Stochastic-dissipative least-action framework for self-organizing biological systems, Part I: Variational rationale and Lyapunov-type behavior.

Maintained by environmental fluxes, biological systems are thermodynamic processes that operate far from equilibrium without detailed-balance dynamics. Yet, they often exhibit well defined nonequilibrium steady states (NESSs). More importantly, critical thermodynamic functionality arises directly from transitions among their NESSs, driven by environmental switching. Here, we identify constraints on excess thermodynamic quantities that ride above the NESS housekeeping background. We do this by extending the Crooks fluctuation theorem to transitions among NESSs, without invoking an unphysical dual dynamics. This and corresponding integral fluctuation theorems determine how much work must be expended when controlling systems maintained far from equilibrium. This generalizes feedback control theory, showing that Maxwellian Demons can leverage mesoscopic-state information to take advantage of the excess energetics in NESS transitions. Altogether, these point to universal thermodynamic laws that are immediately applicable to the accessible degrees of freedom within the effective dynamic at any emergent level of hierarchical organization. By way of illustration, this readily allows analyzing a voltage-gated sodium ion channel whose molecular conformational dynamics play a critical functional role in propagating action potentials in mammalian neuronal membranes.

We study out-of-equilibrium energy transport in a quantum critical fluid with Lifshitz scaling symmetry following a local quench between two semi-infinite fluid reservoirs. The late time energy flow is universal and is accommodated via a steady state occupying an expanding central region between outgoing shock and rarefaction waves. We consider the admissibility and entropy conditions for the formation of such a non-equilibrium steady state for a general dynamical critical exponent z in arbitrary dimensions and solve the associated Riemann problem. The Lifshitz fluid with z = 2 can be obtained from a Galilean boost invariant field theory and the non-equilibrium steady state is identified as a boosted thermal state. A Lifshitz fluid with generic z is scale invariant but without boost symmetry and in this case the non-equilibrium steady state is genuinely non-thermal.

We propose a non-equilibrium thermodynamical description in terms of the Chemical Master Equation (CME) to characterize the dynamics of a chemical cycle chain reaction among m different species. These systems can be closed or open for energy and molecules exchange with the environment, which determines how they relax to the stationary state. Closed systems reach an equilibrium state (characterized by the detailed balance condition (D.B.)), while open systems will reach a non-equilibrium steady state (NESS). The principal difference between D.B. and NESS is due to the presence of chemical fluxes. In the D.B. condition the fluxes are absent while for the NESS case, the chemical fluxes are necessary for the state maintaining. All the biological systems are characterized by their "far from equilibrium behavior," hence the NESS is a good candidate for a realistic description of the dynamical and thermodynamical properties of living organisms. In this work we consider a CME written in terms of a discrete Kolmogorov forward equation, which lead us to write explicitly the non-equilibrium chemical fluxes. For systems in NESS, we show that there is a non-conservative "external vector field" whose is linearly proportional to the chemical fluxes. We also demonstrate that the modulation of these external fields does not change their stationary distributions, which ensure us to study the same system and outline the differences in the system's behavior when it switches from the D.B. regime to NESS. We were interested to see how the non-equilibrium fluxes influence the relaxation process during the reaching of the stationary distribution. By performing analytical and numerical analysis, our central result is that the presence of the non-equilibrium chemical fluxes reduces the characteristic relaxation time with respect to the D.B. condition. Within a biochemical and biological perspective, this result can be related to the "plasticity property" of biological systems and to their capabilities to switch from one state to another as is observed during synaptic plasticity, cell fate determination, and differentiation.

Recently, in their attempt to construct steady state thermodynamics (SST), Komatsu, Nakagawa, Sasa, and Tasaki found an extension of the Clausius relation to nonequilibrium steady states in classical stochastic processes. Here we derive a quantum mechanical version of the extended Clausius relation. We consider a small system of interest attached to large systems which play the role of heat baths. By only using the genuine quantum dynamics, we realize a heat conducting nonequilibrium steady state in the small system. We study the response of the steady state when the parameters of the system are changed abruptly, and show that the extended Clausius relation, in which “heat” is replaced by the “excess heat”, is valid when the temperature difference is small. Moreover we show that the entropy that appears in the relation is similar to von Neumann entropy but has an extra symmetrization with respect to time-reversal. We believe that the present work opens a new possibility in the study of nonequilibrium phenomena in quantum systems, and also confirms the robustness of the approach by Komatsu et al.

Entropy production rate (EPR) is the fundamental theoretical quantity in non-equilibrium thermodynamics whereas reaction rate is the primary experimental quantity for a chemical system out-of-equilibrium. In this work, we explore a connection between the above two quantities for general reaction networks. Both cyclic and linear networks of arbitrary dimension are studied, along with a mixed variety. The systems can attain a non-equilibrium steady state (NESS) under chemiostatic condition, which becomes the state of true thermodynamic equilibrium when detailed balance holds. We show that there exists a universal functional relationship of the EPR with reaction rate close to steady states for all the networks considered. Near a NESS, the former varies linearly with the reaction rate. On the other hand, around a true equilibrium, it varies quadratically with the latter. Numerical experiments justify our analytical findings quite transparently.

Advances in our scientific understanding and technological power in recent decades have dramatically amplified our capacity to intentionally manipulate complex ecological and biological systems. An implication of this is that biological and ecological problems are increasingly understood and approached from an engineering perspective. In environmental contexts, this is exemplified in the pursuits of geoengineering, designer ecosystems, and conservation cloning. In human health contexts, it is exemplified in the development of synthetic biology, bionanotechnology, and human enhancement technologies. Designer Biology: The Ethics of Intensively Engineering Biological and Ecological Systems consists of thirteen chapters (twelve of them original to the collection) that address the ethical issues raised by technological intervention and design across a broad range of biological and ecological systems. Among the technologies addressed are geoengineering, human enhancement, sex selection, genetic modification, and synthetic biology. This collection advances and enriches our understanding of the ethical issues raised by these technologies and identifies general lessons about the ethics of engineering complex biological and ecological systems that can be applied as new technologies and practices emerge. The insights that emerge will be especially valuable to students and scholars of environmental ethics, bioethics, or technology ethics.

The impact of fluctuations on the dynamical behaviour of complex biological systems is a longstanding issue, whose understanding would elucidate how evolutionary pressure tends to modulate intrinsic noise. Using the Itō stochastic differential equation formalism, we performed analytic and numerical analyses of model systems containing different molecular species in contact with the environment and interacting with each other through mass-action kinetics. For networks of zero deficiency, which admit a detailed- or complex-balanced steady state, all molecular species are uncorrelated and their Fano factors are Poissonian. Systems of higher deficiency have non-equilibrium steady states and non-zero reaction fluxes flowing between the complexes. When they model homo-oligomerization, the noise on each species is reduced when the flux flows from the oligomers of lowest to highest degree, and amplified otherwise. In the case of hetero-oligomerization systems, only the noise on the highest-degree species shows this behaviour.

The school from Brussels have found that for the systems maintained far from thermodynamic equilibrium and when the kinetic laws are suitably nonlinear, the excess entropy production, δxP, becomes negative for t > to. In this case, the nonequilibrium steady state becomes unstable and sometimes, when the internal structure permits, the system executes limit cycle oscillations [1–3].

This paper discusses the evaluation of hydrodynamic variables in the presence of spontaneous fluctuations, such as in molecular simulations of fluid flows. The principal point is that hydrodynamic variables such as fluid velocity and temperature must be defined in terms of mechanical variables such as momentum and energy density). Because these relations are nonlinear and because fluctuations of mechanical variables are correlated, care must be taken to avoid introducing a bias when evaluating means, variances, and correlations of hydrodynamic variables. The unbiased estimates are formulated; some alternative, incorrect approaches are presented as cautionary warnings. The expressions are verified by numerical simulations, both at thermodynamic equilibrium and at a nonequilibrium steady state.

The Langevin formalism that describes fluctuations about thermodynamic equilibrium is extended to study hydrodynamic nonequilibrium steady states. The limitations of our generalization are discussed as well as the connection between experimental and theoretical quantities which is more subtle than in equilibrium. The spectrum for Brillouin scattering from a fluid in a shear flow or temperature gradient is simply obtained by Langevin methods. The latter problem exhibits an asymmetry in the height of the peaks inversely proportional to the square of the scattering wave vector. We also construct a microscopic ensemble that is applicable to a variety of hydrodynamic nonequilibrium steady states, and then verify for a particular model that our extension of the Langevin method agrees with a fully microscopic calculation.

The fluctuation-dissipation theorem is a central result of statistical physics, which applies to any system at thermodynamic equilibrium. Its violation is a strong signature of nonequilibrium behavior. We show that for any system with Markovian dynamics, in a nonequilibrium steady state, a proper choice of observables restores a fluctuation-response theorem identical to a suitable version of the equilibrium fluctuation-dissipation theorem. This theorem applies to a broad class of dynamical systems. We illustrate it with linear stochastic dynamics and examples borrowed from the physics of molecular motors and Hopf bifurcations. Finally, we discuss general implications of the theorem.

Many scholars researched social informatization from different perspectives, including profession, economy and technology. In this thesis, the author will studied on social informatization from the perspective of basic characteristics of information. Firstly, the author will describe other scholars’ social informationization theories. Secondly, the definition of information and basic characteristics of information will be given. Then, the production mode informatization and life-style informatization from the perspective of basic characteristics of information will be studied on in this paper. Lastly, the conclusion will be drawn.

Utility of Brownian dynamics simulations in chemistry and biology: A comprehensive review.

We consider chemical reactions occurring in a compartment separated by semipermeable membranes from reservoirs of reactant and product, both held at constant pressure. In earlier work, we have developed a nonequilibrium thermodynamic theory applicable to systems with a single reactive intermediate, and we have established a link between the thermodynamic and stochastic analyses of such systems. Here we show that our results generalize directly to cases with two or more reactive intermediates, if the reaction mechanism is nonautocatalytic, or if the system is evolving toward an equilibrium steady state in the reaction compartment without first exhausting the reactant or product reservoir. Starting with nonautocatalytic mechanisms, we identify effective driving forces for each intermediate; we then obtain the driving force for an arbitrary system by mapping to an instantaneously equivalent nonautocatalytic system. The driving force can be cast thermodynamically in terms of the difference between the actual chemical potential of the intermediate and its chemical potential at a reference state (the steady state of the instantaneously equivalent nonautocatalytic system); it can also be cast kinetically in terms of reactive fluxes in the instantaneously equivalent system. Taking the product of the driving force and the net flux of each intermediate and then summing over the species gives a term in the dissipation that is specific to the intermediates. This term is minimized at nonequilibrium steady states, unlike the total dissipation (or entropy production). For the nonautocatalytic or equilibrating systems, an integral of the driving forces yields a Liapunov function for the evolution of the reaction chamber toward the steady state. The same integral also determines the stationary solution of the birth–death master equation for the species numbers of intermediates in the reaction compartment; this generalizes the Einstein relation for the probability of equilibrium fluctuations to far-from-equilibrium conditions.

Information theory (IT) has been used in the many different disciplines of communication. However, only in few cases an examination for complying with the assumptions of IT have been carried outand thus ensure that the results allow for the generation of theory. In this order, in this review several interpretations of the IT in ecological investigation are examined through consideration of the basis from which the IT algorithms have been derived, mainly H´. It was noted that three versions of the IT are used for describing ecologic phenomena, and that the measurement of information can be used as an indicator of diversity but requires conversion. Likewise, that a discrimination between diversity and informationmeasurements is convenient inasmuch the latter measures statistical structure which can be used todescribe community structure. This allows for exploring further interpretations of H´ such as its predictive capability.