Mechanism Of Energy Transformation Research Articles

Structural basis underlying the electron transfer features of a blue copper protein auracyanin from the photosynthetic bacterium Roseiflexus castenholzii.

Auracyanin (Ac) is a blue copper protein that mediates the electron transfer between Alternative Complex III (ACIII) and downstream electron acceptors in both fort chains of filamentous anoxygenic phototrophs. Here, we extracted and purified the air-oxidized RfxAc from the photoheterotrophically grown Roseiflexus castenholzii, and we illustrated the structural basis underlying its electron transferring features. Spectroscopic and enzymatic analyses demonstrated the reduction of air-oxidized RfxAc by the ACIII upon oxidation of menaquinol-4 and menaquinol-7. Crystal structures of the air-oxidized and Na-dithionite-reduced RfxAc at 2.2 and 2.0Å resolutions, respectively, showed that the copper ions are coordinated by His77, His146, Cys141, and Met151 in minor different geometries. The Cu1-Sδ bond length increase of Met151, and the electron density Fourier differences at Cu1 and His77 demonstrated their essential roles in the dithionite-induced reduction. Structural comparisons further revealed that the RfxAc contains a Chloroflexus aurantiacus Ac-A-like copper binding pocket and a hydrophobic patch surrounding the exposed edge of His146 imidazole, as well as an Ac-B-like Ser- and Thr-rich polar patch located at a different site on the surface. These spectroscopic and structural features allow RfxAc to mediate electron transfers between the ACIII and redox partners different from those of Ac-A and Ac-B. These results provide a structural basis for further investigating the electron transfer and energy transformation mechanism of bacterial photosynthesis, and the diversity and evolution of electron transport chains.

Stereoselective aziridination of imines via ammonium ylides: A molecular electron density theory study

AbstractThe highly trans‐stereoselective reaction of ammonium salt (AS 2) toward (E)‐N‐benzylidene‐4‐methylbenzenesulfonamide (IM 4) in the presence of Na2CO3 leading to an aziridine derivative, trans‐Az 6, was theoretically studied using Molecular Electron Density Theory (MEDT) at the B3LYP/6‐31G(d) computational level to probe energy transformation, selectivities, and molecular mechanism. The reaction starts by a nucleophilic substitution reaction between 1,4‐diazabicyclo [2.2.2]octane (DABCO) and phenacyl bromide (PB) to form AS 2 which undergoes a proton abstraction by Na2CO3 to produce Ammonium Ylide (AY 3). Subsequently, nucleophilic addition of AY 3 to the double bond in IM 4 leads to form a betaine‐like intermediate, namely, IN‐Ta which named IN‐Ta. Finally, trans‐Az 6 is produced as a result of the nucleophilic attack of the negatively charged nitrogen atom on the carbon atom bearing DABCO in IN‐Ta. Analysis of the relative Gibbs free energies shows that the ring closure step is the rate‐determining step (RDS). By an investigation of the conceptual density functional theory, CDFT reactivity indices AY 3 and IM 4 are classified as a strong nucleophilic molecular system and as a strong electrophilic molecular system, respectively, which implies that the addition step of AY 3 to IM 4 has a high polar character. An analysis of the calculated electrophilic and nucleophilic Parr functions at the reactive sites of reagents clarifies the regioselectivity observed experimentally within the C1–C2 bond creation process.

The mechanisms of energy transformation in sharp open-channel bends: Analysis based on experiments in a laboratory flume

In sharp open-channel bends, there exists nonlinear interactions between streamwise and cross-stream velocities, which leads to the adjustment of flow energy transport, increases the energy dissipation and eventually influences the development of river bends. However, previous studies have not yet fully understood the mechanisms underlying the transport and dissipation of energy in open-channel bends. In addition, energy dissipation is directly related to the evolution of enstrophy Ω·Ω/2. However, it has not yet received much attention in the study of the resistance in meandering rivers. To gain an insight into these mechanisms, with the aid of detailed experimental data collected in a sharp open-channel bend, this study quantified the impacts of the key terms in the kinetic energy equation and the enstrophy equation. Results show that the term related to the transport of kinetic energy by cross-stream circulation is at least an order of magnitude larger than the other terms in the kinetic energy equation, which contributes significantly to the redistribution of kinetic energy over the cross section. The term related to the production of turbulent kinetic energy in the kinetic energy equation shows the smallest order of magnitude and thus is almost negligible for the time-averaged flow field. Furthermore, over most of the measured area, the term related to the centrifugal force shows values of at least an order of magnitude larger than the other terms in the enstrophy equation, which means that this term exerts the dominant influence on the energy dissipation. The results also revealed that the transformation process is insensitive to the variations in Froude number. These results are expected to improve the understanding of the complete process of energy transformation, especially the resistance caused by secondary flow in meandering rivers.

Reflections about elementary tribosystem

Friction as a transformational, energy process operates with the concept of a tribosystem. What is a tribosystem? The energy transformation is directly carried out by the friction contact itself. The original reflections on the elementary tribosystem – an object in which there is an implementation of the principle of energy balance are considered. The principle of compliance with the energy balance quantitatively characterizes the friction system. The main mechanism of energy transformation in friction is the mechanism of elastic-plastic deformation. The existence of a critical volume of friction distinguishing the deformation under friction from the traditional volume deformation is indicated. The structural-energy model of energy transformation at the friction is given. The structural-energy diagram of the evolution of friction surfaces is shown, where two main stages of the formation and functioning of the elementary tribosystem are indicated.

Ultrasonic vibration-assisted metal forming: Constitutive modelling of acoustoplasticity and applications

This paper presents a new physics-based constitutive model to accurately describe the deformation behaviour of metals during ultrasonic vibration assisted (UVA) forming. Dislocation dynamics and acoustic energy transformation mechanisms in materials under ultrasonic vibration were considered in the modelling. A user defined subroutine was also developed for modelling the UVA forming processes using the finite element method. To assess the proposed model, upsetting forming, press forming, and incremental forming were simulated separately, and the predicted results were compared with their corresponding experiments. It was found that the application of the ultrasonic vibration can significantly decrease the material flow stress, making the material softer in forming. A large vibration amplitude results in a large reduction in flow stress. Relevant experimental measurements showed that the model has captured the material behaviour and the major mechanics in UVA forming. Different forming processes, due to their difference in tool-workpiece contact condition, would have different acoustic energy and stress transformation efficiency.

(High Temperature Materials Division Outstanding Achievement Award) Recent Advances in Intermediate-Temperature Fuel Cells: Surface Modification and In Situ/Operando Characterization

The performances of electrochemical systems are often limited by the charge and mass transfer along surfaces and across interfaces. Fundamental understanding of these electrochemical processes, especially the rate-limiting steps, is vital to achieving rational design of a new generation of intermediate-temperature fuel cells powered by a wide variety of readily available fuels. Also, surface modification has been successfully used to dramatically enhance electro-catalytic activity and durability of electrode materials. This presentation will highlight some recent advances in surface modifications and characterization of electrodes in energy storage and conversion systems. Surface enhanced Raman spectroscopy (SERS) has been used for probing and mapping new phases and reaction intermediates on electrode surfaces under or near operating conditions. It has also been demonstrated that SiO2 shell isolated Ag nanoparticles have excellent chemical and thermal robustness and stability for in situ SERS study of electrode materials under in situ or operando conditions, providing valuable information on reaction intermediates or structural changes that critically influence the performance and stability of the electrodes. Further, synchrotron-based X-ray absorption spectroscopy (XAS) and XPS have been used to characterize the local atomistic structure and oxidation state of electrode surfaces and interfaces, which may critically affect the activation or degradation processes of electrodes. These experimental studies, together with modeling and simulation, have helped us to gain important insights into the mechanisms of chemical and energy transformation, electro-catalytic reactions, and degradation processes, providing valuable guidelines for rational design of new electrode materials, surfaces, and interfaces with desired functionalities.

Prospects for laser-driven ion acceleration through controlled displacement of electrons by standing waves

During the interaction of intense femtosecond laser pulses with various targets, the natural mechanisms of laser energy transformation inherently lack temporal control and thus commonly do not provide opportunities for a controlled generation of a well-collimated, high-charge beam of ions with a given energy of particular interest. In an effort to alleviate this problem, it was recently proposed that the ions can be dragged by an electron bunch trapped in a controllably moving potential well formed by laser radiation. Such standing-wave acceleration (SWA) can be achieved through reflection of a chirped laser pulse from a mirror, which has been formulated as the concept of chirped-standing-wave acceleration (CSWA). Here, we analyse general feasibility aspects of the SWA approach and demonstrate its reasonable robustness against field structure imperfections, such as those caused by misalignment, ellipticity, and limited contrast. Using this, we also identify prospects and limitations of the CSWA concept.

Negative dissipation gradients in hysteretic materials.

Measuring energy dissipation on the nanoscale is of great interest not only for nanomechanics but also to understand important energy transformation and loss mechanisms that determine the efficiency of energy of data storage devices. Fully understanding the magnetic dynamics and dissipation processes in nanomagnets is of major relevance for a number of basic and applied issues from magnetic recording to spin-based sensor devices to biomedical magnetic-based hyperthermia treatments. Here we present experimental evidence for a counter-intuitive monotonical reduction of energy dissipation as the interaction between two nanomagnets is enhanced. This behavior, which takes place when spins are parallel, can be understood in terms of hysteresis phenomena involved in the reorientation of these spins. The measured magnetic losses of about a few femtowatts are in agreement with quasi-static micromagnetic numerical simulations.

Analytical characterization of damping in gear teeth dynamics under hydrodynamic conditions

Using an analytical method, we characterize damping and stiffness in lightly loaded, lubricated gear pairs at different operating speeds and lubricant temperatures. This is accomplished by employing a trace method to approximate and model the hysteresis loop of the lubricant reaction, thus recording the energy transformation mechanism during the gear teeth oscillatory motion. The method can be expanded for use in a variety of problems where hydrodynamic vibro-impacts lead to energy dissipation.

Effect of shell permutation on electromagnetic properties of ZnFeO4/(PANI, SiO2) core/double-shell nanostructured disks

ZnFe2O4/PANI/SiO2 (ZPS) and ZnFe2O4/SiO2/PANI (ZSP) core/double-shell nanostructured disks comprising PANI conducting dielectric shell and SiO2 insulating dielectric shell on a disk-shaped ZnFe2O4 magnetic core are prepared to study the effect of shell permutation on their electromagnetic properties. The complex relative permittivity (εr=εr′−jεr″) and permeability (μr=μr′−jμr″) of ZPS and ZSP are measured, and the reflection loss (RL) is determined, together with the ZnFe2O4 core, in the 1–18 GHz range. εr′ and εr″ in ZPS and ZSP are smaller than the core because of the induction of disordered dipolar polarizations at various interfaces involving the insulating SiO2 shell. Two obvious dielectric and magnetic abnormalities are observed in ZPS and ZSP. First, εr″ is weakened in the dipolar polarization-rich ZPS when compared to the ZSP of relatively less dipolar polarization. Second, μr′ and μr″ in ZPS become the largest in the 1.5–10.8 and 5.6–18 GHz ranges, respectively, while μr″ in ZSP remains the lowest and changes to be negative in the 10–18 GHz range, among all samples. An electromagnetic energy transformation mechanism is proposed to explain the observed abnormalities and their effects on absorption.

Investigation, modelling and reviewing the effective parameters in microwave-assisted transesterification

Abstract Synthesis of biodiesel using so-called microwave (MW) energy at a frequency of 2.45 GHz is investigated in this work. In this frequency, energy can transfer in the scale of molecular size. Dipolar rotation and ionic conduction are two important mechanisms of energy transformation; Thus, an efficient and localized high temperature is produced that can assist reaction. In this study, we focused on effective parameters during transesterification. It was found that methanol produces a higher yield than the other alcohol types. It is due to methanol reorientation ability under the microwave irradiation, which may result in a better microwave absorption. Furthermore, the requirement for catalyst in this situation was reduced about ten-fold. Besides, an empirical model was generated to analyze and predict the effect of operating parameters. The model was based on fitting a wide range of different experimental results for homogeneous alkalic catalysis. The predictive power of developed model was within the temperature range of 40 and 80 °C, reaction time between 5 and 15 min and alcohol to oil molar ratio between 3 and 12. The optimum values in the mentioned ranges included the alcohol to oil molar ratio of between 1:6 to 1:9 in homogenous catalyst systems and 15:1–18:1 in heterogeneous one, reaction time within 3–5 min and the temperature within 65–90 °C. Finally a very good agreement between the model and experimental data was observed with error of±8% even with the other catalysts types.

DNA nanotechnology based on i-motif structures.

CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this structure can serve as the stem of one-dimensional nanowires, and a four-strand stem can provide a new basis for three-dimensional DNA structures such as pillars. By sacrificing some accuracy in assembly, we used these properties to prepare the first fast-responding pure DNA supramolecular hydrogel. This hydrogel does not swell and cannot encapsulate small molecules. These unique properties could lead to new developments in smart materials based on DNA assembly and support important applications in fields such as tissue engineering. We expect that DNA nanotechnology will continue to develop rapidly. At a fundamental level, further studies should lead to greater understanding of the energy transformation and material transportation mechanisms at the nanometer scale. In terms of applications, we expect that many of these elegant molecular devices will soon be used in vivo. These further studies could demonstrate the power of DNA nanotechnology in biology, material science, chemistry, and physics.

Specific features of the kinetics of H2-O2-O2(a 1Δ g ) mixtures: II. Quenching of O2(a 1Δ g ) excited in a discharge behind the shock front at temperatures of 500–1020 K

Results of experiments on the quenching of singlet delta oxygen (SDO) O2(a 1Δ g ) in lean hydrogen-oxygen mixtures at temperatures of 500–1020 K and pressures of 26–90 Torr behind the shock front are analyzed theoretically. The processes affecting SDO quenching are simulated taking into account the temporal characteristics of the experiment and various mechanisms of energy transformation in an O2(a 1Δ g )-H2-H-HO2 system. It is demonstrated that the approximations of both fast and slow (in comparison with the vibrational relaxation time of the HO2 radical) quenching of the electronically excited state of the radical are in good agreement with the experimental data on the effective rate constant of SDO deexcitation at temperatures of up to 700 K. It is shown that the available data on the kinetics of reactions involving SDO in H2-O2-O2(a 1Δ g ) mixtures overestimate the SDO quenching rate in comparison with the experimental results obtained at temperatures above 850 K. The decrease in the rate constant of the reaction H + O2(a 1Δ g )→ products by one order of magnitude makes it possible to match the simulation results to the experimental data. The existence of the processes restoring SDO in the presence of atomic hydrogen that are not considered in the current models of the H2-O2-O2(a 1Δ g ) kinetics is supposed.

Изучение атомных механизмов преобразования энергии тонкопленочными металлическими наноструктурами методом молекулярной динамики

Изучение атомных механизмов преобразования энергии тонкопленочными металлическими наноструктурами методом молекулярной динамики

Stability and dynamics analysis of time delayed eutrophication ecological model based upon the Zeya reservoir

In this paper, within the framework of ordinary differential equation and eutrophication ecological theory, a time delayed eutrophication ecological model based upon the Zeya reservoir is studied analytically and numerically. A key advantage of time delayed term is that it can be quite accurate to describe food energy transformation mechanism, which enables a systematic and logical procedure for fitting eutrophication model to real monitoring data. Mathematical theoretical works have been pursuing the investigation of some stability conditions for the equilibria, which in turn provides a theoretical basis for the numerical simulation. Numerical analysis indicates that the time delayed term has an important role in complex dynamics using comparative analysis of the bifurcation diagram. It should also be stressed that chaos spontaneously appears with increase of a critical parameter for the system without time delayed term. In addition, it is successful to show that the time delayed term may be a critical factor for complex dynamics, which can directly suppress the emergence of chaos and promote the system to enter into a steady state. All these results are expected to be useful in the study of the dynamic complexity of eutrophication ecosystems.

Negotiating energy dynamics through embodied action in a materially structured environment

We provide evidence that a learning activity called Energy Theater engages learners with key conceptual issues in the learning of energy, including disambiguating matter flow and energy flow and theorizing mechanisms for energy transformation. A participationist theory of learning, in which learning is indicated by changes in speech and behavior, supports ethnographic analysis of learners' embodied interactions with each other and the material setting. We conduct detailed analysis to build plausible causal links between specific features of Energy Theater and the conceptual engagement that we observe. Disambiguation of matter and energy appears to be promoted especially by the material structure of the Energy Theater environment, in which energy is represented by participants, while objects are represented by areas demarcated by loops of rope. Theorizing mechanisms of energy transformation is promoted especially by Energy Theater's embodied action, which necessitates modeling the time ordering of energy transformations.

Preparation methods of thermoluminescent materials for dosimetric applications: An overview

Many different natural minerals and synthetic inorganic compounds present the phenomenon of thermoluminescence (TL); however, only a part of them satisfy the requirements to be used as TL dosimeters. The mechanism of excitation energy transformation into the output of light is one of the most important points in the TL materials designing. Both the threshold detection dose and accuracy of measurements depend on the efficiency of energy transformation.The role of diverse mechanisms of energy transfer and energy losses is very different depending on the nature of the TL material and its composition including intrinsic defects and those induced by impurities. The structure of these defects can be controlled to a high extent by the preparation method. That is why the most important fact is to find the interrelations among the preparation methods, the structural defects and the TL properties of the material.The aim of this paper is to give a selected review on the preparation methods of the most popular and commercially available phosphors as well as those less used or “homemade” for special studies.

Modeling the Confinement and Prestress Effects on Dynamic Failure of Ceramic Deep Beam

The present study performs numerical experiments to investigate the confinement and prestress effects on the dynamic failure of a ceramic deep beam. Johnson-Holmquist ceramic model (JH-2) is implemented into LS-DYNA through its user subroutines. The implementation and the effectiveness of the model are validated by a single element compression test and available plate impact test results. Failure of ceramics is isolated into two modes, i.e. tension induced cracking and compression generated crushing. Three different setups, i.e. bare ceramic beam, the beam with lateral constraints, and the beam with lateral constraints and a 100 MPa pre-applied pressure are considered in the numerical experiments. The results show that, in lower velocity impact, few tension induced cracks connecting the impactor head and the supports happened on the specimen, minor crush zone is found around the supports. Under higher velocity impact, however, a relative larger crush zone is also observed near the impact head, spreading tension cracks occurred in a triangular zone on the specimen. The lateral confinement affects the tension induced failure under both lower velocity and higher velocity impacts. The pre-applied pressure has only minor effect on the failure of the deep beam in low velocity impact. In higher velocity impact, however, the pre-applied stress may change the distribution profile of the tensile cracks. Both pre-stress and the lateral constraints have negligible effect on the compression crush happened near the impactor head in the higher velocity impacts. The dynamic failure patterns of the ceramic deep beam and the confinement and prestress effects are demonstrated clearly in the present study. Energy transformation mechanism during the impacts is briefly discussed.

Structure of the Fo/Vo-hybrid ATP synthase rotor ring from Acetobacterium woodii at 2.4 Å resolution

Energetic status of the cell is one the most important factors of its normal physiological functioning. Meanwhile its experimental evaluation is not always possible and reasonable due to high costs and invasiveness. Theoretical description of ATP production in the cell can be possible using existing data about the structure, functioning and spatial distribution of energoproducing systems. The FoF1ATPsynthase is one of the key enzymes in energy supplying in almost all living systems. This enzyme is an attractive research target due to its high mechanical complexity. Nevertheless, some key issues regarding energy conversation during the FoF1-ATPsynthase catalytic cycle are still unclear. The issue of rotational catalysis convertibility arises in the step that describes the rotormovement and proton translocation. This is one of the features that causes difficulty in the creation of a universal model of ATP synthesis. In this work, we provide a theoretical description of FoF1ATPsynthase catalytic cycle using combined mathematical approaches. Thus, the mechanism of Fo can be nominally described as the complexity of the rotation of protein subunits and proton translocation through membrane half-channels, which is an obligatory step in the transformation of the accumulated energy. The description of the above processes can yield the time of proton translocation and the mechanism of energy transformation and its transition to ATP-binding sites. Langevin dynamics is used for the rotation of the central protein core and the Monte-Carlo method helps to model nucleotide and proton binding. This approach is the first in which both ATP synthesis and hydrolysis can occur depending on the nucleotide concentration and system conditions. The calculated rates are close to the experimentally measured rates of ATP functioning. The model has been formalized as a computer simulation Program of ATP Synthesis and Hydrolysis (PASH) that allows researchers to evaluate ATP production both for one enzyme and for dirrefent types of cells. Flexibility of parameter settings in synthesis and hydrolysis of active enzymes and their regulation allows universal application of this approach in the evaluation of cell energetic status.

Molecular insights into the terminal energy acceptor in cyanobacterial phycobilisome

The linker protein L(CM) (ApcE) is postulated as the major component of the phycobilisome terminal energy acceptor (TEA) transferring excitation energy from the phycobilisome to photosystem II. L(CM) is the only phycobilin-attached linker protein in the cyanobacterial phycobilisome through auto-chromophorylation. However, the underlying mechanism for the auto-chromophorylation of L(CM) and the detailed molecular architecture of TEA is still unclear. Here, we demonstrate that the N-terminal phycobiliprotein-like domain of L(CM) (Pfam00502, LP502) can specifically recognize phycocyanobilin (PCB) by itself. Biochemical assays indicated that PCB binds into the same pocket in LP502 as that in the allophycocyanin α-subunit and that Ser152 and Asp155 play a vital role in LP502 auto-chromophorylation. By carefully conducting computational simulations, we arrived at a rational model of the PCB-LP502 complex structure that was supported by extensive mutational studies. In the PCB-LP502 complex, PCB binds into a deep pocket of LP502 with a distorted conformation, and Ser152 and Asp155 form several hydrogen bonds to PCB fixing the PCB Ring A and Ring D. Finally, based on our results, the dipoles and dipole-dipole interactions in TEA are analysed and a molecular structure for TEA is proposed, which gives new insights into the energy transformation mechanism of cyanobacterial phycobilisome.