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1. Thermodynamic consistency and fluctuations in mesoscopic stochastic simulations of reactive gas mixtures

   https://doi.org/10.1063/5.0251770  

   Polimeno, Matteo; Kim, Changho; Blanchette, François; Srivastava, Ishan; Garcia, Alejandro_L; Nonaka, Andy_J; Bell, John_B (April 2025, The Journal of Chemical Physics)

   It is essential that mesoscopic simulations of reactive systems reproduce the correct statistical distributions at thermodynamic equilibrium. By considering a compressible fluctuating hydrodynamics (FHD) simulation method of ideal gas mixtures undergoing reversible reactions described by the chemical Langevin equations, we show that thermodynamic consistency in reaction rates and the use of instantaneous temperatures for the evaluation of reaction rates is required for fluctuations for the overall system to be correct. We then formulate the required properties of a thermodynamically consistent reaction (TCR) model. As noted in the literature, while reactions are often discussed in terms of forward and reverse rates, these rates should not be modeled independently because they must be compatible with thermodynamic equilibrium for the system. Using a simple TCR model where each chemical species has constant heat capacity, we derive the explicit condition that the forward and reverse reaction rate constants must satisfy in order for the system to be thermodynamically consistent. We perform equilibrium and non-equilibrium simulations of ideal gas mixtures undergoing a reversible dimerization reaction to measure the fluctuational behavior of the system numerically. We confirm that FHD simulations with the TCR model give the correct static structure factor of equilibrium fluctuations. For the statistically steady simulation of a gas mixture between two isothermal walls with different temperatures, we show using the TCR model that the temperature variance agrees with the corresponding thermodynamic-equilibrium temperature variance in the interior of the system, whereas noticeable deviations are present in regions near walls, where chemistry is far from equilibrium. 

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2. Beyond equilibrium thermodynamics in the low temperature plasma processor

   https://doi.org/10.1116/1.5022470  

   Thimsen, Elijah (June 2018, Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena)

   Low temperature plasmas are open driven thermodynamic systems capable of increasing the free energy of the mass that flows through them. An interesting thing about low temperature plasmas is that different species have different temperatures at the same location in space. Since thermal equilibrium cannot be assumed, many of the familiar results of equilibrium thermodynamics cannot be applied in their familiar form to predict, e.g., the direction of a chemical reaction. From the perspective of classical processing governed by thermal equilibrium, examples of highly unexpected gas-phase chemical reactions (CO2 dissociation, NO, N2H4, O3 synthesis) and solid material transformations (surface activation, size-focusing, and hyperdoping) promoted by low temperature plasmas are presented. The lack of a known chemical reaction equilibrium criterion prevents assessment of predictive kinetics models of low temperature plasmas, to ensure that they comply with the laws of thermodynamics. There is a need for a general method to predict chemical reaction equilibrium in low temperature plasmas or an alternative method to establish the thermodynamic admissibility of a proposed kinetics model. Toward those ends, two ideas are explored in this work. The first idea is that chemical reactions in low temperature plasmas proceed toward a thermal equilibrium state at an effective temperature intermediate between the neutral gas temperature and the electron temperature. The effective temperature hypothesis is simple, and surprisingly is adequate for elucidation in some systems, but it lacks generality. The general equation for nonequilibrium reversible–irreversible coupling (GENERIC) is a general beyond equilibrium thermodynamics framework that can be used to rigorously establish the thermodynamic admissibility of a set of dynamic modeling equations, such as a kinetic model, without knowledge of the final state that the system is tending toward. The use of GENERIC is described by way of example using a two-temperature hydrodynamic model from the literature. The conclusion of the GENERIC analysis presented in this work is that the concept of superlocal equilibrium is thermodynamically admissible and may be applied to describe low temperature plasmas, provided that appropriate terms are included for exchange of internal energy and momentum between different species that may have different temperatures and bulk velocities at the same location in space. The concept of superlocal equilibrium is expected to be of utility in future work focused on deriving equilibrium criteria for low temperature plasmas. 

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3. Advances in dynamically controlled catalytic reaction engineering

   https://doi.org/10.1039/d0re00330a  

   Armstrong, Cameron D.; Teixeira, Andrew R. (November 2020, Reaction Chemistry & Engineering)

   null (Ed.)

   Transient reaction modulation has found its place in many branches of chemical reaction engineering over the past hundred years. Historically, catalytic reactions have been dominated by the impulse to reduce spatial and temporal perturbations in favor of steady, static systems due to their ease of operation and scalability. Transient reactor operation, however, has seen remarkable growth in the past few decades, where new operating regimes are being revealed to enhance catalytic reaction rates beyond the statically achievable limits classically described by thermodynamics and the Sabatier principle. These theoretical and experimental studies suggest that there exists a resonant frequency which coincides with its catalytic turnover that can be exploited and amplified for a given reaction to overcome classical barriers. This review discusses the evolution of thought from thermostatic (equilibrium), to thermodynamic (dynamic equilibrium), and finally dynamic (non-equilibrium) catalysis. Natural and forced dynamic oscillations are explored with periodic reactor operation of catalytic systems that modulate energetics and local concentrations through a multitude of approaches, and the challenges to unlock this new class of catalytic reaction engineering is discussed. 

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4. Power of stochastic kinetic models: From biological signaling and antibiotic activities to T cell activation and cancer initiation dynamics

   https://doi.org/10.1002/wcms.1612  

   Teimouri, Hamid; Kolomeisky, Anatoly B. (February 2022, WIREs Computational Molecular Science)

   All chemical processes exhibit two main universal features. They are stochastic because chemical reactions might happen only after random successful collisions of reacting species, and they are dynamic because the amount of reactants and products change with time. Since biological processes rely heavily on specific chemical reactions, stochasticity and dynamics are also crucial features for all living systems. To understand the molecular mechanisms of chemical and biological processes, it is important to develop and apply theoretical methods that fully incorporate the randomness and dynamic nature of these systems. In recent years, there have been significant advances in formulating and exploring such theoretical methods. As an illustration of such developments, in this review, the recent applications of stochastic kinetic models for various biological processes are discussed. Specifically, we focus on applying these theoretical approaches to investigate the biological signaling, clearance of bacteria under antibiotics, T cells activation in the immune system, and cancer initiation dynamics. The main advantage of the presented stochastic kinetic models is that they generally can be solved analytically, allowing to clarify the underlying microscopic picture, as well as explain the existing experimental observations and make new testable predictions. This theoretical approach becomes a powerful tool in uncovering the molecular mechanisms of complex natural phenomena. 

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5. Single-Molecule Kinetic Analysis of Oxygenation of Co(II) Porphyrin at the Solution/Solid Interface

   https://doi.org/10.1021/acs.jpclett.2c01254  

   Johnson, Kristen N.; Mazur, Ursula; Hipps, K. W. (June 2022, The Journal of Physical Chemistry Letters)

   Kinetic analysis of surface reactions at the single molecule level is important for understanding the influence of the substrate and solvent on reaction dynamics and mechanisms, but it is difficult with current methods. Here we present a stochastic kinetic analysis of the oxygenation of cobalt octaethylporphyrin (CoOEP) at the solution/solid interface by monitoring fluctuations from equilibrium using scanning tunneling microscopy (STM) imaging. Image movies were used to monitor the oxygenated and deoxygenated state dwell times. The rate constants for CoOEP oxygenation are ka = 4.9×10-6 s-1∙torr-1 and kd = 0.018 s-1. This is the first use of stochastic dwell time analysis with STM to study a chemical reaction and the results suggest that it has great potential for application to a wide range of surface reactions. Expanding these stochastic studies to further systems is key to unlocking kinetic information for surface confined reactions at the molecular level -- especially at the solution/solid interface. 

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