Search Results (86)

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

Friston proposed the Minimum Free Energy Principle (FEP) based on the Variational Bayesian (VB) method. This principle emphasizes that the brain and behavior coordinate with the environment, promoting self-organization. However, it has a theoretical flaw, a possibility of being misunderstood, and a limitation (only likelihood functions are used as constraints). This paper first introduces the semantic information G theory and the R(G) function (where R is the minimum mutual information for the given semantic mutual information G). The G theory is based on the P-T probability framework and, therefore, allows for the use of truth, membership, similarity, and distortion functions (related to semantics) as constraints. Based on the study of the R(G) function and logical Bayesian Inference, this paper proposes the Semantic Variational Bayesian (SVB) and the Maximum Information Efficiency (MIE) principle. Theoretic analysis and computing experiments prove that R − G = F − H(X|Y) (where F denotes VFE, and H(X|Y) is Shannon conditional entropy) instead of F continues to decrease when optimizing latent variables; SVB is a reliable and straightforward approach for latent variables and active inference. This paper also explains the relationship between information, entropy, free energy, and VFE in local non-equilibrium and equilibrium systems, concluding that Shannon information, semantic information, and VFE are analogous to the increment of free energy, the increment of exergy, and physical conditional entropy. The MIE principle builds upon the fundamental ideas of the FEP, making them easier to understand and apply. It needs to combine deep learning methods for wider applications. Full article

Generative diffusion models have achieved spectacular performance in many areas of machine learning and generative modeling. While the fundamental ideas behind these models come from non-equilibrium physics, variational inference, and stochastic calculus, in this paper we show that many aspects of these models can be understood using the tools of equilibrium statistical mechanics. Using this reformulation, we show that generative diffusion models undergo second-order phase transitions corresponding to symmetry breaking phenomena. We show that these phase transitions are always in a mean-field universality class, as they are the result of a self-consistency condition in the generative dynamics. We argue that the critical instability arising from these phase transitions lies at the heart of their generative capabilities, which are characterized by a set of mean-field critical exponents. Finally, we show that the dynamic equation of the generative process can be interpreted as a stochastic adiabatic transformation that minimizes the free energy while keeping the system in thermal equilibrium. Full article

Peusner’s network thermodynamics (PNT) is an important way of describing processes in nonequilibrium thermodynamics. PNT allows energy transport and conversion processes in membrane systems to be described. This conversion concerns internal energy transformation into free and dissipated energies linked with the membrane transport of solutes. A transformation of the Kedem–Katchalsky (K-K) equations into the R variant of Kedem–Katchalsky–Peusner (K-K-P) equations was developed for the transport of binary electrolytic solutions through a membrane. The procedure was verified for a system in which a membrane Ultra Flo 145 Dialyser separated aqueous NaCl solutions. Peusner coefficients were calculated by the transformation of the K-K coefficients. Next, the coupling coefficients of the membrane processes and energy fluxes for electrolyte solutions transported through the membrane were calculated based on the Peusner coefficients. The efficiency of energy conversion in the membrane transport processes was estimated, and this coefficient increased nonlinearly with the increase in the solute concentration in the membrane. In addition, the energy fluxes as functions of ionic current density for constant solute fluxes were also investigated for membrane transport processes in the Ultra Flo 145 Dialyser membrane. Full article

Maximizing the amount of work harvested from an environment is important for a wide variety of biological and technological processes, from energy-harvesting processes such as photosynthesis to energy storage systems such as fuels and batteries. Here, we consider the maximization of free energy—and by extension, the maximum extractable work—that can be gained by a classical or quantum system that undergoes driving by its environment. We consider how the free energy gain depends on the initial state of the system while also accounting for the cost of preparing the system. We provide simple necessary and sufficient conditions for increasing the gain of free energy by varying the initial state. We also derive simple formulae that relate the free energy gained using the optimal initial state rather than another suboptimal initial state. Finally, we demonstrate that the problem of finding the optimal initial state may have two distinct regimes, one easy and one difficult, depending on the temperatures used for preparation and work extraction. We illustrate our results on a simple model of an information engine. Full article

Two-dimensional (2D) materials have drawn extensive attention due to their exceptional characteristics and potential uses in electronics and energy storage. This investigation employs simulations using molecular dynamics to examine the mechanical and thermal transport attributes of the 2D silicene–germanene (Si-Ge) lateral heterostructure. The pre-existing cracks of the Si-Ge lateral heterostructure are addressed with external strain. Then, the effect of vacancy defects and temperature on the mechanical attributes is also investigated. By manipulating temperature and incorporating vacancy defects and pre-fabricated cracks, the mechanical behaviors of the Si-Ge heterostructure can be significantly modulated. In order to investigate the heat transport performance of the Si-Ge lateral heterostructure, a non-equilibrium molecular dynamics approach is employed. The efficient phonon average free path is obtained as 136.09 nm and 194.34 nm, respectively, in the Si-Ge heterostructure with a zigzag and armchair interface. Our results present the design and application of thermal management devices based on the Si-Ge lateral heterostructure. Full article

Peusner’s network thermodynamics (PNT) is one of the more important formalisms of nonequilibrium thermodynamics used to describe membrane transport and the conversion of the internal energy of the system into energy dissipated in the environment and free energy used for the work involved in the transport of solution components in membrane processes. A procedure of transformation the Kedem–Katchalsky (K-K) equations for the transport of binary electrolytic solutions through a membrane to the Kedem–Katchalsky–Peusner (K-K-P) equations based on the PNT formalism for liquid junction potentials was developed. The subject of the study was a membrane used for hemodialysis (Ultra Flo 145 Dialyser) and aqueous NaCl solutions. The research method was the L version of the K-K-P formalism for binary electrolyte solutions. The Peusner coefficients obtained from the transformations of the K-K formalism coefficients for the transport of electrolyte solutions through the artificial polymer membrane were used to calculate the coupling coefficients of the membrane processes and to calculate the dissipative energy flux. In addition, the dissipative energy flux, as a function of thermodynamic forces, made it possible to investigate the energy conversion of transport processes in the membrane system. Full article

This paper investigates the performance of vacuum gate dielectric doping-free carbon nanotube/nanoribbon field-effect transistors (VGD-DL CNT/GNRFETs) via computational analysis employing a quantum simulation approach. The methodology integrates the self-consistent solution of the Poisson solver with the mode space non-equilibrium Green’s function (NEGF) in the ballistic limit. Adopting the vacuum gate dielectric (VGD) paradigm ensures radiation-hardened functionality while avoiding radiation-induced trapped charge mechanisms, while the doping-free paradigm facilitates fabrication flexibility by avoiding the realization of a sharp doping gradient in the nanoscale regime. Electrostatic doping of the nanodevices is achieved via source and drain doping gates. The simulations encompass MOSFET and tunnel FET (TFET) modes. The numerical investigation comprehensively examines potential distribution, transfer characteristics, subthreshold swing, leakage current, on-state current, current ratio, and scaling capability. Results demonstrate the robustness of vacuum nanodevices for high-performance, radiation-hardened switching applications. Furthermore, a proposal for extrinsic enhancement via doping gate voltage adjustment to optimize band diagrams and improve switching performance at ultra-scaled regimes is successfully presented. These findings underscore the potential of vacuum gate dielectric carbon-based nanotransistors for ultrascaled, high-performance, energy-efficient, and radiation-immune nanoelectronics. Full article

In this study, recent advances in tailoring the surface properties of polymers for the optimization of the adhesion of various coatings by non-equilibrium gaseous plasma are reviewed, and important findings are stressed. Different authors have used various experimental setups and reported results that scatter significantly and are sometimes contradictory. The correlations between the processing parameters and the adhesion are drawn, and discrepancies are explained. Many authors have explained improved adhesion with the adjustment of the surface free energy or wettability of the polymer substrate and the surface tension of liquids used for the deposition of thin films. The adhesion force between the polymer substrate and the coating does not always follow the evolution of the surface wettability, which is explained by several effects, including the aging effects due to the hydrophobic recovery and the formation of an interlayer rich in loosely bonded low molecular weight fragments. Full article

Wakes produced by underwater vehicles, particularly submarines, in density-stratified fluids play a pivotal role across military, academic, and engineering domains. In comparison to homogeneous fluid environments, wakes in stratified flows exhibit distinctive phenomena, including upstream blocking, pancake eddies, internal waves, and variations in hydrodynamic performance. These phenomena are crucial for optimizing the operation of underwater vehicles. This review critically assesses the hydrodynamic and thermodynamic aspects of these wakes through an integration of theoretical, experimental, and numerical approaches. The hydrodynamic wake evolution, comprising near-wake, non-equilibrium, and quasi-two-dimensional regimes, is scrutinized. The underlying physics, encompassing energy transformation, vertical motion suppression, and momentum dissipation, are analyzed in detail. Special emphasis is placed on numerical methods, encompassing diverse approaches and turbulence models and highlighting their differences in fidelity and computational cost. Numerical simulations not only provide insights into the intricate interplay among various factors but also emerge as a crucial focal point for future research directions. In the realm of thermodynamic wakes, we delve into the thermal wake induced by the discharge of high-temperature cooling water and the cold wake resulting from the stirring of seawater. The generation, evolution, and ascent to the free surface of these wakes are explored. Additionally, this review identifies and analyzes current research shortcomings in each aspect. By systematically addressing existing knowledge gaps, our study contributes novel insights that propel academic progress and bear significant implications for submarine engineering. This work not only enhances our understanding of the intricate dynamics involved but also provides a foundation for future research endeavors in this critical field. 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

In comparison to numerous enhanced sampling methods for equilibrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here, we derive a time-reversal path sampling (tRPS) method based on time reversibility to accelerate simulations for determining the transition rates between free-energy basins. It converts the difficult uphill path sampling into an easy downhill problem. This method is easy to implement, i.e., forward and backward shooting simulations with opposite initial velocities are conducted from random initial conformations within a transition-state region until they reach the basin minima, which are then assembled to give the distribution of transition paths efficiently. The effects of tRPS are demonstrated using a comparison with direct simulations of protein folding and unfolding, where tRPS is shown to give results consistent with direct simulations and increase the efficiency by up to five orders of magnitude. This approach is generally applicable to stochastic processes with microscopic reversibility, regardless of whether the variables are continuous or discrete. Full article

This article presents an overview of an alternative approach to the systematization and evolution of biological organisms on the basis of the fractal-cluster theory. It presents the foundations of the fractal-cluster theory for the self-organizing systems of the organism class. Static and dynamic efficiency criteria based on the fractal-cluster relations and the analytical apparatus of nonequilibrium thermodynamics are presented. We introduce a highly sensitive static criterion, D, which determines the deviation in the value of the clusters and subclusters of the fractal-cluster system structures from their reference values. Other static criteria are the fractal-cluster entropy H and the free energy F of an organism. The dynamic criterion is based on Prigogine’s theorem and is determined by the second differential of the temporal trend of the fractal-cluster entropy H. By using simulations of the cluster variations for biological organisms in the (H, D, F)-space, the criteria for the fractal-cluster stochastics as well as for energy and evolution laws are obtained. The relationship between the traditional and fractal-cluster approaches for identifying an organism is discussed. Full article

Mismatch repair is a critical step in DNA replication that occurs after base selection and proofreading, significantly increasing fidelity. However, the mechanism of mismatch recognition has not been established for any repair enzyme. Speculations in this area mainly focus on exploiting thermodynamic equilibrium and free energy. Nevertheless, non-equilibrium processes may play a more significant role in enhancing mismatch recognition accuracy by utilizing adenosine triphosphate (ATP). This study aimed to investigate this possibility. Considering our limited knowledge of actual mismatch repair enzymes, we proposed a hypothetical enzyme that operates as a quantum system with three discrete energy levels. When the enzyme is raised to its highest energy level, a quantum transition occurs, leading to one of two low-energy levels representing potential recognition outcomes: a correct match or a mismatch. The probabilities of the two outcomes are exponentially different, determined by the energy gap between the two low energy levels. By flipping the energy gap, discrimination between mismatches and correct matches can be achieved. Within a framework that combines quantum mechanics with thermodynamics, we established a relationship between energy cost and the recognition error. Full article

Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from Clostridium Beijerinckii and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes. Full article