Stochastic thermodynamics of chemical reaction networks

For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events. A first-law like energy balance relates internal energy, applied (chemical) work and dissipated heat for every single reaction. Entropy production along a single trajectory involves a sum over changes in the entropy of the network itself and the entropy of the medium. The latter is given by the exchanged heat identified through the first law. Total entropy production is constrained by an integral fluctuation theorem for networks arbitrarily driven by time-dependent rates and a detailed fluctuation theorem for networks in the steady state. Further exact relations like a generalized Jarzynski relation and a generalized Clausius inequality are discussed. We illustrate these results for a three-species cyclic reaction network which exhibits nonequilibrium steady states as well as transitions between different steady states.Comment: 14 pages, 2 figures, accepted for publication in J. Chem. Phy

Comparison of independent proxies in the reconstruction of deep-water circulation in the south-east Atlantic off Namibia

Independent proxies were assessed in two Late Quaternary sediment cores from the eastern South Atlantic to compare deep-water changes during the last 400 kyr. Two cores were recovered from beneath North AtlanticDeep Water (NADW) at approximately 3 000 m depth. Late Quaternary presence of NADW is indicated by the Cibicidoides wuellerstorfi assemblage on the Walvis Ridge (Core GeoB 1214) and the Bulimina alazanensisassemblage on the Namibian continental slope (Core GeoB 1710). The propagation of NADW is exclusively observed during interglacials, with maximum factor loadings in Stages 1, 5, 7, 9 and 11. These maxima are consistent with peaks in kaolinite/chlorite ratios and maxima of poorly crystalline smectite in the clay-mineral record. Kaolinite and poorly crystalline smectite are products of intense chemical weathering. They are injected into the NADW at low latitudes, north of the study area, and advected south. Chlorite, which is stable under cold weatheringregimes, is a characteristic mineral of water masses of southern origin. During glacial stages, it is advected north with Southern Component Water (SCW). Above the NADW/SCW depths, kaolinite/chlorite ratios varyonly slightly without a significant glacial-interglacial pattern, as measured in a core (GeoB 1712) from 1 000 m deep on the same profile of the Namibian continental slope off Walvis Bay

Upper ocean climate of the Eastern Mediterranean Sea during the Holocene Insolation Maximum – a model study

ine thousand years ago (9 ka BP), the Northern Hemisphere experienced enhanced seasonality caused by an orbital configuration close to the minimum of the precession index. To assess the impact of this "Holocene Insolation Maximum" (HIM) on the Mediterranean Sea, we use a regional ocean general circulation model forced by atmospheric input derived from global simulations. A stronger seasonal cycle is simulated by the model, which shows a relatively homogeneous winter cooling and a summer warming with well-defined spatial patterns, in particular, a subsurface warming in the Cretan and western Levantine areas. The comparison between the SST simulated for the HIM and a reconstruction from planktonic foraminifera transfer functions shows a poor agreement, especially for summer, when the vertical temperature gradient is strong. As a novel approach, we propose a reinterpretation of the reconstruction, to consider the conditions throughout the upper water column rather than at a single depth. We claim that such a depth-integrated approach is more adequate for surface temperature comparison purposes in a situation where the upper ocean structure in the past was different from the present-day. In this case, the depth-integrated interpretation of the proxy data strongly improves the agreement between modelled and reconstructed temperature signal with the subsurface summer warming being recorded by both model and proxies, with a small shift to the south in the model results. The mechanisms responsible for the peculiar subsurface pattern are found to be a combination of enhanced downwelling and wind mixing due to strengthened Etesian winds, and enhanced thermal forcing due to the stronger summer insolation in the Northern Hemisphere. Together, these processes induce a stronger heat transfer from the surface to the subsurface during late summer in the western Levantine; this leads to an enhanced heat piracy in this region, a process never identified before, but potentially characteristic of time slices with enhanced insolation

Miocene siliciclastic deposits of Naxos Island: Geodynamic and environmental implications for the evolution of the southern Aegean Sea (Greece)

An interdisciplinary study has been carried out on Naxos Island, located in the southern Aegean Sea (Greece), which shows Miocene geodynamic and environmental changes in a classic example of a collapsing orogen. Early to Mid-Miocene siliciclastic deposits on Naxos have been shed from an uplifting mountainous realm in the south, which included a patchwork of at least four source terrains of different thermal histories.Petrography of pebbles suggests that the source units formed part of a passivecontinental margin succession (external Pelagonian unit), and an ophiolite succession mainly of deep-water cherts and limestones deposited on basalt substratum (Pindos unit). The continental margin source contributed rounded zircon crystals of Late Jurassic to Early Cretaceous age and broadly scattering Paleozoic zircon fission-track cooling ages. A distal pebble assemblage of Paleogene shallow-water carbonates passing into flysch-like, mixed calcarenitic and siliciclastic components with volcanic arc components is subordinately present. High-grade metamorphic components from the nearby metamorphic core complex are not present. The depositional evolution reflects increasing relief and, in some parts, a fluvial succession with rhythmic channel deposition, possibly due to runoff variability forced by orbital cyclicity. Upsection, the depositional trend indicates increasing seasonality and decreasing humidity in the source region. The Miocene sedimentary succession has been deposited on an ophiolite nappe. Juxtaposition of this ophiolite nappe occurred as an extensional allochthon during large-scale extension in the Aegean region at the margins of an exhuming metamorphic core complex

Sediment transport on the inner shelf off Khao Lak (Andaman Sea, Thailand) during the 2004 Indian Ocean tsunami and former storm events: evidence from foraminiferal transfer functions

We have investigated the benthic foraminiferal fauna from sediment event layers associated with the 2004 Indian Ocean tsunami and former storms that have been retrieved in short sediment cores from offshore environments of the Andaman Sea, off Khao Lak, western Thailand. Species composition and test preservation of the benthic foraminiferal faunas exhibit pronounced changes across the studied sections and provide information on the depositional history of the tsunami layer, particularly on the source water depth of the displaced foraminiferal tests. In order to obtain accurate bathymetric information on sediment provenance, we have mapped the distribution of modern faunas in non-tsunamigenic surface sediments and created a calibration data set for the development of a transfer function. Our quantitative reconstructions revealed that the resuspension of sediment particles by the tsunami wave was restricted to a maximum water depth of approximately 20 m. Similar values were obtained for former storm events, thus impeding an easy distinction of different high-energy events

Ignorance based inference of optimality in thermodynamic processes

We derive ignorance based prior distribution to quantify incomplete information and show its use to estimate the optimal work characteristics of a heat engine.Comment: Latex, 10 pages, 3 figure

Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation

Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also rapidly sample uncorrelated configurations. Here, we introduce a new class of moves based on nonequilibrium dynamics: candidate configurations are generated through a finite-time process in which a system is actively driven out of equilibrium, and accepted with criteria that preserve the equilibrium distribution. The acceptance rule is similar to the Metropolis acceptance probability, but related to the nonequilibrium work rather than the instantaneous energy difference. Our method is applicable to sampling from both a single thermodynamic state or a mixture of thermodynamic states, and allows both coordinates and thermodynamic parameters to be driven in nonequilibrium proposals. While generating finite-time switching trajectories incurs an additional cost, driving some degrees of freedom while allowing others to evolve naturally can lead to large enhancements in acceptance probabilities, greatly reducing structural correlation times. Using nonequilibrium driven processes vastly expands the repertoire of useful Monte Carlo proposals in simulations of dense solvated systems

Efficiency of Free Energy Transduction in Autonomous Systems

We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution induced by chemical coupling, adopted, for example, in biological systems, is inevitably an autonomous process. We found that the efficiency is bounded by the ratio between the non-symmetric and the symmetrized Kullback-Leibler distance, which is significantly lower than unity. Consequences of this low efficiency are demonstrated in the simple two-state case, which serves as an important minimal model for studying the energetics of biomolecules.Comment: 4 pages, 4 figure