State Transition Mechanism Research Articles

Mechanism of state transition of a defect causing random-telegraph-noise-induced fluctuation in stress-induced leakage current of SiO2 films

Dynamic fluctuation in stress-induced leakage current, called V-SILC, which is one of the causes of erratic bits in flash memory, was investigated. This investigation showed that V-SILC is attributed to random telegraph noise, which is associated with a state transition of a single defect. To analyze the mechanism of the state transition, dependences of state-transition probabilities on gate current and temperature were investigated. These dependences indicate that the state transitions are caused by current injection, and the mechanism of the state transition causing V-SILC is a defect-structure transition caused by charge collision.

The Study of Nonlinear Correlation between Shanghai, Hongkong and American Stock Returns An Empirical Analysis Based on MS-VAR Model and MS-DCC-MVGARCH Model

Considering the mean and the volatility correlation of Chinese and foreign stock market may undergo structural changes because of the reform and opening-up, the paper attempts to incorporate Markov state transition mechanism(MS) into both the VAR model and DCC-MVGARCH model at the same time. Based on that, it constructs the MS-VAR model and MS-DCC-MVGARCH model to empirically verify the nonlinear mean spillover effect and the volatility correlation among the Shanghai, Hong Kong and American stock markets. Empirical research shows that: firstly, there exists differentiating character among the correlation of these stock markets. USA stock market has positive spillover effect on Shanghai and Hong Kong stock markets, but it is not obvious conversely; at the same time; the volatility correlation between Shanghai and Hong Kong stock market is the highest, and it presents periodic volatility, while the volatility correlation between HK and US is the lowest, and it presents a stable fluctuant feature. Secondly, the interaction among the effects of Shanghai, Hong Kong and American Stock Market presents the obvious non-linear feature. The mean spillover effect among these stock markets in state 2 is significantly greater than in state 1; at the same time, the effects of volatility among these stock markets in state 1 is significantly higher than that of in state 2.

State Transition of a Defect Causing Random-Telegraph-Noise Fluctuation in Stress-Induced Leakage Current of Thin SiO2 Films in a Metal–Oxide–Silicon Structure

Dynamic fluctuation in stress-induced leakage current – called “variable stress-induced leakage current” – in a gate oxide of a metal–oxide–semiconductor structure was investigated. Variable stress-induced leakage current is attributed to random telegraph noise, which is associated with the state-transition of a single defect. To analyze the mechanism of the state-transition, dependence of state-transition probabilities on gate current and on temperature were investigated. These dependences indicate that the state-transition mechanism is a defect-structure transition by charge collision.

State-transitions facilitate robust quantum yields and cause an over-estimation of electron transport in Dunaliella tertiolecta cells held at the CO2 compensation point and re-supplied with DIC

Photosynthetic energy consumption and non-photosynthetic energy quenching processes are inherently linked. Both processes must be controlled by the cell to allow cell maintenance and growth, but also to avoid photodamage. We used the chlorophyte algae Dunaliella tertiolecta to investigate how the interactive regulation of photosynthetic and non-photosynthetic pathways varies along dissolved inorganic carbon (DIC) and photon flux gradients. Specifically, cells were transferred to DIC-deplete media to reach a CO₂ compensation before being re-supplied with DIC at various concentrations and different photon flux levels. Throughout these experiments we monitored and characterized the photophysiological responses using pulse amplitude modulated fluorescence, oxygen evolution, 77 K fluorescence emission spectra, and fast-repetition rate fluorometry. O₂ uptake was not significantly stimulated at DIC depletion, which suggests that O₂ production rates correspond to assimilatory photosynthesis. Fluorescence-based measures of relative electron transport rates (rETRs) over-estimated oxygen-based photosynthetic measures due to a strong state-transitional response that facilitated high effective quantum yields. Adoption of an alternative fluorescence-based rETR calculation that accounts for state-transitions resulted in improved linear oxygen versus rETR correlation. This study shows the extraordinary capacity of D. tertiolecta to maintain stable effective quantum yields by flexible regulation of state-transitions. Uncertainties about the control mechanisms of state-transitions are presented.

Energy–delay tradeoff analysis of user state transition mechanism for mobile web services

From the perspective of mobile users, the most considerable experiences are service delay and battery lifetime, both of which are closely related to the user state transition mechanism adopted in most mobile wireless systems. In this paper, the user state transition mechanism with more than simple two states (active/idle or on/off states) is modeled through Markov chain. Then, its performance is numerically analyzed with respect to the energy consumption and the activation delay by considering the bursty traffic attributes of mobile web services. As a result, we derive the energy–delay tradeoff curves, which show an achievable performance bound of the user state transition mechanism. The derived energy–delay tradeoff curve provides a guideline for network operators to suitably apply the user state transition mechanism so as to minimize the energy consumption of a mobile node while guaranteeing the delay requirement of the service.

Allostery and Folding of the N-terminal Receiver Domain of Protein NtrC

The N-terminal receiver domain of protein NtrC (NtrC(r)) exhibits allosteric transitions between the inactive (unphosphorylated) and active (phosphorylated) state on the microsecond time scale. Using a coarse-grained variational model with coupled energy basins, we illustrate that significant loss of conformational flexibility is the key determinant of the inactive (I) → active (A) state transition mechanism of NtrC(r). In particular, our results reveal that the rearrangements of the native contacts involving the regulatory helix-α4 and the flexible β3-α3 loop upon activation play a crucial role in the activation mechanism. Interestingly, we find that the β3-α3 loop exhibits a gradual decrease in flexibility throughout the activation transition, while helix-α4, in contrast, becomes more rigid abruptly near the free energy barrier separating the two states. To gain further insight into role these flexible regions play in the transition mechanism, we consider folding of NtrC(r) to both states using a similar model. Our calculated folding routes suggest that helix-α4 becomes structured later when folding to the I state compared to folding of the A state, a result consistent with it is relative conformational flexibility in the two states. Finally, we find a good qualitative agreement between our predicted I → A transition mechanism and the measured backbone dynamics from nuclear magnetic resonance experiments.

Mechanisms of Intermittent State Transitions in a Coupled Heterogeneous Oscillator Model of Epilepsy

We investigate the dynamic mechanisms underlying intermittent state transitions in a recently proposed neural mass model of epilepsy. A low dimensional model is constructed, which preserves two key features of the neural mass model, namely (i) coupling between oscillators and (ii) heterogeneous proximity of these oscillators to a bifurcation between distinct limit cycles. We demonstrate that state transitions due to intermittency occur in the abstract model. This suggests that there is a general bifurcation mechanism responsible for this behaviour and that this is independent of the precise form of the evolution equations. Such abstractions of neural mass models allow a deeper insight into underlying dynamic and physiological mechanisms, and also allow the more efficient exploration of large scale brain dynamics in disease.

A phenomenological approach for the chemo-responsive shape memory effect in amorphous polymers

In this work, we present a phenomenological approach to study the state transition and working mechanism of the chemo-responsive shape memory effect (SME) in shape memory polymers (SMPs). The thermodynamics of polymer solution and free-energy theory are initially applied to quantitatively identify the factors that trigger a chemo-responsive SME. After this, a field theory is developed to couple the chemical potential, stress and relaxation time in a polymer system with free-energy functions. Furthermore, by means of combining together and utilizing the Gordon–Taylor (GT) theory and Free-Volume (FV) theory, the intrinsic plasticizing effect and generalized plasticizing effect are decoupled and quantitatively determined as the driving forces for the chemo-responsive SME in SMPs. In addition, the influence of the intrinsic plasticizing effect and generalized plasticizing effect on the glass transition temperature (Tg) is consequently numerically modeled using the GT and FV equations, respectively. Finally, the theoretical model is verified by the available experimental data reported in the literature and then compared with the simulation results of a semi-empirical model. This phenomenological approach is expected to provide a powerful simulation tool for extracting the transition temperature parameter, theoretical prediction and experimental substantiation of the response of chemo-responsive SME in amorphous SMPs.

UMTS 상태 천이 방식에서 에너지 소비와 활성 지연간의 트레이드오프 성능 분석

이동통신 시스템은 무선 자원과 배터리 전력을 효율적으로 관리하기 위해 사용자 상태 천이 방식을 정의하고 있다. 이러한 상태 천이 방식에서는 에너지 소비가 많은 상태가 기본적으로 짧은 접속 지연을 제공하므로 에너지와 지연 성능 사이에 트레이드오프 관계가 존재한다. 본 논문에서는 이동 응용 서비스의 트래픽 속성을 고려하여 UMTS 시스템의 사용자 상태 천이 방식을 분석한다. 상태 천이 방식의 마르코프 모델링을 통하여 에너지 소비량과 활성 지연을 수학적으로 도출하고 운용 파라미터에 따라 이들의 트레이드오프 관계를 파악한다. 분석 결과로 도출된 에너지-지연 트레이드오프 곡선은 주어진 상태 천이 방식이 달성 가능한 성능 한계를 보여주며 지연 요구사항을 보장하면서 에너지 소비를 최소화하는 최적 운용 전략을 제시한다. Mobile communication systems define user state transition mechanisms in order to manage radio resources and battery power efficiently. In the state transition mechanism, a state with a higher energy consumption inherently offers a shorter access delay, so there is a tradeoff between the energy and delay performances. In this paper, we analyze the user state transition mechanism of UMTS by considering the bursty traffic attributes of mobile applications. We perform a numerical evaluation for both the energy consumption and the activation delay by Markov modeling of the state transition mechanism, and investigate their tradeoff relationship as functions of operational parameters. The resulting energy-delay tradeoff curves clearly show an achievable performance bound of the user state transition mechanism and also offer an optimal operation strategy to minimize the energy consumption while guaranteeing the delay requirement.

Effect of cold temperature on regulation of state transitions in Arabidopsis thaliana

Low temperature is one of the most important abiotic factors limiting growth, development and distribution of plants. The effect of cold temperature on phosphorylation and migration of LHCII has been studied by 77K fluorescence emission spectroscopy and immuno-blotting in Arabidopsis thaliana. It has been reported that the mechanism of state transitions has been well operated at optimum growth temperatures. In this study, exposure of leaves to cold conditions (10°C for 180min) along with low light treatment (for 3h) did not show any increase in F726 which corresponds to fluorescence from PSI supercomplex, whereas low light at optimal temperature (26±2°C) could enhanced F726. Therefore these results conclude that low light at cold condition did not enhance PSI absorption cross-section. We have also observed low levels of LHCII phosphorylation in cold exposed leaves in dark or low light. Though LHCII phosphorylation was detectable, the lateral movement of phosphorylated LHCII is reduced due to high granal stacking in cold treated leaves either in light or dark. Apart from these results, it is suggested that increased OJ phase and decreased JI and IP phases of Chl a fluorescence transients were due to reduced electron transport processes in cold treated samples.

Analysis of Tradeoff Between Energy Consumption and Activation Delay in Power Management Mechanisms

Power management mechanisms (PMMs) inherently have a tradeoff between the energy consumption and delay. In this letter, we analyze an active-idle state transition mechanism for power-saving in mobile stations by considering the general traffic pattern of smartphones, which consists of uplink request packets and downlink bursty data. We derive closed-form solutions of both the energy consumption and activation delay, and characterize their tradeoff relationship. The results show that the tradeoff curve is linear and its slope is not affected by the PMM's operational parameters or the traffic arrival rate.

Mechanism of Ion Coupled State Transition in LeuT-fold Transporters

Several highly conserved features, including similarities in the overall architecture and in substrate and ion binding sites, suggest that secondary transporters sharing the LeuT-fold topology might form an emerging superfamily with a similar transport mechanism. Similar to other transporters, LeuT-fold transporters operate via the alternating access mechanism, in which during the transport cycle the transporter protein undergoes conformational transitions between two major states, an inward-facing (IF) and an outward-facing (OF) one. However, despite the availability of a wealth of structural data, a clear and consistent understanding for the transition mechanism and how it might be coupled to ion binding/unbinding events has not been achieved yet.Using microsecond-long equilibrium molecular dynamics (MD) and special-protocol target MD simulations and comparative structural analysis, we demonstrate that the conformational changes of the conserved Na2 site are closely coupled with the global transition between the OF and IF states in the LeuT-fold transporters. In our TMD simulations, we show that inducing structural transitions in only two transmembrane (TM) helices that are directly involved in Na+ binding site in Mhp1, is sufficient to drive the transition between the IF and OF states in the entire protein. Additional data from equilibrium simulations along with structural analyses suggest that the state transitions captured in the simulations are highly relevant to the natural pathway during the transport cycle. Furthermore, the results clearly show a high correlation between Na+-binding TMs and extracellular and cytoplasmic gates, and how the movement of specific TMs switches the states of the transporter. Meanwhile, our extended equilibrium simulations performed in different transport states, and following free energy calculations suggest the effect of Na+-binding in LeuT-fold is to reshape the free energy landscape, and thereby to change the distribution of the states involved the transport cycle.

Workflow Model Design Based on N-Tree for Process Management in PDM

In this paper, a workflow model based on N-tree for process management in PDM system is presented. It streamlines circuits in process management to sequence, branch, parallel, and loop patterns. It also offers this workflow model’s mechanisms of construction, executing, and state transition by definitions of workflow’s node properties, node constraints and state set. Last it exhibits an instance of applying this workflow model to process management of a simple PDM system.

Critical Roles of Interactions among Switch I-preceding Residues and between Switch II and Its Neighboring α-Helix in Conformational Dynamics of the GTP-bound Ras Family Small GTPases

GTP-bound forms of Ras family small GTPases exhibit dynamic equilibrium between two interconverting conformations, "inactive" state 1 and "active" state 2. A great variation exists in their state distribution; H-Ras mainly adopts state 2, whereas M-Ras predominantly adopts state 1. Our previous studies based on comparison of crystal structures representing state 1 and state 2 revealed the importance of the hydrogen-bonding interactions of two flexible effector-interacting regions, switch I and switch II, with the γ-phosphate of GTP in establishing state 2 conformation. However, failure to obtain both state structures from a single protein hampered further analysis of state transition mechanisms. Here, we succeed in solving two crystal structures corresponding to state 1 and state 2 from a single Ras polypeptide, M-RasD41E, carrying an H-Ras-type substitution in residue 41, immediately preceding switch I, in complex with guanosine 5'-(β,γ-imido)triphosphate. Comparison among the two structures and other state 1 and state 2 structures of H-Ras/M-Ras reveal two new structural features playing critical roles in state dynamics; interaction of residues 31/41 (H-Ras/M-Ras) with residues 29/39 and 30/40, which induces a conformational change of switch I favoring its interaction with the γ-phosphate, and the hydrogen-bonding interaction of switch II with its neighboring α-helix, α3-helix, which induces a conformational change of switch II favoring its interaction with the γ-phosphate. The importance of the latter interaction is proved by mutational analyses of the residues involved in hydrogen bonding. These results define the two novel functional regions playing critical roles during state transition.

Protein–protein interactions by molecular modeling and biochemical characterization of PSI-LHCI supercomplexes from Chlamydomonas reinhardtii

The physiological function of Photosystem I (PSI) is a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae and higher plants. The Chlamydomonas reinhardtii PSI structure was not known since it contains a unique structure having additional light harvesting complex I (LHCI) subunits, which play a major role in the transfer of sunlight energy to the reaction center. Here, individual subunits of LHC and core subunits are built based on the PDB taken from RCSB Protein Data Bank. The model gives information about the geometrical existence of subunits following a flanking order of Lhca5, Lhca1, Lhca6, Lhca4, Lhca2, Lhca8, Lhca9, Lhca7, and Lhca3. The new subunit PsaO is located close to the PsaH, PsaI and PsaL subunits, thus it may be involved in the state transition mechanism and stabilization of PSI-LHCI supercomplexes. The modeled PSI-LHCI structure of C. reinhardtii shows a unique arrangement of PsaN, PsaO of PSI core subunits and Lhca5 to Lhca9 of LHCI subunits. There are many non-covalent interactions among the PSI and LHCI subunits, which suggest that C. reinhardtii PSI-LHCI supercomplexes are more complex than higher plants. These results strongly support the experimental data that, even with harsh treatment of the PSI-LHCI supercomplexes with detergent, the complexes do not dissociate due to strong interactions between the PSI core and LHCI. Thus, our 3D model may give valid structural information of the PSI-LHCI arrangement and its physiological role in C. reinhardtii.

Structural Basis for Conformational Dynamics of GTP-bound Ras Protein

Ras family small GTPases assume two interconverting conformations, "inactive" state 1 and "active" state 2, in their GTP-bound forms. Here, to clarify the mechanism of state transition, we have carried out x-ray crystal structure analyses of a series of mutant H-Ras and M-Ras in complex with guanosine 5'-(beta,gamma-imido)triphosphate (GppNHp), representing various intermediate states of the transition. Crystallization of H-RasT35S-GppNHp enables us to solve the first complete tertiary structure of H-Ras state 1 possessing two surface pockets unseen in the state 2 or H-Ras-GDP structure. Moreover, determination of the two distinct crystal structures of H-RasT35S-GppNHp, showing prominent polysterism in the switch I and switch II regions, reveals a pivotal role of the guanine nucleotide-mediated interaction between the two switch regions and its rearrangement by a nucleotide positional change in the state 2 to state 1 transition. Furthermore, the (31)P NMR spectra and crystal structures of the GppNHp-bound forms of M-Ras mutants, carrying various H-Ras-type amino acid substitutions, also reveal the existence of a surface pocket in state 1 and support a similar mechanism based on the nucleotide-mediated interaction and its rearrangement in the state 1 to state 2 transition. Intriguingly, the conformational changes accompanying the state transition mimic those that occurred upon GDP/GTP exchange, indicating a common mechanistic basis inherent in the high flexibility of the switch regions. Collectively, these results clarify the structural features distinguishing the two states and provide new insights into the molecular basis for the state transition of Ras protein.

Evidence that pH can drive state transitions in isolated thylakoid membranes from spinach

Our observation that the F735/F685 ratio at 77 K increased when the lumenal pH decreased led us to investigate the role of pH in explaining the mechanism of state transitions in spinach (Spinacea oleracea L.) thylakoid membranes. As the lumenal pH was changed from pH 7.5 to 5.5, the quantum yield of PS II decreased, while that of PS I increased. In the presence of an uncoupler, NH(4)Cl, which sequesters protons, a reversal of the effects observed at pH 5.5 were noticed. The thylakoid membranes treated with NaF at pH 5.5, when suspended in a buffer of pH 7.5, showed enhanced PS II fluorescence and a decreased PS I fluorescence, suggesting migration of LHC II back to PS II from PS I. The results presented here suggest for the first time that the lumenal pH of thylakoid membranes regulates the migration of antenna, and hence the energy distribution, between the two photosystems, i.e. a low lumenal pH (pH 5.5) favors antenna migration from PS II to PS I. At pH 7.5, the deprotonation of LHC II antenna attached to PS I leads to back migration of LHC II to PS II.

Markov decision processes with multidimensional action spaces

We study controlled Markov processes where multiple decisions need to be made for each state. We present conditions on the cost structure and the state transition mechanism of the process under which optimal decisions are restricted to a subset of the decision space. As a result, the numerical computation of the optimal policy may be significantly expedited.

Fluorescence changes accompanying short-term light adaptations in photosystem I and photosystem II of the cyanobacterium Synechocystis sp. PCC 6803 and phycobiliprotein-impaired mutants: State 1/State 2 transitions and carotenoid-induced quenching of phycobilisomes

The features of the two types of short-term light-adaptations of photosynthetic apparatus, State 1/State 2 transitions, and non-photochemical fluorescence quenching of phycobilisomes (PBS) by orange carotene-protein (OCP) were compared in the cyanobacterium Synechocystis sp. PCC 6803 wild type, CK pigment mutant lacking phycocyanin, and PAL mutant totally devoid of phycobiliproteins. The permanent presence of PBS-specific peaks in the in situ action spectra of photosystem I (PSI) and photosystem II (PSII), as well as in the 77 K fluorescence excitation spectra for chlorophyll emission at 690 nm (PSII) and 725 nm (PSI) showed that PBS are constitutive antenna complexes of both photosystems. The mutant strains compensated the lack of phycobiliproteins by higher PSII content and by intensification of photosynthetic linear electron transfer. The detectable changes of energy migration from PBS to the PSI and PSII in the Synechocystis wild type and the CK mutant in State 1 and State 2 according to the fluorescence excitation spectra measurements were not registered. The constant level of fluorescence emission of PSI during State 1/State 2 transitions and simultaneous increase of chlorophyll fluorescence emission of PSII in State 1 in Synechocystis PAL mutant allowed to propose that spillover is an unlikely mechanism of state transitions. Blue-green light absorbed by OCP diminished the rout of energy from PBS to PSI while energy migration from PBS to PSII was less influenced. Therefore, the main role of OCP-induced quenching of PBS is the limitation of PSI activity and cyclic electron transport under relatively high light conditions.

Kinetics of Solid State Polymorphic Transition of Caffeine

Polymorphic solid state transition of caffeine anhydrate crystals from a metastable Form I to a stable Form II was conducted to investigate the kinetics as a function of temperature and humidity. The kinetics was expressed well with the penetration model proposed in our previous study. The transition rate was independent of the humidity but was dependent on the temperature. The activation energy was comparable to that for the solid state transition of theophylline anhydrates, indicating a similar mechanism of solid state transition.