Quantifying Landscape-Flux via Single-Cell Transcriptomics Uncovers the Underlying Mechanism of Cell Cycle

Recent developments in single-cell sequencing technology enable the acquisition of entire transcriptome data. Understanding the underlying mechanism and identifying the driving force of transcriptional regulation governing cell function directly from these data remains challenging. This study reconstructs a continuous vector field of the cell cycle based on discrete single-cell RNA velocity to quantify the single-cell global nonequilibrium dynamic landscape-flux. It reveals that large fluctuations disrupt the global landscape and genetic perturbations alter landscape-flux, thus identifying key genes in maintaining cell cycle dynamics and predicting associated functional effects. Additionally, it quantifies the fundamental energy cost of the cell cycle initiation and unveils that sustaining the cell cycle requires curl flux and dissipation to maintain the oscillatory phase coherence. This study enables the inference of the cell cycle gene regulatory networks directly from the single-cell transcriptomic data, including the feedback mechanisms and interaction intensity. This provides a golden opportunity to experimentally verify the landscape-flux theory and also obtain its associated quantifications. It also offers a unique framework for combining the landscape-flux theory and single-cell high-through sequencing experiments for understanding the underlying mechanisms of the cell cycle and can be extended to other nonequilibrium biological processes, such as differentiation development and disease pathogenesis.

Omicron BA.2.75 Subvariant of SARS-CoV-2 Is Expected to Have the Greatest Infectivity Compared with the Competing BA.2 and BA.5, Due to Most Negative Gibbs Energy of Binding

Omicron BA.2.75 may become the next globally dominant strain of COVID-19 in 2022. The BA.2.75 sub-variant has acquired more mutations (9) in spike protein and other genes of SARS-CoV-2 than any other variant. Thus, its chemical composition and thermodynamic properties have changed compared with earlier variants. In this paper, the Gibbs energy of the binding and antigen-receptor binding rate was reported for the BA.2.75 variant. Gibbs energy of the binding of the Omicron BA.2.75 variant is more negative than that of the competing variants BA.2 and BA.5.

Mathematical model of solidification of melt with high-speed cooling

A new mathematical model of supercooled melt crystallization based on the variational principles of thermodynamics has been developed. The model takes into account the crystal formation and diffusion growth regularities, as well as the diffusionless crystal growth with the deviation from the local equilibrium at the surface. The model also takes into account the growing crystals mutual influence on the components concentration in the melt. The calculations for the supercooled eutectic melt Fe₈₃B₁₇showed that the nucleation and growth of the phases Fe and Fe₂B with a metastable phase Fe₃B occur in the melt. The local equilibrium on the surface of the growing Fe₃B crystals with the melt probably does not maintained. The regularities of the nucleation and mutual influence of the growing crystals of the phases are studied. The nucleation and growth rate of the Fe₃B nuclei differs from the growth of Fe and Fe₂B nuclei due to the diffusionless capture of boron atoms by the growing Fe₃B crystals surface. The model will help to calculate the melt cooling technology mode for producing amorphous ribbons on a copper rotating drum. The calculation made it possible to analyze changes in the temperature and the crystallization degree in the various ribbon layers. The calculation results have been verified experimentally by x-ray diffraction and calorimetric studies of the obtained ribbons. The correspondence of the calculation and the experimental results confirms the effectiveness developed methodology for studying the regularities of crystal growth in supercooled melts.

Nonequilibrium statistical thermodynamics of multicomponent interfaces

Interfaces and their dynamics are critical in many biological, physical, and industrial processes. However, the thermodynamics of interfaces far from equilibrium are subtle and have not been firmly or rigorously established. In analogy with well-known bulk phenomena, we hypothesize a “local” equilibrium for interfaces in multicomponent, multiphase systems and examine the resulting theoretical implications. We then conduct high-precision molecular dynamics simulations to validate the underlying theory, and show that generalized equilibrium thermodynamic equations can be applied to systems far beyond equilibrium. These results lay the groundwork for accurate and thermodynamically consistent modeling of transport at interfaces.

Nonequilibrium interfacial thermodynamics has important implications for crucial biological, physical, and industrial-scale transport processes. Here, we discuss a theory of local equilibrium for multiphase multicomponent interfaces that builds upon the “sharp” interface concept first introduced by Gibbs, allowing for a description of nonequilibrium interfacial processes such as those arising in evaporation, condensation, adsorption, etc. By requiring that the thermodynamics be insensitive to the precise location of the dividing surface, one can identify conditions for local equilibrium and develop methods for measuring the values of intensive variables at the interface. We then use extensive, high-precision nonequilibrium molecular dynamics (NEMD) simulations to verify the theory and establish the validity of the local equilibrium hypothesis. In particular, we demonstrate that equilibrium equations of state are also valid out of equilibrium, and can be used to determine interfacial temperature and chemical potential(s) that are consistent with nonequilibrium generalizations of the Clapeyron and Gibbs adsorption equations. We also show, for example, that, far from equilibrium, temperature or chemical potential differences need not be uniform across an interface and may instead exhibit pronounced discontinuities. However, even in these circumstances, we demonstrate that the local equilibrium hypothesis and its implications remain valid. These results provide a thermodynamic foundation and computational tools for studying or revisiting a wide variety of interfacial transport phenomena.

Hidden Dissipation and Irreversibility in Maxwell's Demon

Maxwell's demon is an entity in a 150-year-old thought experiment that paradoxically appears to violate the second law of thermodynamics by reducing entropy without doing work. It has increasingly practical implications as advances in nanomachinery produce devices that push the thermodynamic limits imposed by the second law. A well-known explanation claiming that information erasure restores second law compliance fails to resolve the paradox because it assumes the second law a priori, and does not predict irreversibility. Instead, a purely mechanical resolution that does not require information theory is presented. The transport fluxes of mass, momentum, and energy involved in the demon's operation are analyzed and show that they imply "hidden" external work and dissipation. Computing the dissipation leads to a new lower bound on entropy production by the demon. It is strictly positive in all nontrivial cases, providing a more stringent limit than the second law and implying intrinsic thermodynamic irreversibility. The thermodynamic irreversibility is linked with mechanical irreversibility resulting from the spatial asymmetry of the demon's speed selection criteria, indicating one mechanism by which macroscopic irreversibility may emerge from microscopic dynamics.

Fluctuation-Dissipation Theorems for Multiphase Flow in Porous Media

A thermodynamic description of porous media must handle the size- and shape-dependence of media properties, in particular on the nano-scale. Such dependencies are typically due to the presence of immiscible phases, contact areas and contact lines. We propose a way to obtain average densities suitable for integration on the course-grained scale, by applying Hill's thermodynamics of small systems to the subsystems of the medium. We argue that the average densities of the porous medium, when defined in a proper way, obey the Gibbs equation. All contributions are additive or weakly coupled. From the Gibbs equation and the balance equations, we then derive the entropy production in the standard way, for transport of multi-phase fluids in a non-deformable, porous medium exposed to differences in boundary pressures, temperatures, and chemical potentials. Linear relations between thermodynamic fluxes and forces follow for the control volume. Fluctuation-dissipation theorems are formulated for the first time, for the fluctuating contributions to fluxes in the porous medium. These give an added possibility for determination of the Onsager conductivity matrix for transport through porous media. Practical possibilities are discussed.

Crooks Fluctuation Theorem for Single Polymer Dynamics in Time-Dependent Flows: Understanding Viscoelastic Hysteresis

Nonequilibrium work relations have fundamentally advanced our understanding of molecular processes. In recent years, fluctuation theorems have been extensively applied to understand transitions between equilibrium steady-states, commonly described by simple control parameters such as molecular extension of a protein or polymer chain stretched by an external force in a quiescent fluid. Despite recent progress, far less is understood regarding the application of fluctuation theorems to processes involving nonequilibrium steady-states such as those described by polymer stretching dynamics in nonequilibrium fluid flows. In this work, we apply the Crooks fluctuation theorem to understand the nonequilibrium thermodynamics of dilute polymer solutions in flow. We directly determine the nonequilibrium free energy for single polymer molecules in flow using a combination of single molecule experiments and Brownian dynamics simulations. We further develop a time-dependent extensional flow protocol that allows for probing viscoelastic hysteresis over a wide range of flow strengths. Using this framework, we define quantities that uniquely characterize the coil-stretch transition for polymer chains in flow. Overall, generalized fluctuation theorems provide a powerful framework to understand polymer dynamics under far-from-equilibrium conditions.

Notes of a protein crystallographer: the legacy of J.-B. J. Fourier - crystallography, time and beyond

The importance of the Fourier transform as a fundamental tool for crystallography is well known in the field. However, the complete legacy of Jean-Baptiste Joseph Fourier (1768-1830) as a pioneer Egyptologist and premier mathematician and physicist of his time, and the implications of his work in other scientific fields, is less well known. Significantly, his theoretical and experimental work on phenomena related to the transmission of heat founded the mathematical study of irreversible phenomena and introduced the flow of time in physico-chemical processes and geology, with its implications for biological evolution. Fourier's insights are discussed in contrast to the prevalent notion of reversible dynamic time in the early 20th century, which was dominated by Albert Einstein's (1875-1953) theory of general relativity versus the philosophical notion of durée proposed by the French philosopher Henri-Louis Bergson (1859-1941). The current status of the mathematical description of irreversible processes by Ilya Romanovich Prigogine (1917-2003) is briefly discussed as part of the enduring legacy of the pioneering work of J.-B. J. Fourier, first established nearly two centuries ago, in numerous scientific endeavors.

Nonequilibrium Thermodynamics in Biochemical Systems and Its Application

Living systems are open systems, where the laws of nonequilibrium thermodynamics play the important role. Therefore, studying living systems from a nonequilibrium thermodynamic aspect is interesting and useful. In this review, we briefly introduce the history and current development of nonequilibrium thermodynamics, especially that in biochemical systems. We first introduce historically how people realized the importance to study biological systems in the thermodynamic point of view. We then introduce the development of stochastic thermodynamics, especially three landmarks: Jarzynski equality, Crooks' fluctuation theorem and thermodynamic uncertainty relation. We also summarize the current theoretical framework for stochastic thermodynamics in biochemical reaction networks, especially the thermodynamic concepts and instruments at nonequilibrium steady state. Finally, we show two applications and research paradigms for thermodynamic study in biological systems.

Dissipative Structures, Organisms and Evolution

Self-organization in nonequilibrium systems has been known for over 50 years. Under nonequilibrium conditions, the state of a system can become unstable and a transition to an organized structure can occur. Such structures include oscillating chemical reactions and spatiotemporal patterns in chemical and other systems. Because entropy and free-energy dissipating irreversible processes generate and maintain these structures, these have been called dissipative structures. Our recent research revealed that some of these structures exhibit organism-like behavior, reinforcing the earlier expectation that the study of dissipative structures will provide insights into the nature of organisms and their origin. In this article, we summarize our study of organism-like behavior in electrically and chemically driven systems. The highly complex behavior of these systems shows the time evolution to states of higher entropy production. Using these systems as an example, we present some concepts that give us an understanding of biological organisms and their evolution.

Modeling, Simulation, and Reconstruction of 2-Reservoir Heat-to-Power Processes in Finite-Time Thermodynamics

The connection between endoreversible models of Finite-Time Thermodynamics and the corresponding real running irreversible processes is investigated by introducing two concepts which complement each other: Simulation and Reconstruction. In that context, the importance of particular machine diagrams for Simulation and (reconstruction) parameter diagrams for Reconstruction is emphasized. Additionally, the treatment of internal irreversibilities through the use of contact quantities like the contact temperature is introduced into the Finite-Time Thermodynamics description of thermal processes.

Simple, Accurate and User-Friendly Differential Constitutive Model for the Rheology of Entangled Polymer Melts and Solutions from Nonequilibrium Thermodynamics

In a recent reformulation of the Marrucci-Ianniruberto constitutive equation for the rheology of entangled polymer melts in the context of nonequilibrium thermodynamics, rather large values of the convective constraint release parameter β_ccr had to be used in order for the model not to violate the second law of thermodynamics. In this work, we present an appropriate modification of the model, which avoids the splitting of the evolution equation for the conformation tensor into an orientation and a stretching part. Then, thermodynamic admissibility simply dictates that β_ccr ≥ 0, thus allowing for more realistic values of β_ccr to be chosen. Moreover, and in view of recent experimental evidence for a transient stress undershoot (following the overshoot) at high shear rates, whose origin may be traced back to molecular tumbling, we have incorporated additional terms into the model accounting, at least in an approximate way, for non-affine deformation through a slip parameter ξ. Use of the new model to describe available experimental data for the transient and steady-state shear and elongational rheology of entangled polystyrene melts and concentrated solutions shows close agreement. Overall, the modified model proposed here combines simplicity with accuracy, which renders it an excellent choice for managing complex viscoelastic fluid flows in large-scale numerical calculations.

Fluctuation-response inequality out of equilibrium

We present an approach to response around arbitrary out-of-equilibrium states in the form of a fluctuation-response inequality (FRI). We study the response of an observable to a perturbation of the underlying stochastic dynamics. We find that the magnitude of the response is bounded from above by the fluctuations of the observable in the unperturbed system and the Kullback-Leibler divergence between the probability densities describing the perturbed and the unperturbed system. This establishes a connection between linear response and concepts of information theory. We show that in many physical situations, the relative entropy may be expressed in terms of physical observables. As a direct consequence of this FRI, we show that for steady-state particle transport, the differential mobility is bounded by the diffusivity. For a "virtual" perturbation proportional to the local mean velocity, we recover the thermodynamic uncertainty relation (TUR) for steady-state transport processes. Finally, we use the FRI to derive a generalization of the uncertainty relation to arbitrary dynamics, which involves higher-order cumulants of the observable. We provide an explicit example, in which the TUR is violated but its generalization is satisfied with equality.

[Common mathematical-physical essence involved from chromatographic separation to intelligent medicine: irreversibility]

The chromatographic separation processes for many molecules in solute bands by stationary phase-mobile phase separation can be compared to ordering disease severity. The common features of chromatographic processes and machine-disease diagnosis-doctor's advice is the separation (classification) of components (individual disease states), both of which show irreversibility of time evolution; however, the former is caused by linear non-equilibrium thermodynamics and latter by nonlinear non-equilibrium thermodynamics (dissipative structure). When the scientific view is extended from drug detection and preparation to evidence-based medicine (EBM), discrete mathematics (axiomatic set theory and probability measure), and artificial intelligence (AI) cloud computing, the convection-diffusion equation and irreversibility in non-equilibrium thermodynamics form a common and core essence of mathematical physics that crosses fields of chromatographic separation and intelligent medicine. It is of profound scientific and practical significance to construct and develop a unified and all-encompassing mathematical framework by incorporating the generality and characteristics of the two subjects.

Thermodynamics of Majority-Logic Decoding in Information Erasure

We investigate the performance of majority-logic decoding in both reversible and finite-time information erasure processes performed on macroscopic bits that contain N microscopic binary units. While we show that for reversible erasure protocols single-unit transformations are more efficient than majority-logic decoding, the latter is found to offer several benefits for finite-time erasure processes: Both the minimal erasure duration for a given erasure and the minimal erasure error for a given erasure duration are reduced, if compared to a single unit. Remarkably, the majority-logic decoding is also more efficient in both the small-erasure error and fast-erasure region. These benefits are also preserved under the optimal erasure protocol that minimizes the dissipated heat. Our work therefore shows that majority-logic decoding can lift the precision-speed-efficiency trade-off in information erasure processes.

Shear Banding in 4:1 Planar Contraction

We study shear banding in a planar 4:1 contraction flow using our recently developed two-fluid model for semidilute entangled polymer solutions derived from the generalized bracket approach of nonequilibrium thermodynamics. In our model, the differential velocity between the constituents of the solution allows for coupling between the viscoelastic stress and the polymer concentration. Stress-induced migration is assumed to be the triggering mechanism of shear banding. To solve the benchmark problem, we used the OpenFOAM software package with the viscoelastic solver RheoTool v.2.0. The convection terms are discretized using the high-resolution scheme CUBISTA, and the governing equations are solved using the SIMPLEC algorithm. To enter into the shear banding regime, the uniform velocity at the inlet was gradually increased. The velocity increases after the contraction due to the mass conservation; therefore, shear banding is first observed at the downstream. While the velocity profile in the upstream channel is still parabolic, the corresponding profile changes to plug-like after the contraction. In agreement with experimental data, we found that shear banding competes with flow recirculation. Finally, the profile of the polymer concentration shows a peak in the shear banding regime, which is closer to the center of the channel for larger inlet velocities. Nevertheless, the increase in the polymer concentration in the region of flow recirculation was significantly larger for the inlet velocities studied in this work. With our two-fluid finite-volume solver, localized shear bands in industrial applications can be simulated.

BAR-based optimum adaptive steered MD for configurational sampling

The equilibrium and nonequilibrium adaptive alchemical free energy simulation methods optimum Bennett's acceptance ratio and optimum crooks' equation (OCE), based on the statistically optimal bidirectional reweighting estimator named Bennett's Acceptance Ratio or Crooks' equation, perform initial sampling in the staging alchemical transformation and then determine the importance rank of different states via the time-derivative of the variance. The method is proven to give speedups compared with the equal time rule. In the current work, we extend the time derivative of variance guided adaptive sampling method to the configurational space, falling in the term of steered MD (SMD). The SMD approach biasing physically meaningful collective variable (CV) such as one dihedral or one distance to pulling the system from one conformational state to another. By minimizing the variance of the free energy differences along the pathway in an optimized way, a new type of adaptive SMD (ASMD) is introduced. As exhibits in the alchemical case, this adaptive sampling method outperforms the traditional equal-time SMD in nonequilibrium stratification. Also, the method gives much more efficient calculation of potential of mean force than the selection criterion-based ASMD scheme, which is proven to be more efficient than traditional SMD. The OCE workflow is periodicity-of-CV dependent while ASMD is not. The performance is demonstrated in a dihedral flipping case and two distance pulling cases, accounting for periodic and nonperiodic CVs, respectively. © 2019 Wiley Periodicals, Inc.

Transmutable Colloidal Crystals and Active Phase Separation via Dynamic, Directed Self-Assembly with Toggled External Fields

A diverse set of functional materials can be fabricated by assembling dispersions of colloids and nanoparticles. Two principal engineering challenges prevent efficient production of these materials: first, scalable synthesis of particles with carefully tailored interactions required to generate complex structures, and second, the propensity of such materials to arrest in undesirable metastable states. Active assembly processes, such as dynamic, directed self-assembly in which the interactions among particles are externally controlled and vary over time, offer a promising method to address these challenges. For dispersions of polarizable dielectric or paramagnetic nanoparticles, an effective mode of active assembly can be achieved by toggling an external electric or magnetic field, which induces attractive particle interactions, on and off cyclically over time. Here, we develop computational and theoretical models for such active assembly processes and find that cyclically toggling the external field leads to growth of colloidal crystals at significantly faster rates and with many fewer defects than for assembly in a steady field. The active process stabilizes phases that are only metastable in steady fields, including a dense fluid phase and body-centered orthorhombic crystals. The growth mechanism and terminal structure of the dispersion are easily controlled by the toggling protocol, and the toggle parameters can be used to continuously transmute between crystal structures with different lattice parameters. Finally, we show how results from linear irreversible thermodynamics can be used to predict the dissipative terminal states of the active assembly process in terms of parameters of the toggling protocol.

From Lagrangian Mechanics to Nonequilibrium Thermodynamics: A Variational Perspective

In this paper, we survey our recent results on the variational formulation of nonequilibrium thermodynamics for the finite-dimensional case of discrete systems, as well as for the infinite-dimensional case of continuum systems. Starting with the fundamental variational principle of classical mechanics, namely, Hamilton’s principle, we show, with the help of thermodynamic systems with gradually increasing complexity, how to systematically extend it to include irreversible processes. In the finite dimensional cases, we treat systems experiencing the irreversible processes of mechanical friction, heat, and mass transfer in both the adiabatically closed cases and open cases. On the continuum side, we illustrate our theory using the example of multicomponent Navier–Stokes–Fourier systems.

Triphase Separation of a Ternary Symmetric Highly Viscous Mixture

We discuss numerical results of diffusion-driven separation into three phases of a symmetric, three-component highly viscous liquid mixture after an instantaneous quench from the one-phase region into an unstable location within the tie triangle of its phase diagram. Our theoretical approach follows a diffuse-interface model of partially miscible ternary liquid mixtures that incorporates the one-parameter Margules correlation as a submodel for the enthalpic (so-called excess) component of the Gibbs energy of mixing, while its nonlocal part is represented based on a square-gradient (Cahn–Hilliard-type) modeling assumption. The governing equations for this phase-field ternary mixture model are simulated in 3D, showing the segregation kinetics in terms of basic segregation statistics, such as the integral scale of the pair-correlation function and the separation depth for each component. Based on the temporal evolution of the integral scales, phase separation takes place via the simultaneous growth of three phases up until a symmetry-breaking event after which one component continues to separate quickly, while phase separation for the other two seems to be delayed. However, inspection of the separation depths reveals that there can be no symmetry among the three components at any instant in time during a triphase segregation process.

Vacuum Landscaping: Cause of Nonlocal Influences without Signaling

In the quest for an understanding of nonlocality with respect to an appropriate ontology, we propose a “cosmological solution”. We assume that from the beginning of the universe each point in space has been the location of a scalar field representing a zero-point vacuum energy that nonlocally vibrates at a vast range of different frequencies across the whole universe. A quantum, then, is a nonequilibrium steady state in the form of a “bouncer” coupled resonantly to one of those (particle type dependent) frequencies, in remote analogy to the bouncing oil drops on an oscillating oil bath as in Couder’s experiments. A major difference to the latter analogy is given by the nonlocal nature of the vacuum oscillations. We show with the examples of double- and n-slit interference that the assumed nonlocality of the distribution functions alone suffices to derive the de Broglie–Bohm guiding equation for N particles with otherwise purely classical means. In our model, no influences from configuration space are required, as everything can be described in 3-space. Importantly, the setting up of an experimental arrangement limits and shapes the forward and osmotic contributions and is described as vacuum landscaping.

Energy dissipation and fluctuations in a driven liquid

Minimal models of active and driven particles have recently been used to elucidate many properties of nonequilibrium systems. However, the relation between energy consumption and changes in the structure and transport properties of these nonequilibrium materials remains to be explored. We explore this relation in a minimal model of a driven liquid that settles into a time periodic steady state. Using concepts from stochastic thermodynamics and liquid state theories, we show how the work performed on the system by various nonconservative, time-dependent forces-this quantifies a violation of time reversal symmetry-modifies the structural, transport, and phase transition properties of the driven liquid.

A Variational Formulation of Nonequilibrium Thermodynamics for Discrete Open Systems with Mass and Heat Transfer

We propose a variational formulation for the nonequilibrium thermodynamics of discrete open systems, i.e., discrete systems which can exchange mass and heat with the exterior. Our approach is based on a general variational formulation for systems with time-dependent nonlinear nonholonomic constraints and time-dependent Lagrangian. For discrete open systems, the time-dependent nonlinear constraint is associated with the rate of internal entropy production of the system. We show that this constraint on the solution curve systematically yields a constraint on the variations to be used in the action functional. The proposed variational formulation is intrinsic and provides the same structure for a wide class of discrete open systems. We illustrate our theory by presenting examples of open systems experiencing mechanical interactions, as well as internal diffusion, internal heat transfer, and their cross-effects. Our approach yields a systematic way to derive the complete evolution equations for the open systems, including the expression of the internal entropy production of the system, independently on its complexity. It might be especially useful for the study of the nonequilibrium thermodynamics of biophysical systems.

Hierarchy of Relaxation Times and Residual Entropy: A Nonequilibrium Approach

We consider nonequilibrium (NEQ) states such as supercooled liquids and glasses that are described with the use of internal variables. We classify the latter by the state-dependent hierarchy of relaxation times to assess their relevance for irreversible contributions. Given an observation time τobs, we determine the window of relaxation times that divide the internal variables into active and inactive groups, the former playing a central role in the NEQ thermodynamics. Using this thermodynamics, we determine (i) a bound on the NEQ entropy and on the residual entropy and (ii) the nature of the isothermal relaxation of the entropy and the enthalpy in accordance with the second law. A theory that violates the second law such as the entropy loss view is shown to be internally inconsistent if we require it to be consistent with experiments. The inactive internal variables still play an indirect role in determining the temperature T(t) and the pressure P(t) of the system, which deviate from their external values.

Dissolution or Growth of a Liquid Drop via Phase-Field Ternary Mixture Model Based on the Non-Random, Two-Liquid Equation

We simulate the diffusion-driven dissolution or growth of a single-component liquid drop embedded in a continuous phase of a binary liquid. Our theoretical approach follows a diffuse-interface model of partially miscible ternary liquid mixtures that incorporates the non-random, two-liquid (NRTL) equation as a submodel for the enthalpic (so-called excess) component of the Gibbs energy of mixing, while its nonlocal part is represented based on a square-gradient (Cahn-Hilliard-type modeling) assumption. The governing equations for this phase-field ternary mixture model are simulated in 2D, showing that, for a single-component drop embedded in a continuous phase of a binary liquid (which is highly miscible with either one component of the continuous phase but is essentially immiscible with the other), the size of the drop can either shrink to zero or reach a stationary value, depending on whether the global composition of the mixture is within the one-phase region or the unstable range of the phase diagram.

How Simple Could Life Be?

Will we be ever able to produce living matter artificially? Despite our increasingly precise understanding of the details of life, its fundamental principles still lie in the dark. Armed with today's technology and knowledge about living systems, it is high time for us to re-address this persistent challenge in understanding nature. Graphics: Monika Krause, MPIB.

Spontaneous fine-tuning to environment in many-species chemical reaction networks

A chemical mixture that continually absorbs work from its environment may exhibit steady-state chemical concentrations that deviate from their equilibrium values. Such behavior is particularly interesting in a scenario where the environmental work sources are relatively difficult to access, so that only the proper orchestration of many distinct catalytic actors can power the dissipative flux required to maintain a stable, far-from-equilibrium steady state. In this article, we study the dynamics of an in silico chemical network with random connectivity in an environment that makes strong thermodynamic forcing available only to rare combinations of chemical concentrations. We find that the long-time dynamics of such systems are biased toward states that exhibit a fine-tuned extremization of environmental forcing.

Optical Binding of Nanowires

Multiple scattering of light induces structured interactions, or optical binding forces, between collections of small particles. This has been extensively studied in the case of microspheres. However, binding forces are strongly shape dependent: here, we turn our attention to dielectric nanowires. Using a novel numerical model we uncover rich behavior. The extreme geometry of the nanowires produces a sequence of stationary and dynamic states. In linearly polarized light, thermally stable ladder-like structures emerge. Lower symmetry, sagittate arrangements can also arise, whose configurational asymmetry unbalances the optical forces leading to nonconservative, translational motion. Finally, the addition of circular polarization drives a variety of coordinated rotational states whose dynamics expose fundamental properties of optical spin. These results suggest that optical binding can provide an increased level of control over the positions and motions of nanoparticles, opening new possibilities for driven self-organization and heralding a new field of self-assembling optically driven micromachines.

Nonequilibrium thermodynamics of the Markovian Mpemba effect and its inverse

Under certain conditions, it takes a shorter time to cool a hot system than to cool the same system initiated at a lower temperature. This phenomenon-the "Mpemba effect"-was first observed in water and has recently been reported in other systems. Whereas several detail-dependent explanations were suggested for some of these observations, no common underlying mechanism is known. Using the theoretical framework of nonequilibrium thermodynamics, we present a widely applicable mechanism for a similar effect, the Markovian Mpemba effect, derive a sufficient condition for its appearance, and demonstrate it explicitly in three paradigmatic systems: the Ising model, diffusion dynamics, and a three-state system. In addition, we predict an inverse Markovian Mpemba effect in heating: Under proper conditions, a cold system can heat up faster than the same system initiated at a higher temperature. We numerically demonstrate that this inverse effect is expected in a 1D antiferromagnet nearest-neighbors interacting Ising chain in the presence of an external magnetic field. Our results shed light on the mechanism behind anomalous heating and cooling and suggest that it should be possible to observe these in a variety of systems.

Numerical evidence for thermally induced monopoles

Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell's equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis.

Probing kinetic drug binding mechanism in voltage-gated sodium ion channel: open state versus inactive state blockers

The kinetics and nonequilibrium thermodynamics of open state and inactive state drug binding mechanisms have been studied here using different voltage protocols in sodium ion channel. We have found that for constant voltage protocol, open state block is more efficient in blocking ionic current than inactive state block. Kinetic effect comes through peak current for mexiletine as an open state blocker and in the tail part for lidocaine as an inactive state blocker. Although the inactivation of sodium channel is a free energy driven process, however, the two different kinds of drug affect the inactivation process in a different way as seen from thermodynamic analysis. In presence of open state drug block, the process initially for a long time remains entropy driven and then becomes free energy driven. However in presence of inactive state block, the process remains entirely entropy driven until the equilibrium is attained. For oscillating voltage protocol, the inactive state blocking is more efficient in damping the oscillation of ionic current. From the pulse train analysis it is found that inactive state blocking is less effective in restoring normal repolarisation and blocks peak ionic current. Pulse train protocol also shows that all the inactive states behave differently as one inactive state responds instantly to the test pulse in an opposite manner from the other two states.

Dynamic, Directed Self-Assembly of Nanoparticles via Toggled Interactions

Crystals self-assembled from nanoparticles have useful properties such as optical activity and sensing capability. During fabrication, however, gelation and glassification often leave these materials arrested in defective or disordered metastable states. This is a key difficulty preventing adoption of self-assembled nanoparticle materials at scale. Processes which suppress kinetic arrest and defect formation while accelerating growth of ordered materials are essential for bottom-up approaches to creating nanomaterials. Dynamic, directed self-assembly processes in which the interactions between self-assembling components are actuated temporally offer one promising methodology for accelerating and controlling bottom-up growth of nanostructures. In this article, we show through simulation and theory how time-dependent, periodically toggled interparticle attractions can avoid kinetic barriers and yield well-ordered crystalline domains for a dispersion of nanoparticles interacting via a short-ranged, isotropic potential. The growth mechanism and terminal structure of the dispersion are controlled by parameters of the toggling protocol. This control allows for selection of processes that yield rapid self-assembled, low defect crystals. Although self-assembly via periodically toggled attractions is inherently unsteady and out-of-equilibrium, its outcome is predicted by a first-principles theory of nonequilibrium thermodynamics. The theory necessitates equality of the time average of pressure and chemical potential in coexisting phases of the dispersion. These quantities are evaluated using well known equations of state. The phase behavior predicted by this theory agrees well with measurements made in Brownian dynamics simulations of sedimentation equilibrium and homogeneous nucleation. The theory can easily be extended to model dynamic self-assembly directed by other toggled conservative force fields.

Thermodynamical journey in plant biology

Nonequilibrium irreversible thermodynamics constitute a meaningful point of view suitable to explore life with a rich paradigm. This analytical framework can be used to span the gap from molecular processes to plant function and shows great promise to create a holistic description of life. Since living organisms dissipate energy, exchange entropy and matter with their environment, they can be assimilated to dissipative structures. This concept inherited from nonequilibrium thermodynamics has four properties which defines a scale independent framework suitable to provide a simpler and more comprehensive view of the highly complex plant biology. According to this approach, a biological function is modeled as a cascade of dissipative structures. Each dissipative structure, corresponds to a biological process, which is initiated by the amplification of a fluctuation. Evolution of the process leads to the breakage of the system symmetry and to the export of entropy. Exporting entropy to the surrounding environment corresponds to collecting information about it. Biological actors which break the symmetry of the system and which store information are by consequence, key actors on which experiments and data analysis focus most. This paper aims at illustrating properties of dissipative structure through familiar examples and thus initiating the dialogue between nonequilibrium thermodynamics and plant biology.

Nonequilibrium landscape theory of neural networks

The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape-flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments.

Energetics of glucose metabolism: a phenomenological approach to metabolic network modeling

A new formalism to describe metabolic fluxes as well as membrane transport processes was developed. The new flux equations are comparable to other phenomenological laws. Michaelis-Menten like expressions, as well as flux equations of nonequilibrium thermodynamics, can be regarded as special cases of these new equations. For metabolic network modeling, variable conductances and driving forces are required to enable pathway control and to allow a rapid response to perturbations. When applied to oxidative phosphorylation, results of simulations show that whole oxidative phosphorylation cannot be described as a two-flux-system according to nonequilibrium thermodynamics, although all coupled reactions per se fulfill the equations of this theory. Simulations show that activation of ATP-coupled load reactions plus glucose oxidation is brought about by an increase of only two different conductances: a [Ca²⁺] dependent increase of cytosolic load conductances, and an increase of phosphofructokinase conductance by [AMP], which in turn becomes increased through [ADP] generation by those load reactions. In ventricular myocytes, this feedback mechanism is sufficient to increase cellular power output and O₂ consumption several fold, without any appreciable impairment of energetic parameters. Glucose oxidation proceeds near maximal power output, since transformed input and output conductances are nearly equal, yielding an efficiency of about 0.5. This conductance matching is fulfilled also by glucose oxidation of β-cells. But, as a price for the metabolic mechanism of glucose recognition, β-cells have only a limited capability to increase their power output.

Dissipative metabolic patterns respond during neutrophil transmembrane signaling

Self-organization is a common theme in biology. One mechanism of self-organization is the creation of chemical patterns by the diffusion of chemical reactants and their nonlinear interactions. We have recently observed sustained unidirectional traveling chemical redox [NAD(P)H - NAD(P)(+)] waves within living polarized neutrophils. The present study shows that an intracellular metabolic wave responds to formyl peptide receptor agonists, but not antagonists, by splitting into two waves traveling in opposite directions along a cell's long axis. Similar effects were noted with other neutrophil-activating substances. Moreover, when cells were exposed to an N-formyl-methionyl-leucyl-phenylalanine (FMLP) gradient whose source was perpendicular to the cell's long axis, cell metabolism was locally perturbed with reorientation of the pattern in a direction perpendicular to the initial cellular axis. Thus, extracellular activating signals and the signals' spatial cues are translated into distinct intracellular dissipative structures.

Thermodynamic efficiency of microbial growth is low but optimal for maximal growth rate

Thermodynamic efficiency of microbial growth on substrates that are more oxidized than biomass approaches 24%. This is the theoretical value for a linear energy converter optimized for maximal output flow at optimal efficiency. For growth on substrates more reduced than biomass, thermodynamic efficiencies correspond to those predicted for optimization to maximal growth rate (or yield) only.