Mean Potential Energy Research Articles

The Nature of Piezoelectricity of Ferroelectric SbSI Crystal

The contribution of Sb atoms soft mode to the temperature dependences of the piezoelectric modulus e(T) and atomic equilibrium position's difference Δz(T) has been studied theoretically, when SbSI crystal is deformed along crystallographic x(a), y(b) and z(c)—axes. The largest change of e(T) occurs in the ferrophase near the phase transition (when T ≈ TC ). At T < TC , the e(T) changes become slow. It has been found that value and anomalous temperature dependence of e(T) and Δz(T) is influenced by the change of mean potential energy of Sb atoms in soft mode due to its interaction with phonons.

A general circulation model ensemble study of the atmospheric circulation of Venus

The response of three numerical model dynamical cores to Venus‐like forcing and friction is described in this paper. Each dynamical core simulates a super‐rotating atmospheric circulation with equatorial winds of 35 ± 10 m/s, maintained by horizontally propagating eddies leaving the equatorial region and inducing a momentum convergence there. We discuss the balance between the mean circulation and eddies with reference to the production of a super‐rotating equatorial flow. The balance between the horizontal eddies and vertical eddies in the polar region is discussed and shown to produce an indirect overturning circulation above the jet. The indirect overturning may be related to the observed region of the polar dipole in the Venus atmosphere. Reservoirs of energy and momentum are calculated for each dynamical core and explicit sources and sinks are diagnosed from the general circulation model (GCM). The effect of a strong “sponge layer” damping to rest is compared with eddy damping and found to change significantly the momentum balance within the top “sponge layer” but does not significantly affect the super‐rotation of the bulk of the atmosphere. The Lorenz (1955) energy cycle is calculated and the circulation is shown to be dominated by energy conversion between the mean potential energy and mean kinetic energy reservoirs, with barotropic energy conversion between the mean kinetic energy and eddy kinetic energy reservoirs. We suggest modifications to the GCM parameterizations on the basis of our analysis of the atmospheric circulation and discuss the effect of numerical parameterizations on the simulated atmosphere.

Computer Simulation of Chiral Nanoporous Networks on Solid Surfaces

A lattice Monte Carlo (MC) model was proposed with the aim of understanding the factors affecting the chiral self-assembly of tripod-shaped molecules in two dimensions. To that end a system of flat symmetric molecules adsorbed on a triangular lattice was simulated by using the canonical ensemble method. Special attention was paid to the influence of size and composition of the building block on the morphology of the adsorbed overlayer. The obtained results demonstrated a spontaneous self-assembly into extended chiral networks with hexagonal cavities, highlighting the ability of the model to reproduce basic structural features of the corresponding experimental systems. The simulated assemblies were analyzed with respect to their structural and energetic properties resulting in quantitative estimates of the unit cell parameters and mean potential energy of the adsorbed layer. The predictive potential of the model was additionally illustrated by comparison of the obtained superstructures with the recent STM images that have been recorded for different organic tripod-shaped molecules adsorbed at the liquid/pyrolytic graphite interface.

Balancing Simulation Accuracy and Efficiency with the Amber United Atom Force Field

We have analyzed the quality of a recently proposed Amber united-atom model and its overall efficiency in ab initio folding and thermodynamic sampling of two stable beta-hairpins. It is found that the mean backbone structures are quite consistent between the simulations in the united-atom and its corresponding all-atom models in Amber. More importantly, the simulated beta turns are also consistent between the two models. Finally, the chemical shifts on H alpha are highly consistent between simulations in the two models, although the simulated chemical shifts are lower than experiment, indicating less structured peptides, probably due to the omission of the hydrophobic term in the simulations. More interestingly, the stabilities of both beta-hairpins at room temperature are similar to those derived from the NMR measurement, whether the united-atom or the all-atom model is used. Detailed analysis shows high percentages of backbone torsion angles within the beta region and high percentages of native contacts. Given the reasonable quality of the united-atom model with respect to experimental data, we have further studied the simulation efficiency of the united-atom model over the all-atom model. Our data shows that the united-atom model is a factor of 6-8 faster than the all-atom model as measured with the ab initio first pass folding time for the two tested beta-hairpins. Detailed structural analysis shows that all ab initio folded trajectories enter the native basin, whether the united-atom model or the all-atom model is used. Finally, we have also studied the simulation efficiency of the united-atom model as measured in terms of how fast thermodynamic convergence can be achieved. It is apparent that the united-atom simulations reach convergence faster than the all-atom simulations with respect to both mean potential energies and mean native contacts. These findings show that the efficiency of the united-atom model is clearly beyond the per-step dynamics simulation of about 2 over the all-atom model. Thus, reasonable reduction of a protein model can be achieved with improved sampling efficiency while still preserving a high level of accuracy for applications in both ab initio folding and thermodynamic sampling. This study motivates us to develop more simplified protein models with sufficient consistency with the all-atom models for enhanced conformational sampling.

Aqueous Solution of [bmim][PF6]: Ion and Solvent Effects on Structure and Dynamics

A dilute aqueous solution of the salt 1-n-butyl,3-methylimidazolium hexafluorophosphate ([bmim][PF(6)]) has been studied using molecular dynamics simulations to investigate the effect of ions on water and vice versa. The anion is found to diffuse faster than the cation in the solution, in contrast to observations in the pure ionic liquid. Distributions of pair energies have been employed to identify ion association, and around 13% of the ions were found to exist as pairs. The mean potential energy of water molecules present in the coordination shell of an anion is less than that of water molecules coordinated to a cation. The former kind also exhibit two distinct orientational preferences with respect to the anion. The larger diffusion coefficient of the anion is related to the faster dynamics of water molecules in its hydration layer, as evidenced from the relaxation of their residence time correlation function.

Vertical dispersion by stratified turbulence

We derive a relation for the growth of the mean square of vertical displacements, δz, of fluid particles of stratified turbulence. In the case of freely decaying turbulence, we find that for large times 〈δz2〉 goes to a constant value 2(EP(0) +aE(0))/N2, whereEP(0) andE(0) are the initial mean potential and total turbulent energy per unit mass, respectively,a&lt; 1 andNis the Brunt–Väisälä frequency. In the case of stationary turbulence, we find that 〈δz2〉 = 〈δb2〉/N2+ 2εPt/N2, where εPis the mean dissipation of turbulent potential energy per unit mass and 〈δb2〉 is the Lagrangian structure function of normalized buoyancy fluctuations. The first term is the same as that obtained in the case of adiabatic fluid particle dispersion. This term goes to the finite limit 4EP/N2ast→ ∞. Assuming that the second term represents irreversible mixing, we show that the Osborn &amp; Cox model for vertical diffusion is retained. In the case where the motion is dominated by a turbulent cascade with an eddy turnover timeT≫N−1, rather than linear gravity waves, we suggest that there is a range of time scales,t, betweenN−1andT, where 〈δb2〉 = 2πCPLεPt, whereCPLis a constant of the order of unity. This means that for such motion the ratio between the adiabatic and the diabatic mean-square displacement is universal and equal to πCPLin this range. Comparing this result with observations, we make the estimateCPL≈ 3.

Global gravity wave activity in the tropopause region from CHAMP radio occultation data

We discuss the global gravity wave (GW) activity expressed by the specific potential energy in the altitude range from 5 km below to 10 km above the tropopause, derived from GPS radio occultation data from CHAMP (2001–2008). The GW analysis is based on vertical detrending of the individual measured temperature profiles by applying a Gaussian filter in two different ways: (i) filtering of the complete temperature profiles and (ii) separate filtering of the profiles for the tropospheric and lower stratospheric parts. The separate filtering method significantly reduces the usually observed wave activity enhancement in the tropopause region which highly depends on the performance of the complete filtering method to reproduce the change in the temperature gradient at the tropopause. We only consider vertical wavelengths less than 10 km. The global mean potential energy in the tropopause region deduced with these different background temperatures will be analyzed, differences will be emphasized and possible error sources of the new method will be considered.

Delayed baroclinic response of the Antarctic circumpolar current to surface wind stress

The Antarctic Circumpolar Current (ACC) responds to the surface windstress via two processes, i.e., the instant barotropic process and the delayed baroclinic process. This study focuses on the baroclinic instability mechanism in ACC, which was less reported in the literatures. Results show that the strengthening of surface zonal windstress causes the enhanced tilting of the isopycnal surface, leading to more intense baroclinic instability. Simultaneously, the mesoscale eddies resulting from the baroclinic instability facilitate the transformation of mean potential energy to eddy energy, which causes the remarkable decrease of the ACC volume transport with the 2-year lag time. This delayed negative correlation between the ACC transport and the zonal windstress may account for the steadiness of the ACC transport during last two decades.

Os processos de conversão de energia nos oceanos: uma revisão do Diagrama de Lorenz

A análise energética é uma importante ferramenta diagnóstica para a identificação de processos dinâmicos associados a eventos de conversão de energia no oceano. Esta análise, de uma forma sucinta, procura mostrar as interações energéticas que ocorrem entre os campos médio e turbulento de um determinado escoamento geofísico, bem como as transferências entre os reservatórios de energia nos oceanos. Estes processos são sumarizados pelo Diagrama de Lorenz que representa, através de quatro caixas, os reservatórios das energias cinética média, cinética turbulenta, potencial média e potencial turbulenta do escoamento do fluido geofísico, identificando as interações que ocorrem entre estas quatro formas de energia, bem como as trocas com o meio externo (fontes e sumidouros). Notadamente a literatura especializada é escassa em textos que detalhem os diversos mecanismos de conversão energética entre as principais formas de energia nos oceanos, havendo algumas publicações que, dependendo da abordagem, detalham apenas alguns deles. Este trabalho apresenta uma revisão sobre o assunto, reunindo informações de diversas fontes e tendo como objetivo principal a construção, passo a passo, do Diagrama de Lorenz, com suas respectivas formulações. A discussão de cada termo do Diagrama é apresentada objetivamente, o que possibilitará um melhor entendimento desta ferramenta, a qual é de real importância para a sumarização de uma estimativa energética para uma dada região do oceano.

Enhanced mixing downstream of a pile in an estuarine flow

We studied the impact on stratification and mixing of a bridge pile in a stratified shear flow at the Western Bridge of the Great Belt Fixed Link, Denmark, in January and April 2006. Stratification was measured with high horizontal resolution by towed CTD chains and dissipation of turbulent kinetic energy was measured by a free-falling MSS 90 microstructure profiler equipped with shear probes. Background stratification and current were measured by standard CTD and a bottom-mounted ADCP, respectively. The spatial and temporal variability of the flow field close behind a single pile was measured by an ADCP mounted on a small catamaran tethered to this pile. A shear background flow of varying strength was observed with an inflow of up to 80 cm s − 1 in the surface layer and an outflow of 10 cm s − 1 in the bottom layer. The brackish surface layer was separated from the saline Kattegat water in the bottom layer by an intermediate layer resulting in a Brunt–Väisälä frequency of up to 100 cycles per hour (cph). The maximum Reynolds number ( Re) and internal Froude number ( Fr) were 4.6 × 10 6 and 1.3, respectively. Eddies occurred downstream of a pile with a characteristic diameter of the pile and a frequency corresponding to a von Kármán vortex street when near-surface Fr > 0.7. Enhanced mixing was observed in the von Kármán vortex streets, which caused an increase in salinity by a few psu in the surface mixed layer of the eddy up to 400 m downstream of the piles. Differential advection by cross-channel circulation smeared out laterally from the wakes' salinity anomalies and turbulence. The dissipation of turbulent kinetic energy in the intermediate layer increased by an order of magnitude downstream of the piles as a function of Fr when Fr > 0.7. This enhanced mixing reduced the mean potential energy anomaly downstream by some 10 Jm − 3 in the upper 15 m depth and caused an upstream-directed baroclinic pressure gradient of the same order as the barotropic pressure gradient, which forced reversed flow in the bottom layer.

Lorenz energy cycle of the global atmosphere based on reanalysis datasets

The mean state of the global atmospheric energy cycle is re‐examined using the two reanalysis datasets — NCEP2 and ERA40 (1979–2001). The general consistency between the two datasets suggests that the present estimates of the energy cycle are probably the most reliable ones. The comparison between the present and a previous study shows noticeable discrepancies in some of the energy components and conversion rates. The current estimate of the transformations from mean potential energy to mean kinetic energy C(PM, KM) further suggests that the near‐surface processes play an important role in the conversion rate C(PM, KM), along with the Ferrel cell and Hadley cells, which probably change the direction of the conversion rate C(PM, KM).

Atomic dynamics in different regions of the potential energy surface

The atomic dynamics in two (bulk) metallic glasses, Ni40Pd40P20 and Zr55Cu30Al10Ni5, were investigated by neutron inelastic scattering in different regions of the potential energy landscape, which are reached by slow cooling the bulk glasses and by hyper-quenching the same alloys. The results prove that the atomic dynamics depends also on the fictive temperature, i.e. the region of the potential energy surface, in which the glass is frozen in. Obviously the shapes of the basins or inherent structures are not the same everywhere on the potential energy surface, and the glass with a higher fictive temperature has more low energy modes than has the same glass with a lower fictive temperature. As results from computer simulation have suggested already, on moving to regions of lower mean potential energy (aging), part of theses low energy modes are transferred to the energy region of the calculated Debye cut-off energy. The difference between the vibrational entropies, calculated from the generalized vibrational density-of-states, which have been determined for both fictive temperatures, shows that the contribution from the vibrational entropy to the total entropy change, when moving through the potential energy landscape, is small for the two metallic glasses investigated. Structural relaxation of the hyper-quenched glass removes part of the additional low energy modes, but quantitatively possibly only at the low and perhaps also at the high-energy limit of the density-of-states. The wavelength dependence of the dynamics suggests that the additional low energy modes in the glass with the higher fictive temperature are not dominated by extended but more likely by localized modes.

Investigation of a new mean temperature-dependent potential energy function for methane and its use for the prediction of transport properties

In this work an improved mean potential energy function for the interaction of an isolated pair of methane is obtained, from which the non-equilibrium properties of methane at zero pressure limit are calculated, accurately. The potential energy function of 21 different fixed orientations of (CH4)2 dimer has been obtained via the coupled cluster method. In order to obtain a mean potential energy function, the Boltzmann-average of the obtained potentials of the selected fixed orientations has been used. Unlike the full potential energy surface with the angle-dependent, the parameters of the mean potential are found to be temperature-dependent. The mean potential energy function is fitted well by an analytical expression at different temperatures. The mean absolute percentage deviation of analytical expression compare to the calculated value is about 0.6%. In studying a system with a great number of configurations, calculation of the potential energy function for all configurations is an impossible task; in the proposed model, 21 important fixed orientations have been selected. Introduction of a new approach for calculating the potential energy in methane and investigation of the temperature dependence of mean potential energy are the most important claims of this work. The mean potential function is used to calculate the viscosity, self-diffusion coefficient, and thermal conductivity at the zero pressure limit. The mean absolute percentage deviation in the calculated viscosity, self-diffusion coefficient and thermal conductivity is 3.1, 2.4, and 5.3%, respectively. Also, the second virial coefficient has been calculated for some temperatures.

Fluid-structure interaction in atomic force microscope cantilever dynamics and thermal response

This paper discusses the effects of fluid loading on structures at low Reynolds numbers, a regime commonly found in the case of atomic force microscope cantilevers. In order to provide insight to the problem, the effect of fluid loading is analyzed from a feedback/systems approach, a perspective that considers the response of the fluid loaded system using the open-loop characteristics of the in vacuo cantilever and hydrodyamic effects. Increased mass ratio is shown to increase the bandwidth of the fluid-structure feedback loop with corresponding decrease in system quality for high fluid loading. The nondimensional natural frequency plays the role of a Reynolds number and determines the phase margin of the system. An analysis of the frequency response of the fluid loaded system, using the fluctuation-dissipation theorem, shows the fluctuating force is not spectrally white, but is related to the imaginary part of the hydrodynamic function. The mean potential energy of the cantilever is shown to be 12kBT, however, the kinetic energy is shown to be less than this value, decreasing with increasing fluid loading.

Ondas de gravidade na estratosfera terrestre inferida através da técnica de rádio ocultação de GPS

Perfis de temperatura obtidos pelo satélite CHAMP nos anos de 2001 a 2005 foram utilizados para determinar a atividade de ondas de gravidade na região da baixa estratosfera sobre a América do Sul. Os resultados encontrados para a energia potencial integrada, entre 24 e 34 km de altitude, mostraram uma variação interanual na atividade de ondas de gravidade, com uma maior atividade de ondas em torno da região equatorial. Para melhor avaliar a variação da atividade de ondas de gravidade, foi determinada a energia potencial média integrada entre (10ºN-10ºS) e (100ºO- 20ºO). Os resultados da energia potencial média mostraram uma variação sazonal da atividade de ondas de gravidade. O inverno foi a estação do ano com a menor atividade de ondas, enquanto que a primavera apresentou um aumento na atividade de ondas. A atividade de ondas de gravidade na baixa estratosfera, inferida através da energia potencial média, apresenta claramente um aumento nos anos de 2002 e 2004 e uma diminuição nos anos de 2003 e 2005.

A global analysis of wave potential energy in the lower stratosphere derived from 5 years of GPS radio occultation data with CHAMP

This paper presents the first results of the global long‐term potential energy and mean potential energy per unit mass associated to wave activity (WA) in the lower and middle stratosphere, obtained from Global Positioning System radio occultation (GPS‐RO) temperature profiles, retrieved during the last 5 years from the CHAMP (CHAllenging Minisatellite Payload) satellite. We excluded temperature variations corresponding to the wavelike character of the Quasi Biennial oscillation (QBO). Possible limitations and distortions expected from our analysis are pointed out. Systematic annual and interannual features, clearly evidenced through 5 years of observations as a function of height, latitude and time are shown. We confirm some previously reported characteristics, in particular interannual requiring a sufficiently long period of observation, in addition to others not reported yet. In particular, a general stronger (weaker) wave activity is observed associated to apparent vertical wavelengths longer (shorter) than 4 km. The tropical/extratropical signatures decrease/increase with increasing altitude. At equatorial latitudes, WA interannual enhancements, related to QBO, are observed just below zonal wind zero contours corresponding to westerly shears. A significant decrease of WA is seen where the zonal wind is minimum. Both at equatorial and middle latitudes, an increased WA appears close above the TP, following its annual height oscillation and above 30 km height. At higher latitudes, a systematic annual variation of WA is observed, exhibiting stronger enhancements in winter SH respect to NH, but in SH, taking place during late winter and early spring. This enhanced WA, associated during 2002 to the stratospheric warming observed in that year, appears here as a systematic annual stratospheric feature. Its intensity increases with altitude, from 25 to 35 km. Inertio‐gravity waves generated by geostrophic adjustment during the maximum of the southern polar vortex (polar night jet) between late August and mid‐ September, could constitute a main source of this WA enhancement.

A Cascade-Type Global Energy Conversion Diagram Based on Wave–Mean Flow Interactions

A cascade-type energy conversion diagram is proposed for the purpose of diagnosing the atmospheric general circulation based on wave–mean flow interactions. Mass-weighted isentropic zonal means facilitate the expression of nongeostrophic wave effects, conservation properties, and lower boundary conditions. To gain physical insights into energetics based on the nonacceleration theorem, the wave energy W is defined as the sum of the eddy available potential energy PE and the eddy kinetic energy KE. The mainstream of the energy cascade is as follows: The diabatic heating produces the zonal mean available potential energy PZ, which is converted into the zonal mean kinetic energy KZ through the mean meridional circulation. The KZ is mainly converted to W through zonal wave–mean flow interactions and the rest is dissipated through friction. Not only the dynamical conversion but also the diabatic heating generates W, which is dissipated through friction. A diagnosis package is designed to analyze actual atmospheric data on the standard pressure surfaces. A validation study of the package is made by using the output from a general circulation model. The scheme accurately expresses tendencies of the zonal mean and eddy available potential energy equations, showing the diagnosis capability. On shorter time scales, PE changes in accordance with KE, good correlation indicating the relevance of the definition of wave energy. A preliminary study is made of the climate in December–February (DJF), and June–August (JJA), using the NCEP–NCAR reanalysis. The dynamical wave energy generation rate C(KZ, W) is about 60% of the conversion rate C(PZ, KZ), which means that KZ is dissipated through friction at a rate of about 40%. In the extratropics, C(KZ, W) is almost equal to C(PZ, KZ), as is expected from quasigeostrophic balance. In the subtropics, however, C(KZ, W) is much smaller than C(PZ, KZ), which suggests the importance of nongeostrophic effects on the energetics. The energetics is substantially different between the two solstices. Both C(PZ, KZ) and C(KZ, W) are about 30% larger in DJF than those in JJA, reflecting differences in wave activity. Stationary waves contribute considerably to energy conversions in the Northern Hemispheric winter, while baroclinic instability waves do more in the Southern Hemispheric winter than in the Northern Hemispheric winter.

새만금해역에서 밀도성층의 계절 변동

Seasonal and tidal variations of density stratification in the Saemangeum waters are investigated based on synoptic CTD observations between July 2003 and September 2005. CTD data used in this study are those obtained after closing the dike No. 4 and before closing the two final gaps, the Sinsi and the Garyeok, on the Saemangeum tidal harrier. A total of 19 field campaigns comprehend a wide temporal spectrum, that is, few seasons, spring and neap tides, and high and low waters. In addition, ADCPs were anchored and CTDs were cast at three stations for 25 h in July 2005. Water columns are vertically homogeneous in autumn and winter. The vertical homogeneity persists in spring but with an occasional weak stratification in i:he northern part of the Gogunsan Islands. Increased reshwater runoff tends to stabilize the water columns and strong density stratification is established in summer. The mean potential energy anomaly (PEA) in summer used as a stratification parameter is the largest <TEX>$(27.7\;J\;m^{-3})$</TEX> in the northern part of the Gogunsan Islands where the Geum River discharge dominates, the smallest <TEX>$(16.9\;J\;m^{-3})$</TEX> is in the inner area of the barrier, in between the two <TEX>$(21.6\;J\;m^{-3})$</TEX> in the southern part of the Gogunsan Islands. Whereas the stratification is generally strengthened in summer, strong winds or large tidal currents over the shallow depths frequently destratify the water column near the mouth of river runoff inside the tidal barrier. Periodic stratification, the development of stratification on the ebb and its breakdown on the flood, occurs in the mid-area inside the barrier induced by the tidal straining, which can also be found in the results of 25 h observation.

Allosteric Disulfide Bonds

Disulfide bonds have been generally considered to be either structural or catalytic. Structural bonds stabilize a protein, while catalytic bonds mediate thiol-disulfide interchange reactions in substrate proteins. There is emerging evidence for a third type of disulfide bond that can control protein function by triggering a conformational change when it breaks and/or forms. These bonds can be thought of as allosteric disulfides. To better define the properties of allosteric disulfides, we have analyzed the geometry and dihedral strain of 6874 unique disulfide bonds in 2776 X-ray structures. A total of 20 types of disulfide bonds were identified in the dataset based on the sign of the five chi angles that make up the bond. The known allosteric disulfides were all contained in 1 of the 20 groups, the -RHStaple bonds. This bond group has a high mean potential energy and narrow energy distribution, which is consistent with a functional role. We suggest that the -RHStaple configuration is a hallmark of allosteric disulfides. About 1 in 15 of all structurally determined disulfides is a potential allosteric bond.

Low-frequency dynamical heterogeneity in simulated amorphousNi0.5Zr0.5below its glass temperature: Correlations with cage volume and local order fluctuations

From molecular dynamics simulations results are reported concerning correlations between low-frequency (lf) heterogeneous dynamics in simulated Ni0.5Zr0.5 melts at 700, 760, and 810 K, which means around the Kauzmann temperature of the model, TK approximately 750 K. A method is presented to separate lf dynamics, reflecting the slow relaxation dynamics in the vitrifying melt, and high-frequency (hf) dynamics, characteristic of the thermal fluctuations at the considered temperatures. By means of a suitable quantitative measure of the distribution of heterogeneous lf dynamics in space and time, correlation parameters are evaluated between the spatial distribution of lf dynamics and structural inhomogeneities in the thermodynamically homogeneous melt. Relevant correlations are found between lf dynamics and some involved structure quantities such as the cage volume around Ni atoms, Omega Ni, or the Theta Ni parameter which reflects the geometry of the nearest-neighbor cage around Ni atoms. Further, at 810 K there is a weak correlation between heterogeneous dynamics and fluctuations of the mean potential energy per atom and a comparable weak anticorrelation with the particle density and Ni-atom density inhomogeneities, where these three correlations decrease with decreasing temperature. The present results indicate the existence of long-living regions of enhanced Omega Ni in the structure, which may act as regions of preferential initiation of irreversible lf dynamics and slow relaxation.