Isothermal titration calorimetry study of epicatechin binding to serum albumin

The interaction of epicatechin with bovine serum albumin (BSA) was studied by isothermal titration calorimetry. The binding constant (K) and associated thermodynamic binding parameters (n, Delta H) were determined for the interaction at three solution concentrations of BSA using a binding model assuming independent binding sites. These data show weak non-covalent binding of epicatechin to BSA. The interaction energetics varied with BSA concentration in the calorimeter cell, suggesting that the binding of epicatechin induced BSA aggregation. The free energy (Delta G) remained constant within a range of 2 kJ mol(-1) and negative entropy was observed, indicating an enthalpy driven exothermic interaction. It is concluded that the non-covalent epicatechin-BSA complex is formed by hydrogen bonding. (c) 2006 Elsevier B.V. All rights reserved.

Tracking and mean structure of easterly waves over the Intra-Americas Sea

Easterly waves (EWs) are prominent features of the intertropical convergence zone (ITCZ), found in both the Atlantic and Pacific during the Northern Hemisphere summer and fall, where they commonly serve as precursors to hurricanes over both basins.Alarge proportion of Atlantic EWs are known to form over Africa, but the origin of EWs over the Caribbean and east Pacific in particular has not been established in detail. In this study reanalyses are used to examine the coherence of the large-scale wave signatures and to obtain track statistics and energy conversion terms for EWs across this region. Regression analysis demonstrates that some EW kinematic structures readily propagate between the Atlantic and east Pacific, with the highest correlations observed across Costa Rica and Panama. Track statistics are consistent with this analysis and suggest that some individual waves are maintained as they pass from the Atlantic into the east Pacific, whereas others are generated locally in the Caribbean and east Pacific. Vortex anomalies associated with the waves are observed on the leeward side of the Sierra Madre, propagating northwestward along the coast, consistent with previous modeling studies of the interactions between zonal flow and EWs with model topography similar to the Sierra Madre. An energetics analysis additionally indicates that the Caribbean low-level jet and its extension into the east Pacific—known as the Papagayo jet—are a source of energy for EWs in the region. Two case studies support these statistics, as well as demonstrate the modulation of EW track and storm development location by the MJO.

Baroclinic stationary waves in aquaplanet models

An aquaplanet model is used to study the nature of the highly persistent low-frequency waves that have been observed in models forced by zonally symmetric boundary conditions. Using the Hayashi spectral analysis of the extratropical waves, the authors find that a quasi-stationary wave 5 belongs to a wave packet obeying a well-defined dispersion relation with eastward group velocity. The components of the dispersion relation with k ≥ 5 baroclinically convert eddy available potential energy into eddy kinetic energy, whereas those with k < 5 are baroclinically neutral. In agreement with Green’s model of baroclinic instability, wave 5 is weakly unstable, and the inverse energy cascade, which had been previously proposed as a main forcing for this type of wave, only acts as a positive feedback on its predominantly baroclinic energetics. The quasi-stationary wave is reinforced by a phase lock to an analogous pattern in the tropical convection, which provides further amplification to the wave. It is also found that the Pedlosky bounds on the phase speed of unstable waves provide guidance in explaining the latitudinal structure of the energy conversion, which is shown to be more enhanced where the zonal westerly surface wind is weaker. The wave’s energy is then trapped in the waveguide created by the upper tropospheric jet stream. In agreement with Green’s theory, as the equator-to-pole SST difference is reduced, the stationary marginally stable component shifts toward higher wavenumbers, while wave 5 becomes neutral and westward propagating. Some properties of the aquaplanet quasi-stationary waves are found to be in interesting agreement with a low frequency wave observed by Salby during December–February in the Southern Hemisphere so that this perspective on low frequency variability, apart from its value in terms of basic geophysical fluid dynamics, might be of specific interest for studying the earth’s atmosphere.

Potential energy surface and moleculardynamics of MbNO: existence of an unsuspected FeON minimum

Ligands such as CO, O2, or NO are involved in the biological function of myoglobin. Here we investigate the energetics and dynamics of NO interacting with the Fe(II) heme group in native myoglobin using ab initio and molecular dynamics simulations. At the global minimum of the ab initio potential energy surface (PES), the binding energy of 23.4 kcal/mol and the Fe-NO structure compare well with the experimental results. Interestingly, the PES is found to exhibit two minima: There exists a metastable, linear Fe-O-N minimum in addition to the known, bent Fe-N-O global minimum conformation. Moreover, the T-shaped configuration is found to be a saddle point, in contrast to the corresponding minimum for NO interacting with Fe(III). To use the ab initio results for finite temperature molecular dynamics simulations, an analytical function was fitted to represent the Fe-NO interaction. The simulations show that the secondary minimum is dynamically stable up to 250 K and has a lifetime of several hundred picoseconds at 300 K. The difference in the topology of the heme-NO PES from that assumed previously (one deep, single Fe-NO minimum) suggests that it is important to use the full PES for a quantitative understanding of this system. Why the metastable state has not been observed in the many spectroscopic studies of myoglobin interacting with NO is discussed, and possible approaches to finding it are outlined.

Photochromic dithienylethene derivatives containing Ru(II) or Os(II) metal units. Sensitized photocyclization from a triplet state

Efficient photocyclization from a low-lying triplet state is reported for a photochromic dithienylperfluorocyclopentene with Ru(bpy)(3) units attached via a phenylene linker to the thiophene rings. The ring-closure reaction in the nanosecond domain is sensitized by the metal complexes. Upon photoexcitation into the lowest Ru-to-bpy (MLCT)-M-1 state followed by intersystem crossing to emitting (MLCT)-M-3 states, photoreactive (IL)-I-3 states are populated by an efficient energy-transfer process. The involvement of these (IL)-I-3 states explains the quantum yield of the photocyclization, which is independent of the excitation wavelength but decreases strongly in the presence of dioxygen. This behavior differs substantially from the photocyclization of the nonemissive dithienylperfluorocyclopentene free ligand, which occurs from the lowest (IL)-I-1 state on a picosecond time scale and is insensitive to oxygen quenching. Cyclic voltammetric studies have also been performed to gain further insight into the energetics of the system. The very high photocyclization quantum yields, far above 0.5 in both cases, are ascribed to the strong steric repulsion between the bulky substituents on the dithienylperfluorocyclopentene bridge bearing the chelating bipyridine sites or the Ru(bpy)(3) moieties, forcing the system to adopt nearly exclusively the reactive antiparallel conformation. In contrast, replacement of both Ru(II) centers by Os(II) completely prevents the photocyclization reaction upon light excitation into the low-lying Os-to-bpy (MLCT)-M-1 state. The photoreaction can only be triggered by optical population of the higher lying (IL)-I-1 excited state of the central photochromic unit, but its yield is low due to efficient energy transfer to the luminescent lowest (MLCT)-M-3 state.

Reversible sphere-to-lamellar wetting transition at the interface of a diblock copolymer system

We use ellipsometry to investigate a transition in the morphology of a sphere-forming diblock copolymer thin-film system. At an interface the diblock morphology may differ from the bulk when the interfacial tension favours wetting of the minority domain, thereby inducing a sphere-to-lamella transition. In a small, favourable window in energetics, one may observe this transition simply by adjusting the temperature. Ellipsometry is ideally suited to the study of the transition because the additional interface created by the wetting layer affects the polarisation of light reflected from the sample. Here we study thin films of poly(butadiene-ethylene oxide) (PB-PEO), which order to form PEO minority spheres in a PB matrix. As temperature is varied, the reversible transition from a partially wetting layer of PEO spheres to a full wetting layer at the substrate is investigated.

Energetic constraints on precipitation under climate change

Energetic constraints on precipitation are useful for understanding the response of the hydrological cycle to ongoing climate change, its response to possible geoengineering schemes, and the limits on precipitation in very warm climates of the past. Much recent progress has been made in quantifying the different forcings and feedbacks on precipitation and in understanding how the transient responses of precipitation and temperature might differ qualitatively. Here, we introduce the basic ideas and review recent progress. We also examine the extent to which energetic constraints on precipitation may be viewed as radiative constraints and the extent to which they are confirmed by available observations. Challenges remain, including the need to better demonstrate the link between energetics and precipitation in observations and to better understand energetic constraints on precipitation at sub-global length scales.

The key role of the western boundary in linking the AMOC strength to the north-south pressure gradient

A key idea in the study of the Atlantic meridional overturning circulation (AMOC) is that its strength is proportional to the meridional density gradient, or more precisely, to the strength of the meridional pressure gradient. A physical basis that would tell us how to estimate the relevant meridional pressure gradient locally from the density distribution in numerical ocean models to test such an idea, has been lacking however. Recently, studies of ocean energetics have suggested that the AMOC is driven by the release of available potential energy (APE) into kinetic energy (KE), and that such a conversion takes place primarily in the deep western boundary currents. In this paper, we develop an analytical description linking the western boundary current circulation below the interface separating the North Atlantic Deep Water (NADW) and Antarctic Intermediate Water (AAIW) to the shape of this interface. The simple analytical model also shows how available potential energy is converted into kinetic energy at each location, and that the strength of the transport within the western boundary current is proportional to the local meridional pressure gradient at low latitudes. The present results suggest, therefore, that the conversion rate of potential energy may provide the necessary physical basis for linking the strength of the AMOC to the meridional pressure gradient, and that this could be achieved by a detailed study of the APE to KE conversion in the western boundary current.

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Rensch's rule in large herbivorous mammals derived from metabolic scaling

Rensch’s rule, which states that the magnitude of sexual size dimorphism tends to increase with increasing body size, has evolved independently in three lineages of large herbivorous mammals: bovids (antelopes), cervids (deer), and macropodids (kangaroos). This pattern can be explained by a model that combines allometry,life-history theory, and energetics. The key features are thatfemale group size increases with increasing body size and that males have evolved under sexual selection to grow large enough to control these groups of females. The model predicts relationships among body size and female group size, male and female age at first breeding,death and growth rates, and energy allocation of males to produce body mass and weapons. Model predictions are well supported by data for these megaherbivores. The model suggests hypotheses for why some other sexually dimorphic taxa, such as primates and pinnipeds(seals and sea lions), do or do not conform to Rensh’s rule.

Available potential energy and exergy in stratified fluids

Lorenz’s theory of available p otential energy (APE) remains the main framework for studying the atmospheric and oceanic energy cycles. Because the APE generation rate is the volume integral of a thermodynamic efficiency times the local diabatic heating/cooling rate, APE theory is often regarded as an extension of the theory of heat engines. Available energetics in classical thermodynamics, however, usually relies on the concept of exergy, and is usually measured relative to a reference state maximising entropy at constant energy, whereas APE’s reference state minimises p otential energy at constant entropy. This review seeks to shed light on the two concepts; it covers local formulations of available energetics, alternative views of the dynamics/thermodynamics coupling, APE theory and the second law, APE production/dissipation, extensions to binary fluids, mean/eddy decomp ositions, APE in incompressible fluids, APE and irreversible turbulent mixing, and the role of mechanical forcing on APE production.

Extended Canadian middle atmosphere model: zonal-mean climatology and physical parameterizations

This paper describes the energetics and zonal-mean state of the upward extension of the Canadian Middle Atmosphere Model, which extends from the ground to ~210 km. The model includes realistic parameterizations of the major physical processes from the ground up to the lower thermosphere and exhibits a broad spectrum of geophysical variability. The rationale for the extended model is to examine the nature of the physical and dynamical processes in the mesosphere/lower thermosphere (MLT) region without the artificial effects of an imposed sponge layer which can modify the circulation in an unrealistic manner. The zonal-mean distributions of temperature and zonal wind are found to be in reasonable agreement with observations in most parts of the model domain below ~150 km. Analysis of the global-average energy and momentum budgets reveals a balance between solar extreme ultraviolet heating and molecular diffusion and a thermally direct viscous meridional circulation above 130 km, with the viscosity coming from molecular diffusion and ion drag. Below 70 km, radiative equilibrium prevails in the global mean. In the MLT region between ~70 and 120 km, many processes contribute to the global energy budget. At solstice, there is a thermally indirect meridional circulation driven mainly by parameterized nonorographic gravity-wave drag. This circulation provides a net global cooling of up to 25 K d^-1.

Irreversible compressible work and APE dissipation in turbulent stratified fluid

Although it plays a key role in the theory of stratified turbulence, the concept of available potential energy (APE) dissipation has remained until now a rather mysterious quantity, owing to the lack of rigorous result about its irreversible character or energy conversion type. Here, we show by using rigorous energetics considerations rooted in the analysis of the Navier-Stokes for a fully compressible fluid with a nonlinear equation of state that the APE dissipation is an irreversible energy conversion that dissipates kinetic energy into internal energy, exactly as viscous dissipation. These results are established by showing that APE dissipation contributes to the irreversible production of entropy, and by showing that it is a part of the work of expansion/contraction. Our results provide a new interpretation of the entropy budget, that leads to a new exact definition of turbulent effective diffusivity, which generalizes the Osborn-Cox model, as well as a rigorous decomposition of the work of expansion/contraction into reversible and irreversible components. In the context of turbulent mixing associated with parallel shear flow instability, our results suggests that there is no irreversible transfer of horizontal momentum into vertical momentum, as seems to be required when compressible effects are neglected, with potential consequences for the parameterisations of momentum dissipation in the coarse-grained Navier-Stokes equations.

Aluminium distribution in ZSM-5 revisited: the role of Al-Al interactions

We present a theoretical study of the distribution of Al atoms in zeolite ZSM-5 with Si/Al=47, where we focus on the role of Al-Al interactions rather than on the energetics of Al/Si substitutions at individual sites. Using interatomic potential methods, we evaluate the energies of the full set of symmetrically independent configurations of Al siting in a Si94Al2O192 cell. The equilibrium Al distribution is determined by the interplay of two factors: the energetics of the Al/Si substitution at an individual site, which tends to populate particular T sites (e.g. the T14 site), and the Al-Al interaction, which at this Si/Al maximises Al-Al distances in agreement with Dempsey’s rule. However, it is found that the interaction energy changes approximately as the inverse of the square of the distance between the two Al atoms, rather than the inverse of the distance expected if this were merely charge repulsion. Moreover, we find that the anisotropic nature of the framework density plays an important role in determining the magnitude of the interactions, which are not simply dependent on Al-Al distances.

Estimating Lorenz's reference state in an ocean with a nonlinear equation of state for seawater

The study of the mechanical energy budget of the oceans using Lorenz available potential energy (APE) theory is based on knowledge of the adiabatically re-arranged Lorenz reference state of minimum potential energy. The compressible and nonlinear character of the equation of state for seawater has been thought to cause the reference state to be ill-defined, casting doubt on the usefulness of APE theory for investigating ocean energetics under realistic conditions. Using a method based on the volume frequency distribution of parcels as a function of temperature and salinity in the context of the seawater Boussinesq approximation, which we illustrate using climatological data, we show that compressibility effects are in fact minor. The reference state can be regarded as a well defined one-dimensional function of depth, which forms a surface in temperature, salinity and density space between the surface and the bottom of the ocean. For a very small proportion of water masses, this surface can be multivalued and water parcels can have up to two statically stable levels in the reference density profile, of which the shallowest is energetically more accessible. Classifying parcels from the surface to the bottom gives a different reference density profile than classifying in the opposite direction. However, this difference is negligible. We show that the reference state obtained by standard sorting methods is equivalent, though computationally more expensive, to the volume frequency distribution approach. The approach we present can be applied systematically and in a computationally efficient manner to investigate the APE budget of the ocean circulation using models or climatological data.