Dissipative Pathways Research Articles

The Pigment World: Life's Origins as Photon-Dissipating Pigments.

Many of the fundamental molecules of life share extraordinary pigment-like optical properties in the long-wavelength UV-C spectral region. These include strong photon absorption and rapid (sub-pico-second) dissipation of the induced electronic excitation energy into heat through peaked conical intersections. These properties have been attributed to a "natural selection" of molecules resistant to the dangerous UV-C light incident on Earth's surface during the Archean. In contrast, the "thermodynamic dissipation theory for the origin of life" argues that, far from being detrimental, UV-C light was, in fact, the thermodynamic potential driving the dissipative structuring of life at its origin. The optical properties were thus the thermodynamic "design goals" of microscopic dissipative structuring of organic UV-C pigments, today known as the "fundamental molecules of life", from common precursors under this light. This "UV-C Pigment World" evolved towards greater solar photon dissipation through more complex dissipative structuring pathways, eventually producing visible pigments to dissipate less energetic, but higher intensity, visible photons up to wavelengths of the "red edge". The propagation and dispersal of organic pigments, catalyzed by animals, and their coupling with abiotic dissipative processes, such as the water cycle, culminated in the apex photon dissipative structure, today's biosphere.

Synchronously manipulating absorption and nonradiative transition of croconaine via donor engineering for efficient NIR-II photothermal theranostics

Organic molecules with strong absorption in the near-infrared (NIR)-II region are highly desired for cancer photothermal theranostics. However, it remains challenges to construct NIR-II photothermal agents with desired optical properties. This study reports a donor engineering approach to simultaneously manipulate the absorption and nonradiative transitions of croconaine dyes. By introducing different donor units with increasing electron donating ability to the backbone, the absorption of the synthesized croconaines were gradually red-shifted to NIR-II region, especially the benzo[c,d]indolium conjugated croconaine (CR1045). The extensive conjugation of CR1045 had a narrower HOMO-LUMO energy gap and strong NIR-II light responsiveness. Importantly, the steric repulsion between this large planar donor and croconate acceptor of CR1045 promotes the formation of a twisted intramolecular charge transfer (TICT) state, making it more prone to direct the absorbed energy towards heat-producing non-radiative decay rather than other dissipative pathways. And the nanoformulated CR1045 exhibits excellent optoacoustic generation capability and ultrahigh photothermal conversion efficiency (∼84%). In vitro and in vivo investigations confirm good optoacoustic imaging and effective photothermal treatment of tumors. Therefore, this work offers insights into donor regulation for the future development of efficient NIR-II photothermal agents.

Soil water availability modulates the response of grapevine leaf gas exchange and PSII traits to a simulated heat wave

Background and aimsA better understanding of plant carbon assimilation, water status and photosystem performance responses to combined heat and drought stress would help to optimize grapevine management under such limiting conditions.MethodsGas exchange and chlorophyll fluorescence parameters were measured in potted grapevines, cv Sauvignon Blanc, before, during and after simulated six-day heat (Tmax = 40 °C) wave using heated well-watered (HW), heated drought-stressed (HD), non-heated well-watered (CW) and non-heated dry (CD) vines.ResultsPhotosynthesis and stomatal conductance in HW vines increased during the morning and dropped in the afternoon with respect to CW vines. Daily plant transpiration in HW almost doubled that of CW vines. When grapevines were already exposed to drought, the effects of the heat wave were negligible, with HD plants showing similar leaf photosynthesis and transpiration to their CD counterparts. Heat, but not drought stress, decreased the maximum (Fv/Fm) and effective photochemical quantum yield of PSII (φPSII), and also affected the use of absorbed energy. HW plants dissipated more radiative energy as heat, a protective mechanism of the photosystem, while HD vines increased the energy dissipated by non-regulated non-photochemical pathways, which might lead to photoinhibition damages. The different behavior could be due to the enhanced transpiration rate and consequent decrease in leaf temperature in HW as compared to HD vines. After the heat wave, only HW vines recovered the afternoon values of photosynthesis, stomatal conductance and φPSII to similar levels as those in CW vines.ConclusionDrought had a more significant effect than heat stress on photosynthesis, stomatal conductance and transpiration. The combined heat and drought stress, however, increased the proportion of energy lost by the leaves through harmful non-regulated dissipative pathways. With adequate soil water availability, grapevines withstood the heat wave period through an increase in leaf transpiration, which decreased leaf temperature and protected the PSII from heat damage.

Anti-Dissipative Strategies toward More Efficient Solar Energy Conversion.

In natural and artificial photosynthesis, light absorption and catalysis are separate processes linked together by exergonic electron transfer. This leads to free energy losses between the initial excited state, formed after light absorption, and the active catalyst formed after the electron transfer cascade. Additional deleterious processes, such as internal conversion (IC) and vibrational relaxation (VR), also dissipate as much as 20-30% of the absorbed photon energy. Minimization of these energy losses, a holy grail in solar energy conversion and solar fuel production, is a challenging task because excited states are usually strongly coupled which results in negligible kinetic barriers and very fast dissipation. Here, we show that topological control of oligomeric {Ru(bpy)3} chromophores resulted in small excited-state electronic couplings, leading to activation barriers for IC by means of inter-ligand electron transfer of around 2000 cm-1 and effectively slowing down dissipation. Two types of excited states are populated upon visible light excitation, that is, a bridging-ligand centered metal-to-ligand charge transfer [MLCT(Lm)], and a 2,2'-bipyridine-centered MLCT [MLCT(bpy)], which lies 800-1400 cm-1 higher in energy. As a proof-of-concept, bimolecular electron transfer with tri-tolylamine (TTA) as electron donor was performed, which mimics catalyst activation by sacrificial electron donors in typical photocatalytic schemes. Both excited states were efficiently quenched by TTA. Hence, this novel strategy allows to trap higher energy excited states before IC and VR set in, saving between 100 and 170 meV. Furthermore, transient absorption spectroscopy suggests that electron transfer reactions with TTA produced the corresponding Lm•--centered and bpy•--centered reduced photosensitizers, which involve different reducing abilities, that is, -0.79 and -0.93 V versus NHE for Lm•- and bpy•-, respectively. Thus, this approach probably leads in fine to a 140 meV more potent reductant for energy conversion schemes and solar fuel production. These results lay the first stone for anti-dissipative energy conversion schemes which, in bimolecular electron transfer reactions, harness the excess energy saved by controlling dissipative conversion pathways.

Nonreciprocal conversion between radio-frequency and optical photons with an optoelectromechanical system

Nonreciprocal systems breaking time-reversal symmetry are essential tools in modern quantum technologies enabling the suppression of unwanted reflected signals or extraneous noise entering through detection ports. Here we propose a scheme enabling nonreciprocal conversion between optical and radio-frequency (rf) photons using exclusively optomechanical and electromechanical interactions. The nonreciprocal transmission is obtained by interference of two dissipative pathways of transmission between the two electromagnetic modes established through two distinct intermediate mechanical modes. In our protocol, we apply a bichromatic drive to the cavity mode and a single-tone drive to the rf resonator, and use the relative phase between the drive tones to obtain nonreciprocity. We show that perfect nonreciprocal transduction can be obtained in the limit of large cooperativity in both directions, from optical to rf and vice versa. We also study the transducer noise and show that mechanical thermal noise is always reflected back onto the isolated port. In the limit of large cooperativity, the input noise is instead transmitted in an unaltered way in the allowed direction; in particular one has only vacuum noise in the output rf port in the case of optical-to-rf conversion.

Do We Understand the Mechanisms Used by Biological Systems to Correct Their Errors?

Most cellular processes involved in biological information processing display a surprisingly low error rate despite the stochasticity of the underlying biochemical reactions and the presence of competing chemical species. Such high fidelity is the result of nonequilibrium kinetic proofreading mechanisms, i.e., the existence of dissipative pathways for correcting the reactions that went in the wrong direction. While proofreading was often studied from the perspective of error minimization, a number of recent studies have demonstrated that the underlying mechanisms need to consider the interplay of other characteristic properties such as speed, energy dissipation, and noise reduction. Here, we present current views and new insights on the mechanisms of error-correction phenomena and various trade-off scenarios in the optimization of the functionality of biological systems. Existing challenges and future directions are also discussed.

Observation of dissipative chlorophyll-to-carotenoid energy transfer in light-harvesting complex II in membrane nanodiscs

Plants prevent photodamage under high light by dissipating excess energy as heat. Conformational changes of the photosynthetic antenna complexes activate dissipation by leveraging the sensitivity of the photophysics to the protein structure. The mechanisms of dissipation remain debated, largely due to two challenges. First, because of the ultrafast timescales and large energy gaps involved, measurements lacked the temporal or spectral requirements. Second, experiments have been performed in detergent, which can induce non-native conformations, or in vivo, where contributions from homologous antenna complexes cannot be disentangled. Here, we overcome both challenges by applying ultrabroadband two-dimensional electronic spectroscopy to the principal antenna complex, LHCII, in a near-native membrane. Our data provide evidence that the membrane enhances two dissipative pathways, one of which is a previously uncharacterized chlorophyll-to-carotenoid energy transfer. Our results highlight the sensitivity of the photophysics to local environment, which may control the balance between light harvesting and dissipation in vivo.

Nonequilibrium states of a plasmonic Dicke model with coherent and dissipative surface-plasmon–quantum-emitter interactions

Hybrid photonic-plasmonic nanostructures allow one to engineer coupling of quantum emitters and cavity modes accounting for the direct coherent and environment mediated dissipative pathways. Using generalized plasmonic Dicke model, we explore the non-equilibrium phase diagram with respect to these interactions. The analysis shows that their interplay results in the extension of the superradiant and regular lasing states to the dissipative coupling regime and an emergent lasing phase without population inversion having boundary with the superradiant and normal states. Calculated photon emission spectra are demonstrated to carry distinct signatures of these phases.

Analysis of Membrane Phononic Crystals with Wide Band Gaps and Low-Mass Defects

We present techniques to model and design membrane phononic crystals with low-mass defects, optimized for force sensing. Further, we identify the importance of the phononic crystal mass contrast as it pertains to the size of acoustic bandgaps and to the dissipation properties of defect modes. In particular, we quantify the tradeoff between high mass contrast phononic crystals with their associated robust acoustic isolation, and a reduction of soft clamping of the defect mode. We fabricate a set of phononic crystals with a variety of defect geometries out of high stress stoichiometric silicon nitride membranes, and measured at both room temperature and 4 K in order to characterize the dissipative pathways across a variety of geometries. Analysis of these devices highlights a number of design principles integral to the implementation of low-mass, low-dissipation mechanical modes into optomechanical systems.

Dissipation in noisy chemical networks: The role of deficiency.

We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of complex behavior such as multistability and oscillations, is shown to also characterize the entropic balance. In particular, when deficiency is zero the average stochastic dissipation rate equals that of the corresponding deterministic model, where correlations are disregarded. In fact, dissipation can be reduced by the effect of noise, as occurs in a toy model of metabolism that we employ to illustrate our findings. This phenomenon highlights that there is a close interplay between deficiency and the activation of new dissipative pathways at low molecule numbers.

Heat dissipation guides activation in signaling proteins

Life is fundamentally a nonequilibrium phenomenon. At the expense of dissipated energy, living things perform irreversible processes that allow them to propagate and reproduce. Within cells, evolution has designed nanoscale machines to do meaningful work with energy harnessed from a continuous flux of heat and particles. As dictated by the Second Law of Thermodynamics and its fluctuation theorem corollaries, irreversibility in nonequilibrium processes can be quantified in terms of how much entropy such dynamics produce. In this work, we seek to address a fundamental question linking biology and nonequilibrium physics: can the evolved dissipative pathways that facilitate biomolecular function be identified by their extent of entropy production in general relaxation processes? We here synthesize massive molecular dynamics simulations, Markov state models (MSMs), and nonequilibrium statistical mechanical theory to probe dissipation in two key classes of signaling proteins: kinases and G-protein-coupled receptors (GPCRs). Applying machinery from large deviation theory, we use MSMs constructed from protein simulations to generate dynamics conforming to positive levels of entropy production. We note the emergence of an array of peaks in the dynamical response (transient analogs of phase transitions) that draw the proteins between distinct levels of dissipation, and we see that the binding of ATP and agonist molecules modifies the observed dissipative landscapes. Overall, we find that dissipation is tightly coupled to activation in these signaling systems: dominant entropy-producing trajectories become localized near important barriers along known biological activation pathways. We go on to classify an array of equilibrium and nonequilibrium molecular switches that harmonize to promote functional dynamics.

Single-Molecule Identification of Quenched and Unquenched States of LHCII

In photosynthetic light harvesting, absorbed sunlight is converted to electron flow with near-unity quantum efficiency under low light conditions. Under high light conditions, plants avoid damage to their molecular machinery by activating a set of photoprotective mechanisms to harmlessly dissipate excess energy as heat. To investigate these mechanisms, we study the primary antenna complex in green plants, light-harvesting complex II (LHCII), at the single-complex level. We use a single-molecule technique, the Anti-Brownian Electrokinetic trap, which enables simultaneous measurements of fluorescence intensity, lifetime, and spectra in solution. With this approach, including the first measurements of fluorescence lifetime on single LHCII complexes, we access the intrinsic conformational dynamics. In addition to an unquenched state, we identify two partially quenched states of LHCII. Our results suggest that there are at least two distinct quenching sites with different molecular compositions, meaning multiple dissipative pathways in LHCII. Furthermore, one of the quenched conformations significantly increases in relative population under environmental conditions mimicking high light.

Light energy allocation at PSII under field light conditions: How much energy is lost in NPQ-associated dissipation?

In the field, plants are exposed to fluctuating light, where photosynthesis occurs under conditions far from a steady state. Excess energy dissipation associated with energy quenching of chlorophyll fluorescence (qE) functions as an efficient photo-protection mechanism in photosystem II. PsbS is an important regulator of qE, especially for the induction phase of qE. Beside the regulatory energy dissipation, some part of energy is lost through relaxation of excited chlorophyll molecules. To date, several models to quantify energy loss through these dissipative pathways in PSII have been proposed. In this short review, we compare and evaluate these models for PSII energy allocation when they are applied to non-steady state photosynthesis. As a case study, an investigation on energy allocation to qE-associated dissipation at PSII under non-steady state photosynthesis using PsbS-deficient rice transformants is introduced. Diurnal and seasonal changes in PSII energy allocation in rice under natural light are also presented. Future perspective of studies on PSII energy allocation is discussed.

PLASTICITY OF THE PSYCHROPHILIC GREEN ALGA CHLAMYDOMONAS RAUDENSIS (UWO 241) (CHLOROPHYTA) TO SUPRAOPTIMAL TEMPERATURE STRESS(1).

Chlamydomonas raudensis H. Ettl (UWO 241) is a psychrophilic green alga endemic to Lake Bonney, Antarctica. The objective of this study was to investigate the response of UWO 241 to incubation at 24°C, a temperature close to optimum for related mesophilic species. Using chl a fluorescence analysis, shifting cells from a growth temperature of 10°C-24°C resulted in a decline in PSII photochemical efficiency with light energy being directed away from photochemistry and toward dissipative pathways. Using the SYTOX Green assay, it was determined that UWO 241 cells die when incubated at 24°C under growth irradiance with a half-time of 34.9 h. The role of light in cell death was minor as cell death occurred in darkness at 24°C with a half-time of 43.7 h. To examine the plasticity of UWO 241 to temperature stress, 10°C-grown cells were shifted to 24°C for 12 h and then returned to 10°C to recover. The 12 h incubation at 24°C, which resulted in <10% cell death, led to declines in both light-saturated rates of photosynthesis and respiration, PSII photochemistry and energy partitioning, and changes to transcript abundances-those associated with the light-harvesting protein of PSII and ferredoxin declining rapidly, whereas transcripts of specific heat-shock proteins (HSPs) increased. Within 24-48 h of being transferred back to 10°C, all parameters returned to levels occurring in 10°C-grown cells. This research shows, for the first time, that 24°C is a temperature that is lethal to UWO 241, and yet this organism displays considerable physiological and molecular plasticity.

Hypoxic responses of Na+/K+ ATPase in trout hepatocytes

Reduction in oxygenation induces inhibition of Na+/K+ ATPase in a number of cells and tissues, including hepatocytes. When not reversed, decrease in Na+/K+ pump activity leads to a gradual Na+ accumulation, cell swelling and death. However, when accompanied by suppression of dissipative cation pathways, it has also been shown to be a beneficial adaptive strategy used by some hypoxia-tolerant species to reduce ATP consumption during prolonged periods of anoxia. This study aims to investigate acute hypoxic responses of the Na+/K+ ATPase in primary cultures of trout hepatocytes. Gradual decrease in oxygenation was followed by an instantaneous transient dose-dependent downregulation of the Na+/K+ ATPase transport activity, but was without an effect on hydrolytic function of the enzyme. Hypoxia-induced inhibition of active K+ influx was reversed spontaneously when hypoxic incubation time exceeded 20 min. The stimulating effect of prolonged hypoxic exposure on the Na+/K+ pump is most probably secondary to hypoxia-induced activation of the Na+/H+ exchanger with the following Na+ accumulation leading to Na+/K+ ATPase activation. Hypoxia-induced inhibition of the Na+/K+ pump was not caused by ATP depletion or global oxidative stress. However, local controlled production of reactive oxygen species seems to play an important role in hypoxia-induced regulation of the Na+/K+ ATPase. Treatment of cells with mercaptopropionyl glycine (MPG), a scavenger of OH*-, abolished hypoxia-induced inhibition of the Na+/K+ ATPase. Earlier on we have shown that activation of Na+/H+ exchanger under hypoxic conditions can be opposed by MPG treatment as well. Taken together our results suggest that regulation of both oxygen-sensitive transporters may be accomplished by local changes in free radical production.

Changes in net photosynthesis, chlorophyll fluorescence and xanthophyll cycle interconversions during freeze-thaw cycles in the Mediterranean moss Leucodon sciuroides

The tolerance to freezing and thawing of Leucodon sciuroides, a moss growing in mountainous areas of the Mediterranean (south-east Spain), was investigated by means of CO2 gas exchange, modulated chlorophyll (Chl) a fluorescence and pigment analysis by high-performance liquid chromatography. Evidence is presented for freezing-induced decreases in CO2 fixation that enhance non-radiative dissipation of absorbed light energy, a process which protects the photosynthetic apparatus. The photosynthetic apparatus of L. sciuroides remained fully recuperable after freezing, as indicated by the recovery of photosynthetic CO2 fixation and Chl fluorescence parameters to pre-freezing values during thawing. The rapid recovery of photosynthesis activity during thawing in L. sciuroides suggests that this moss is capable of tolerating freeze-thaw cycles in a manner similar to that found at higher latitudes or in the Antarctic. The resistance of the photosynthetic apparatus of this moss to freezing might be achieved, at least partially, through the employment of dissipative pathways, such as non-radiative dissipation of absorbed light energy.

A re-evaluation of the ATP :NADPH budget during C3 photosynthesis: a contribution from nitrate assimilation and its associated respiratory activity?

The purpose of this review in reanalysing the ATP :reluctant balance in illuminated leaf cells is to stress that photosynthesis in vivo does not involve CO2 fixation alone, but embraces other processes, chief among which is N assimilation. Prior to the demonstration of CO2 fixation and photophosphorylation by isolated chloroplasts, the mitochondria were thought likely to provide all the ATP required for CO2 fixation (discussed in Arnon et al., 1954). During the 1960s, the development of techniques for the isolation of chloroplasts able to fix CO2 at rates approaching those of the parent tissue induced a paradigm shift, leading to the establishment of a dominant (if not unanimous) view that chloroplasts in vivo must by themselves meet all their ATP requirements. More recent studies, however, indicate that the reality lies somewhere between these two extremes. The present work places emphasis on the integrated nature of photosynthesis and proposes that much of the respiratory ATP necessary for whole cell photosynthesis may be generated during the production of C skeletons for N assimilation. Rather than considering dissipative electron transport pathways as necessary to uncouple respiratory precursor synthesis from ATP production, the present analysis emphasizes the metabolic value of ATP produced during N-linked respiration, with cellular ATP supply being tailored to ATP demand.

Control of maximum sarcoplasmic reticulum Ca load in intact ferret ventricular myocytes. Effects Of thapsigargin and isoproterenol.

In steady state, the Ca content of the sarcoplasmic reticulum (SR) of cardiac myocytes is determined by a balance among influx and efflux pathways. The SR Ca content may be limited mainly by the ATP-supplied chemical potential that is inherent in the gradient between SR and cytosol. That is, forward Ca pumping from cytosol to SR may be opposed by energetically conservative reverse pumping dependent on intra-SR free [Ca]. On the other hand, SR Ca loading may be limited by dissipative pathways (pump slippage and/or pump-independent leak). To assess how SR Ca content is limited, we loaded voltage-clamped ferret ventricular myocytes cumulatively with known amounts of Ca via L-type Ca channels (ICa), using Na-free solutions to prevent Na/Ca exchange. We then measured the maximal resulting caffeine-released SR Ca content under control conditions, as well as when SR Ca pumping was accelerated by isoproterenol (1 micro M) or slowed by thapsigargin (0.2-0.4 micro M). Under control conditions, SR Ca content reached a limit of 137 micro mol.liter cytosol-1 (nonmitochondrial volume) when measured by integrating caffeine-induced Na/Ca exchange currents lintegraINaCaXdt) and of 119 micro mol.liter cytosol-1 when measured using fluorescence signals dependent on changes in cytosolic free Ca ([Ca]i). When Ca-ATPase pumping rate was slowed 39% by thapsigargin, the maximal SR Ca content decreased by 5 (integralINaCaXdt method) or 23% (fluorescence method); when pumping rate was increased 74% by isoproterenol, SR Ca content increased by 10% (fluorescence method) or 20% (integralINaCaXdt method). The relative stability of the SR Ca load suggests that dissipative losses have only a minor influence in setting the SR Ca content. Indeed, it appears that the SR Ca pump in intact cells can generate a [Ca] gradient approaching the thermodynamic limit.

A mathematical model of amphibian skin epithelium with two types of transporting cellular units.

A computer model of ion transport across amphibian skin epithelium containing two types of cellular units, their relative number and sizes, and a paracellular pathway has been developed. The two cellular units are, a large Na+ transporting compartment representing the major epithelium from stratum granulosum to str. germinativum, and a small, Cl- transporting compartment representing the mitochondria rich cell. The cellular units both contain dissipative and active pathways according to the two-membrane model. The Na+ transporting unit includes a (Na+, K+, 2 Cl-) co-transport system in the inward facing membrane. The outward facing membrane of the Cl- transporting units contains a potential gated Cl- permeability. Effects of ion distributions and changes in gating variables on the time course of transepithelial voltage clamp currents and their steady states are analyzed. The model predicts communication between the two cellular units under open circuit conditions.

Volume regulation by flounder red blood cells in anisotonic media.

The nucleated high K, low Na red blood cells of the winter flounder demonstrated a volume regulatory response subsequent to osmotic swelling or shrinkage. During volume regulation the net water flow was secondary to net inorganic cation flux. Volume regulation the net water flow was secondary to net inorganic cation flux. Volume regulation after osmotic swelling is referred to as regulatory volume decrease (RVD) and was characterized by net K and water loss. Since the electrochemical gradient for K is directed out of the cell there is no need to invoke active processes to explain RVD. When osmotically shrunken, the flounder erythrocyte demonstrated a regulatory volume increase (RVI) back toward control cell volume. The water movements characteristic of RVI were a consequence of net cellular NaCl and KCl uptake with Na accounting for 75 percent of the increase in intracellular cation content. Since the Na electrochemical gradient is directed into the cell, net Na uptake was the result of Na flux via dissipative pathways. The addition of 10(-4)M ouabain to suspensions of flounder erythrocytes was without effect upon net water movements during volume regulation. The presence of ouabain did however lead to a decreased ration of intracellular K:Na. Analysis of net Na and K fluxes in the presence and absence of ouabain led to the conclusion that Na and K fluxes via both conservative and dissipative pathways are increased in response to osmotic swelling or shrinkage. In addition, the Na and K flux rate through both pump and leak pathways decreased in a parallel fashion as cell volume was regulated. Taken as a whole, the Na and K movements through the flounder erythrocyte membrane demonstrated a functional dependence during volume regulation.