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Clathrate hydrates are vital in energy research and environmental applications. Understanding their stability is crucial for harnessing their potential. In this work, we employ direct coexistence simulations to study finite-size effects in the determination of the three-phase equilibrium temperature (T3) for methane hydrates. Two popular water models, TIP4P/Ice and TIP4P/2005, are employed, exploring various system sizes by varying the number of molecules in the hydrate, liquid, and gas phases. The results reveal that finite-size effects play a crucial role in determining T3. The study includes nine configurations with varying system sizes, demonstrating that smaller systems, particularly those leading to stoichiometric conditions and bubble formation, may yield inaccurate T3 values. The emergence of methane bubbles within the liquid phase, observed in smaller configurations, significantly influences the behavior of the system and can lead to erroneous temperature estimations. Our findings reveal finite-size effects on the calculation of T3 by direct coexistence simulations and clarify the system size convergence for both models, shedding light on discrepancies found in the literature. The results contribute to a deeper understanding of the phase equilibrium of gas hydrates and offer valuable information for future research in this field. [ABSTRACT FROM AUTHOR]

Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute equilibrium properties at a target temperature using reweighting or through Monte Carlo exchanges between replicas at higher temperatures. A recent paper [G. M. Rotskoff and E. Vanden-Eijnden, Phys. Rev. Lett. 122, 150602 (2019)] demonstrated that accurate equilibrium densities of states can also be computed through a nonequilibrium "quench" process, where sampling is performed at a higher temperature to encourage rapid mixing and then quenched to lower energy states with dissipative dynamics. Here, we provide an implementation of the quench dynamics in LAMMPS and evaluate a new formulation of nonequilibrium estimators for the computation of partition functions or free energy surfaces (FESs) of molecular systems. We show that the method is exact for a minimal model of N-independent harmonic springs and use these analytical results to develop heuristics for the amount of quenching required to obtain accurate sampling. We then test the quench approach on alanine dipeptide, where we show that it gives an FES that is accurate near the most stable configurations using the quench approach but disagrees with a reference umbrella sampling calculation in high FE regions. We then show that combining quenching with umbrella sampling allows the efficient calculation of the free energy in all regions. Moreover, by using this combined scheme, we obtain the FES across a range of temperatures at no additional cost, making it much more efficient than standard umbrella sampling if this information is required. Finally, we discuss how this approach can be extended to solute tempering and demonstrate that it is highly accurate for the case of solvated alanine dipeptide without any additional modifications. [ABSTRACT FROM AUTHOR]

Time-aging-time superposition and the concept of single-parameter aging refer to the experimentally verified scenario in which the relaxation profile is shifted as a whole along the logarithmic time or frequency scale during physical aging, i.e., without changing the shape of the susceptibility spectrum or decay function. This homogeneous aspect of aging and structural recovery appears to contrast the heterogeneous nature of structural relaxation in equilibrium. A picture is proposed in which both structural recovery and relaxation are heterogeneous, but lacking a local correlation of time constants. This scenario is consistent with time-aging-time superposition and single-parameter aging, as well as with recovery and relaxation processes being subject to practically the same time constant dispersion. [ABSTRACT FROM AUTHOR]

We conduct dissipative particle dynamics simulations of nonionic surfactant solutions to investigate the statistical properties of micellar recombination. We categorize the recombination events into self-recombination, where two micelles created by scission join together, and non-self-recombination. We find that these two recombination events exhibit distinct statistical properties. The probability density function of the recombination time for self-recombination follows a power law, and we show that the mean squared displacement of the surfactants determines the exponent of the power law. In contrast, the survival function for non-self-recombination is exponential, which is consistent with the mean-field model. For non-self-recombination, we evaluate the mean recombination time for various aggregation numbers, temperatures, and surfactant volume fractions. We find a scaling law describing the mean recombination time of the micelles at equilibrium. [ABSTRACT FROM AUTHOR]

We extend our recently proposed theoretical framework for estimating cavity-modified equilibrium Fermi's golden rule (FGR) rate constants beyond the single cavity mode case to cases where the molecular system is coupled to multiple cavity modes. We show that the cumulative effect of simultaneous coupling to multiple modes can enhance FGR rate constants by orders of magnitude relative to the single mode case. We also present an analysis of the conditions necessary for maximizing this effect in the Marcus limit of FGR-based rate theory. [ABSTRACT FROM AUTHOR]

In this study we derive analytically the equilibrium melting probabilities for basepairs of a DNA molecule with a defect site. We assume that the defect is characterized by a change in the Watson–Crick basepair energy of the defect basepair, and in the associated two stacking energies for the defect, as compared to the remaining parts of the DNA. The defect site could, for instance, occur due to DNA basepair mismatching, cross-linking, or by the chemical modifications when attaching fluorescent labels, such as fluorescent-quencher pairs, to DNA. Our exact solution of the Poland–Scheraga model for DNA melting provides the probability that the labeled basepair, and its neighbors, are open at different temperatures. Our work is of direct importance, for instance, for studies where fluorophore-quencher pairs are used for studying single basepair fluctuations of designed DNA molecules. [ABSTRACT FROM AUTHOR]

We report a method to predict equilibrium concentration profiles of hard ellipses in nonuniform fields, including multiphase equilibria of fluid, nematic, and crystal phases. Our model is based on a balance of osmotic pressure and field mediated forces by employing the local density approximation. Implementation of this model requires development of accurate equations of state for each phase as a function of hard ellipse aspect ratio in the range k = 1–9. The predicted density profiles display overall good agreement with Monte Carlo simulations for hard ellipse aspect ratios k = 2, 4, and 6 in gravitational and electric fields with fluid–nematic, fluid–crystal, and fluid–nematic–crystal multiphase equilibria. The profiles of local order parameters for positional and orientational order display good agreement with values expected for bulk homogeneous hard ellipses in the same density ranges. Small discrepancies between predictions and simulations are observed at crystal–nematic and crystal–fluid interfaces due to limitations of the local density approximation, finite system sizes, and uniform periodic boundary conditions. The ability of the model to capture multiphase equilibria of hard ellipses in nonuniform fields as a function of particle aspect ratio provides a basis to control anisotropic particle microstructure on interfacial energy landscapes in diverse materials and applications. [ABSTRACT FROM AUTHOR]

We describe a multiple electronic state adaptation of the mapping approach to surface hopping introduced recently by Mannouch and Richardson [J. Chem. Phys. 158, 104111 (2023)]. Our modification treats populations and coherences on an equal footing and is guaranteed to give populations in any electronic basis that tend to the correct quantum–classical equilibrium values in the long-time limit (assuming ergodicity). We demonstrate its accuracy by comparison with exact benchmark results for three- and seven-state models of the Fenna–Matthews–Olson complex, obtaining electronic populations and coherences that are significantly more accurate than those of fewest switches surface hopping and at least as good as those of any other semiclassical method we are aware of. Since these results were obtained by adapting the scheme of Mannouch and Richardson, we go on to compare our results with theirs for a variety of problems with two electronic states. We find that their method is sometimes more accurate, especially in the Marcus inverted regime. However, in other situations, the accuracies are comparable, and since our scheme can be used with multiple electronic states it can be applied to a wider variety of electronically nonadiabatic systems. [ABSTRACT FROM AUTHOR]

Determining the role of non-native interactions in folding dynamics, kinetics, and mechanisms is a classic problem in protein folding. More recently, this question has witnessed a renewed interest in light of the hypothesis that knotted proteins require the assistance of non-native interactions to fold efficiently. Here, we conduct extensive equilibrium and kinetic Monte Carlo simulations of a simple off-lattice C-alpha model to explore the role of non-native interactions in the thermodynamics and kinetics of three proteins embedding a trefoil knot in their native structure. We find that equilibrium knotted conformations are stabilized by non-native interactions that are non-local, and proximal to native ones, thus enhancing them. Additionally, non-native interactions increase the knotting frequency at high temperatures, and in partially folded conformations below the transition temperatures. Although non-native interactions clearly enhance the efficiency of transition from an unfolded conformation to a partially folded knotted one, they are not required to efficiently fold a knotted protein. Indeed, a native-centric interaction potential drives the most efficient folding transition, provided that the simulation temperature is well below the transition temperature of the considered model system. [ABSTRACT FROM AUTHOR]

The Robeson bound is a theoretical limit that applies to kinetics-driven membrane separations of gas mixtures. However, this bound does not apply to sorption-driven membrane processes such as CO2/N2 separation, which lacks a theoretical explanation. As a result, we are uncertain about the factors that control the limiting behavior of sorption-driven separations. To address this issue, we employed a simple lattice model and dynamic mean field theory to examine the transport properties of disordered model structures, isolating sorption effects from purely kinetic effects. Our findings indicate that transport effects play a crucial role in sorption-driven processes, and perm-selectivity is consistently lower than sorption selectivity, which is an unattainable limit. We used basic geometric fragments of the structure to explain how transport effects emerge and manifest themselves in sorption-driven processes. [ABSTRACT FROM AUTHOR]

The vibrational dynamics of solids is described by phonons constituting basic collective excitations in equilibrium crystals. Here, we consider a non-equilibrium active solid, formed by self-propelled particles, which bring the system into a non-equilibrium steady-state. We identify novel vibrational collective excitations of non-equilibrium (active) origin, which coexist with phonons and dominate over them when the system is far from equilibrium. These vibrational excitations are interpreted in the framework of non-equilibrium physics, in particular, stochastic thermodynamics. We call them "entropons" because they are the modes of spectral entropy production (at a given frequency and wave vector). The existence of entropons could be verified in future experiments on dense self-propelled colloidal Janus particles and granular active matter, as well as in living systems, such as dense cell monolayers. [ABSTRACT FROM AUTHOR]

Solid–liquid friction plays a key role in nanofluidic systems. Following the pioneering work of Bocquet and Barrat, who proposed to extract the friction coefficient (FC) from the plateau of the Green–Kubo (GK) integral of the solid–liquid shear force autocorrelation, the so-called plateau problem has been identified when applying the method to finite-sized molecular dynamics simulations, e.g., with a liquid confined between parallel solid walls. A variety of approaches have been developed to overcome this problem. Here, we propose another method that is easy to implement, makes no assumptions about the time dependence of the friction kernel, does not require the hydrodynamic system width as an input, and is applicable to a wide range of interfaces. In this method, the FC is evaluated by fitting the GK integral for the timescale range where it slowly decays with time. The fitting function was derived based on an analytical solution of the hydrodynamics equations [Oga et al., Phys. Rev. Res. 3, L032019 (2021)], assuming that the timescales related to the friction kernel and the bulk viscous dissipation can be separated. By comparing the results with those of other GK-based methods and non-equilibrium molecular dynamics, we show that the FC is extracted with excellent accuracy by the present method, even in wettability regimes where other GK-based methods suffer from the plateau problem. Finally, the method is also applicable to grooved solid walls, where the GK integral displays complex behavior at short times. [ABSTRACT FROM AUTHOR]

The equilibrium structure of selenophenol has been investigated using rotational spectroscopy and high-level quantum mechanical calculations, offering electronic and structural insight into the scarcely studied selenium compounds. The jet-cooled broadband microwave spectrum was measured in the 2–8 GHz cm-wave region using broadband (chirped-pulse) fast-passage techniques. Additional measurements up to 18 GHz used narrow-band impulse excitation. Spectral signatures were obtained for six isotopic species of selenium (80Se, 78Se, 76Se, 82Se, 77Se, and 74Se), together with different monosubstituted 13C species. The (unsplit) rotational transitions associated with the non-inverting μa-dipole selection rules could be partially reproduced with a semirigid rotor model. However, the internal rotation barrier of the selenol group splits the vibrational ground state into two subtorsional levels, doubling the dipole-inverting μb transitions. The simulation of the double-minimum internal rotation gives a very low barrier height (B3PW91: 42 cm−1), much smaller than for thiophenol (277 cm−1). A monodimensional Hamiltonian then predicts a huge vibrational separation of 72.2 GHz, justifying the non-observation of μb transitions in our frequency range. The experimental rotational parameters were compared with different MP2 and density functional theory calculations. The equilibrium structure was determined using several high-level ab initio calculations. A final Born–Oppenheimer ( r e BO ) structure was obtained at the coupled-cluster CCSD(T)_ae/cc-wCVTZ level of theory, including small corrections for the wCVTZ → wCVQZ basis set enlargement calculated at the MP2 level. The mass-dependent method with predicates was used to produce an alternative r m (2) structure. The comparison between the two methods confirms the high accuracy of the r e BO structure and offers information on other chalcogen-containing molecules. [ABSTRACT FROM AUTHOR]

We present a time-dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off of the variational path sampling methodology by approximating the time-dependent commitment probability within a neural network ansatz. The reaction mechanisms inferred through this approach are elucidated by a novel decomposition of the rate in terms of the components of a stochastic path action conditioned on a transition. This decomposition affords an ability to resolve the typical contribution of each reactive mode and their couplings to the rare event. The associated rate evaluation is variational and systematically improvable through the development of a cumulant expansion. We demonstrate this method in both over- and under-damped stochastic equations of motion, in low-dimensional model systems, and in the isomerization of a solvated alanine dipeptide. In all examples, we find that we can obtain quantitatively accurate estimates of the rates of the reactive events with minimal trajectory statistics and gain unique insights into transitions through the analysis of their commitment probability. [ABSTRACT FROM AUTHOR]

A new approach for generating Gaussian basis sets is reported and tested for atoms from H to Ne. The basis sets thus calculated, named SIGMA basis sets, range from DZ to QZ sizes and have the same composition per shell as Dunning basis sets but with different treatment of the contractions. The standard SIGMA basis sets and their augmented versions have proven to be very suitable for providing good results in atomic and molecular calculations. The performance of the new basis sets is analyzed in terms of total, correlation, and atomization energies, equilibrium distances, and vibrational frequencies in several molecules, and the results are compared at several computational levels with those obtained with the corresponding Dunning and other basis sets. [ABSTRACT FROM AUTHOR]

Monochromatic waves incident on an array of structures give rise to nonlinear, time-constant mean drift forces (MDFs). These forces depend on the array's spatial configuration; their magnitude and the direction is, in general, different for every structure in the array. If the spatial configuration of an array is not fixed, as is the case in arrays of individually anchor-moored structures, the time-constant differences in MDF on individual bodies can lead to a change in spatial configuration, which could, in turn, significantly affect both the first-order, time-harmonic response of the array, as well as the downwave component of the MDF. Here, we explore the dependency of these deviatoric forces on array configurations and on the frequency of the incident monochromatic waves. We consider configurations of line arrays (consisting of 2–5 vertical circular cylinders) that are described by 1 or 2 parameters, and we focus on the along-array component of deviatoric forces. Using multiple scattering computational simulations, we identify the array configurations in which the deviatoric drift forces are zero, and we discuss the stability of these equilibrium configurations with respect to class-preserving configuration perturbations. Both stable and unstable equilibria exist, but the relative number of unstable equilibria grows as the number of degrees of freedom of the configuration perturbations increases. Interestingly, the stable configurations experience a generally lower downwave mean drift force on the entire array than the unstable ones. Overall, the variations in the deviatoric and the downwave MDFs between equilibria are significant (on the order of the isolated body MDF). [ABSTRACT FROM AUTHOR]

In striking contrast to equilibrium systems, inertia can profoundly alter the structure of active systems. Here, we demonstrate that driven systems can exhibit effective equilibrium-like states with increasing particle inertia, despite rigorously violating the fluctuation–dissipation theorem. Increasing inertia progressively eliminates motility-induced phase separation and restores equilibrium crystallization for active Brownian spheres. This effect appears to be general for a wide class of active systems, including those driven by deterministic time-dependent external fields, whose nonequilibrium patterns ultimately disappear with increasing inertia. The path to this effective equilibrium limit can be complex, with finite inertia sometimes acting to accentuate nonequilibrium transitions. The restoration of near equilibrium statistics can be understood through the conversion of active momentum sources to passive-like stresses. Unlike truly equilibrium systems, the effective temperature is now density dependent, the only remnant of the nonequilibrium dynamics. This density-dependent temperature can in principle introduce departures from equilibrium expectations, particularly in response to strong gradients. Our results provide additional insight into the effective temperature ansatz while revealing a mechanism to tune nonequilibrium phase transitions. [ABSTRACT FROM AUTHOR]

We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of hard spheres in d = 3 dimensions and, thus, obtain an estimate of the random close packing volume fraction, ϕRCP, as a function of size polydispersity. We first consider mixtures of particle sizes with discrete distributions. For binary systems, we show agreement between our predictions and simulations using both our own results and results reported in previous studies, as well as agreement with recent experiments from the literature. We then apply our approach to systems with continuous polydispersity using three different particle size distributions, namely, the log-normal, Gamma, and truncated power-law distributions. In all cases, we observe agreement between our theoretical findings and numerical results up to rather large polydispersities for all particle size distributions when using as reference our own simulations and results from the literature. In particular, we find ϕRCP to increase monotonically with the relative standard deviation, sσ, of the distribution and to saturate at a value that always remains below 1. A perturbative expansion yields a closed-form expression for ϕRCP that quantitatively captures a distribution-independent regime for sσ < 0.5. Beyond that regime, we show that the gradual loss in agreement is tied to the growth of the skewness of size distributions. [ABSTRACT FROM AUTHOR]

Thermogalvanic cells convert waste heat directly to electric work. There is an abundance of waste heat in the world and thermogalvanic cells may be underused. We discuss theoretical tools that can help us understand and therefore improve on cell performance. One theory is able to describe all aspects of the energy conversion: nonequilibrium thermodynamics. We recommend to use the theory with operationally defined, independent variables, as others have done before. These describe well-defined experiments. Three invariance criteria serve as a basis for any description: of local electroneutrality, entropy production invariance, and emf's independence of the frame of reference. Alternative formalisms, using different sets of variables, start with ionic or neutral components. We show that the heat flux is not the same in the two formalisms and derive a new relationship between the heat fluxes. The heat flux enters the definition of the Peltier coefficient and is essential for the understanding of the Peltier heat at the electrode interfaces and of the Seebeck coefficient of the cell. The Soret effect can occur independently of any Seebeck effect, but the Seebeck effect will be affected by the presence of a Soret effect. Common misunderstandings are pointed out. Peltier coefficients are needed for the interpretation and design of experiments. [ABSTRACT FROM AUTHOR]

For a molecular glass-former, propylene glycol, we directly compare the equilibrium fluctuations, measured as "structural" relaxation in the regime of linear response, with structural recovery, i.e., field induced physical aging in the limit of a small perturbation. The two distinct correlation functions are derived from a single experiment. Because the relaxation time changes only 2% during structural recovery, no aging model is needed to analyze the results. Although being conceptually different processes, dielectric relaxation and recovery dynamics are observed to be identical for propylene glycol, whereas single-particle dynamics as seen by photon correlation spectroscopy are significantly faster. This confirms the notion that structural recovery and aging are governed by all modes observed by dielectric spectroscopy, i.e., including cross correlations, not only by single-particle dynamics. A comparison with analogous results for other materials suggests that the relation between relaxation and recovery time scales may be material specific rather than universal. [ABSTRACT FROM AUTHOR]

Physical kinetic roughening processes are well-known to exhibit universal scaling of observables that fluctuate in space and time. Are there analogous dynamic scaling laws that are unique to the chemical reaction mechanisms available synthetically and occurring naturally? Here, we formulate an approach to the dynamic scaling of stochastic fluctuations in thermodynamic observables at and away from equilibrium. Both analytical expressions and numerical simulations confirm our dynamic scaling ansatz with associated scaling exponents, function, and law. A survey of common chemical mechanisms reveals classes that organize according to the molecularity of the reactions involved, the nature of the reaction vessel and external reservoirs, (non)equilibrium conditions, and the extent of autocatalysis in the reaction network. Varying experimental parameters, such as temperature, can cause coupled reactions capable of chemical feedback to transition between these classes. While path observables, such as the dynamical activity, have scaling exponents that are time-independent, the variance in the entropy production and flow can have time-dependent scaling exponents and self-averaging properties as a result of temporal correlations that emerge during thermodynamically irreversible processes. Altogether, these results establish dynamic universality classes in the nonequilibrium fluctuations of thermodynamic observables for well-mixed chemical reactions. [ABSTRACT FROM AUTHOR]

Pyrene fluorescence after a high-energy electronic excitation exhibits a prominent band shoulder not present after excitation at low energies. The standard assignment of this shoulder as a non-Kasha emission from the second-excited state (S2) has been recently questioned. To elucidate this issue, we simulated the fluorescence of pyrene using two different theoretical approaches based on vertical convolution and nonadiabatic dynamics with nuclear ensembles. To conduct the necessary nonadiabatic dynamics simulations with high-lying electronic states and deal with fluorescence timescales of about 100 ns of this large molecule, we developed new computational protocols. The results from both approaches confirm that the band shoulder is, in fact, due to S2 emission. We show that the non-Kasha behavior is a dynamic-equilibrium effect not caused by a metastable S2 minimum. However, it requires considerable vibrational energy, which can only be achieved in collisionless regimes after transitions into highly excited states. This strict condition explains why the S2 emission was not observed in some experiments. [ABSTRACT FROM AUTHOR]

A long-standing question in the Reynolds-averaged modeling of turbulent flow is how to predict accurately flows with temporal or spatial unsteadiness. In this paper, we present a "return to equilibrium" approach to modeling the unsteady Reynolds stress anisotropy bij in terms of differential transport equations, the solutions to which are constrained by algebraic closures for bij in flows at equilibrium and by the corresponding rapid-distortion-theory solutions for flows far from equilibrium. When coupled with scale equations for the turbulent kinetic energy and the dissipation rate, these anisotropy evolution equations comprise a complete closure scheme for which no additional model coefficients are required. Evaluations of this closure scheme, in which two different existing equilibrium algebraic models for bij were employed, were carried out for homogeneous turbulence in flows with a step imposition of shear, with continuously oscillatory shear at different frequencies and with a prescribed time-dependent plane-strain rate. Good agreement was achieved between model predictions and experimental/simulation target data in all test cases, with either Girimaji's bij model or a structure-based bij model used as the equilibrium algebraic closure. [ABSTRACT FROM AUTHOR]

Air Taylor bubbles in a millichannel filled with water are characterized by an elongated shape, a bullet-shaped nose (head), and a comparatively flat tail. Many experimental and numerical investigations have been performed in the past. Yet, most of them consider Taylor bubbles in a straight channel with constant cross section. The effect of a local change in the channel geometry on both the bubble shape and the flow fields on each side of the gas–liquid interface is, however, difficult to predict. In this work, we present experimental data obtained in a vertical millichannel, where the flow is moderately obstructed by a constriction, whose ratio ranges from 10% to 36%. We find that the Taylor bubble takes an equilibrium position for downward liquid flow with 264.36 < Re < 529.67 and 264.36 < Re < 728.29 for 10.17% and 18.06% constriction ratios, respectively. In this area, an empirical correlation characterizing the bubble head is provided. Other flow regimes, such as bubble breakup, co- and countercurrent configurations, are identified and shown in the form of a regime map. The results, besides their relevance in process engineering, exhibit high reproducibility and will serve as a reference for future interface-resolving two-phase flow simulations. [ABSTRACT FROM AUTHOR]

A large number of magnetohydrodynamic (MHD) equilibrium calculations are often required for uncertainty quantification, optimization, and real-time diagnostic information, making MHD equilibrium codes vital to the field of plasma physics. In this paper, we explore a method for solving the Grad–Shafranov equation by using physics-informed neural networks (PINNs). For PINNs, we optimize neural networks by directly minimizing the residual of the partial differential equation as a loss function. We show that PINNs can accurately and effectively solve the Grad–Shafranov equation with several different boundary conditions, making it more flexible than traditional solvers. This method is flexible as it does not require any mesh and basis choice, thereby streamlining the computational process. We also explore the parameter space by varying the size of the model, the learning rate, and boundary conditions to map various tradeoffs such as between reconstruction error and computational speed. Additionally, we introduce a parameterized PINN framework, expanding the input space to include variables such as pressure, aspect ratio, elongation, and triangularity in order to handle a broader range of plasma scenarios within a single network. Parameterized PINNs could be used in future work to solve inverse problems such as shape optimization. [ABSTRACT FROM AUTHOR]

We use the 3D magnetohydrodynamic (MHD) code M3D-C1 [Jardin et al., Comput. Sci. Discovery 5, 014002 (2012)] to examine the MHD stability and subsequent evolution of NSTX shot 129169. This discharge had a period with a non-monotonic safety factor profile, q (reversed shear), which was terminated by a MHD event that abruptly lowered the central safety factor, q0, and greatly reduced the peakedness of the pressure profile. We show that the equilibrium just before the MHD event occurred was linearly unstable to many pressure-driven infernal modes. Modes with toroidal mode number n ≥ 3 all had rational surfaces very close to the minimum value of q. However, a non-resonant pressure-driven (1, 1) mode was also present, and this dominated the nonlinear evolution. The final state in the simulation, after the MHD activity subsided, had a reduced and flattened pressure profile and a nearly monotonic q-profile, in qualitative agreement with experimental results. The initial state was also unstable to the resistive interchange criteria in the reversed-shear region, but the final state was stable everywhere. The "double tearing mode" (DTM) does not appear to play a role in the MHD activity of this discharge. In Appendix A, we show that in a torus, the DTM is strongly stabilized by pressure, but it is destabilized in cylindrical geometry (which has been the most extensively analyzed in the literature). [ABSTRACT FROM AUTHOR]

In this paper, we explore the local dynamics, chaos, and bifurcations of a discrete Rosenzweig–Macarthur prey–predator model. More specifically, we explore local dynamical characteristics at equilibrium solutions of the discrete model. The existence of bifurcations at equilibrium solutions is also studied, and that at semitrivial and trivial equilibrium solutions, the model does not undergo flip bifurcation, but at positive equilibrium solutions, it undergoes flip and Neimark–Sacker bifurcations when parameters go through certain curves. Fold bifurcation does not exist at positive equilibrium, and we have studied these bifurcations by the center manifold theorem and bifurcation theory. We also studied chaos by the feedback control method. The theoretical results are confirmed numerically. [ABSTRACT FROM AUTHOR]

The paper presents a simple yet rigorous analysis of the transient of the spatial distribution of the kinetic energy of a classical ideal monoatomic dilute gas that passes from non-equilibrium to equilibrium. The proposed approach is event-based, in the sense that the evolution of the system is analyzed as a function of the random number of collisions in a given time interval. Taking a very simple yet realistic model of collision, the paper shows that collisions between atoms lead exponentially to energy equipartition. [ABSTRACT FROM AUTHOR]

This paper investigated a multi-modular magnetic microrobot/millirobot (MMM) with a serial chain structure consisting of multiple identical modules. Depending on the magnet pattern used for the MMM's modules, an MMM can have different equilibrium postures under an external magnetic field, such as assembled ring and disassembled straight-line postures. In this study, we investigated the equilibrium and locomotion characteristics of the MMM by applying two different representative magnet patterns, considered to be effective for magnetic actuation, to the robots. We established various equations to determine and control the assembly, disassembly, and locomotion of the MMM with each magnet pattern. We also conducted various experiments demonstrating the assembly, disassembly, and cargo delivery capabilities of the MMM under different external magnetic fields. Results confirmed that each MMM and their magnet pattern have distinctive and useful characteristics, demonstrating that the two magnet patterns can be selectively and effectively used as MMM in different applications. [ABSTRACT FROM AUTHOR]

The equilibrium states of multisublattice magnets with spin s = 3/2 are studied. The developed approach essentially uses the symmetry properties of the Hamiltonian, the idea of the residual symmetry of the equilibrium state, and the form of order parameters. On this basis, without using any model assumptions, classification equations for order parameters are obtained. Solutions of these equations are given in cases of broken SU(3) and SU(4) symmetries. The equilibrium structure of order parameters is presented in terms of the spontaneous anisotropy parameters of the residual symmetry generator. [ABSTRACT FROM AUTHOR]

In this paper, an improved probability model is introduced to provide a more comprehensive prediction of annular flow. Unlike previous work, which did not consider atomization and deposition, as well as breakup and coalescence, simultaneously, the improved model integrates all four processes into its framework. The mechanisms of these processes are described in detail by the present model. When annular flow is fully developed, the four processes reach dynamic equilibrium. A numerical program is compiled based on the influence of the four processes on the droplets. Five important parameters, including the droplet-diameter probability density distribution, characteristic droplet diameters, entrainment ratio, liquid film thickness, and interfacial shear-stress coefficient, are calculated when the annular flow is in dynamic equilibrium. The validity and accuracy of the improved model are assessed by comparison with 377 cases from 12 experiments. For most cases used to validate the predicted droplet-diameter probability density distribution, the prediction curves closely match the experimental data. The mean absolute percentage errors (MAPEs) for the two experiments used to validate the predicted characteristic droplet diameters are 20.74% and 24.04%, respectively. Additionally, the mean MAPEs of the entrainment ratio, liquid film thickness, and interfacial shear-stress coefficient are found to be 34.11%, 20.60%, and 27.28%, respectively. This demonstrates the effectiveness and reliability of the improved probability model in predicting annular flow. [ABSTRACT FROM AUTHOR]

The outbreak of infectious diseases often exhibits periodicity, and this periodic behavior can be mathematically represented as a limit cycle. However, the periodic behavior has rarely been considered in demonstrating the cluster phenomenon of infection induced by diffusion (the instability modes) in the SIR model. We investigate the emergence of Turing instability from a stable equilibrium and a limit cycle to illustrate the dynamical and biological mechanisms of pattern formation. We identify the Hopf bifurcation to demonstrate the existence of a stable limit cycle using First Lyapunov coefficient in our spatiotemporal diffusion-driven SIR model. The competition between different instability modes induces different types of patterns and eventually spot patterns emerge as stable patterns. We investigate the impact of susceptible, infected, and recovered individuals on the type of patterns. Interestingly, these instability modes play a vital role in selecting the pattern formations, which is directly related to the number of observed spot patterns. Subsequently, we explain the dynamical and biological mechanisms of spot patterns to develop an effective epidemic prevention strategy. [ABSTRACT FROM AUTHOR]

The recent pandemic has highlighted the need to understand how we resist infections and their causes, which may differ from the ways we often think about treating epidemic diseases. The current study presents an improved version of the susceptible-infected-recovered (S I R) epidemic model, to better comprehend the community's overall dynamics of diseases, involving numerous infectious agents. The model deals with a non-monotone incidence rate that exhibits psychological or inhibitory influence and a saturation treatment rate. It has been identified that depending on the measure of medical resources and the effectiveness of their supply, the model exposes both forward and backward bifurcations where two endemic equilibria coexist with infection-free equilibrium. The model also experiences local and global bifurcations of codimension two, including saddle-node, Hopf, and Bogdanov–Takens bifurcations. Additionally, the stability of equilibrium points is investigated. For a spatially extended S I R model system, we have shown that cross-diffusion allows S and I populations to coexist in a habitat. Also, the Turing instability requirements and Turing bifurcation regime are derived. The relationship between distinct role-playing model parameters and various pattern formations like spot and stripe patterns is validated by carrying out in-depth numerical simulations. The findings in the vicinity of the endemic equilibrium solution demonstrate the significance of positive and negative valued cross-diffusion coefficients in regulating the genesis of spatial patterns in susceptible as well as diseased individuals. The discussion of the findings of epidemiological ramifications concludes the manuscript. [ABSTRACT FROM AUTHOR]

We experimentally investigate the motion of a pendulum on a turntable. The dynamics of this conical pendulum experiment are very rich and can be studied both at the undergraduate and graduate levels. At low rotational frequency of the turntable, we measure the Coriolis acceleration. Increasing the rotational frequency, we experimentally demonstrate a supercritical pitchfork bifurcation: above a critical rotational frequency, the pendulum arm spontaneously rises up. Beyond the characterization of the equilibrium pendulum angle, we evidence the so-called critical slowing down corresponding to the increase in the pendulum period when approaching the critical rotational frequency. Bifurcation and critical slowing down are key concepts in the study of critical phenomena that are seldom illustrated experimentally. All our experimental measurements are in excellent quantitative agreement with the theory we provide. [ABSTRACT FROM AUTHOR]

Extensive experimental evidence has shown that the presence of poloidal flow in tokamaks can dramatically improve transport properties. However, theory indicates that poloidal flows are damped by poloidal viscosity, thus necessitating external drivers, such as neutral beam injection or radio frequency heating. In this work, ideal magnetohydrodynamic equilibria are calculated via the FORTRAN code FLOW [Guazzotto et al., Phys. Plasmas 11, 604 (2004)] and a postprocessor is used to estimate the neoclassical poloidal viscosity. The equilibrium inputs, which correspond to intuitive physical quantities, are then numerically optimized to reduce a viscosity figure of merit. We present supersonic equilibria in tokamak geometry with minimized neoclassical poloidal viscosities for various velocity free function inputs, plasma aspect ratios, and collisionality regimes. Benchmarks are made against an analytic theory as well as a classical expression of poloidal viscosity. Numerical confirmation of the analytic theory is obtained in the high aspect ratio and high collisionality limit. Good agreement is also seen near the plasma core and edge, with discrepancies arising in the intermediate region. Outside of these limits, rotation input function profiles are found that provide ∼order of magnitude improvements over the analytic theory, with additional progress being made toward predictions for tokamak-relevant equilibria. [ABSTRACT FROM AUTHOR]

The bulk viscosity, ηb, of the hard sphere (HS) fluid is computed by equilibrium and nonequilibrium molecular dynamics (NEMD) simulations, the latter using an adaptation of the time-stepping method for continuous potential systems invented by Hoover et al. [Phys. Rev. A 21, 1756 (1980)], which employs an imposed cyclic density variation on the system by affine scaling of the particle coordinates. The time-stepping method employed for HS is validated against exact event-driven hard sphere methodology for a series of equilibrium quantities over a wide density range, including the pressure, singular parts of the hard sphere viscosities, and the nonsingular parts of the shear viscosity time correlation functions. The time steps used are typically only a little smaller than those employed in continuous potential simulations. Exact pressure tensor fluctuation expressions are derived for the singular (or infinite limiting frequency) equilibrium parts of the viscosities, which were employed in the simulations. The values obtained agree well with the predictions of the Enskog theory for all densities considered. The bulk viscosity obtained by NEMD is shown to be noticeably frequency dependent for densities in excess of ∼0.8, decaying approximately exponentially to the Enskog and equilibrium simulation values at all densities considered for frequencies in excess of ∼5 in hard sphere units. Temperature profiles during the cycle and the effects of strain amplitude on the computed frequency dependent bulk viscosity are presented. The bulk viscosity increases with the maximum density amplitude. [ABSTRACT FROM AUTHOR]

We present a classical molecular-dynamics study of the collective dynamical properties of the coexisting liquid phase at equilibrium body-centered cubic (BCC) Fe crystal–melt interfaces. For the three interfacial orientations (100), (110), and (111), the collective dynamics are characterized through the calculation of the intermediate scattering functions, dynamical structure factors, and density relaxation times in a sequential local region of interest. An anisotropic speedup of the collective dynamics in all three BCC crystal–melt interfacial orientations is observed. This trend differs significantly from the previously observed slowing down of the local collective dynamics at the liquid–vapor interface [del Rio and González, Acta Mater. 198, 281 (2020)]. Examining the interfacial density relaxation times, we revisit the validity of the recently developed time-dependent Ginzburg–Landau theory for the solidification crystal–melt interface kinetic coefficients, resulting in excellent agreement with both the magnitude and the kinetic anisotropy of the crystal–melt interface kinetic coefficients measured from the non-equilibrium molecular-dynamics simulations. [ABSTRACT FROM AUTHOR]

The 1H- and 2H-1,2,3-triazoles are isomeric five-membered ring, aromatic heterocycles that may undergo chemical equilibration by virtue of intramolecular hydrogen migration (tautomerization). Using millimeter-wave spectroscopy in the 130–375 GHz frequency range, we measured the spectroscopic constants for thirteen 1H-1,2,3-triazole and sixteen 2H-1,2,3-triazole isotopologues. Herein, we provide highly accurate and highly precise semi-experimental equilibrium (reSE) structures for the two tautomers based on the spectroscopic constants of each set of isotopologues, together with vibration–rotation interaction and electron-mass distribution corrections calculated using coupled-cluster singles, doubles, and perturbative triples calculations [CCSD(T)/cc-pCVTZ]. The resultant structures are compared with a "best theoretical estimate" (BTE), which has recently been shown to be in exceptional agreement with the semi-experimental equilibrium structures of other aromatic molecules. Bond distances of the 1H tautomer are determined to <0.0008 Å and bond angles to <0.2°. For the 2H tautomer, bond angles are also determined to <0.2°, but bond distances are less precise (2σ ≤ 0.0015). Agreement between BTE and reSE values is discussed. [ABSTRACT FROM AUTHOR]

We present a general method for computing interfacial free energies from atomistic simulations, which is particularly suitable for solid/liquid interfaces. Our method uses an Einstein crystal as a universal reference state and is more flexible than previous approaches. Surfaces with dipoles, complex reconstructions, and miscible species are all easily accommodated within the framework. It may also be extended to calculating the relative free energies of different phases and other types of defect. We have applied our method to interfaces of bassanite and gypsum with water and obtained interfacial free energies of the order of 0.12 J/m2, of which ∼45% is due to entropic contributions. Our calculations of the interfacial free energy of NaCl with water obtained a value of 0.13 J/m2, of which only 19% is from entropic contributions. We have also predicted equilibrium morphologies for bassanite and gypsum that compare well with experiments and previous calculations. [ABSTRACT FROM AUTHOR]

While many physical processes are non-equilibrium in nature, the theory and modeling of such phenomena lag behind theoretical treatments of equilibrium systems. The diversity of powerful theoretical tools available to describe equilibrium systems has inspired strategies that map non-equilibrium systems onto equivalent equilibrium analogs so that interrogation with standard statistical mechanical approaches is possible. In this work, we revisit the mapping from the non-equilibrium random sequential addition process onto an equilibrium multi-component mixture via the replica method, allowing for theoretical predictions of non-equilibrium structural quantities. We validate the above approach by comparing the theoretical predictions to numerical simulations of random sequential addition. [ABSTRACT FROM AUTHOR]

We measured the solid–liquid–vapor (SLV) equilibrium of binary mixtures during experiments that alternated between cooling the mixture and injecting the more-volatile component into the sample chamber; thus, the composition of the mixture changed (non-isoplethic) throughout the experiment. Four binary mixtures were used in the experiments to represent mixtures with miscible solid phases (N2/CO) and barely miscible solid solutions (N2/C2H6), as well as mixtures with intermediate solid miscibility (N2/CH4 and CO/CH4). We measured new SLV pressure data for the binary mixtures, except for N2/CH4, which are also available in the literature for verification in this work. While these mixtures are of great interest in planetary science and cryogenics, the resulting pressure data are also needed for modeling purposes. We found the results for N2/CH4 to be consistent with the literature. The resulting new SLV curve for CO/CH4 shows similarities to N2/CH4. Both have two density inversion points (bracketing the temperature range where the solid floats). This result is important for places such as Pluto, Triton, and Titan, where these mixtures exist in vapor, liquid, and solid phases. Based on our experiments, the presence of a eutectic is unlikely for the N2/CH4 and CO/CH4 systems. An azeotrope with or without a peritectic is likely, but further investigations are needed to confirm. The N2/CO system does not have a density inversion point, as the ice always sinks in its liquid. For N2/C2H6, new SLV pressure data were measured near each triple point of the pure components. [ABSTRACT FROM AUTHOR]

Modulating the interaction potential between colloids suspended in a fluid can trigger equilibrium phase transitions as well as the formation of non-equilibrium "arrested states," such as gels and glasses. Faithful representation of such interactions is essential for using simulation to interrogate the microscopic details of non-equilibrium behavior and for extrapolating observations to new regions of phase space that are difficult to explore in experiments. Although the extended law of corresponding states predicts equilibrium phases for systems with short-ranged interactions, it proves inadequate for equilibrium predictions of systems with longer-ranged interactions and for predicting non-equilibrium phenomena in systems with either short- or long-ranged interactions. These shortcomings highlight the need for new approaches to represent and disambiguate interaction potentials that replicate both equilibrium and non-equilibrium phase behavior. In this work, we use experiments and simulations to study a system with long-ranged thermoresponsive colloidal interactions and explore whether a resolution to this challenge can be found in regions of the phase diagram where temporal effects influence material state. We demonstrate that the conditions for non-equilibrium arrest by colloidal gelation are sensitive to both the shape of the interaction potential and the thermal quench rate. We exploit this sensitivity to propose a kinetics-based algorithm to extract distinct arrest conditions for candidate potentials that accurately selects between potentials that differ in shape but share the same predicted equilibrium structure. The algorithm selects the candidate that best matches the non-equilibrium behavior between simulation and experiments. Because non-equilibrium behavior in simulation is encoded entirely by the interparticle potential, the results are agnostic to the particular mechanism(s) by which arrest occurs, and so we expect our method to apply to a range of arrested states, including gels and glasses. Beyond its utility in constructing models, the method reveals that each potential has a quantitatively distinct arrest line, providing insight into how the shape of longer-ranged potentials influences the conditions for colloidal gelation. [ABSTRACT FROM AUTHOR]

A system's configurational state can be manipulated using dynamic variation of control parameters, such as temperature, pressure, or magnetic field; for finite-duration driving, excess work is required above the equilibrium free-energy change. Minimum-work protocols in multidimensional control-parameter space have the potential to significantly reduce work relative to one-dimensional control. By numerically minimizing a linear-response approximation to the excess work, we design protocols in control-parameter spaces of a 2D Ising model that efficiently drive the system from the all-down to all-up configuration. We find that such designed multidimensional protocols take advantage of more flexible control to avoid control-parameter regions of high system resistance, heterogeneously input and extract work to make use of system relaxation, and flatten the energy landscape, making accessible many configurations that would otherwise have prohibitively high energy and, thus, decreasing spin correlations. Relative to one-dimensional protocols, this speeds up the rate-limiting spin-inversion reaction, thereby keeping the system significantly closer to equilibrium for a wide range of protocol durations and significantly reducing resistance and, hence, work. [ABSTRACT FROM AUTHOR]

In the present study, using dynamic mean field theory complemented by grand canonical molecular dynamics simulations, we investigate the extent to which the density distributions encountered during the dynamics of capillary condensation are related to those distributions at equilibrium or metastable equilibrium in a system at fixed average density (canonical ensemble). We find that the states encountered can be categorized as out of equilibrium or quasi-equilibrium based on the magnitude of the driving force for mass transfer. More specifically, in open-ended slit pores, pore filling via double bridging is an out of equilibrium process, induced by the dynamics of the system, while pore filling by single bridge formation is connected to a series of configurations that are equilibrium configurations in the canonical ensemble and that cannot be observed experimentally by a standard adsorption process, corresponding to the grand canonical ensemble. Likewise, in closed cap slits, the formation of a liquid bridge near the pore opening and its subsequent growth while the initially detached meniscus from the capped end remains immobilized are out of equilibrium processes that occur at large driving forces. On the other hand, at small driving forces, there is a continuous acceleration of the detached meniscus from the capped end, which is associated with complete reversibility in the limit of an infinitesimally small driving force. [ABSTRACT FROM AUTHOR]