The oscillating Fischer-Tropsch reaction.

The mechanistic steps that underlie the formation of higher hydrocarbons in catalytic carbon monoxide (CO) hydrogenation at atmospheric pressure over cobalt-based catalysts (Fischer-Tropsch synthesis) have remained poorly understood. We reveal nonisothermal rate-and-selectivity oscillations that are self-sustained over extended periods of time (>24 hours) for a cobalt/cerium oxide catalyst with an atomic ratio of cobalt to cerium of 2:1 (Co2Ce1) at 220°C and equal partial pressures of the reactants. A microkinetic mechanism was used to generate rate-and-selectivity oscillations through forced temperature oscillations. Experimental and theoretical oscillations were in good agreement over an extended range of reactant pressure ratios. Additionally, phase portraits for hydrocarbon production were constructed that support the thermokinetic origin of our rate-and-selectivity oscillations.

Comment on "Validity of path thermodynamic description of reactive systems: Microscopic simulations".

The assertions made in a recent paper [Phys. Rev. E 107, 014106 (2023)10.1103/PhysRevE.107.014106] regarding the validity of path thermodynamics are ill founded and contradict well-known results. Following up on a previous Comment, I show that, for both models of chemical reaction networks considered in the aforementioned paper, path thermodynamics yields values of the entropy production rates fully consistent with those expected from standard chemical thermodynamics in the large-system limit.

Quantum local-equilibrium approach to dissipative hydrodynamics.

The macroscopic hydrodynamic equations are derived for many-body systems in the local-equilibrium approach, using the Schrödinger picture of quantum mechanics. In this approach, statistical operators are defined in terms of microscopic densities associated with the fundamentally conserved quantities and other slow modes possibly emerging from continuous symmetry breaking, as well as macrofields conjugated to these densities. Functional identities can be deduced, allowing us to identify the reversible and dissipative parts of the mean current densities, to obtain general equations for the time evolution of the conjugate macrofields, and to establish the relationship to projection-operator methods. The entropy production is shown to be nonnegative by applying the Peierls-Bogoliubov inequality to a quantum integral fluctuation theorem. Using the expansion in the gradients of the conjugate macrofields, the transport coefficients are given by Green-Kubo formulas and the entropy production rate can be expressed in terms of quantum Einstein-Helfand formulas, implying its nonnegativity in agreement with the second law of thermodynamics. The results apply to multicomponent fluids and can be extended to condensed matter phases with broken continuous symmetries.

Comment on "Validity of path thermodynamics in reactive systems".

The paper by Malek Mansour and Garcia [Phys. Rev. E 101, 052135 (2020)2470-004510.1103/PhysRevE.101.052135] is shown to be based on misconceptions in the stochastic formulation of chemical thermodynamics in reactive systems. Their erroneous claims, asserting that entropy production cannot be correctly evaluated using path probabilities whenever the reactive system involves more than one elementary reaction leading to the same composition changes, are refuted.

Emergence of homochirality in large molecular systems.

The selection of a single molecular handedness, or homochirality across all living matter, is a mystery in the origin of life. Frank's seminal model showed in the '50s how chiral symmetry breaking can occur in nonequilibrium chemical networks. However, an important shortcoming in this classic model is that it considers a small number of species, while there is no reason for the prebiotic system, in which homochirality first appeared, to have had such a simple composition. Furthermore, this model does not provide information on what could have been the size of the molecules involved in this homochiral prebiotic system. Here, we show that large molecular systems are likely to undergo a phase transition toward a homochiral state, as a consequence of the fact that they contain a large number of chiral species. Using chemoinformatics tools, we quantify how abundant chiral species are in the chemical universe of all possible molecules of a given length. Then, we propose that Frank's model should be extended to include a large number of species, in order to possess the transition toward homochirality, as confirmed by numerical simulations. Finally, using random matrix theory, we prove that large nonequilibrium reaction networks possess a generic and robust phase transition toward a homochiral state.

Stochastic approach to entropy production in chemical chaos.

Methods are presented to evaluate the entropy production rate in stochastic reactive systems. These methods are shown to be consistent with known results from nonequilibrium chemical thermodynamics. Moreover, it is proved that the time average of the entropy production rate can be decomposed into the contributions of the cycles obtained from the stoichiometric matrix in both stochastic processes and deterministic systems. These methods are applied to a complex reaction network constructed on the basis of Rössler's reinjection principle and featuring chemical chaos.

Molecular theory of Langevin dynamics for active self-diffusiophoretic colloids.

Active colloidal particles that are propelled by a self-diffusiophoretic mechanism are often described by Langevin equations that are either postulated on physical grounds or derived using the methods of fluctuating hydrodynamics. While these descriptions are appropriate for colloids of micrometric and larger size, they will break down for very small active particles. A fully microscopic derivation of Langevin equations for self-diffusiophoretic particles powered by chemical reactions catalyzed asymmetrically by the colloid is given in this paper. The derivation provides microscopic expressions for the translational and rotational friction tensors, as well as reaction rate coefficients appearing in the Langevin equations. The diffusiophoretic force and torque are expressed in terms of nonequilibrium averages of fluid fields that satisfy generalized transport equations. The results provide a description of active motion on small scales where descriptions in terms of coarse grained continuum fluid equations combined with boundary conditions that account for the presence of the colloid may not be appropriate.

Active Matter, Microreversibility, and Thermodynamics.

Active matter, comprising many active agents interacting and moving in fluids or more complex environments, is a commonly occurring state of matter in biological and physical systems. By its very nature, active matter systems exist in nonequilibrium states. In this paper, the active agents are small Janus colloidal particles that use chemical energy provided by chemical reactions occurring on their surfaces for propulsion through a diffusiophoretic mechanism. As a result of interactions among these colloids, either directly or through fluid velocity and concentration fields, they may act collectively to form structures such as dynamic clusters. A general nonequilibrium thermodynamics framework for the description of such systems is presented that accounts for both self-diffusiophoresis and diffusiophoresis due to external concentration gradients, and is consistent with microreversibility. It predicts the existence of a reciprocal effect of diffusiophoresis back onto the reaction rate for the entire collection of colloids in the system, as well as the existence of a clustering instability that leads to nonequilibrium inhomogeneous system states.

Template-directed growth of copolymers.

The theory of multistate template-directed reversible copolymerization is developed by extending the method based on iterated function systems to matrices, taking into account the possibility of multiple activation states instead of a single one for the growth process. In this extended theory, the mean growth velocity is obtained with an iterated matrix function system and the probabilities of copolymer sequences are given by matrix products defined along the template. The theory allows us to understand the effects of template heterogeneity, which include a fractal distribution of local growth velocities far enough from equilibrium, and a regime of sublinear growth in time close to equilibrium.

The 2020 motile active matter roadmap.

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of 'active matter' in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines. The 2020 motile active matter roadmap of Journal of Physics: Condensed Matter addresses the current state of the art of the field and provides guidance for both students as well as established scientists in their efforts to advance this fascinating area.

Multistate reversible copolymerization of non-Markovian chains under low conversion conditions.

The reversible kinetics of copolymerization is solved analytically for the multistate mechanism proposed by Coleman and Fox [J. Chem. Phys. 38, 1065 (1963)] under low conversion conditions where the concentrations of monomeric species are chemostatted and stay constant in time. Although the rates of this mechanism only depend on the currently attached or detached monomer, the growing macromolecular chain forms a non-Markovian sequence that is characterized by matrices associated with every monomeric unit composing the sequence. These matrices are obtained by solving the kinetic equations, and they determine the growth velocity of the copolymers, the statistical properties of its possible sequences, as well as the thermodynamics of the copolymerization process.

From single particle motion to collective dynamics in Janus motor systems.

The single-particle and collective dynamics of systems comprising Janus motors, solvent, and reactive solute species maintained in nonequilibrium states are investigated. Reversible catalytic reactions with the solute species take place on the catalytic faces of the motors, and the nonequilibrium states are established either by imposing constant-concentration reservoirs that feed and remove reactive species or through out-of-equilibrium fluid phase reactions. We consider general intermolecular interactions between the Janus motor hemispheres and the reactive species. For single motors, we show that the reaction rate depends nonlinearly on an applied external force when the system is displaced far from equilibrium. We also show that a finite-time fluctuation formula derived for fixed catalytic particles describes the nonequilibrium reactive fluctuations of moving Janus motors. Simulation of the collective dynamics of small ensembles of Janus motors with reversible kinetics under nonequilibrium conditions is carried out, and the spatial and orientational correlations of dynamic cluster states are discussed. The conditions leading to the instability of the homogeneous motor distribution and the onset of nonequilibrium dynamical clustering are described.

Microreversibility, fluctuations, and nonlinear transport in transistors.

We present a stochastic approach for charge transport in transistors. In this approach, the electron and hole densities are governed by diffusion-reaction stochastic differential equations satisfying local detailed balance and the electric field is determined with the Poisson equation. The approach is consistent with the laws of electricity, thermodynamics, and microreversibility. In this way, the signal amplifying effect of transistors is verified under their working conditions. We also perform the full counting statistics of the two electric currents coupled together in transistors and we show that the fluctuation theorem holds for their joint probability distribution. Similar results are obtained including the displacement currents. In addition, the Onsager reciprocal relations and their generalizations to nonlinear transport properties deduced from the fluctuation theorem are numerically shown to be satisfied.

Nonequilibrium thermodynamics and boundary conditions for reaction and transport in heterogeneous media.

Nonequilibrium interfacial thermodynamics is formulated in the presence of surface reactions for the study of diffusiophoresis in isothermal systems. As a consequence of microreversibility and Onsager-Casimir reciprocal relations, diffusiophoresis, i.e., the coupling of the tangential components of the pressure tensor to the concentration gradients of solute species, has a reciprocal effect where the interfacial currents of solutes are coupled to the slip velocity. The presence of surface reactions is shown to modify the diffusiophoretic and reciprocal effects at the fluid-solid interface. The thin-layer approximation is used to describe the solution flowing near a reactive solid interface. Analytic formulas describing the diffusiophoretic and reciprocal effects are deduced in the thin-layer approximation and tested numerically for the Poiseuille flow of a solution between catalytic planar surfaces.

Reconstructing stochastic attractors from nanoscale experiments on a non-equilibrium reaction.

We studied the catalytic NO2(g) + H2(g)/Pt system on model platinum catalysts with nanoscale spatial resolution by means of field emission microscopy (FEM). While the surface of the catalyst is in a non-reactive state at low H2 partial pressure, bursts of activity are observed when increasing this parameter. These kinetic instabilities subsequently evolve towards self-sustained periodic oscillations for a wide range of pressures. Combining time series analyses and numerical simulations of a simple reaction model, we clarify how these observations fit in the traditional classification of dynamical systems. In particular, reconstructions of the probability density around oscillating trajectories show that the experimental system defines a crater-like structure in probability space. The experimental observations thus correspond to a noise-perturbed limit cycle emerging from a nanometric reactive system. This conclusion is further supported by comparison with stochastic simulations of the proposed chemical model. The obtained results and simulations pave the way towards a better understanding of reactive nanosystems.

Dynamics of Janus motors with microscopically reversible kinetics.

Janus motors with chemically active and inactive hemispheres can operate only under nonequilibrium conditions where detailed balance is broken by fluxes of chemical species that establish a nonequilibrium state. A microscopic model for reversible reactive collisions on a Janus motor surface is constructed and shown to satisfy detailed balance. The model is used to study Janus particle reactive dynamics in systems at equilibrium where generalized chemical rate laws that include time-dependent rate coefficients with power-law behavior are shown to describe reaction rates. While maintaining reversible reactions on the Janus catalytic hemisphere, the system is then driven into a nonequilibrium steady state by fluxes of chemical species that control the chemical affinity. The statistical properties of the self-propelled Janus motor in this nonequilibrium steady state are investigated and compared with the predictions of a fluctuating thermodynamics theory. The model has utility beyond the examples presented here, since it allows one to explore various aspects of nonequilibrium fluctuations in systems with self-diffusiophoretic motors from a microscopic perspective.

Stochastic approach and fluctuation theorem for charge transport in diodes.

A stochastic approach for charge transport in diodes is developed in consistency with the laws of electricity, thermodynamics, and microreversibility. In this approach, the electron and hole densities are ruled by diffusion-reaction stochastic partial differential equations and the electric field generated by the charges is determined with the Poisson equation. These equations are discretized in space for the numerical simulations of the mean density profiles, the mean electric potential, and the current-voltage characteristics. Moreover, the full counting statistics of the carrier current and the measured total current including the contribution of the displacement current are investigated. On the basis of local detailed balance, the fluctuation theorem is shown to hold for both currents.

Fluctuating chemohydrodynamics and the stochastic motion of self-diffusiophoretic particles.

The propulsion of active particles by self-diffusiophoresis is driven by asymmetric catalytic reactions on the particle surface that generate a mechanochemical coupling between the fluid velocity and the concentration fields of fuel and product in the surrounding solution. Because of thermal and molecular fluctuations in the solution, the motion of micrometric or submicrometric active particles is stochastic. Coupled Langevin equations describing the translation, rotation, and reaction of such active particles are deduced from fluctuating chemohydrodynamics and fluctuating boundary conditions at the interface between the fluid and the particle. These equations are consistent with microreversibility and the Onsager-Casimir reciprocal relations between affinities and currents and provide a thermodynamically consistent basis for the investigation of the dynamics of active particles propelled by diffusiophoretic mechanisms.

Reaction kinetics in open reactors and serial transfers between closed reactors.

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with a finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.