Search Results (53)

In this position paper, we argue that the conventional understanding of ‘information’ (as generally conceived in science, in a digital fashion) is overly simplistic and not consistently applicable to living systems, which are open systems that cannot be reduced to any kind of ‘portion’ (building block) ascribed to the category of quantity. Instead, it is a matter of relationships and qualities in an indivisible analogical (and ontological) relationship between any presumed ‘software’ and ‘hardware’ (information/matter, psyche/soma). Furthermore, in biological systems, contrary to Shannon’s definition, which is well-suited to telecommunications and informatics, any kind of ‘information’ is the opposite of internal entropy, as it depends directly on order: it is associated with distinction and differentiation, rather than flattening and homogenisation. Moreover, the high degree of structural compartmentalisation of living matter prevents its energetics from being thermodynamically described by using a macroscopic, bulk state function. This requires the Second Principle of Thermodynamics to be redefined in order to make it applicable to living systems. For these reasons, any static, bit-related concept of ‘information’ is inadequate, as it fails to consider the system’s evolution, it being, in essence, the organized coupling to its own environment. From the perspective of quantum field theory (QFT), where many vacuum levels, symmetry breaking, dissipation, coherence and phase transitions can be described, a consistent picture emerges that portrays any living system as a relational process that exists as a flux of context-dependent meanings. This epistemological shift is also associated with a transition away from the ‘particle view’ (first quantisation) characteristic of quantum mechanics (QM) towards the ‘field view’ possible only in QFT (second quantisation). This crucial transition must take place in life sciences, particularly regarding the methodological approaches. Foremost because biological systems cannot be conceived as ‘objects’, but rather as non-confinable processes and relationships. Full article

We present a thermodynamically consistent energetic variational model for active nematics driven by ATP hydrolysis. Extending the classical Toner–Tu framework, we introduce a chemo-mechanical coupling mechanism in which the self-advection and polarization dynamics are modulated by the ATP hydrolysis rate. The model is derived using an energetic variational approach that integrates both chemical free energy and mechanical energy into a unified energy dissipation law. The reaction rate equation explicitly incorporates mechanical feedback, revealing how active transport and alignment interactions influence chemical fluxes and vice versa. This formulation not only preserves consistency with non-equilibrium thermodynamics but also provides a transparent pathway for modeling energy transduction in active systems. We also present numerical simulations demonstrating the positive energy transduction under a specific choice of model parameters. The new modeling framework offers new insights into energy transduction and regulation mechanisms in biologically related active systems. Full article

This work presents a robust box-constrained nonlinear least-squares algorithm for accurately fitting the Jones–Wilkins–Lee (JWL) equation of state parameters, which describes the isentropic expansion of detonation products from high-energy materials. In the energetic material literature, there are plenty of methods that address this problem, and in some cases, it is not fully clear which method is employed. We provide a fully detailed numerical framework that explicitly enforces Chapman–Jouguet (CJ) constraints and systematically separates the contributions of different terms in the JWL expression. The algorithm leverages a trust-region Gauss–Newton method combined with singular value decomposition to ensure numerical stability and rapid convergence, even in highly overdetermined systems. The methodology is validated through comprehensive comparisons with leading thermochemical codes such as CHEETAH 2.0, ZMWNI, and EXPLO5. The results demonstrate that the proposed approach yields lower residual fitting errors and improved consistency with CJ thermodynamic conditions compared to standard fitting routines. By providing a reproducible and theoretically based methodology, this study advances the state of the art in JWL parameter determination and improves the reliability of energetic material simulations. Full article

The concept of thermodynamic efficiency is central to the theoretical understanding of tropical cyclone intensity and intensification, but the issue has remained controversial owing to the existence of distinct and incompatible definitions. Physically, thermodynamic efficiency relates to the fraction of the surface enthalpy fluxes and diabatic processes that contributes to the generation of the potential energy available (APE) for conversions into kinetic energy, so that the main difficulty is how best to define APE. In this study, we revisit the available energetics of axisymmetric vortex motions by redefining APE relative to a non-resting reference state in gradient wind balance instead of a resting state. Our approach, which accounts for both diabatic and frictional effects, reveals that the choice of reference state significantly impacts the prediction of APE generation and its conversion to kinetic energy. By using idealised numerical experiments of axisymmetric tropical cyclone intensification, we demonstrate that the APE production estimated from a non-resting reference state is a much more accurate predictor of APE to KE conversion than those based on other choices of reference states such as initial, mean, and sorted profiles. These findings suggest that incorporating the balanced dynamical structure of tropical cyclones into APE-based theories could lead to improved potential intensity models, with implications for forecasting and understanding cyclone behaviour. Full article

This study integrates molecular dynamics (MD) simulations and density functional theory (DFT) computations to elucidate the unique adsorption characteristics of phenol and para-chlorophenol onto sepiolite by examining structural deformation, electronic properties, and adsorption energetics. The hydroxyl group (-OH) of phenol mainly determines its adsorption process since it has a quite negative Mulliken charge (−0.428) and significant electrophilic reactivity (fi⁺ = 0.090), therefore enabling strong hydrogen bonding with the silanol (-SiOH) groups of sepiolite. By π-π interactions with the electron-rich siloxane (-Si-O-Si-) surfaces, the aromatic carbons in phenol improve stability. The close molecular structure allows minimum deformation energy (E_def = 94.18 kcal/mol), hence optimizing alignment with the sepiolite surface. The much negative adsorption energy (E_ads = −349.26 kcal/mol) of phenol supports its further thermodynamic stability. Conversely, because of its copious chlorine (-Cl) component, para-chlorophenol runs against steric and electrical obstacles. The virtually neutral Mulliken charge (−0.020) limits electrostatic interactions even if the chlorine atom shows great electrophilicity (fi⁺ = 0.278). Chlorine’s electron-withdrawing action lowers the hydroxyl group’s (fi⁺ = 0.077) reactivity, hence lowering hydrogen bonding. Moreover, para-chlorophenol shows strong deformation energy (E_def = 102.33 kcal/mol), which causes poor alignment and less access to high-affinity sites. With less negative than phenol, the adsorption energy for para-chlorophenol (E_ads = −317.53 kcal/mol) indicates its reduced thermodynamic affinity. Although more evident in para-chlorophenol because of the polarizable chlorine atom, van der Waals interactions do not balance its steric hindrance and reduced electrostatic interactions. With a maximum Qmax = 0.78 mmol/g, isotherm models confirm the remarkable adsorption capability of phenol in contrast to Qmax = 0.66 mmol/g for para-chlorophenol. By hydrogen bonding and π-cation interactions, phenol builds a dense and structured adsorption layer, and para-chlorophenol shows a chaotic organization with reduced site use. Supported by computational approaches and experimental validation, the results provide a comprehensive knowledge of adsorption mechanisms and provide a basis for the design of adsorbents catered for particular organic pollutants. Full article

Brassinosteroids, as unique plant steroid hormones that bear structural similarity to animal steroids, play a crucial role in modulating plant growth and development. These hormones have a positive impact on plant resistance and, under stressful conditions, stimulate photosynthesis and antioxidative systems (enzymatic and non-enzymatic), leading to a reduced impact of environmental cues on plant metabolism and growth. Although these plant hormones have been studied for several decades, most studies analyze the primary site of action of the brassinosteroid phytohormone, with a special emphasis on the activation of various genes (mainly nuclear) through different signaling processes that influence plant metabolism, growth, and development. This review explores another issue, the secondary influence (the so-called mode of action) of brassinosteroids on changes in growth, development, and chemical composition, as well as thermodynamic and energetic changes, mainly during the early growth of corn seedlings. The interactions of brassinosteroids with other phytohormones and physiologically active substances and the influence of these interactions on the mode of action of brassinosteroid phytohormones were also discussed. Seen from a cybernetic point of view, the approach can be labeled as “black box” or “gray box”. “Black box” and “gray box” are terms for cybernetic systems, for which we know the inputs and outputs (in an energetic, biochemical, kinetic, informational, or some other sense), but whose internal structure and/or organization are completely or partially unknown to us. The findings of many researchers have indicated an important role of reactive species, such as oxygen and nitrogen reactive species, in these processes. This ultimately results in the redistribution of matter and energy from source organs to sink organs, with a decrease in Gibbs free energy from the source to sink organs. This quantitative evidence speaks of the exothermic nature and spontaneity of early (corn) seedling development and growth under the influence of 24-epibrassinolide. Based on these findings and a review of the literature on the mode of action of brassinosteroids, a hypothesis was put forward about the secondary effects of BRs on germination and the early growth of plant seedlings. Full article

In this work, we studied the main decomposition reactions on the ground state of nitromethane (CH₃NO₂) with the CASPT2 approach. The energetics of the main elementary reactions of the title molecule have been analyzed on the basis of Gibbs free energies obtained from standard expressions of statistical thermodynamics. In addition, we describe a mapping method (orthogonalized 3D representation) for the potential energy surfaces (PESs) by defining an orthonormal basis consisting of two $R^n$ orthonormal vectors (n, internal degrees of freedom) that allows us to obtain a set of ordered points in the plane (vector subspace) spanned by such a basis. Geometries and harmonic frequencies of all species and orthogonalized 3D representations of the PESs have been computed with the CASPT2 approach. It is found that all of the analyzed kinetically controlled reactions of nitromethane are endergonic. For such a class of reactions, the dissociation of nitromethane into CH₃ and NO₂ is the process with the lower activation energy barrier (ΔG); that is, the C-N bond cleavage is the most favorable process. In contrast, there exists a dynamically controlled process that evolves through a roaming reaction mechanism and is an exergonic reaction at high temperatures: CH₃NO₂ → [CH₃^…NO₂]* → [CH₃ONO]* → CH₃O + NO. The above assertions are supported by CASPT2 mappings of the potential energy surfaces (PESs) and classical trajectories obtained by “on-the fly” CASSCF molecular dynamics calculations. Full article

Methylene blue (MB), a widely used organic dye, poses significant environmental challenges due to its stability and persistence in aquatic ecosystems. This study employs density functional theory (DFT) to investigate the demethylation mechanisms of MB mediated by reactive oxygen species (ROS), a critical initial step in its photocatalytic degradation. Computational analyses reveal that demethylation is energetically favorable, particularly when mediated by hydroxyl radicals (^•OH) and hydroxyl ions (OH⁻) with reaction energies of −154 kcal/mol and −214 kcal/mol, respectively. These pathways lead to the formation of key intermediates, such as Azure B, methanol (CH₃OH), and formaldehyde (CH₂O), which align with experimentally detected degradation byproducts. The study further demonstrates that the dissociation of hydrogen peroxide species (H₂O₂, H₂O₂⁻, H₂O₂⁺) plays a fundamental role in generating the ROS required for MB degradation. Potential energy surface analyses confirm that these ROS-driven processes are thermodynamically and kinetically viable. The findings provide a theoretical framework that bridges existing knowledge gaps in MB degradation, reinforcing the role of ROS in advanced photocatalytic systems and contributing to the optimization of wastewater treatment strategies. This work underscores the importance of integrating computational and experimental approaches to develop more effective strategies for the remediation of recalcitrant pollutants in wastewater. Full article

The study of solid–liquid equilibria offers critical insights into the molecular interactions between constituents in binary mixtures. Predicting these equilibria often requires comprehensive thermodynamic models, yet simplified approaches can provide valuable perspectives. In this work, we explore the application of the Bragg–Williams model to solid–liquid equilibria in binary mixtures leading to the formation of eutectic solvents. This model relies on a single parameter—the molar energy change upon mixing compounds—and demonstrates noteworthy features: the parameter can be estimated from a few (in principle, from a single) experimental melting points, and it correlates strongly with interaction energy parameters from more complex models, such as the PC-SAFT molecular-based equation of state. By using the Bragg–Williams model, we provide a straightforward and informative framework for characterizing solid–liquid equilibria, enabling insights into molecular interactions while requiring few data points as input. Despite its simplicity, the model effectively captures the essence of binary mixture energetics, positioning it as a practical tool for advancing the understanding of phase behavior in eutectic solvent systems. Full article

Background: Breast cancer remains a significant global health concern, with approximately 2.3 million diagnosed cases and 670,000 deaths annually. Current targeted therapies face challenges such as resistance and adverse side effects. This study aimed to explore natural compounds as potential multitargeted breast cancer therapeutics, focusing on Lucidin, an anthraquinone derived from Rubia cordifolia, and comparing its efficacy with Lapatinib, an FDA-approved drug. Methods: We performed multitargeted molecular docking studies on key breast cancer proteins using a natural compound library from ZINC. Comparative analyses of Lucidin and Lapatinib included molecular interaction fingerprints, pharmacokinetics, WaterMap computations (5 ns) to assess water thermodynamics and binding interactions, and Molecular Dynamics Simulations (100 ns) in water to evaluate complex stability and dynamic behaviour. Results: Lucidin demonstrated significant binding affinity and interaction potential with multiple breast cancer targets, outperforming Lapatinib in stability and binding interactions. WaterMap analysis revealed favourable hydration site energetics for Lucidin, enhancing its efficacy. The multitargeted profile of Lucidin suggests a broader therapeutic approach with potential to overcome resistance and side effects associated with Lapatinib. Conclusions: Lucidin shows promise as a novel, multitargeted anti-breast cancer agent with improved efficacy over Lapatinib. These findings provide a foundation for further in vitro and in vivo validation to develop Lucidin as a potential therapeutic option for breast cancer treatment. Full article

Aromatic esters such as phenyl acetates are of interest as promising liquid organic hydrogen carriers (LOHCs) due to the presence of double bonds. However, the key factor for the development of green hydrogen fuel is the production of LOHCs from renewable sources. Since the synthesis and isolation of such esters is a complex task, understanding the relationship between the chemical structures of aromatic esters and their thermodynamic properties is of great importance for their further practical use as LOHCs. Obtaining reliable thermodynamic and thermochemical properties of phenyl and benzyl phenyl acetates formed the basis of this work. Vapour pressures, enthalpies of vaporisation, and enthalpies of formation were systematically studied. An approach based on the structure–property correlation was used to confirm these quantities. Additionally, the high-level quantum-chemical method G4 was used to estimate the enthalpy of formation in the gas phase. The final stage was the assessment of the energetics of chemical reactions based on aromatic esters and their partially and fully hydrogenated analogues. Full article

The coupling processes among the lithosphere, atmosphere, and ionosphere (LAI) during the earthquake preparation phase are still an open scientific debate. Comprehensive LAI coupling effects around the 2022 Ms6.8 Luding earthquake in China are investigated with a multi-parameter and multi-layer approach, including the b-value, revised accelerated moment release, Earth resistivity, ELF magnetic field emissions, atmospheric electric field, surface temperature, foF2 from ionosonde, GNSS TEC, Ne and magnetic field from CSES and Swarm satellites, and energetic electrons from CSES and NOAA satellites. It is found that the anomalies start from the lithospheric parameters as Earth resistivity and b-values 1–2 years before to reflect the local stress loading in the seismic region, then the ionospheric and atmospheric disturbances occur and accelerate −50 days before and −15 days before, and finally the electrons precipitate a few days before. The simultaneous perturbations in LAI illustrate the thermodynamic coupling channel, such as on 24 August, −12 days before. Meanwhile, the abundant developed ionospheric anomalies without atmospheric disturbances demonstrate the electromagnetic coupling way from the lithosphere to the ionosphere directly. Finally, the results demonstrate a two-way model of LAIC: one way is characterized by a slow chain of processes, of thermodynamic nature, starting from the ground and proceeding to the above atmosphere and ionosphere, showing an exponential trend in the cumulative number of anomalies; the second way is characterized by oscillating electromagnetic coupling between the lithosphere and ionosphere, showing intermittent fluctuations in the corresponding cumulative number of anomalies. Full article

The plasma membrane forms the boundary between a living entity and its environment and acts as a barrier to permeation and flow of substances. Several computational means of calculating permeability have been implemented for molecular dynamics (MD) simulations-based approaches. Except for double bilayer systems, most permeability studies have been performed under equilibrium conditions, in large part due to the challenges associated with creating concentration gradients in simulations utilizing periodic boundary conditions. To enhance the scientific understanding of permeation and complement the existing computational means of characterizing membrane permeability, we developed a non-equilibrium method that enables the generation and maintenance of steady-state gradients in MD simulations. We utilize PBCs advantageously by imposing a directional bias to the motion of permeants so that their crossing of the boundary replenishes the gradient, like a previous study on ions. Under these conditions, a net flow of permeants across membranes may be observed to determine bulk permeability by a direct application of $J=P\Delta c$. In the present study, we explore the results of its application to an exemplary ${\mathrm{O}}_2$ and POPC bilayer system, demonstrating accurate and precise permeability measurements. In addition, we illustrate the impact of permeant concentration and the choice of thermostat on the permeability. Moreover, we demonstrate that energetics of permeation can be closely examined by the dissipation of the gradient across the membrane to gain nuanced insights into the thermodynamics of permeability. Full article

Symmetry breaking is a phenomenon that is observed in various contexts, from the early universe to complex organisms, and it is considered a key puzzle in understanding the emergence of life. The importance of this phenomenon is underscored by the prevalence of enantiomeric amino acids and proteins.The presence of enantiomeric amino acids and proteins highlights its critical role. However, the origin of symmetry breaking has yet to be comprehensively explained, particularly from an energetic standpoint. This article explores a novel approach by considering energy dissipation, specifically lost free energy, as a crucial factor in elucidating symmetry breaking. By conducting a comprehensive thermodynamic analysis applicable across scales, ranging from elementary particles to aggregated structures such as crystals, we present experimental evidence establishing a direct link between nonequilibrium free energy and energy dissipation during the formation of the structures. Results emphasize the pivotal role of energy dissipation, not only as an outcome but as the trigger for symmetry breaking. This insight suggests that understanding the origins of complex systems, from cells to living beings and the universe itself, requires a lens focused on nonequilibrium processes Full article

This study introduces a mathematical model for electrolytic chemical reactions, employing an energy variation approach grounded in classical thermodynamics. Our model combines electrostatics and chemical reactions within well-defined energetic and dissipative functionals. Extending the energy variation method to open systems consisting of charge, mass, and energy inputs, this model explores energy transformation from one form to another. Electronic devices and biological channels and transporters are open systems. By applying this generalized approach, we investigate the conversion of an electrical current to a proton flow by cytochrome c oxidase, a vital mitochondrial enzyme contributing to ATP production, the ‘energetic currency of life’. This model shows how the enzyme’s structure directs currents and mass flows governed by energetic and dissipative functionals. The interplay between electron and proton flows, guided by Kirchhoff’s current law within the mitochondrial membrane and the mitochondria itself, determines the function of the systems, where electron flows are converted into proton flows and gradients. This important biological system serves as a practical example of the use of energy variation methods to deal with electrochemical reactions in open systems. We combine chemical reactions and Kirchhoff’s law in a model that is much simpler to implement than a full accounting of all the charges in a chemical system. Full article