Fundamental Molecules of Life are Pigments which Arose and Evolved to Dissipate the Solar Spectrum

The driving force behind the origin and evolution of life has been the thermodynamic imperative of increasing the entropy production of the biosphere through increasing the global solar photon dissipation rate. In the upper atmosphere of today, oxygen and ozone derived from life processes are performing the short wavelength UVC and UVB dissipation. On Earth's surface, water and organic pigments in water facilitate the near UV and visible photon dissipation. The first organic pigments probably formed, absorbed, and dissipated at those photochemically active wavelengths in the UVC that could have reached Earth's surface during the Archean. Proliferation of these pigments can be understood as an autocatalytic photochemical process obeying non-equilibrium thermodynamic directives related to increasing solar photon dissipation rate. Under these directives, organic pigments would have evolved over time to increase the global photon dissipation rate by; 1) increasing the ratio of their effective photon cross sections to their physical size, 2) decreasing their electronic excited state life times, 3) quenching non-radiative de-excitation channels (e.g. fluorescence), 4) covering ever more completely the solar spectrum, and 5) dispersing into an ever greater surface area of Earth. From knowledge of the evolution of the spectrum of G-type stars, and considering the most probable history of the transparency of Earths atmosphere, we construct the most probable surface solar spectrum as a function of time and compare this with the history of molecular absorption maxima obtained from the available data in the literature. This comparison supports the thermodynamic dissipation theory for the origin of life, constrains models for Earth's early atmosphere, and sheds some new light on the origin of photosynthesis.Comment: 43 pages, 3 figure

Maximum Entropy Production Theorem for Transitions between Enzyme Functional States and Its Applications

Transitions between enzyme functional states are often connected to conformational changes involving electron or proton transport and directional movements of a group of atoms. These microscopic fluxes, resulting in entropy production, are driven by non-equilibrium concentrations of substrates and products. Maximal entropy production exists for any chosen transition, but such a maximal transitional entropy production (MTEP) requirement does not ensure an increase of total entropy production, nor an increase in catalytic performance. We examine when total entropy production increases, together with an increase in the performance of an enzyme or bioenergetic system. The applications of the MTEP theorem for transitions between functional states are described for the triosephosphate isomerase, ATP synthase, for β-lactamases, and for the photochemical cycle of bacteriorhodopsin. The rate-limiting steps can be easily identified as those which are the most efficient in dissipating free-energy gradients and in performing catalysis. The last step in the catalytic cycle is usually associated with the highest free-energy dissipation involving proton nanocurents. This recovery rate-limiting step can be optimized for higher efficiency by using corresponding MTEP requirements. We conclude that biological evolution, leading to increased optimal catalytic efficiency, also accelerated the thermodynamic evolution, the synergistic relationship we named the evolution-coupling hypothesis

Thermodynamic limits on oxygenic photosynthesis around M-dwarf stars: Generalized models and strategies for optimization

We explore the feasibility and potential characteristics of photosynthetic light-harvesting on exo-planets orbiting in the habitable zone of low mass stars ($< 1$ M$_{\odot}$). As stellar temperature, $T_{s}$, decreases, the irradiance maximum red-shifts out of the $400 \textrm{nm} \leq \lambda < 750$ nm range of wavelengths that can be utilized by \emph{oxygenic} photosynthesis on Earth. However, limited irradiance in this region does not preclude oxygenic photosynthesis and Earth's plants, algae and cyanobacteria all possess very efficient \emph{light-harvesting antennae} that facilitate photosynthesis in very low light. Here we construct general models of photosynthetic light-harvesting structures to determine how an oxygenic photosystem would perform in different irradiant spectral fluxes. We illustrate that the process of light-harvesting, capturing energy over a large antenna and concentrating it into a small \emph{reaction centre}, must overcome a fundamental \emph{entropic barrier}. We show that a plant-like antenna cannot be adapted to the light from stars of $T_{s}<3400$ K, as increasing antenna size offers diminishing returns on light-harvesting. This can be overcome if one introduces a slight \emph{enthalpic gradient}, to the antenna. Interestingly, this strategy appears to have been adopted by Earth's oxygenic cyanobacteria, and we conclude that \emph{bacterial} oxygenic photosynthesis is feasible around even the lowest mass M-dwarf stars.Comment: 5 Figures, submitted to Astrobiology and awaiting return of revie

Simultaneous Extrema in the Entropy Production for Steady-State Fluid Flow in Parallel Pipes

Steady-state flow of an incompressible fluid in parallel pipes can simultaneously satisfy two contradictory extremum principles in the entropy production, depending on the flow conditions. For a constant total flow rate, the flow can satisfy (i) a pipe network minimum entropy production (MinEP) principle with respect to the flow rates, and (ii) the maximum entropy production (MaxEP) principle of Ziegler and Paltridge with respect to the choice of flow regime. The first principle - different to but allied to that of Prigogine - arises from the stability of the steady state compared to non-steady-state flows; it is proven for isothermal laminar and turbulent flows in parallel pipes with a constant power law exponent, but is otherwise invalid. The second principle appears to be more fundamental, driving the formation of turbulent flow in single and parallel pipes at higher Reynolds numbers. For constant head conditions, the flow can satisfy (i) a modified maximum entropy production (MaxEPMod) principle of \v{Z}upanovi\'c and co-workers with respect to the flow rates, and (ii) an inversion of the Ziegler-Paltridge MaxEP principle with respect to the flow regime. The interplay between these principles is demonstrated by examples.Comment: Revised version 2; 5 figure

In the light of time

The concept of time is examined using the second law of thermodynamics that was recently formulated as an equation of motion. According to the statistical notion of increasing entropy, flows of energy diminish differences between energy densities that form space. The flow of energy is identified with the flow of time. The non-Euclidean energy landscape, i.e. the curved space–time, is in evolution when energy is flowing down along gradients and levelling the density differences. The flows along the steepest descents, i.e. geodesics are obtained from the principle of least action for mechanics, electrodynamics and quantum mechanics. The arrow of time, associated with the expansion of the Universe, identifies with grand dispersal of energy when high-energy densities transform by various mechanisms to lower densities in energy and eventually to ever-diluting electromagnetic radiation. Likewise, time in a quantum system takes an increment forwards in the detection-associated dissipative transformation when the stationary-state system begins to evolve pictured as the wave function collapse. The energy dispersal is understood to underlie causality so that an energy gradient is a cause and the resulting energy flow is an effect. The account on causality by the concepts of physics does not imply determinism; on the contrary, evolution of space–time as a causal chain of events is non-deterministic

From steam engine to solar cells: can thermodynamics guide the development of future generations of photovoltaics?

Thermodynamics has played a singular role in the development of virtually all energy technologies to-date. This review argues that it also has a role to play in the understanding and design of solar cell operation, particularly looking toward the future, high-efficiency solar cells. After a historical overview of the key developments in the ‘thermodynamics of light,’ the conversion of a monochromatic light beam is used as a starting point to analyze the conversion process, examine the fundamental losses in terms of irreversible entropy generation, and consider in detail one of the key applications: the Shockley–Queisser detailed balance. We review and compare the principal suggestions for the highest theoretical efficiency of solar energy conversion, and analyze one possible embodiment of such a third-generation structure: the hot-carrier solar cell. A somewhat different application of the statistical approach—light trapping—is reviewed at a fundamental level, and the future potential is considered for devices which combine such a ‘thermodynamic squeezing’ of light with latest developments in photonics, leading to a photonic bandgap solar cell. We argue that the widespread use of thermodynamic tools in the current photovoltaics research, especially when combined with the potential benefits to future devices, already indicates that our thinking should not be about if but how thermodynamics can guide us to make better solar cells

Commercial-Scale Conversion of Algae to Biofuel

Biodiesel, derived from renewable feedstocks like algae, has the potential to replace traditional, petroleum-based fuels — providing a carbon-neutral, sustainable transportation fuel. However, with plummeting oil prices, alternative fuels have become less competitive. Thus, process modeling and optimization are needed to reduce costs. Extensive modeling has been done for the conversion of algae and plant lipids to biofuels, but the upstream operations remain poorly understood. We partnered with other organizations to create an overall techno-economic model for a commercial-scale algae-to-biodiesel venture, using software packages like ASPEN PLUS, the ASPEN Process Economic Analyzer, gPROMS, and AIMMS. The two most important findings from this model were that: (1) cultivation represented 90% of the total capital expense because of the massive fields required to grow the algae, and (2) extraction of the oil from algae had highly variable cost estimates, which spanned three orders of magnitude. The low photosynthetic efficiency of the algae was the major limiting factor in terms of algae growth. Therefore an exergy analysis was undertaken to rigorously calculate the efficiency (3.9%) and determine what could be done to improve it. Overall, the algae cell’s absorption of sunlight was the largest loss of exergy, and therefore the most crucial factor in decreasing capital expenditures for this venture. Regarding the extraction of the oils, supercritical carbon dioxide is a green, non-toxic solvent that can be used to extract and convert algae-oils to biodiesel in a single step, eliminating the need for pre- or post-processing of the oil or biodiesel product. The statistical associating fluid theory equations-of-state in ASPEN PLUS (PC-SAFT) and gProms (SAFT-γ Mie) were used to perform the fluid-phase equilibria calculations because of their improved robustness and higher accuracy for long-chain hydrocarbons when compared with cubic equations-of-state. A multi-phase reactor model was formulated to account for the effects of changing phase equilibria on reaction conversions. While further research is required to obtain cost estimates, preliminary results for this system show that it is possible to achieve high oil-to-biodiesel conversions at much lower pressures than previous anticipated

Thermodynamics of quantum systems under dynamical control

In this review the debated rapport between thermodynamics and quantum mechanics is addressed in the framework of the theory of periodically-driven/controlled quantum-thermodynamic machines. The basic model studied here is that of a two-level system (TLS), whose energy is periodically modulated while the system is coupled to thermal baths. When the modulation interval is short compared to the bath memory time, the system-bath correlations are affected, thereby causing cooling or heating of the TLS, depending on the interval. In steady state, a periodically-modulated TLS coupled to two distinct baths constitutes the simplest quantum heat machine (QHM) that may operate as either an engine or a refrigerator, depending on the modulation rate. We find their efficiency and power-output bounds and the conditions for attaining these bounds. An extension of this model to multilevel systems shows that the QHM power output can be boosted by the multilevel degeneracy. These results are used to scrutinize basic thermodynamic principles: (i) Externally-driven/modulated QHMs may attain the Carnot efficiency bound, but when the driving is done by a quantum device ("piston"), the efficiency strongly depends on its initial quantum state. Such dependence has been unknown thus far. (ii) The refrigeration rate effected by QHMs does not vanish as the temperature approaches absolute zero for certain quantized baths, e.g., magnons, thous challenging Nernst's unattainability principle. (iii) System-bath correlations allow more work extraction under periodic control than that expected from the Szilard-Landauer principle, provided the period is in the non-Markovian domain. Thus, dynamically-controlled QHMs may benefit from hitherto unexploited thermodynamic resources

Working at the limit: A review of thermodynamics and optimality of the Earth system

Optimality concepts related to energy and entropy have long been proposed to govern Earth system processes, for instance in the form of propositions that certain processes maximize or minimize entropy production. These concepts, however, remain quite obscure, seem contradictory to each other, and have so far been mostly disregarded. This review aims to clarify the role of thermodynamics and optimality in Earth system science by showing that they play a central role in how, and how much, work can be derived from solar forcing and that this imposes a major constraint on the dynamics of dissipative structures of the Earth system. This is, however, not as simple as it may sound. It requires a consistent formulation of Earth system processes in thermodynamic terms, including their linkages and interactions. Thermodynamics then constrains the ability of the Earth system to derive work and generate free energy from solar radiative forcing, which limits the ability to maintain motion, mass transport, geochemical cycling, and biotic activity. It thus limits directly the generation of atmospheric motion and other processes indirectly through their need for transport. I demonstrate the application of this thermodynamic Earth system view by deriving first-order estimates associated with atmospheric motion, hydrologic cycling, and terrestrial productivity that agree very well with observations. This supports the notion that the emergent simplicity and predictability inherent in observed climatological variations can be attributed to these processes working as hard as they can, reflecting thermodynamic limits directly or indirectly. I discuss how this thermodynamic interpretation is consistent with established theoretical concepts in the respective disciplines, interpret other optimality concepts in light of this thermodynamic Earth system view, and describe its utility for Earth system science.</p