Computer simulations of structures, energetics and dynamics of myoglobin center dot center dot center dot ligand complexes

Myoglobin has been studied in considerable detail using different experimental and computational techniques over the past decades. Recent developments in time-resolved spectroscopy have provided experimental data amenable to detailed atomistic simulations. The main theme of the present review are results on the structures, energetics and dynamics of ligands ( CO, NO) interacting with myoglobin from computer simulations. Modern computational methods including free energy simulations, mixed quantum mechanics/molecular mechanics simulations, and reactive molecular dynamics simulations provide insight into the dynamics of ligand dynamics in confined spaces complementary to experiment. Application of these methods to calculate and understand experimental observations for myoglobin interacting with CO and NO are presented and discussed.

Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

How well do coupled models replicate ocean energetics relevant to ENSO?

Accurate replication of the processes associated with the energetics of the tropical ocean is necessary if coupled GCMs are to simulate the physics of ENSO correctly, including the transfer of energy from the winds to the ocean thermocline and energy dissipation during the ENSO cycle. Here, we analyze ocean energetics in coupled GCMs in terms of two integral parameters describing net energy loss in the system using the approach recently proposed by Brown and Fedorov (J Clim 23:1563–1580, 2010a) and Fedorov (J Clim 20:1108–1117, 2007). These parameters are (1) the efficiency c of the conversion of wind power into the buoyancy power that controls the rate of change of the available potential energy (APE) in the ocean and (2) the e-folding rate a that characterizes the damping of APE by turbulent diffusion and other processes. Estimating these two parameters for coupled models reveals potential deficiencies (and large differences) in how state-of-the-art coupled GCMs reproduce the ocean energetics as compared to ocean-only models and data assimilating models. The majority of the coupled models we analyzed show a lower efficiency (values of c in the range of 10–50% versus 50–60% for ocean-only simulations or reanalysis) and a relatively strong energy damping (values of a-1 in the range 0.4–1 years versus 0.9–1.2 years). These differences in the model energetics appear to reflect differences in the simulated thermal structure of the tropical ocean, the structure of ocean equatorial currents, and deficiencies in the way coupled models simulate ENSO.

Energetics, lifestyle, and reproduction in birds

Theoretical and empirical studies of life history aim to account for resource allocation to the different components of fitness: survival, growth, and reproduction. The pioneering evolutionary ecologist David Lack [(1968) Ecological Adaptations for Breeding in Birds (Methuen and Co.,London)] suggested that reproductive output in birds reflects adaptation to environmental factors such as availability of food and risk of predation, but subsequent studies have not always supported Lack’s interpretation. Here using a dataset for 980 bird species (Dataset S1), a phylogeny, and an explicit measure of reproductive productivity, we test predictions for how mass-specific productivity varies with body size, phylogeny,and lifestyle traits. We find that productivity varies negatively with body size and energetic demands of parental care and positively with extrinsic mortality. Specifically: (i) altricial species are 50% less productive than precocial species; (ii) species with female-only care of offspring are about 20% less productive than species with other methods of parental care; (iii) nonmigrants are 14% less productive than migrants; (iv) frugivores and nectarivores are about 20% less productive than those eating other foods; and (v) pelagic foragers are 40% less productive than those feeding in other habitats. A strong signal of phylogeny suggests that syndromes of similar life-history traits tend to be conservative within clades but also to have evolved independently in different clades. Our results generally support both Lack’s pioneering studies and subsequent research on avian life history.

Energetics of a symmetric circulation including momentum constraints

A theory of available potential energy (APE) for symmetric circulations, which includes momentum constraints, is presented. The theory is a generalization of the classical theory of APE, which includes only thermal constraints on the circulation. Physically, centrifugal potential energy is included along with gravitational potential energy. The generalization relies on the Hamiltonian structure of the conservative dynamics, although (as with classical APE) it still defines the energetics in a nonconservative framework. It follows that the theory is exact at finite amplitude, has a local form, and can be applied to a variety of fluid models. It is applied here to the f -plane Boussinesq equations. It is shown that, by including momentum constraints, the APE of a symmetrically stable flow is zero, while the energetics of a mechanically driven symmetric circulation properly reflect its causality.

The importance of moisture distribution for the growth and energetics of mid-latitude systems

A primitive equation model is used to study the sensitivity of baroclinic wave life cycles to the initial latitude-height distribution of humidity. Diabatic heating is parametrized only as a consequence of condensation in regions of large-scale ascent. Experiments are performed in which the initial relative humidity is a simple function of model level, and in some cases latitude bands are specified which are initially relatively dry. It is found that the presence of moisture can either increase or decrease the peak eddy kinetic energy of the developing wave, depending on the initial moisture distribution. A relative abundance of moisture at mid-latitudes tends to weaken the wave, while a relative abundance at low latitudes tends to strengthen it. This sensitivity exists because competing processes are at work. These processes are described in terms of energy box diagnostics. The most realistic case lies on the cusp of this sensitivity. Further physical parametrizations are then added, including surface fluxes and upright moist convection. These have the effect of increasing wave amplitude, but the sensitivity to initial conditions of relative humidity remains. Finally, 'control' and 'doubled CO2' life cycles are performed, with initial conditions taken from the time-mean zonal-mean output of equilibrium GCM experiments. The attenuation of the wave resulting from reduced baroclinicity is more pronounced than any effect due to changes in initial moisture.

On the validity of single-parcel energetics to assess the importance of internal energy and compressibility effects in stratified fluids

It is often assumed on the basis of single-parcel energetics that compressible effects and conversions with internal energy are negligible whenever typical displacements of fluid parcels are small relative to the scale height of the fluid (defined as the ratio of the squared speed of sound over gravitational acceleration). This paper shows that the above approach is flawed, however, and that a correct assessment of compressible effects and internal energy conversions requires considering the energetics of at least two parcels, or more generally, of mass conserving parcel re-arrangements. As a consequence, it is shown that it is the adiabatic lapse rate and its derivative with respect to pressure, rather than the scale height, which controls the relative importance of compressible effects and internal energy conversions when considering the global energy budget of a stratied fluid. Only when mass conservation is properly accounted for is it possible to explain why available internal energy can account for up to 40 percent of the total available potential energy in the oceans. This is considerably larger than the prediction of single-parcel energetics, according to which this number should be no more than about 2 percent.

Observational and energetics constraints on the non-conservation of potential/Conservative Temperature and implications for ocean modelling

This paper seeks to elucidate the fundamental differences between the nonconservation of potential temperature and that of Conservative Temperature, in order to better understand the relative merits of each quantity for use as the heat variable in numerical ocean models. The main result is that potential temperature is found to behave similarly to entropy, in the sense that its nonconservation primarily reflects production/destruction by surface heat and freshwater fluxes; in contrast, the nonconservation of Conservative Temperature is found to reflect primarily the overall compressible work of expansion/contraction. This paper then shows how this can be exploited to constrain the nonconservation of potential temperature and entropy from observed surface heat fluxes, and the nonconservation of Conservative Temperature from published estimates of the mechanical energy budgets of ocean numerical models. Finally, the paper shows how to modify the evolution equation for potential temperature so that it is exactly equivalent to using an exactly conservative evolution equation for Conservative Temperature, as was recently recommended by IOC et al. (2010). This result should in principle allow ocean modellers to test the equivalence between the two formulations, and to indirectly investigate to what extent the budget of derived nonconservative quantities such as buoyancy and entropy can be expected to be accurately represented in ocean models.

Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design

Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids.

An analysis of the environmental energetics associated with the transition of the first South Atlantic hurricane

This study presents the first analysis of the energetics associated with a hybrid cyclone`s transition in the Southern Hemisphere, Hurricane Catarina ( March 2004). Catarina has earned a place in history as the first documented South Atlantic hurricane, but its unusual tropical transition is still poorly understood. Here we show that Catarina`s transition was preceded by marked environmental changes in the Lorenz energy cycle, with an abrupt shift from a baroclinic to a predominantly barotropic state. Such changes help to explain the unusual vortex`s growth until its transition was completed. Although the vortex`s energy flux is not explicitly calculated, a likely mechanism linking the environmental energetics with Catarina is the extraction of eddy kinetic energy from horizontal momentum and heat transfers within the through component of the blocking. The results advance the understanding of this rare event and suggest that the technique has a great potential to study transitioning systems in general.

Energetics and stability of vacancies in carbon nanotubes

In this work we present ab initio calculations of the formation energies and stability of different types of multi-vacancies in carbon nanotubes. We demonstrate that, as in the case of graphene, the reconstruction of the defects has drastic effects on the energetics of the tubes. In particular, the formation of pentagons eliminates the dangling bonds thus lowering the formation energy. This competition leads to vacancies having an even number of carbon atoms removed to be more stable. Finally the appearance of magic numbers indicating more stable defects can be represented by a model for the formation energies that is based on the number of dangling bonds of the unreconstructed system, the pentagons and the relaxation of the final form of the defect formed after the relaxation. (C) 2011 Elsevier Ltd. All rights reserved.

Furan interaction with the Si(001)-(2 x 2) surface: structural, energetics, and vibrational spectra from first-principles

In this work we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of furan on the silicon (001) surface. A direct comparison of different adsorption structures with x-ray photoelectron spectroscopy (XPS), ultra-violet photoelectron spectroscopy (UPS), high resolution electron energy loss spectroscopy (HREELS), near edge x-ray absorption fine structure (NEXAFS), and high resolution spectroscopy experimental data allows us to identify the [4 + 2] cycloaddition reaction as the most probable adsorbate. In addition, theoretical scanning tunnelling microscopy (STM) images are presented, with a view to contributing to further experimental investigations.

Exploring new molecular species on the (1)[H, Se, F] singlet potential energy surface: Energetics, structures, IR spectra, and heats of formation

Structural, energetic, and vibrational properties of new molecular species, HSeF and HFSe, the associated transition state, and dissociation fragments are investigated using a state-of-the-art theoretical approach, CCSD(T)/CBS. HSeF is a normal covalently bonded molecule 38.98 kcal mol (1) more stable than the complex HF-Se, which shows an unusual structure with a central fluorine atom and a bond angle of 101.8 degrees.A barrier (Delta G(#)) of 49.01 kcal mol (1) separates the two species. Vibrational frequencies are also quite distinct. Heats of formation are evaluated for the diatomic fragments and HSeF. Final Delta(f)H values depend on the experimental accuracy of those of Se(g) and H(2)Se. (c) 2009 Elsevier B.V. All rights reserved.

Temperature and meal size effects on the postprandial metabolism and energetics in a boid snake

We investigated the combined effect of meal size and temperature on the aerobic metabolism and energetics of digestion in Boa constrictor amarali. Oxygen uptake rates ((V) over dot o(2)) and the. duration of the digestion were determined in snakes fed with meals equaling to 5%, 10%, 20%, and 40% of the snake's body mass at 25degrees and 30 degreesC. The maximum (V) over dot o(2) values attained during digestion were greater at 30 degreesC than at 25 degreesC. Both maximal (V) over dot (o2) values and the duration of the specific dynamic action. (SDA) were attained sooner at 30 degreesC than at 25 degreesC. Therefore, the temperature effect on digestion in Boa is characterized by the shortening of the SDA duration at the expense of increased. Energy allocated to SDA was not affected by meal size but. was greater at 25 degreesC compared to 30 degreesC. This indicates that a postprandial thermophilic response can be advantageous not only by decreasing the duration of digestion but also by improving digestive efficiency. Maximal (V) over dot o(2) and SDA duration. increased with meal size at both temperatures.