Thermodynamics of Chemical Waves

Chemical waves constitute a known class of dissipative structures emerging in reaction-diffusion systems. They play a crucial role in biology, spreading information rapidly to synchronize and coordinate biological events. We develop a rigorous thermodynamic theory of reaction-diffusion systems to characterize chemical waves. Our main result is the definition of the proper thermodynamic potential of the local dynamics as a nonequilibrium free energy density and establishing its balance equation. This enables us to identify the dynamics of the free energy, of the dissipation, and of the work spent to sustain the wave propagation. Two prototypical classes of chemical waves are examined. From a thermodynamic perspective, the first is sustained by relaxation towards equilibrium and the second by nonconservative forces generated by chemostats. We analytically study step-like waves, called wavefronts, using the Fisher-Kolmogorov equation as representative of the first class and oscillating waves in the Brusselator model as representative of the second. Given the fundamental role of chemical waves as message carriers in biosystems, our thermodynamic theory constitutes an important step toward an understanding of information transfers and processing in biology.Comment: 12 pages, 2 figure

On phases and interference of local communications in molecules

The role of phases in local Communication Theory of the Chemical Bond is investigated. Probability amplitudes of such molecular ( fine -grained) information systems originate from the superposition principle of quantum mechanics involving the projection onto the bond system defined by the subspace of the state occupied Molecular Orbitals. They are explicitly phase -dependent, thus being capable of inter- ference effects. The phase factors of the local direct and indirect (bridge, cascade) channels are examined and the associated amplitude/probability sum rules are estab- lished. The entropic descriptors of the local channels, providing the system “covalent” (communication- noise ) and “ionic” (information- flow ) components, are investigated using prototype one -electron systems. The competition between these information- theoretic measures of the chemical bond covalency (electron delocalization) and ion- icity (electron localization) is illustrated in H + 2 and H 2

Nonequilibrium Thermodynamics. Transport and Rate Processes in Physical, Chemical and Biological Systems. 4th Edition

Nonequilibrium Thermodynamics: Transport and Rate Processes in Physical, Chemical and Biological Systems, Fourth Edition emphasizes the unifying role of thermodynamics in analyzing natural phenomena. This updated edition expands on the third edition by focusing on the general balance equations for coupled processes of physical, chemical and biological systems. Updates include stochastic approaches, self-organization criticality, ecosystems, mesoscopic thermodynamics, constructual law, quantum thermodynamics, fluctuation theory, information theory, and modeling the coupled biochemical systems. The book also emphasizes nonequilibrium thermodynamics tools, such as fluctuation theories, mesoscopic thermodynamic analysis, information theories, and quantum thermodynamics in describing and designing small scale systems

Rigorous and General Definition of Thermodynamic Entropy

The physical foundations of a variety of emerging technologies --- ranging from the applications of quantum entanglement in quantum information to the applications of nonequilibrium bulk and interface phenomena in microfluidics, biology, materials science, energy engineering, etc. --- require understanding thermodynamic entropy beyond the equilibrium realm of its traditional definition. This paper presents a rigorous logical scheme that provides a generalized definition of entropy free of the usual unnecessary assumptions which constrain the theory to the equilibrium domain. The scheme is based on carefully worded operative definitions for all the fundamental concepts employed, including those of system, property, state, isolated system, environment, process, separable system, system uncorrelated from its environment, and parameters of a system. The treatment considers also systems with movable internal walls and/or semipermeable walls, with chemical reactions and/or external force fields, and with small numbers of particles. The definition of reversible process is revised by introducing the new concept of scenario. The definition of entropy involves neither the concept of heat nor that of quasistatic process; it applies to both equilibrium and nonequilibrium states. The role of correlations on the domain of definition and on the additivity of energy and entropy is discussed: it is proved that energy is defined and additive for all separable systems, while entropy is defined and additive only for separable systems uncorrelated from their environment; decorrelation entropy is defined. The definitions of energy and entropy are extended rigorously to open systems. Finally, to complete the discussion, the existence of the fundamental relation for stable equilibrium states is proved, in our context, for both closed and open systems.Comment: 19 pages, RevTex

Atomically resolved scanning force studies of vicinal Si(111)

Well-ordered stepped semiconductor surfaces attract intense attention owing to the regular arrangements of their atomic steps that makes them perfect templates for the growth of one- dimensional systems, e.g. nanowires. Here, we report on the atomic structure of the vicinal Si(111) surface with 10 degree miscut investigated by a joint frequency-modulation scanning force microscopy (FM-SFM) and ab initio approach. This popular stepped surface contains 7 x 7-reconstructed terraces oriented along the Si(111) direction, separated by a stepped region. Recently, the atomic structure of this triple step based on scanning tunneling microscopy (STM) images has been subject of debate. Unlike STM, SFM atomic resolution capability arises from chemical bonding of the tip apex with the surface atoms. Thus, for surfaces with a corrugated density of states such as semiconductors, SFM provides complementary information to STM and partially removes the dependency of the topography on the electronic structure. Our FM-SFM images with unprecedented spatial resolution on steps confirm the model based on a (7 7 10) orientation of the surface and reveal structural details of this surface. Two different FM-SFM contrasts together with density functional theory calculations explain the presence of defects, buckling and filling asymmetries on the surface. Our results evidence the important role of charge transfers between adatoms, restatoms, and dimers in the stabilisation of the structure of the vicinal surface

Three People Can Synchronize as Coupled Oscillators during Sports Activities

We experimentally investigated the synchronized patterns of three people during sports activities and found that the activity corresponded to spatiotemporal patterns in rings of coupled biological oscillators derived from symmetric Hopf bifurcation theory, which is based on group theory. This theory can provide catalogs of possible generic spatiotemporal patterns irrespective of their internal models. Instead, they are simply based on the geometrical symmetries of the systems. We predicted the synchronization patterns of rings of three coupled oscillators as trajectories on the phase plane. The interactions among three people during a 3 vs. 1 ball possession task were plotted on the phase plane. We then demonstrated that two patterns conformed to two of the three patterns predicted by the theory. One of these patterns was a rotation pattern (R) in which phase differences between adjacent oscillators were almost 2π/3. The other was a partial anti-phase pattern (PA) in which the two oscillators were anti-phase and the third oscillator frequency was dead. These results suggested that symmetric Hopf bifurcation theory could be used to understand synchronization phenomena among three people who communicate via perceptual information, not just physically connected systems such as slime molds, chemical reactions, and animal gaits. In addition, the skill level in human synchronization may play the role of the bifurcation parameter

Quality Coding by Neural Populations in the Early Olfactory Pathway: Analysis Using Information Theory and Lessons for Artificial Olfactory Systems

In this article, we analyze the ability of the early olfactory system to detect and discriminate different odors by means of information theory measurements applied to olfactory bulb activity images. We have studied the role that the diversity and number of receptor neuron types play in encoding chemical information. Our results show that the olfactory receptors of the biological system are low correlated and present good coverage of the input space. The coding capacity of ensembles of olfactory receptors with the same receptive range is maximized when the receptors cover half of the odor input space - a configuration that corresponds to receptors that are not particularly selective. However, the ensemble’s performance slightly increases when mixing uncorrelated receptors of different receptive ranges. Our results confirm that the low correlation between sensors could be more significant than the sensor selectivity for general purpose chemo-sensory systems, whether these are biological or biomimetic