly, and maximally at zero temperature where the mode ceases to exist. A detailed calculation indicates that the ultra-soft excitation persists as long as Tgtrsim μ.

In this paper we consider a particular class of solutions of the Rayleigh-Boltzmann equation, known in the nonlinear setting as homoenergetic solutions, which have the form gleft( x,v,t right) =fleft( v-Lleft( tright)x,tright) where the matrix L(t) describes a shear flow deformation. We began this analysis in [22] where we rigorously proved the existence of a stationary non-equilibrium solution and established the different behaviour of the solutions for small and large values of the shear parameter, for cut-off collision kernels with homogeneity parameter 0leq gamma <1, including Maxwell molecules and hard potentials. In this paper, we concentrate in the case where the deformation term dominates the collision term for large times (hyperbolic-dominated regime). This occurs for collision kernels with gamma < 0 and in particular we focus on gamma in (-1,0). In such a hyperbolic-dominated regime, it appears challenging to provide a clear description of the long-term asymptotics of the solutions. Here we present a formal analysis of the long-time asymptotics for the distribution of velocities and provide the explicit form for the asymptotic profile. Additionally, we discuss the different asymptotic behaviour expected in the case of homogeneity gamma < -1. Furthermore, we provide a probabilistic interpretation describing a stochastic process consisting in a combination of collisions and shear flows. The tagged particle velocity {v(t)}_{tgeq 0} is a Markov process that arises from the combination of free flights in a shear flow along with random jumps caused by collisions.

Critical temperature, T_c, and the transition width, ΔT_c, are two primary parameters of the superconducting transition. The latter parameter reflects the superconducting state disturbance originating from the thermodynamic fluctuations, atomic disorder, applied magnetic field, the presence of secondary crystalline phases, applied pressure, etc. Recently, Hirsch and Marsiglio (2020 arXiv:2012.12796) performed an analysis of the transition width in several near-room-temperature superconductors (NRTS) and reported that the reduced transition width, ΔT_c/T_c, in these materials does not follow a conventional trend of transition width broadening on applied magnetic field observed in low- and high-T_c superconductors. Here we present thorough mathematical analysis of the magnetoresistive data, R(T,B), for the high-entropy alloy (ScZrNb)_{0.65}[RhPd]_{0.35} and hydrogen-rich superconductors of Im-3m-H_{3}S, C2/m-LaH_{10} and P63/mmc-CeH_9. We found that the reduced transition width, ΔT_c/T_c, in these materials does follow a conventional broadening trend on applied magnetic field.

The superfluid phase transition dynamics and associated spontaneous vortex formation with the crossing of the critical temperature in a disk geometry is studied in the framework of the AdS/CFT correspondence by solving the Einstein-Abelian-Higgs model in an AdS_4 black hole. For a slow quench, the vortex density admits a universal scaling law with the cooling rate as predicted by the Kibble-Zurek mechanism (KZM), while for fast quenches, the density shows a universal scaling behavior as a function of the final temperature, that lies beyond the KZM prediction. The vortex number distribution in both the power-law and saturation regimes can be approximated by a normal distribution. However, the study of the universal scaling of the cumulants reveals non-normal features and indicates that vortex statistics in the newborn superfluid is best described by the Poisson binomial distribution, previously predicted in the KZM regime [Phys. Rev. Lett. 124, 240602 (2020)]. This is confirmed by studying the cumulant scalings as a function of the quench time and the quench depth. Our work supports the existence of a universal defect number distribution that accommodates the KZM scaling, its breakdown at fast quenches, and the additional universal scaling laws as a function of the final value of the control parameter.

In this paper, we develop and implement an efficient asymptotic-preserving (AP) scheme to solve the gas mixture of Boltzmann equations under the disparate mass scaling relevant to the so-called "epochal relaxation" phenomenon. The disparity in molecular masses, ranging across several orders of magnitude, leads to significant challenges in both the evaluation of collision operators and the designing of time-stepping schemes to capture the multi-scale nature of the dynamics. A direct implementation of the spectral method faces prohibitive computational costs as the mass ratio increases due to the need to resolve vastly different thermal velocities. Unlike [I. M. Gamba, S. Jin, and L. Liu, Commun. Math. Sci., 17 (2019), pp. 1257-1289], we propose an alternative approach based on proper truncation of asymptotic expansions of the collision operators, which significantly reduces the computational complexity and works well for small varepsilon. By incorporating the separation of three time scales in the model's relaxation process [P. Degond and B. Lucquin-Desreux, Math. Models Methods Appl. Sci., 6 (1996), pp. 405-436], we design an AP scheme that captures the specific dynamics of the disparate mass model while maintaining computational efficiency. Numerical experiments demonstrate the effectiveness of the proposed scheme in handling large mass ratios of heavy and light species, as well as capturing the epochal relaxation phenomenon.

Markov jump processes are continuous-time stochastic processes which describe dynamical systems evolving in discrete state spaces. These processes find wide application in the natural sciences and machine learning, but their inference is known to be far from trivial. In this work we introduce a methodology for zero-shot inference of Markov jump processes (MJPs), on bounded state spaces, from noisy and sparse observations, which consists of two components. First, a broad probability distribution over families of MJPs, as well as over possible observation times and noise mechanisms, with which we simulate a synthetic dataset of hidden MJPs and their noisy observation process. Second, a neural network model that processes subsets of the simulated observations, and that is trained to output the initial condition and rate matrix of the target MJP in a supervised way. We empirically demonstrate that one and the same (pretrained) model can infer, in a zero-shot fashion, hidden MJPs evolving in state spaces of different dimensionalities. Specifically, we infer MJPs which describe (i) discrete flashing ratchet systems, which are a type of Brownian motors, and the conformational dynamics in (ii) molecular simulations, (iii) experimental ion channel data and (iv) simple protein folding models. What is more, we show that our model performs on par with state-of-the-art models which are finetuned to the target datasets.

While attaining external field control of bimolecular chemical reactions has long been a coveted goal of physics and chemistry, the role of hyperfine interactions and dc magnetic fields in achieving such control has remained elusive. We develop an extended coupled-channel statistical theory of barrierless atom-diatom chemical reactions, and apply it to elucidate the effects of magnetic fields and hyperfine interactions on the ultracold chemical reaction Li(^2S_{1/2}) + CaH(^2Σ^+) to LiH(^1Σ^+) + Ca(^1S_{0}) on a newly developed set of ab initio potential energy surfaces. We observe large field effects on the reaction cross sections, opening up the possibility of controlling ultracold barrierless chemical reactions by tuning selected hyperfine states of the reactants with an external magnetic field.

In geometrically frustrated magnetic systems, weak interactions or slight changes to the structure can tip the delicate balance of exchange interactions, sending the system into a different ground state. Brochantite, Cu_4SO_4(OH)_6, has a copper sublattice composed of distorted triangles, making it a likely host for frustrated magnetism, but exhibits stacking disorder. The lack of synthetic single crystals has limited research on the magnetism in brochantite to powders and natural mineral crystals. We grew crystals which we find to be a new polytype with a tendency toward ABAC stacking and some anion disorder, alongside the expected stacking disorder. Comparison to previous results on natural mineral specimens suggests that cation disorder is more deleterious to the magnetism than anion and stacking disorder. Our specific heat data suggest a double transition on cooling into the magnetically ordered state.

Permutation Entropy and statistiCal Complexity Analysis for astRophYsics (PECCARY) is a computationally inexpensive, statistical method by which any time-series can be characterized as predominantly regular, complex, or stochastic. Elements of the PECCARY method have been used in a variety of physical, biological, economic, and mathematical scenarios, but have not yet gained traction in the astrophysical community. This study introduces the PECCARY technique with the specific aims to motivate its use in and optimize it for the analysis of astrophysical orbital systems. PECCARY works by decomposing a time-dependent measure, such as the x-coordinate or orbital angular momentum time-series, into ordinal patterns. Due to its unique approach and statistical nature, PECCARY is well-suited for detecting preferred and forbidden patterns (a signature of chaos), even when the chaotic behavior is short-lived or when working with a relatively short duration time-series or small sets of time-series data. A variety of examples are used to demonstrate the capabilities of PECCARY. These include mathematical examples (sine waves, varieties of noise, sums of sine waves, well-known chaotic functions), a double pendulum system, and astrophysical tracer particle simulations with potentials of varying intricacies. Since the adopted timescale used to diagnose a given time-series can affect the outcome, a method is presented to identify an ideal sampling scheme, constrained by the overall duration and the natural timescale of the system. The accompanying PECCARY Python package and its usage are discussed.

The study demonstrates the capabilities of a vector-based approach for calculating stoichiometric coefficients in chemical equations, using black powder as an illustrative example. A method is proposed for selecting and constraining intermediate interactions between reactants, as well as for identifying final products. It is shown that even a small number of components can lead to a large number of final and intermediate products. Through concrete calculations, a correlation is established between the number of possible chemical equations and the number of reactants. A methodology is proposed for computing all possible chemical equations within a reaction system for arbitrary component ratios, enabling the derivation of all feasible chemical reactions. Additionally, a method is developed for calculating the chemical composition for a fixed set of reactants, allowing for the evaluation of the set of products resulting from all possible chemical interactions given a specified initial composition.

[Abridged] This review paper discussed which chemical effects may be at play in a planet-forming disk midplane, which effects are relevant under different conditions, and which tools are available for modelling chemical kinetics in a disk midplane. The review goes on to discuss some important efforts in the planet formation modelling community to treat chemical evolution, and, vice versa, efforts in the chemical modelling community to implement more physical effects related to planet formation into the chemical modelling. The aim of this review is both to outline some concepts related to planet formation chemistry, but also to encourage, not just collaboration between the planet formation modelling community and the astrochemical community, but also assistance and guidance from one community to the other. Guidance, regarding which effects, out of many, might be more relevant than others under certain planet formation conditions, and regarding why certain included effects lead to certain important modelling outcomes. As the research fields of exoplanet atmospheres and protoplanetary disks near new frontiers in observational insights with upcoming facilities, developing appropriate modelling frameworks (including physical and chemical effects) is paramount to ultimately enable the linking of a chemically characterised exoplanet atmospheres to its formation history in its natal protoplanetary disk.

This work aims to develop a method based on a structurally reliable ice model and a statistically and physico-chemically robust approach for BE distribution inference, with the aim to be applicable to various relevant interstellar species. A multiscale computational approach is presented, with a Molecular Dynamics (MD) Heat & Quench protocol for the amorphous water ice model, and an ONIOM(B3LYP-D3(BJ)/6-311+G**:GFN2-xtb) scheme for the BE inference, with a prime emphasis onto the BE/real system size convergence. The sampling of the binding configurations is twofold, exploring both regularly spaced binding sites, as well as various adsorbate-to-substrate orientations on each locally distinct site. This second source of BE diversity accounts for the local roughness of the potential energy landscape of the substrate. Three different adsorbate test cases are considered, i.e. NH3, CO and CH4, owing to their significance in dust icy mantles, and their distinct binding behavior with water ices. The BE distributions for NH3, CO and CH4 have been inferred, with converged statistics. The distribution for NH3 is better represented by a double Gaussian component profile. Three starting adsorbate orientations per site are required to reach convergence for both Gaussian components of NH3, while 2 orientations are sufficient for CO, and one unique for CH4 (symmetric). Further geometrical and molecular surrounding insights have been provided. These results encompass previously reported results.

We establish a fundamental connection between score-based diffusion models and non-equilibrium thermodynamics by deriving performance limits based on entropy rates. Our main theoretical contribution is a lower bound on the negative log-likelihood of the data that relates model performance to entropy rates of diffusion processes. We numerically validate this bound on a synthetic dataset and investigate its tightness. By building a bridge to entropy rates - system, intrinsic, and exchange entropy - we provide new insights into the thermodynamic operation of these models, drawing parallels to Maxwell's demon and implications for thermodynamic computing hardware. Our framework connects generative modeling performance to fundamental physical principles through stochastic thermodynamics.

Applying the method of moments to the chemical master equation (CME) appearing in stochastic chemical kinetics often leads to the so-called closure problem. Recently, several authors showed that this problem can be partially overcome using moment-based semidefinite programs (SDPs). In particular, they showed that moment-based SDPs can be used to calculate rigorous bounds on various descriptions of the stochastic chemical kinetic system's stationary distribution(s) -- for example, mean molecular counts, variances in these counts, and so on. In this paper, we show that these ideas can be extended to the corresponding dynamic problem, calculating time-varying bounds on the same descriptions.

We study the scalar curvature of the Fisher information metric on the microscopic coupling-parameter manifold of lattice spin models at criticality. For a d-dimensional lattice with periodic boundary conditions and n = L^d sites, the Fisher manifold has m = d cdot n dimensions (one per bond), and we find |R(J_c)| sim n^{d_R} with d_R = (dν+ 2η)/(dν+ η), where ν and η are the correlation-length and anomalous-dimension critical exponents. For 2D Ising (ν= 1, η= 1/4), this predicts d_R = 10/9, confirmed by exact transfer-matrix computations (L = 6--9: d_R = 1.1115 pm 0.0002) and multi-seed MCMC through L = 24. For 3D Ising (ν= 0.630, η= 0.0363), the prediction d_R = 1.019 is consistent with MCMC on L^3 tori up to L = 10 (power-law fit: d_R = 1.040). For 2D Potts q = 3 (predicted 33/29 approx 1.138), FFT-MCMC through L = 40 shows d_eff oscillating non-monotonically around sim 1.20, consistent with O(1/(ln L)^2) logarithmic corrections. For q = 4 (predicted 22/19), effective exponents oscillate with strong logarithmic corrections. The Ricci decomposition identity R_3 = -R_1/2, R_4 = -R_2/2 holds to 5--6 digits for all models. This exponent is distinct from Ruppeiner thermodynamic curvature and reflects the collective geometry of the growing Fisher manifold. We provide falsification criteria and predictions for additional universality classes.