Theoretical Studies on CH_3SiH_3+H→CH_3SiH_2+H_2 Reaction with the Variational Transitional State Theory

In this paper. the abstraction reaction of CH_3SiH_3 with H has been studied by using the 'direct dynamics' method of variational transition-state theory. which is based on the information on geometries. frequencies and energies calculalcd by ab inito along the minimum energy path. The rate constants of the title reaction were calculated for the range of temperature 298-1700 K. The rate constants calculated match well with the experimental values.

State Transition, Is It a Photochemical or Non-photochemical Processin Leaf in Response to Irradiance?

The response of steady-state fluorescence (Fs) to irradiance in apple (Malus pumila Mill. cv. Tengmu No.1/Malus hupehensis Rehd.) leaf increased and decreased at light levels below and above 400 mumol(.)m(-2.)s(-1) photosynthetic photon flux density (PPFD), respectively, while the light-adapted maximal fluorescence (Fm') and minimal fluorescence (Fo') decreased constantly with the increasing PPFD, and the closure of photosystem 11 reaction center (PS 11 RC) increased continuously, reflected by the chlorophyll fluorescence parameter of (Fs-Fo')/(Fm'-Fo'). These facts indicated that decrease of Fs above 400 mumol(.)m(-2.)s(-1) PPFD was not caused by closure of PS 11 RC, but was mainly resulted from the process of light transfer from light-harvesting complex II (LHC II) to PS II RC. In the presence of N- ethylmaleimide (NEM), an inhibitor of photosynthetic state transition, Fs kept on increasing in apple leaf at light levels from 400 to 700 mumol(.)m(-1.)s(-1), which was the photosynthetic saturation irradiance of apple leaves. In addition, Fs still increased at light levels over 700 mumol(.)m(-2.)s(-1) in apple leaf pre-treated with dithiothreitol (DTT), an inhibitor of xanthophyll cycle. These changes showed that state transition and xanthophyll cycle caused a decrease of Fs in apple leaf at light levels below and above the photosynthetic saturation irradiance, respectively. When apple leaf was pre-treated with NEM, the PS II apparent rate of photochemical reaction (P-rate) and photochemical quenching (qP) decreased significantly in the light range of 600-800 mumol(.)m(-2.)s(-1), but the non-photochemical quenching (qN) existed a small increase at 600-800 mumol(.)m(-2.)s(-1) and a decrease above 800 mumol(.)m(-2.)s(-1). These phenomena suggested that state transition was mainly a photochemical and a non-photochemical process in apple leaf responding to light lower and higher than photosynthetic saturation irradiance, respectively.

Theoretical Study of Reaction Paths and Transition States on Conversion Methane into C_2 Hydrocarbons Through Plasma

The direct synthesis of C2 hydrocarbons （ethylene, acetylene and ethane） from methane is one of the most important task in C1 chemistry. Higher conversion of methane and selectivity to C2 hydrocarbons can be real-ized through plasma reaction. In order to explore the reaction process and mechanism, the possible reaction paths （1）—（4） were proposed on coupling reaction of methane through plasma and studied theoretically using semi-PM3 method [PM3 is parameterization method of modified neglect of diatomic overlap （MNDO）] including determining the transition state, calculating the activation energy and thermodynamic state functions and analyzing the bond or-der and intrinsic reaction coordinate. The reaction heat results indicate that the reactions （2） and （4） are exothermic, while reactions of （1） and （3） are endothermic. The activation energy results show that activation energy for reac-tions （1） and （2） was much lower than that of reaction paths （3） and （4）. Therefore, paths （1） and （2） is the favorable reaction path energetically. More interestingly by comparing the intrinsic reaction coordinated （IRC） of the reaction paths （1） and （2）, it is found that the variations of bond lengths in reaction path （1） has a crucial effect on the poten-tial energy, while in reaction path （2）, the adjustment of the system geometry also contributes to the whole potential energy of the system.

Optimal Precursors Triggering the Kuroshio Extension State Transition Obtained by the Conditional Nonlinear Optimal Perturbation Approach

In this study, the initial perturbations that are the easiest to trigger the Kuroshio Extension （KE） transition connecting a basic weak jet state and a strong, fairly stable meandering state, are investigated using a reduced-gravity shallow water ocean model and the CNOP （Conditional Nonlinear Optimal Perturbation） approach. This kind of initial perturbation is called an optimal precursor （OPR）. The spatial structures and evolutionary processes of the OPRs are analyzed in detail. The results show that most of the OPRs are in the form of negative sea surface height （SSH） anomalies mainly located in a narrow band region south of the KE jet, in basic agreement with altimetric observations. These negative SSH anomalies reduce the merid- ional SSH gradient within the KE, thus weakening the strength of the jet. The KE jet then becomes more convoluted, with a high-frequency and large-amplitude variability corresponding to a high eddy kinetic energy level; this gradually strengthens the KE jet through an inverse energy cascade. Eventually, the KE reaches a high-energy state characterized by two well defined and fairly stable anticyclonic meanders. Moreover, sensitivity experiments indicate that the spatial structures of the OPRs are not sensitive to the model parameters and to the optimization times used in the analysis.

A circular zone counting method of identifying a Duffing oscillator state transition and determining the critical value in weak signal detection

Identifying state transition and determining the critical value of the Duffing oscillator are crucial to indicating external signal existence and have a great influence on detection accuracy in weak signal detection. A circular zone counting （CZC） method is proposed in this paper, by combining the Duffing oscillator＇s phase trajectory feature and numerical calculation for quickly and accurately identifying state transition and determining the critical value, to realize a high- efficiency weak signal detection. Detailed model analysis and method construction of the CZC method are introduced. Numerical experiments into the reliability of the proposed CZC method compared with the maximum Lyapunov exponent （MLE） method are carried out. The CZC method is demonstrated to have better detecting ability than the MLE method, and furthermore it is simpler and clearer in calculation to extend to engineering application.

Transition state to mode locking in a passively mode-locked erbium-doped fibre ring laser

The transition state between the continuous wave region and the mode-locked region in a passively mode-locked erbium-doped fibre ring laser has been experimentally observed by utilizing the nonlinear polarization rotation technique. When the pump power reaches the mode-locked threshold, the metastable pulse train with a tunable repetition rate is obtained in the transition from the continuous wave state to the passive mode-locked state via proper adjustment of the polarization controller. A simpie model has been established to explain the experimental observation.

Transition state and formation process of Stone–Wales defects in graphene

Stone–Wales(SW) defects are possibly formed in graphene and other two-dimensional materials, and have multiple influence on their physical and chemical properties. In this study, the transition state of SW defects in graphene is determined with the fully discrete Peierls theory. Furthermore, the atomic formation process is investigated by means of ab-initio simulations. The atomic structure change and energetics of the SW transformation are revealed. It is found that the transition state is at the SW bond rotation of 34.5°and the activation energy barrier is about 12 eV. This work provides a new method to investigate SW transformations in graphene-like materials and to explore unknown SW-type defects in other 2D materials.

Theoretical Study on the Transition State of N-nitropyrazoles Rearrangement Reaction

Theoretical studies on the rearrangement reactions of nitropyrazoles have beeninvestigated. In order to gain a better understanding of the intermediate process of rearrangementreactions, the transition states of the rearrangement reactions were obtained by TS method at theB3LYP/6-311G（d, p） level of theory. The natural bond orbital charge, electrostatic potential andfrontier molecular orbital of the molecules in the process of rearrangement were analyzed, and thesolvent effect was also discussed. The rearrangement of nitropyrazoles involves two transitionstates and one intermediate, and the nitro group and hydrogen atom are two transfer groups forrearrangement reactions. The migration of these two groups leads to the change of chargedistribution and molecular structure. The structural changes of the molecules in different solventsare not significant, but the dipole moment of the molecule has obvious change.

Instantaneous Formulation for Transitions Between Two Instantaneous Bound States and Its Gauge Invariance

We have precisely derived a ＂rigorous instantaneous formulation＂ for transitions between two bound states when the bound states are well-described by instantaneous Bethe-Salpeter （BS） equation （i.e. the kernel of the equation is instantaneous ＂occasionally＂）. The obtained rigorous instantaneous formulation, in fact, is expressed as an operator sandwiched by two ＂reduced BS wave functions＂ properly, while the reduced BS wave functions appearing in the formulation are the rigorous solutions of the instantaneous BS equation, and they may relate to Schroedinger wave functions straightforwardly. We also show that the rigorous instantaneous formulation is gauge-invariant with respect to the Uem（1） transformation precisely, if the concerned transitions are radiative. Some applications of the formulation are outlined.

Coarse-Grained Free-Energy Simulations of Conformational State Transitions in an Adenosine 5′-Triphosphate-binding Cassette Exporter

ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.

Research on the railway construction process quality model based on the state space method

In the ISO9000"input-output"process model,the concept of process quality is difficult to get the correct interpretation. From the"white box"theory of process,this paper puts forward the scientific meaning of the concept of process quality and the process quality model by taking the basic operating unit of 6M1E in the railway construction project for example. The basic operating unit system consists of technological natural process,operation process and management process;the process quality of the basic operating unit system depends on the interrelation and interaction among those three sub-processes,and also subjects to the impact of the external disturbance input factors. Finally,the cast-in-situ prestressed concrete continuous box girder construction process is utilized to elaborate the specific application of this theory in the quality management of the railway construction project.

Charge Density Wave States and Structural Transition in Layered Chalcogenide TaSe_(2-x)Te_x

The structural features and three-dimensional nature of the charge density wave （CDW） state of the layered chalcogenide 1T-TaSe2-xTex （0≤x≤2.0） are characterized by Cs-corrected transmission electron microscopy measurements. Notable changes of both average structure and the CDW state arising from Te substitution for Se are clearly demonstrated in samples with x〉0.3. The commensurate CDW state characterized by the known star-of-David clustering in the 1T-TaSe2 crystal becomes visibly unstable with Te substitution and vanishes when x=0.3. The 1T-TaSe2-xTex （0.3≤x≤1.3） samples generally adopt a remarkable incommensurate CDW state with monoclinic distortion, which could be fundamentally in correlation with the strong qq-dependent electron-phonon coupling-induced period-lattice-distortion as identified in TaTe22. Systematic analysis demonstrates that the occurrence of superconductivity is related to the suppression of the commensurate CDW phase and the presence of discommensuration is an evident structural feature observed in the superconducting samples.

Combined multi-level quantum mechanics theories and molecular mechanics study of water-induced transition state of OH^- + CO_2 reaction in aqueous solution

The presence of a solvent interacting with a system brings about qualitative changes from the corresponding gas-phase reactions. A solvent can not only change the energetics along the reaction pathway, but also radically alter the reaction mechanism. Here, we investigated the water-induced transition state of the OH^-＋CO2→HCO3^- reaction using a multi-level quantum mechanics and molecular mechanics method with an explicit water model. The solvent energy contribution along the reaction pathway has a maximum value which induces the highest energy point on the potential of mean force. The charge transfer from OH^- to CO2 results in the breaking of the OH^- solvation shell and the forming of the CO2 solvation shell. The loss of hydrogen bonds in the OH^- solvation shell without being compensated by the formation of hydrogen bonds in the CO2 solvation shell induces the transition state in the aqueous solution. The calculated free energy reaction barrier at the CCSD（T）/MM level of theory, 11.8 kcal/mol, agrees very well with the experimental value, 12.1 kcal/mol.

Theoretical investigation on the excited state intramolecular proton transfer in Me_(2)N substituted flavonoid by the time-dependent density functional theory method

Time-dependent density functional theory(TDDFT)method is used to investigate the details of the excited state intramolecular proton transfer(ESIPT)process and the mechanism for temperature effect on the Enol^(*)/Keto^(*)emission ratio for the Me_(2)N-substited flavonoid(MNF)compound.The geometric structures of the S_(0) and S_(1) states are denoted as the Enol,Enol^(*),and Keto*.In addition,the absorption and fluorescence peaks are also calculated.It is noted that the calculated large Stokes shift is in good agreement with the experimental result.Furthermore,our results confirm that the ESIPT process happens upon photoexcitation,which is distinctly monitored by the formation and disappearance of the characteristic peaks of infrared(IR)spectra involved in the proton transfer and in the potential energy curves.Besides,the calculations of highest occupied molecular orbital(HOMO)and lowest unoccupied molecular orbital(LUMO)reveal that the electronegativity change of proton acceptor due to the intramolecular charge redistribution in the S_(1) state induces the ESIPT.Moreover,the thermodynamic calculation for the MNF shows that the Enol^(*)/Keto^(*)emission ratio decreasing with temperature increasing arises from the barrier lowering of ESIPT.

Transition State and Catastrophe Set

The study on transition states is one of the most important pathways to understand the essence of chemical reactions. With the development of femtoseeond pulse technique, Zewail et al. have carried out a number of experimental studies on the transition states, while the theoretical chemists has a great interest in the topic. In the previous

The impact of N-terminal phosphorylation on LHCII conformation in state transition

State transition is an important protection mechanism of plants for maintaining optimal efficiency through redistributing unbalanced excitation energy between photosystem II （PSII） and photosystem I （PSI）. This process depends on the reversible phosphorylation/dephosphorylation of the major light-harvesting complex II （LHCII） and its bi-directional migration between PSII and PSI. But it remains unclear how phosphorylation/dephosphorylation modulates the LHCII conformation and further regulates its reversible migration. Here molecular dynamics simulations （MDS） were employed to elucidate the impact of phosphorylation on LHCII conformation. The results indicated that N-terminal phosphorylation loosened LHCII trimer with decreased hydrogen bond （H-bond） interactions and extended the distances between neighboring monomers, which stemmed from the conformational ad- justment of each monomer itself. Global conformational change of LHCII monomer started from its stromal N- terminal （including the phosphorylation sites） by enhancing its interaction to lipid membrane and by adjusting the interaction network with surrounded inter-monomer andintra-monomer transmembrane helixes of B, C, and A, and finally triggered the reorientation of transmembrane helixes and transferred the conformational change to luminal side helixes and loops. These results further our understanding in molecular mechanism of LHCII migration during state transition from the phosphorylation-induced microstructural feature of LHCII.

Fabrication of pillar-array superhydrophobic silicon surface and thermodynamic analysis on the wetting state transition

Textured silicon （Si） substrates decorated with regular microscale square pillar arrays of nearly the same side length, height, but different intervals are fabricated by inductively coupled plasma, and then silanized by self-assembly octadecyl- trichlorosilane （OTS） film. The systematic water contact angle （CA） measurements and micro/nanoscale hierarchical rough structure models are used to analyze the wetting behaviors of original and silanized textured Si substrates each as a function of pillar interval-to-width ratio. On the original textured Si substrate with hydrophilic pillars, the water droplet possesses a larger apparent CAs （〉 90~） and contact angle hysteresis （CAH）, induced by the hierarchical roughness of microscale pil- lar arrays and nanoscale pit-like roughness. However, the silanized textured substrate shows superhydrophobicity induced by the low free energy OTS overcoat and the hierarchical roughness of microscale pillar arrays, and nanoscale island-like roughness. The largest apparent CA on the superhydrophobic surface is 169.8~. In addition, the wetting transition of a gently deposited water droplet is observed on the original textured substrate with pillar interval-to-width ratio increasing. Furthermore, the wetting state transition is analyzed by thermodynamic approach with the consideration of the CAH effect. The results indicate that the wetting state changed from a Cassie state to a pseudo-Wenzel during the transition.

Transition Between Solid-like and Liquid-like States in Soft Silica Suspensions

The influences of silica volume fraction, electrolyte concentration and pH value upon the stress dependence of elastic modulus G′and viscous modulus G″ were investigated. The results show that the suspension transforms from a liquid-like state to a solid-like state with increasing the volume fraction of silica. Such a solid-like state can be transformed back into a liquid-like state under the application of a larger stress. At the higher volume fraction, the larger critical stress is required to induce the transition from solid-like to liquid-like state. As the electrolyte concentration decreases or pH value increases, the inter-particle force increases, which causes the state transition to occur at a higher stress.

Multiple steady state phenomenon in martensitic transformation

Based on the basic facts that the martensitic transformation is a physical phenomenon which occurs in non equilibrium conditions and there exists the feedback mechanism in the martensitic transformation, the dynamical processes of the isothermal and athermal martensitic transformations were analyzed by using nonlinear theory and a bifurcation theory model was established. It is shown that a multiple steady state phenomenon can take place as austenite is cooled, and the transitions of the steady state temperature between the branches of stable steady states can be considered the transformation from austenite to martensite. This model can estimate the starting temperature of the martensitic transformation and explain some experimental features of the martensitic transformation such as the effects of cooling rate, fluctuation and austenitic grain size on the martensitic transformation. [

Bayesian estimation for nonlinear stochastic hybrid systems with state dependent transitions

The Bayesian approach is considered as the most general formulation of the state estimation for dynamic systems. However, most of the existing Bayesian estimators of stochastic hybrid systems only focus on the Markov jump system, few liter- ature is related to the estimation problem of nonlinear stochastic hybrid systems with state dependent transitions. According to this problem, a new methodology which relaxes quite a restrictive as- sumption that the mode transition process must satisfy Markov properties is proposed. In this method, a general approach is presented to model the state dependent transitions, the state and output spaces are discreted into cell space which handles the nonlinearities and computationally intensive problem offline. Then maximum a posterior estimation is obtained by using the Bayesian theory. The efficacy of the estimator is illustrated by a simulated example .