Internal Energy Transfer Research Articles

Structural and functional dynamics of tyrosine amino acid in phycocyanin of hot-spring cyanobacteria: A possible pathway for internal energy transfer

Phycocyanin (PC) is the most abundant accessory light-harvesting pigmented protein found in cyanobacteria. In the present investigation, prominent roles of tyrosine residue (Tyr) in excitation energy transfer between chromophores in PC of hot-spring cyanobacteria were studied. The expression pattern of codons suggests that Tyr was most abundant amino acids in α subunits as compared to β subunits in total aromatic amino acids. The α subunits of PC model (PDB 3O18) have one chromophore at cysteine (Cys) α-84 position (~10 Tyr) and β subunits contains two chromophores located at β-84 (~5 Tyr) and β-155 (~3 Tyr) in the cyanobacterium Thermosynechococcus vulcanus. The hydrophobic and hydrogen bond interaction was most favored between Tyr and buried amino acids near α-84 chromophore. The aromatic-aromatic interaction, aromatic-sulphur interaction, cation-pi interaction were mostly linked with Cys (α-84) as compared to β-84 and β-155. Phenylalanine (Phe) was demonstrating fewer interactions with chromophores due to nature of weak internal fluorescence. The coordinates of PC chromophore showed that internal fluorescence was very high close to Cys (α-84) residue which transmits excited photonic energy between intra-monomeric subunits Cys α84adg-Cys β84bch and inter-monomer Cys β84b-Cys β84c-Cys β84h. The lateral transmission of energy between adjacent hexamer-hexamer was feasible by Cys β155 chromophore. In contrast to total aromatic amino acids, tyrosine appeared exclusive for internal energy transfer by property of high internal fluorescence. These findings provide the illustrated role of tyrosine amino acids in rapid energy transfer mechanism inside PC which may be incorporated for making energy devices and various biotechnological sciences.

Numerical simulation of blast wave mitigation achieved by water inside a subsurface magazine model

This paper visualizes explosions in a subsurface magazine model constructed underground to mitigate the effects of blast waves. Numerical simulations discuss the effect of water that is put inside the magazine model. In the case of the explosion inside the magazine with water, the peak overpressure on the ground becomes smaller than that in the case of the explosion on the ground. The peak overpressures on the ground agree with those in the previous experiment. The increases of kinetic and internal energies of water are then estimated, and that the internal energy transfer at the interface of water and air is one of important factors to mitigate the blast wave on the ground in the present numerical method. As high-pressure gas at the exit of the magazine model drives the blast wave, the exit impulse and pressure are calculated and well reduced in the case with water inside the magazine model. Our study confirms that the exit pressure can scale the peak overpressure on the ground.

Ultraviolet fluorescence of coelenteramide and coelenteramide-containing fluorescent proteins. Experimental and theoretical study

Coelenteramide-containing fluorescent proteins are products of bioluminescent reactions of marine coelenterates. They are called ‘discharged photoproteins’. Their light-induced fluorescence spectra are variable, depending considerably on external conditions. Current work studies a dependence of light-induced fluorescence spectra of discharged photoproteins obelin, aequorin, and clytin on excitation energy. It was demonstrated that photoexcitation to the upper electron-excited states (260–300nm) of the discharged photoproteins initiates a fluorescence peak in the near UV region, in addition to the blue-green emission. To characterize the UV fluorescence, the light-induced fluorescence spectra of coelenteramide (CLM), fluorophore of the discharged photoproteins, were studied in methanol solution. Similar to photoproteins, the CLM spectra depended on photoexcitation energy; the additional peak (330nm) in the near UV region was observed in CLM fluorescence at higher excitation energy (260–300nm). Quantum chemical calculations by time depending method with B3LYP/cc-pVDZ showed that the conjugated pyrazine-phenolic fragment and benzene moiety of CLM molecule are responsible for the additional UV fluorescence peak. Quantum yields of CLM fluorescence in methanol were 0.028±0.005 at 270–340nm photoexcitation. A conclusion was made that the UV emission of CLM might contribute to the UV fluorescence of the discharged photoproteins. The study develops knowledge on internal energy transfer in biological structures – complexes of proteins with low-weight aromatic molecules.

Influence of microwave heating on the extractions of fluorine and Rare Earth elements from mixed rare earth concentrate

A novel process was proposed to treat the mixed rare earth concentrate by utilizing the microwave radiation. The influences of microwave heating on the mechanism of decomposition, microstructure of mixed rare earth concentrate, the behavior of fluorine leaching by water and the rare earth elements(REEs) leaching by hydrochloric acid were investigated. The results showed that bastnaesite and monazite were decomposed efficiently to rare earth oxide, and fluorine containing compounds were converted to fluoride after the microwave treatment. However, the bastnaesite and monazite were partly decomposed to REEs hydrate after treating with the conventional heating (convective heating). The recoveries of fluoride in the solutions of water and REEs in the solution of hydrochloric acid by leaching the concentrate treated with microwave radiation reached 67.1% and 82.5%, which were much higher than for those with conventional heating process (38.5% and 47.4% respectively). The increase in the recovery of fluorine and REEs is attributed to the phase transformation of REEs minerals due to the microwave characteristics of the rapid internal heating and energy transfer.

Internal Energy Transfer in Dynamical Behavior of Slightly Curved Shear Deformable Microplates

This paper investigates the internal energy transfer and modal interactions in the dynamical behavior of slightly curved microplates. Employing the third-order shear deformation theory, the microplate model is developed taking into account geometric nonlinearities as well as the modified couple stress theory; the initial curvature is modeled by an initial imperfection in the out-of-plane direction. The in-plane displacements and inertia are retained, and the coupled out-of-plane, rotational, and in-plane motion characteristics are analyzed. Specifically, continuous models are developed for kinetic and potential energies as well as damping and external works; these are balanced and reduced via Lagrange's equations along with an assumed-mode technique. The reduced-order model is then solved numerically by means of a continuation technique; stability analysis is performed by means of the Floquet theory. The possibility of the occurrence of modal interactions and internal energy transfers is verified via a linear analysis on different natural frequencies of the system. The nonlinear resonant response of the system is obtained for the cases with internal energy transfer, and energy transfer mechanisms are analyzed; as we shall see, the presence of an initial curvature affects the system dynamics substantially. The importance of taking into account small-size effects is also shown by discovering this fact that both the linear and nonlinear internal energy transfer mechanisms are shifted substantially if this effect is ignored.

γ-Secretase Modulators and Inhibitors Induce Different Conformational Changes of Presenilin 1 Revealed by FLIM and FRET.

Elucidation of γ-secretase structure and dynamic conformational changes is of importance to drug discovery targeting this enzyme. Electron microscopy analyses provided important structural information, but the dynamic changes of γ-secretase in cells need to be explored further. We found that PS1 internal fluorescence resonance energy transfer (FRET) probes can incorporate into γ-secretase complex and possess secretase activity. Our results from fluorescence lifetime image microscopy (FLIM) and acceptor photobleaching FRET show different PS1 internal FRET when PS1 fluorescent probes expressed alone or with other secretase subunits Aph1aL, Nicastrin, and Pen2, indicating that PS1 internal FRET could be applied for probing conformational change of γ-secretase complex. Further, we accessed whether γ-secretase activity interfering compounds induced different conformational changes of PS1. Our results show that both γ-secretase modulators and inhibitors affect PS1 internal FRET but in different manners. These results demonstrate that FLIM and acceptor photobleaching FRET could be applied to monitor different PS1 conformational changes in γ-secretase.

A11 Towards an integrated evaluation of the effects on health from smoke or toxic gas dispersion in the evacuation of subway tunnels

Background Understanding how subway tunnels perform during accidents or malicious attacks resulting in the release of smoke or hazardous toxins is key in establishing evacuation strategies that reduce the loss of life or effects on public health. During such emergency situation, the natural background air current caused by the air exchange between the station and outside, has an important influence on the dispersion of smoke and/or toxic agents. Over 60% of deaths in fires are caused either wholly or partially by inhalation of smoke or toxic gases. Thus evacuation strategies that provide routes which reduce the exposure time of individuals to a toxic environment could potentially reduce the loss of life or effects on an evacuee's health. The strategy go up and take the nearest exit to the surface might not be the best response. To support this assessment an understanding of; the air flow driving the motion of smoke, its links with internal climatology and external weather conditions and the evacuation capabilities of subway tunnels, is needed. Methods To support this exploration, 3D Computational Fluid Dynamic models have been developed, to validate field measurements and to gain an understanding of the internal airflow momentum and energy transfer capacity of subway stations in relation to external climatic factors and its effect on the dispersion of smoke and/or toxic agents. By integrating results with evacuation simulations, visual diagnostic and predictive tools which display; the background air flow within the subway, the dispersion of smoke and/or toxic substances, the resulting reduction of visibility and the evacuation of pedestrians, are in development to further our understanding in both subway climatology and integrated evacuation strategies. Results Initial results show promising links between external climatic factors, the subway climatology and the ability to predict the dispersal of smoke/toxins. It has also been established that by navigating pedestrians on routes away from smoke and/or toxic dispersion can significantly reduce the number of fatalities and effect on evacuee's health. The possibilities of integrating these findings is allowing for a more integrated assessment to be carried out. Conclusions The study discussed demonstrates that by integrating the datasets mentioned, a greater understanding of the effect subway climatology has on evacuations strategies of subway stations can be understood. It is shown that accessible technology and software, along with methodologies developed, supports the assessment and development of integrated evacuation strategies that reduce the loss of life or effects on public health. Language: en

General multi-group macroscopic modeling for thermo-chemical non-equilibrium gas mixtures.

This paper opens a new door to macroscopic modeling for thermal and chemical non-equilibrium. In a game-changing approach, we discard conventional theories and practices stemming from the separation of internal energy modes and the Landau-Teller relaxation equation. Instead, we solve the fundamental microscopic equations in their moment forms but seek only optimum representations for the microscopic state distribution function that provides converged and time accurate solutions for certain macroscopic quantities at all times. The modeling makes no ad hoc assumptions or simplifications at the microscopic level and includes all possible collisional and radiative processes; it therefore retains all non-equilibrium fluid physics. We formulate the thermal and chemical non-equilibrium macroscopic equations and rate coefficients in a coupled and unified fashion for gases undergoing completely general transitions. All collisional partners can have internal structures and can change their internal energy states after transitions. The model is based on the reconstruction of the state distribution function. The internal energy space is subdivided into multiple groups in order to better describe non-equilibrium state distributions. The logarithm of the distribution function in each group is expressed as a power series in internal energy based on the maximum entropy principle. The method of weighted residuals is applied to the microscopic equations to obtain macroscopic moment equations and rate coefficients succinctly to any order. The model's accuracy depends only on the assumed expression of the state distribution function and the number of groups used and can be self-checked for accuracy and convergence. We show that the macroscopic internal energy transfer, similar to mass and momentum transfers, occurs through nonlinear collisional processes and is not a simple relaxation process described by, e.g., the Landau-Teller equation. Unlike the classical vibrational energy relaxation model, which can only be applied to molecules, the new model is applicable to atoms, molecules, ions, and their mixtures. Numerical examples and model validations are carried out with two gas mixtures using the maximum entropy linear model: one mixture consists of nitrogen molecules undergoing internal excitation and dissociation and the other consists of nitrogen atoms undergoing internal excitation and ionization. Results show that the original hundreds to thousands of microscopic equations can be reduced to two macroscopic equations with almost perfect agreement for the total number density and total internal energy using only one or two groups. We also obtain good prediction of the microscopic state populations using 5-10 groups in the macroscopic equations.

Work transfer theory for mechanical non-equilibrium, quasi-equilibrium, and equilibrium

Work transfer is the mechanical process of energy transfer, which attracts great attention in multidisciplinary fields. A work transfer theory for mechanical non-equilibrium, quasi-equilibrium, and equilibrium is proposed as a special case of an internal energy transfer theory under a postulate that pressure, time, and displacement are independent and orthogonal variables in extended phase spaces. The statistical thermodynamic work transfer theory is applicable to providing the equation of state in various mechanical phenomena in nature, and the work fluxes are expressed as a function of pressure, time, and displacement. The theory is the unification of internal convection and external diffusion work transfer, which is a non-equilibrium generalization beyond the quasi-equilibrium theories of isobaric and isochoric processes. Two internal phase space dimensions of pressure and volume are introduced for the intensive and extensive property dimensions. The theory explicitly demonstrates diffusion, convection, internal convection, and equilibrium work fluxes. The work transfer theory is applied to investigate the mechanical mechanisms in the liquid–vapor phase transition. Three variable separation constants infer particle number constants and play the major roles in describing the distinct phase transition mechanisms. Qualitative predictions of the work transfer theory in liquid–vapor phase transition are carried out, and comparisons between quasi-equilibrium and non-equilibrium processes are discussed. In the kinetics of work transfer, the four control mechanisms of forced convection, turbulence, transient, and film work are considered. The work fluxes in the phase transition are dynamically characterized and the corresponding equations of state are predicted.

The effects of internal energy transfers on power cycle efficiency

The effects of internal energy transfers on power cycle efficiency

Internal energy transfer in dynamical behaviour of Timoshenko microarches

The internal energy transfer and modal interactions in the motion characteristics of Timoshenko microarches are investigated numerically. The length-scale parameter is introduced to the strain energy of the system and the equations of motion are obtained via Hamilton’s principle based on the modified couple stress theory; these equations are discretized into a set of nonlinear ordinary differential equations through use of the Galerkin scheme. The possibility of the occurrence of modal interactions and internal energy transfers is verified by obtaining the ratios of the linear natural frequencies of the system. The nonlinear response of the system is obtained for the cases with the modal interactions and internal energy transfer.

Light-Emission Properties and Internal Energy Transfer Phenomenon of Calcium Zirconate Phosphor Doped with Mn2+

Light-Emission Properties and Internal Energy Transfer Phenomenon of Calcium Zirconate Phosphor Doped with Mn2+

Internal energy transfer theory for thermodynamic non-equilibrium, quasi-equilibrium, and equilibrium

Abstract Internal energy transfer is one of the most principal processes in the dynamic universe, but its exact thermodynamic processes have not been completely unveiled. We here propose an internal energy transfer theory for thermodynamic non-equilibrium, quasi-equilibrium, and equilibrium as a new paradigm for internal energy transfer, based on the first and the second laws of thermodynamics. The internal generation mechanisms of heat, work, and chemical energy transfer are considered. The internal energy fluxes are obtained as functions of temperature, pressure, chemical potential, time, and displacement under a postulate that the intensive variables are independent and orthogonal in extended phase spaces. The internal energy transfer theory is applicable to exploring the internal equilibrium, internal convection, external convection, and diffusion (or conduction) transfer mechanisms of heat, work, and chemical energy. The theory is a statistical thermodynamic generalization of thermal, mechanical, and chemical energy transfer as well as the conventional convection energy transfer. Six phase spaces consist of three intensive property dimensions of temperature, pressure, and chemical potential and three extensive property dimensions of entropy, volume, and particle number. The theory is a non-equilibrium generalization beyond the quasi-equilibrium theories of isothermal, isentropic, isobaric, isochoric, migration, and diffusion processes.

Direct analysis of complex mixtures by mass spectrometry

Mixture analysis can provide information on individual components if the sample is first subjected to chromatographic separation. Two critical capabilities, soft ionization and the ability to mass-select and then dissociate ions of a particular m/z, coalesced in 1975, allowing direct analysis of complex mixtures by mass spectrometry. Chemical ionization was used as the soft ionization method and mass-analysis used the ion kinetic energy spectrometer (MIKES). Soft molecular ionization produces a set of ions that are structural surrogates of the neutral molecules; they can be mass-selected and allowed to spontaneously dissociate (i.e. as metastable ions) or fragmented upon energy transfer e.g. in the course of collision-induced dissociation (CID). The second stage of mass analysis provides information about the atomic connectivity in the precursor ion and by implication in the original molecule. This review focuses on the development of complex mixture analysis by mass spectrometry and allied topics. Discussion of the activation techniques associated with (collision-induced dissociation, surface-induced dissociation and metastable ion dissociation) emphasizes the importance of energy transfer phenomena and the internal energies distributions of ions to explain the observed mass spectra. The translational to internal energy transfer in collisions is readily accessed in the MIKES where the second stage mass analyzer is a kinetic energy/charge analyzer. Collisions in the keV range can also be used to change ion the charge state via the processes of charge exchange, electron stripping, or charge inversion. New ionization sources for analysis of non-volatile compounds that were introduced during the time period (1975–1990) of this review included secondary ion mass spectrometry, plasma desorption and field ionization and they are briefly discussed. Several types of scans were developed to rapidly access information of the individual components, including chemically specific scans (e.g. neutral loss scans of mass 30 for nitro compounds).

Thermal self-action effects of acoustic beam in a vibrationally relaxing gas

Thermal self-action of acoustic beam in a molecular gas with excited internal degrees of molecules’ freedom, is studied. This kind of thermal self-action differs from that in a Newtonian fluid. Heating or cooling of a medium takes place due to transfer of internal vibrational energy. Equilibrium and non-equilibrium gases, which may be acoustically active, are considered. A beam in an acoustically active gas is self-focusing unlike a beam in a standard viscous gas. The self-action effects relating to wave beams containing shock fronts, are discussed. Stationary and non-stationary kinds of self-action are considered.

Modeling of Nitrogen Monoxide Formation and Radiation in Nonequilibrium Hypersonic Flows

The interaction between nitrogen vibrational-translational relaxation with different chemistry models in a hypersonic shock is studied. The vibrational-translational transition models considered include the Larsen–Borgnakke, Schwartz-Slawsky-Herzfeld, and forced harmonic oscillator models; and the nitrogen monoxide formation reaction was studied using the total collision energy chemistry model and reaction cross sections obtained from quasi-classical trajectory simulations. Using direct simulation Monte Carlo solutions that incorporate these models, improved nitrogen monoxide spectral radiation modeling was performed by employing quenching rates from recent experiments. Comparisons of electronic state populations and the corresponding radiative spectra for the different vibrational-translational and chemistry models are presented, and it is shown that the vibronic spectral structure of the nitrogen monoxide radiation could provide a way to test the fidelity of the internal energy transfer and chemistry models.

Nonadiabatic Excited-State Molecular Dynamics: Modeling Photophysics in Organic Conjugated Materials

To design functional photoactive materials for a variety of technological applications, researchers need to understand their electronic properties in detail and have ways to control their photoinduced pathways. When excited by photons of light, organic conjugated materials (OCMs) show dynamics that are often characterized by large nonadiabatic (NA) couplings between multiple excited states through a breakdown of the Born-Oppenheimer (BO) approximation. Following photoexcitation, various nonradiative intraband relaxation pathways can lead to a number of complex processes. Therefore, computational simulation of nonadiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons. Over the years, we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework that efficiently and accurately describes photoinduced phenomena in extended conjugated molecular systems. We use the fewest-switches surface hopping (FSSH) algorithm to treat quantum transitions among multiple adiabatic excited state potential energy surfaces (PESs). Extended molecular systems often contain hundreds of atoms and involve large densities of excited states that participate in the photoinduced dynamics. We can achieve an accurate description of the multiple excited states using the configuration interaction single (CIS) formalism with a semiempirical model Hamiltonian. Analytical techniques allow the trajectory to be propagated "on the fly" using the complete set of NA coupling terms and remove computational bottlenecks in the evaluation of excited-state gradients and NA couplings. Furthermore, the use of state-specific gradients for propagation of nuclei on the native excited-state PES eliminates the need for simplifications such as the classical path approximation (CPA), which only uses ground-state gradients. Thus, the NA-ESMD methodology offers a computationally tractable route for simulating hundreds of atoms on ~10 ps time scales where multiple coupled excited states are involved. In this Account, we review recent developments in the NA-ESMD modeling of photoinduced dynamics in extended conjugated molecules involving multiple coupled electronic states. We have successfully applied the outlined NA-ESMD framework to study ultrafast conformational planarization in polyfluorenes where the rate of torsional relaxation can be controlled based on the initial excitation. With the addition of the state reassignment algorithm to identify instances of unavoided crossings between noninteracting PESs, NA-ESMD can now be used to study systems in which these so-called trivial unavoided crossings are expected to predominate. We employ this technique to analyze the energy transfer between poly(phenylene vinylene) (PPV) segments where conformational fluctuations give rise to numerous instances of unavoided crossings leading to multiple pathways and complex energy transfer dynamics that cannot be described using a simple Förster model. In addition, we have investigated the mechanism of ultrafast unidirectional energy transfer in dendrimers composed of poly(phenylene ethynylene) (PPE) chromophores and have demonstrated that differential nuclear motion favors downhill energy transfer in dendrimers. The use of native excited-state gradients allows us to observe this feature.

Two-dimensional simulation of fast gas heating in an atmospheric pressure streamer discharge and humidity effects

Gas heating in an atmospheric-pressure streamer discharge was analysed by a two-dimensional streamer discharge simulation model describing internal molecular energy transfer. Our two-dimensional streamer simulation model incorporates concepts from the fast gas heating mechanism proposed by Popov (2011 J. Phys. D: Appl. Phys. 44 285201) and our self-developed state-to-state vibrational kinetics. In dry air, gas heating occurs mainly from electron-impact dissociation reactions of O2 molecules and from quenching processes of electronically excited N2(B 3Πg, C 3Πu) molecules and O(1D) atoms. In humid air, rapid vibration-to-translation transitions of H2O and the exothermicity of the OH formation reactions additionally increase the gas temperature. It is shown that gas heating during the discharge pulse increases with humidity.

A full-dimensional quantum dynamical study of H2+H2 collisions: Coupled-states versus close-coupling formulation

Collision-induced energy transfer involving H2 molecules plays an important role in many areas of physics. Kinetic models often require a complete set of state-to-state rate coefficients for H2+H2 collisions in order to interpret results from spectroscopic observations or to make quantitative predictions. Recent progress in full-dimensional quantum dynamics using the numerically exact close-coupling (CC) formulation has provided good agreement with existing experimental data for low-lying states of H2 and increased the number of state-to-state cross sections that may be reliably determined over a broad range of energies. Nevertheless, there exist many possible initial states (e.g., states with high rotational excitation) that still remain elusive from a computational standpoint even at relatively low collision energies. In these cases, the coupled-states (CS) approximation offers an alternative full-dimensional formulation. We assess the accuracy of the CS approximation for H2+H2 collisions by comparison with benchmark results obtained using the CC formulation. The results are used to provide insight into the orientation effects of the various internal energy transfer mechanisms. A statistical CS approximation is also investigated and cross sections are reported for transitions which would otherwise be impractical to compute.

Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows

A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.