Calcium oscillations optimize the energetic efficiency of mitochondrial metabolism.

Energy transduction is central to living organisms, but the impact of enzyme regulation and signaling on its thermodynamic efficiency is generally overlooked. Here, we analyze the efficiency of ATP production by the tricarboxylic acid cycle and oxidative phosphorylation, which generate most of the chemical energy in eukaryotes. Calcium signaling regulates this pathway and can affect its energetic output, but the concrete energetic impact of this cross-talk remains elusive. Calcium enhances ATP production by activating key enzymes of the tricarboxylic acid cycle while calcium homeostasis is ATP-dependent. We propose a detailed kinetic model describing the calcium-mitochondria cross-talk and analyze it using nonequilibrium thermodynamics: after identifying the effective reactions driving mitochondrial metabolism out of equilibrium, we quantify the mitochondrial thermodynamic efficiency for different conditions. Calcium oscillations, triggered by extracellular stimulation or energy deficiency, boost the thermodynamic efficiency of mitochondrial metabolism, suggesting a compensatory role of calcium signaling in mitochondrial bioenergetics.

Validity and reliability of the Questionnaire of Olfactory Disorders for Italian-speaking patients with olfactory dysfunction.

Objective: To translate and validate an Italian version of the Questionnaire of Olfactory Disorders (IT-QOD). Materials and methods: This is a prospective, multicentre study that involved patients with olfactory dysfunction (OD). Both cases and controls underwent administration of the IT-QOD, Sino-Nasal Outcome Test-22 (SNOT-22) and psychophysical evaluation of orthonasal and retronasal olfactory function. Results: The IT-QOD was administered to 96 patients and 38 controls. The Cronbach's alpha exceeded 0.90, indicating satisfactory internal consistency. The test-retest reliability was found to be high for both parosmia (rs = 0.944) and life quality (rs = 0.969). Patients with OD had significantly higher IT-QOD scores compared to healthy individuals (p < 0.001), indicating strong internal validity. The external validity was also satisfactory, as shown by the significant correlation with SNOT-22 (rs = -0.54) and the threshold, discrimination, and identification score (rs = -0.63). Conclusions: The IT-QOD was demonstrated to be reliable and valid to assess the impact of OD on the quality of life of Italian-speaking patients.

Nonideal Reaction-Diffusion Systems: Multiple Routes to Instability.

We develop a general classification of the nature of the instabilities yielding spatial organization in open nonideal reaction-diffusion systems, based on linear stability analysis. This encompasses dynamics where chemical species diffuse, interact with each other, and undergo chemical reactions driven out of equilibrium by external chemostats. We find analytically that these instabilities can be of two types: instabilities caused by intermolecular energetic interactions (E type), and instabilities caused by multimolecular out-of-equilibrium chemical reactions (R type). Furthermore, we identify a class of chemical reaction networks, containing unimolecular networks but also extending beyond them, that can only undergo E-type instabilities. We illustrate our analytical findings with numerical simulations on two reaction-diffusion models, each displaying one of the two types of instability and generating stable patterns.

Deficiency, kinetic invertibility, and catalysis in stochastic chemical reaction networks.

Stochastic chemical processes are described by the chemical master equation satisfying the law of mass-action. We first ask whether the dual master equation, which has the same steady state as the chemical master equation, but with inverted reaction currents, satisfies the law of mass-action and, hence, still describes a chemical process. We prove that the answer depends on the topological property of the underlying chemical reaction network known as deficiency. The answer is yes only for deficiency-zero networks. It is no for all other networks, implying that their steady-state currents cannot be inverted by controlling the kinetic constants of the reactions. Hence, the network deficiency imposes a form of non-invertibility to the chemical dynamics. We then ask whether catalytic chemical networks are deficiency-zero. We prove that the answer is no when they are driven out of equilibrium due to the exchange of some species with the environment.

Information thermodynamics for deterministic chemical reaction networks.

Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance. Here, we expand the scope of information thermodynamics to deterministic bipartite chemical reaction networks, namely, composed of two coupled subnetworks sharing species but not reactions. We do so by introducing a meaningful notion of mutual information between different molecular features that we express in terms of deterministic concentrations. This allows us to formulate separate second laws for each subnetwork, which account for their energy and information exchanges, in complete analogy with stochastic systems. We then use our framework to investigate the working mechanisms of a model of chemically driven self-assembly and an experimental light-driven bimolecular motor. We show that both systems are constituted by two coupled subnetworks of chemical reactions. One subnetwork is maintained out of equilibrium by external reservoirs (chemostats or light sources) and powers the other via energy and information flows. In doing so, we clarify that the information flow is precisely the thermodynamic counterpart of an information ratchet mechanism only when no energy flow is involved.

Thermodynamics of concentration vs flux control in chemical reaction networks.

We investigate the thermodynamic implications of two control mechanisms of open chemical reaction networks. The first controls the concentrations of the species that are exchanged with the surroundings, while the other controls the exchange fluxes. We show that the two mechanisms can be mapped one into the other and that the thermodynamic theories usually developed in the framework of concentration control can be applied to flux control as well. This implies that the thermodynamic potential and the fundamental forces driving chemical reaction networks out of equilibrium can be identified in the same way for both mechanisms. By analyzing the dynamics and thermodynamics of a simple enzymatic model, we also show that while the two mechanisms are equivalent at steady state, the flux control may lead to fundamentally different regimes where systems achieve stationary growth.

Nonequilibrium thermodynamics of non-ideal chemical reaction networks.

All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory that accounts for interactions between chemical species within a mean-field approach using activity coefficients. Thermodynamic consistency requires that rate equations do not obey standard mass-action kinetics but account for the interactions with concentration dependent kinetic constants. Many features of the ideal formulations are recovered. Crucially, the thermodynamic potential and the forces driving non-ideal chemical systems out of equilibrium are identified. Our theory is general and holds for any mean-field expression of the interactions leading to lower bounded free energies.

Chemical cloaking.

Hiding an object in a chemical gradient requires one to suppress the distortions it would naturally cause on it. To do so, we propose a strategy based on coating the object with a chemical reaction-diffusion network which can act as an active cloaking device. By controlling the concentration of some species in its immediate surrounding, the chemical reactions redirect the gradient as if the object was not there. We also show that a substantial fraction of the energy required to cloak can be extracted from the chemical gradient itself.

Thermodynamics of chemical waves.

Chemical waves constitute a known class of dissipative structures emerging in reaction-diffusion systems. They play a crucial role in biology, spreading information rapidly to synchronize and coordinate biological events. We develop a rigorous thermodynamic theory of reaction diffusion systems to characterize chemical waves. Our main result consists of defining the proper thermodynamic potential of the local dynamics as a nonequilibrium free energy density and establishing its balance equation. This enables us to identify the dynamics of the free energy, of the dissipation, and of the work spent to sustain the wave propagation. Two prototypical classes of chemical waves are examined. From a thermodynamic perspective, the first is sustained by relaxation toward equilibrium and the second by nonconservative forces generated by chemostats. We analytically study step-like waves, called wavefronts, using the Fisher-Kolmogorov equation as a representative of the first class and oscillating waves in the Brusselator model as a representative of the second. Given the fundamental role of chemical waves as message carriers in biosystems, our thermodynamic theory constitutes an important step toward an understanding of information transfers and processing in biology.

Linguistic Skills in Bilingual Children With Developmental Language Disorders: A Pilot Study.

The current pilot study compared the linguistic characteristics of a cohort of simultaneous bilingual children (Italian, L1; German L2) with developmental language disorders (DLDs) and those of bilingual peers with typical language development (TLD). Importantly, the two groups were balanced for a number of environmental variables (e.g., age of first exposure to the L2, acquisition contexts, degree of exposure to both languages) known to affect linguistic development in both TLD and DLDs. The analyses included the assessment of the participants' phonological short-term memory. Their lexical, grammatical and narrative abilities were analyzed in both languages by administering the Italian and German equivalent forms of the Battery for the assessment of language in children aged 4 to 12 - BVL_4-12 (Marini et al., 2015). The children with DLDs had reduced phonological short-term memory and lexical skills that, in turn, contributed to the reduced levels of local coherence and informativeness of their narratives. Such difficulties were found at similar levels in their two languages. These results suggest that reduced phonological short-term memory and lexical selection skills may reflect a core symptom in both mono- and bilingual children with developmental language disorders.

Quantum Stochastic Trajectories: The Fokker-Planck-Bohm Equation Driven by the Reduced Density Matrix.

The quantum molecular trajectory is the deterministic trajectory, arising from the Bohm theory, that describes the instantaneous positions of the nuclei of molecules by assuring the agreement with the predictions of quantum mechanics. Therefore, it provides the suitable framework for representing the geometry and the motions of molecules without neglecting their quantum nature. However, the quantum molecular trajectory is extremely demanding from the computational point of view, and this strongly limits its applications. To overcome such a drawback, we derive a stochastic representation of the quantum molecular trajectory, through projection operator techniques, for the degrees of freedom of an open quantum system. The resulting Fokker-Planck operator is parametrically dependent upon the reduced density matrix of the open system. Because of the pilot role played by the reduced density matrix, this stochastic approach is able to represent accurately the main features of the open system motions both at equilibrium and out of equilibrium with the environment. To verify this procedure, the predictions of the stochastic and deterministic representation are compared for a model system of six interacting harmonic oscillators, where one oscillator is taken as the open quantum system of interest. The undeniable advantage of the stochastic approach is that of providing a simplified and self-contained representation of the dynamics of the open system coordinates. Furthermore, it can be employed to study the out of equilibrium dynamics and the relaxation of quantum molecular motions during photoinduced processes, like photoinduced conformational changes and proton transfers.

Quantum stochastic trajectories: the Smoluchowski-Bohm equation.

Molecular systems are quantum systems, but the complete characterization of molecular motions within a fully quantum framework might appear to be an unfeasible task because it would require that the actual nuclear positions are established at any time. One would like to use a quantum molecular trajectory that defines the instantaneous nuclear positions and satisfies the predictions of quantum mechanics in terms of its statistical properties. Even though it can be proven that the single Bohm trajectory provides a representation of the quantum molecular trajectory, this solves the issue only on a theoretical ground: exact solutions of the Schrödinger-Bohm dynamical system are extremely computationally demanding. Therefore, we derive a stochastic equation of Smoluchowski type from the Schrödinger-Bohm dynamics, through projection operator techniques, in order to characterize the molecular motions of open quantum systems. The main quantum features of the motions emerge from the equilibrium distribution, i.e., the wave function's squared modulus integrated on the environment degrees of freedom. Furthermore, we verify the accuracy of the stochastic equation by comparing its predictions with those of the deterministic dynamics for a model system of six interacting harmonic oscillators. The indisputable advantage of this full quantum mechanical approach is that of representing the molecular dynamics, which controls important phenomena like vibrational relaxation, conformational transitions and activated processes, in a self consistent way and at the low computational cost of solving simple stochastic equations.

Quantum Molecular Trajectory and Its Statistical Properties.

Despite the quantum nature of molecules, classical mechanics is often employed to describe molecular motions that play a fundamental role in a wide range of phenomena including chemical reactions. This is due to the need of assigning well-defined positions to the atomic nuclei during the time evolution of the system in order to describe unambiguously the molecular motions, whereas quantum mechanics provides information on probabilistic nature only. One would like to employ a quantum molecular trajectory that defines rigorously the instantaneous nuclear positions and, simultaneously, guarantees the conservation of all quantum mechanics predictions unlike the classical trajectory. We argue that such a quantum molecular trajectory can be formally defined and we prove that it corresponds to a single Bohm trajectory. Our analysis establishes a clear correspondence between the statistical properties of the trajectory and the quantum expectation values. The obvious and undeniable benefit is that of dealing with a quantum methodology fully characterizing the molecular motions without any reference to classical mechanics.