Ligand dynamics in myoglobin: calculation of infrared spectra for photodissociated NO

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

The circulation response to idealized changes in stratospheric water vapor

Observations show that stratospheric water vapor (SWV) concentrations increased by ~30% between 1980 and 2000. SWV has also been projected to increase by up to a factor of two over the 21st century. Trends in SWV impact on stratospheric temperatures, which may lead to changes in the stratospheric circulation. Perturbations in temperature and wind in the stratosphere have been shown to influence the extratropical tropospheric circulation. This study investigates the response to a uniform doubling in SWV from 3 to 6 ppmv in a comprehensive stratosphere-resolving atmospheric-GCM. The increase in SWV causes stratospheric cooling with a maximum amplitude of 5-6 K in the polar lower stratosphere and 2-3 K in the tropical lower stratosphere. The zonal wind on the upper flanks of the subtropical jets is more westerly by up to ~5 m s−1. Changes in resolved wave drag in the stratosphere result in an increase in the strength of tropical upwelling associated with the Brewer-Dobson circulation of ~10% throughout the year. In the troposphere, the increase in SWV causes significant meridional dipole changes in the midlatitude zonal-mean zonal wind of up to 2.8 m s−1 at 850 hPa, which are largest in boreal winter in both hemispheres. This suggests a more poleward storm track under uniformly increased stratospheric water vapor. The circulation changes in both the stratosphere and troposphere are almost entirely due to the increase in SWV at pressures greater than 50 hPa. The results show that long-term trends in SWV may impact on stratospheric temperatures and wind, the strength of the Brewer-Dobson circulation and extratropical surface climate.

Wave-breaking characteristics of midlatitude blocking

In this article, Northern Hemisphere winter midlatitude blocking is analysed through its wave-breaking characteristics. Rossby wave breaking is identified as a key process in blocking occurrence, as it provides the mechanism for the meridional reversal pattern typical of blocking. Two indices are designed to detect the major properties of wave breaking, i.e. the orientation (cyclonic/anticyclonic–direction of breaking or DB index) and the relative contribution of air masses (warm/cold–relative intensity or RI index). The use of the DB index differentiates between the anticyclonic cases over Europe and Asia and the cyclonic events over the oceanic basins. One of the three regions displaying cyclonic type was found over the Atlantic Ocean, the other two being over the Pacific Ocean. The first of these is located over the western side of the Pacific and is dominated by warm air extrusions, whereas the second is placed northward of the exit region of the jet stream, where the meridional θ gradient is much weaker. Two European blocking types have been detected using the RI index, which separates out the cases dominated by warm and cold air masses. The latter cases in particular exhibited a well-structured dipole, with associated strong anomalies in both temperature and precipitation. Copyright © 2011 Royal Meteorological Society

Diabatic processes modifying potential vorticity in a North Atlantic cyclone

Potential vorticity (PV) succinctly describes the evolution of large-scale atmospheric flow because of its material conservation and invertibility properties. However, diabatic processes in extratropical cyclones can modify PV and influence both mesoscale weather and the evolution of the synoptic-scale wave pattern. In this investigation, modification of PV by diabatic processes is diagnosed in a Met Office Unified Model (MetUM) simulation of a North Atlantic cyclone using a set of PV tracers. The structure of diabatic PV within the extratropical cyclone is investigated and linked to the processes responsible for it. On the mesoscale, a tripole of diabatic PV is generated across the tropopause fold extending down to the cold front. The structure results from a dipole in heating across the frontal interface due to condensation in the warm conveyor belt flanking the upper side of the fold and evaporation of precipitation in the dry intrusion and below. On isentropic surfaces intersecting the tropopause, positive diabatic PV is generated on the stratospheric side, while negative diabatic PV is generated on the tropospheric side. The stratospheric diabatic PV is generated primarily by long-wave cooling which peaks at the tropopause itself due to the sharp gradient in humidity there. The tropospheric diabatic PV originates locally from the long-wave radiation and non-locally by advection out of the top of heating associated with the large-scale cloud, convection and boundary layer schemes. In most locations there is no diabatic modification of PV at the tropopause itself but diabatic PV anomalies would influence the tropopause indirectly through the winds they induce and subsequent advection. The consequences of this diabatic PV dipole for the evolution of synoptic-scale wave patterns are discussed.

Synergetic effect of carbon nanopore size and surface oxidation on CO2 capture from CO2/CH4 mixtures

We have studied the synergetic effect of confinement (carbon nanopore size) and surface chemistry (the number of carbonyl groups) on CO2 capture from its mixtures with CH4 at typical operating conditions for industrial adsorptive separation (298 K and compressed CO2CH4 mixtures). Although both confinement and surface oxidation have an impact on the efficiency of CO2/CH4 adsorptive separation at thermodynamics equilibrium, we show that surface functionalization is the most important factor in designing an efficient adsorbent for CO2 capture. Systematic Monte Carlo simulations revealed that adsorption of CH4 either pure or mixed with CO2 on oxidized nanoporous carbons is only slightly increased by the presence of functional groups (surface dipoles). In contrast, adsorption of CO2 is very sensitive to the number of carbonyl groups, which can be examined by a strong electric quadrupolar moment of CO2. Interestingly, the adsorbed amount of CH4 is strongly affected by the presence of the co-adsorbed CO2. In contrast, the CO2 uptake does not depend on the molar ratio of CH4 in the bulk mixture. The optimal carbonaceous porous adsorbent used for CO2 capture near ambient conditions should consist of narrow carbon nanopores with oxidized pore walls. Furthermore, the equilibrium separation factor was the greatest for CO2/CH4 mixtures with a low CO2 concentration. The maximum equilibrium separation factor of CO2 over CH4 of ∼18–20 is theoretically predicted for strongly oxidized nanoporous carbons. Our findings call for a review of the standard uncharged model of carbonaceous materials used for the modeling of the adsorption separation processes of gas mixtures containing CO2 (and other molecules with strong electric quadrupolar moment or dipole moment).

Influence of shape and absorbing surface: a numerical study of railway noise barriers

Results are presented of a study of a performance of various track-side railway noise barriers, determined by using a two- dimensional numerical boundary element model. The basic model uses monopole sources and has been adapted to allow the sources to exhibit dipole-type radiation characteristics. A comparison of boundary element predictions of the performance of simple barriers and vehicle shapes is made with results obtained by using the standard U.K. prediction method. The results obtained from the numerical model indicate that modifying the source to exhibit dipole characteristics becomes more significant as the height of the barrier increases, and suggest that for any particular shape, absorbent barriers provide much better screening efficiency than the rigid equivalent. The cross-section of the rolling stock significantly affects the performance of rigid barriers. If the position of the upper edge is fixed, the results suggest that simple absorptive barriers provide more effective screening than tilted barriers. The addition of multiple edges to a barrier provides additional insertion loss without any increase in barrier height.

The effect of windstress change on future sea level change in the Southern Ocean

AOGCMs of the two latest phases (CMIP3 and CMIP5) of the Coupled Model Intercomparison Project, like earlier AOGCMs, predict large regional variations in future sea level change. The model-mean pattern of change in CMIP3 and CMIP5 is very similar, and its most prominent feature is a zonal dipole in the Southern Ocean: sea level rise is larger than the global mean north of 50°S and smaller than the global mean south of 50°S in most models. The individual models show widely varying patterns, although the inter-model spread in local sea level change is smaller in CMIP5 than in CMIP3. Here we investigate whether changes in windstress can explain the different patterns of projected sea level change, especially the Southern Ocean feature, using two AOGCMs forced by the changes in windstress from the CMIP3 and CMIP5 AOGCMs. We show that the strengthening and poleward shift of westerly windstress accounts for the most of the large spread among models in magnitude of this feature. In the Indian, North Pacific and Arctic Oceans, the windstress change is influential, but does not completely account for the projected sea level change.

A multi-model analysis of the role of the ocean on the African and Indian monsoon during mid-Holocene

We investigate the role of the ocean feedback on the climate in response to insolation forcing during the mid-Holocene (6,000 year BP) using results from seven coupled ocean–atmosphere general circulation models. We examine how the dipole in late summer sea-surface temperature (SST) anomalies in the tropical Atlantic increases the length of the African monsoon, how this dipole structure is created and maintained, and how the late summer SST warming in the northwest Indian Ocean affects the monsoon retreat in this sector. Similar mechanisms are found in all of the models, including a strong wind evaporation feedback and changes in the mixed layer depth that enhance the insolation forcing, as well as increased Ekman transport in the Atlantic that sharpens the Atlantic dipole pattern. We also consider changes in interannual variability over West Africa and the Indian Ocean. The teleconnection between variations in SST and Sahelian precipitation favor a larger impact of the Atlantic dipole mode in this region. In the Indian Ocean, the strengthening of the Indian dipole structure in autumn has a damping effect on the Indian dipole mode at the interannual time scale

The impact of sea ice dynamics on the Arctic climate system

Five paired global climate model experiments, one with an ice pack that only responds thermodynamically (TI) and one including sea-ice dynamics (DI), were used to investigate the sensitivity of Arctic climates to sea-ice motion. The sequence of experiments includes situations in which the Arctic was both considerably colder (Glacial Inception, ca 115,000 years ago) and considerably warmer (3 × CO2) than today. Sea-ice motion produces cooler anomalies year-round than simulations without ice dynamics, resulting in reduced Arctic warming in warm scenarios and increased Arctic cooling in cold scenarios. These changes reflect changes in atmospheric circulation patterns: the DI simulations favor outflow of Arctic air and sea ice into the North Atlantic by promoting cyclonic circulation centered over northern Eurasia, whereas the TI simulations favor southerly inflow of much warmer air from the North Atlantic by promoting cyclonic circulation centered over Greenland. The differences between the paired simulations are sufficiently large to produce different vegetation cover over >19% of the land area north of 55°N, resulting in changes in land-surface characteristics large enough to have an additional impact on climate. Comparison of the DI and TI experiments for the mid-Holocene (6000 years ago) with paleovegetation reconstructions suggests the incorporation of sea-ice dynamics yields a more realistic simulation of high-latitude climates. The spatial pattern of sea-ice anomalies in the warmer-than-modern DI experiments strongly resembles the observed Arctic Ocean sea-ice dipole structure in recent decades, consistent with the idea that greenhouse warming is already impacting the high-northern latitudes.

Extreme rainfall variability in Australia: Patterns, drivers and predictability

Leading patterns of observed monthly extreme rainfall variability in Australia are examined using an Empirical Orthogonal Teleconnection (EOT) method. Extreme rainfall variability is more closely related to mean rainfall variability during austral summer than in winter. The leading EOT patterns of extreme rainfall explain less variance in Australia-wide extreme rainfall than is the case for mean rainfall EOTs. We illustrate that, as with mean rainfall, the El Niño-Southern Oscillation (ENSO) has the strongest association with warm-season extreme rainfall variability, while in the cool-season the primary drivers are atmospheric blocking and the subtropical ridge. The Indian Ocean Dipole and Southern Annular Mode also have significant relationships with patterns of variability during austral winter and spring. Leading patterns of summer extreme rainfall variability have predictability several months ahead from Pacific sea surface temperatures (SSTs) and as much as a year in advance from Indian Ocean SSTs. Predictability from the Pacific is greater for wetter than average summer months than for months that are drier than average, whereas for the Indian Ocean the relationship has greater linearity. Several cool-season EOTs are associated with mid-latitude synoptic-scale patterns along the south and east coasts. These patterns have common atmospheric signatures denoting moist onshore flow and strong cyclonic anomalies often to the north of a blocking anti-cyclone. Tropical cyclone activity is observed to have significant relationships with some warm season EOTs. This analysis shows that extreme rainfall variability in Australia can be related to remote drivers and local synoptic-scale patterns throughout the year.

Transmission of wireless power by magnetic resonance

The work involves investigation of a type of wireless power system wherein its analysis will yield the construction of a prototype modeled as a singular technological artifact. It is through exploration of the artifact that forms the intellectual basis for not only its prototypical forms, but suggestive of variant forms not yet discovered. Through the process it is greatly clarified the role of the artifact, its most suitable application given the constraints on the delivery problem, and optimization strategies to improve it. In order to improve maturity and contribute to a body of knowledge, this document proposes research utilizing mid-field region, efficient inductive-transfer for the purposes of removing wired connections and electrical contacts. While the description seems enough to state the purpose of this work, it does not convey the compromises of having to redraw the lines of demarcation between near and far-field in the traditional method of broadcasting. Two striking scenarios are addressed in this thesis: Firstly, the mathematical explanation of wireless power is due to J.C. Maxwell's original equations, secondly, the behavior of wireless power in the circuit is due to Joseph Larmor's fundamental works on the dynamics of the field concept. A model of propagation will be presented which matches observations in experiments. A modified model of the dipole will be presented to address the phenomena observed in the theory and experiments. Two distinct sets of experiments will test the concept of single and two coupled-modes. In a more esoteric context of the zero and first-order magnetic field, the suggestion of a third coupled-mode is presented. Through the remaking of wireless power in this context, it is the intention of the author to show the reader that those things lost to history, bound to a path of complete obscurity, are once again innovative and useful ideas.

The drivers of projected North Atlantic sea level change

Sea level change predicted by the CMIP5 atmosphere–ocean general circulation models (AOGCMs) is not spatially homogeneous. In particular, the sea level change in the North Atlantic is usually characterised by a meridional dipole pattern with higher sea level rise north of 40°N and lower to the south. The spread among models is also high in that region. Here we evaluate the role of surface buoyancy fluxes by carrying out simulations with the FAMOUS low-resolution AOGCM forced by surface freshwater and heat flux changes from CO2-forced climate change experiments with CMIP5 AOGCMs, and by a standard idealised surface freshwater flux applied in the North Atlantic. Both kinds of buoyancy flux change lead to the formation of the sea level dipole pattern, although the effect of the heat flux has a greater magnitude, and is the main cause of the spread of results among the CMIP5 models. By using passive tracers in FAMOUS to distinguish between additional and redistributed buoyancy, we show that the enhanced sea level rise north of 40°N is mainly due to the direct steric effect (the reduction of sea water density) caused by adding heat or freshwater locally. The surface buoyancy forcing also causes a weakening of the Atlantic meridional overturning circulation, and the consequent reduction of the northward ocean heat transport imposes a negative tendency on sea level rise, producing the reduced rise south of 40°N. However, unlike previous authors, we find that this indirect effect of buoyancy forcing is generally less important than the direct one, except in a narrow band along the east coast of the US, where it plays a major role and leads to sea level rise, as found by previous authors.

Boundary condition effects in the simulation study of equilibrium properties of magnetic dipolar fluids

In this paper we investigate the equilibrium properties of magnetic dipolar (ferro-) fluids and discuss finite-size effects originating from the use of different boundary conditions in computer simulations. Both periodic boundary conditions and a finite spherical box are studied. We demonstrate that periodic boundary conditions and subsequent use of Ewald sum to account for the long-range dipolar interactions lead to a much faster convergence (in terms of the number of investigated dipolar particles) of the magnetization curve and the initial susceptibility to their thermodynamic limits. Another unwanted effect of the simulations in a finite spherical box geometry is a considerable sensitivity to the container size. We further investigate the influence of the surface term in the Ewald sum-that is, due to the surrounding continuum with magnetic permeability mu(BC)-on the convergence properties of our observables and on the final results. The two different ways of evaluating the initial susceptibility, i.e., (1) by the magnetization response of the system to an applied field and (2) by the zero-field fluctuation of the mean-square dipole moment of the system, are compared in terms of speed and accuracy.

Regimes of conformational transitions of a diblock polyampholyte

The conformational properties of symmetric flexible diblock polyampholytes are investigated by scaling theory and molecular dynamics simulations. The electrostatically driven coil-globule transition of a symmetric diblock polyampholyte is found to consist of three regimes identified with increasing electrostatic interaction strength. In the first (folding) regime the electrostatic attraction causes the chain to fold through the overlap of the two blocks, while each block is slightly stretched by self-repulsion. The second (weak association or scrambled egg) regime is the classical collapse of the chain into a globule dominated by the fluctuation-induced attractions between oppositely charged sections of the chain. The structure of the formed globule can be represented as a dense packing of the charged chain sections (electrostatic attraction blobs). The third (strong association or ion binding) regime starts with direct binding of oppositely charged monomers (dipole formation), followed by a cascade of multipole formation (quadrupole, hexapole, octupole, etc.), leading to multiplets analogous to those found in ionomers. The existence of the multiplet cascade has also been confirmed in the simulations of solutions of short polymers with only one single charge (either positive or negative) in the middle of each chain. We use scaling theory to estimate the average chain size and the electrostatic correlation length as functions of the chain length, strength of electrostatic interactions, charge fraction, and solvent quality. The theoretically predicted scaling laws of these conformational properties are in very good agreement with our simulation results.