Recombination kinetics of impurities during a major disruption in tokamak plasmas

The investigations of major disruptions in the TVD and DAMAVAND tokamaks showed that, in the rapid phase of disruption, accelerated (～1 keV) ions and charge-exchange neutrals are generated near the rational magnetic surfaces; this is accompanied by the bursts of line emission from light impurities (C, O). In the present paper, an analysis is made of the bursts of the CV triplet emission (2271–2278 Å) observed over all of the viewing chords in high-current discharges and also of a decrease in the spectral line emission below its initial (predisruption) level both in the plasma core and at the plasma edge in low-current discharges. The data from measurements of the spatial and temporal parameters of the CV line emission from the central and peripheral plasma regions in the rapid phase of disruption in the DAMAVAND tokamak are compared to the results from model calculations of the kinetics of the charge-state distribution of carbon impurity ions (during the disruption, their kinetics is governed by the increase in the effective recombination rate). A key result of the kinetic model is an increase in the effective rate of charge exchange of impurity ions by two orders of magnitude. Numerical simulations show that the dispersion of the charge-state distribution increases substantially; this is attributed to the rapid phase of disruption being dominated by the recombination of impurity ions through charge exchange with neutrals rather than by the anomalous transport. In this case, carbon impurities in the plasma are transported to the region of increased radiative losses on a time scale of 50 μs.     

生理信号回归问题的一种解法

一自适应在线过程可通过Kalman滤波表示为时间变多变量的的自回归模型。时变模型的参数的估计能被用以计算线相关的瞬时测量,此方法对生理信号的分析非常有用。本文着重讨论了在呼吸运动,心率波动,血压的分析中的应用。     

Radiative decay engineering: biophysical and biomedical applications.

Fluorescence spectroscopy is a widely used research tool in biochemistry and molecular biology. Fluorescence has also become the dominant method enabling the revolution in medical diagnostics, DNA sequencing, and genomics. To date all the fluorescence observables, including spectral shifts, anisotropies, quantum yields, and lifetimes, have all been utilized in basic and applied uses of fluorescence. In this forward-looking article we describe a new opportunity in fluorescence, radiative decay engineering (RDE). By RDE we mean modifying the emission of fluorophores or chromophores by increasing or decreasing their radiative decay rates. In most fluorescence experiments the radiative rates are not changed because these rates depend on the extinction coefficient of the fluorophore. This intrinsic rate is not changed by quenching and is only weakly dependent on environmental effects. Spectral changes are usually caused by changes in the nonradiative rates resulting from quenching or resonance energy transfer. These processes affect the emission by providing additional routes for decay of the excited states without emission. In contrast to the relatively constant radiative rates in free solution, it is known that the radiative rates can be modified by placing the fluorophores at suitable distances from metallic surfaces and particles. This Review summarizes results from the physics literature which demonstrate the effects of metallic surfaces, colloids, or islands on increasing or decreasing emissive rates, increasing the quantum yields of low quantum yield chromophores, decreasing the lifetimes, and directing the typically isotropic emission in specific directions. These effects are not due to reflection of the emitted photons, but rather as the result of the fluorophore dipole interacting with free electrons in the metal. These interactions change the intensity and temporal and spatial distribution of the radiation. We describe the unusual effects expected from increases in the radiative rates with reference to intrinsic and extrinsic biochemical fluorophores. For instance, the decreased lifetime can result in an effective increase in photostability. Proximity to nearby metallic surfaces can also increase the local field and modify the rate of excitation. We predict that the appropriate localization of fluorophores near particles can result in usefully high emission from "nonfluorescent" molecules and million-fold increases in the number of photons observable from each fluorophore. We also describe how RDE can be applied to medical testing and biotechnology. As one example we predict that nearby metal surfaces can be used to increase the low intrinsic quantum yields of nucleic acids and make unlabeled DNA detectable using its intrinsic metal-enhanced fluorescence.     

Transients and tradeoffs of phenotypic switching in a fluctuating limited environment

Phenotypic variability in a microorganism population is thought to be advantageous in fluctuating environments, however much remains unknown about the precise conditions for this advantage to hold. In particular competition for a growth-limiting resource and the dynamics of that resource in the environment modify the tradeoff between different effects of variability. Here we investigate theoretically a model system for variable populations under competition for a flowing resource that governs growth (chemostat model) and changes with time. This environment generally induces density-dependent selection among competing sub-populations. We characterize quantitatively the transient dynamics in this system, and find that equilibration between total population density and environment can occur separately and with a distinct timescale from equilibration between competing sub-populations. We analyze quantitatively the two opposing effects of heterogeneity-transient response to change, and fitness at equilibrium-and find the optimal strategy in a fluctuating environment. We characterize the phase diagram of the system in term of its optimal strategy and find it to be strongly dependent on the typical timescale of the environment and weakly dependent on the internal parameters of the population.     

Pathway phase waveform characteristics correlated with length and rate of stylet advancement and partial stylet withdrawal in AC electrical penetration graphs of adult whiteflies

A technique was developed for measuring the length of stylet insertion during adult whitefly probing. The distance that the labium shortens during a probe was shown to be equal to the length of stylets that were inserted into the plant tissue. The length of labial shortening then was measured in high-magnification video recordings of adult female silverleaf whitefly, Bemisia argentifolii, in conjunction with recording electrical penetration graphs (EPGs – AC method). Using a split-screen device, video images of the whitefly's labium during a probe and the EPG waveforms produced during the probe were recorded simultaneously on the same video tape. On playback, changes in labial length could be measured during specific EPG waveforms to determine the length of stylet insertion that occurred during the waveforms. The focus of the study was on two characteristics of the pathway phase sawtooth waveform: the frequency of voltage peaks and the increase in voltage level that occurs over time during sawtooth waveforms. The rate of stylet penetration was significantly and positively correlated with frequency of sawtooth waveform voltage peaks (r ²=0.33) and the length of stylet penetration was significantly and positively correlated (second-order polynomial) with the relative difference in voltage level between the beginning and end of the sawtooth waveform (r ²=0.43). Stylet advancement did not appear to occur during the few low-flat waveforms (unknown behavioral correlation) and high-flat waveforms (phloem phase) that were observed. Voltage drops occur sporadically during sawtooth waveforms, and these were associated with partial stylet withdrawal (indicated when the labium increased in length, but the probe was not terminated) with an accuracy of 99%.     

Elucidation of neuroprotective role of endogenous GABA and energy metabolites middle cerebral artery occluded model in rats

The excitatory amino acids (EAA) like glutamate, aspartate and inhibitory neurotransmitter GABA (gama amino butyric acid) play an important role in the pathophysiology of cerebral ischemia. The objective of the present study is to elucidate the role of endogenous GABA against EAA release in different regions during ischemia. The transient focal ischemia was induced in rats by using middle cerebral artery occlusion model (MCAo). The results indicate gradual elevation of brain glutamate, aspartate and GABA level at different brain regions and attained peak level at 72 h of ischemic reperfusion (IR). At 168 h of IR the EAA levels declined to base line but GABA level was found to be still elevated. The biochemical analysis shows the depleted brain ATP, Na+K+ATPase content and triphasic response of glutathione activity. It can be concluded that time dependent variation in the EAA and GABA release, endogenous GABA can be neuroprotective and earlier restoration of energy deprivation is essential to prevent further neurodegeneration. To have efficient treatment in ischemic condition, multiple approaches like energy supply, antagonism of EAA, controlling calcium function are essential.     

Intramolecular conformational transitions "random coil-helix-folded structure" in polypeptides.

A general theory has been developed for conformational intramolecular transitions in a single macromolecule with a high degree of polymerization (an infinite length model) capable of forming two types of ordered structures: the α-helix and the folded β-structure, as well as acquiring the random coil conformation. The phase diagram analysis of this system has shown that the regular β-structure state is separated from all other states of the chain by the phase boundary line. Any intersection of the phase boundary is a phase transition which can be either of the first order or second order, depending on values of the energy parameters of the system. Mechanisms of intramolecular rearrangements: β-structure–random coil and α-helix–β-structure have been discussed. It has been shown that there exist two different mechanisms for each of these rearrangements, and the regions of parameter variation corresponding to each mechanism have been specified.     

A Process-Based Mathematical Model on Methane Production with Emission Indices for Control

In this paper, a process-based mathematical model is developed for the production of methane through biodegradation. It is a three-dimensional model given by ordinary differential equations. The results of the analysis of the model are interpreted through three emission indices, which are introduced for the first time. The estimation of either one or all of them can interpret the feasibility of the equilibrium and the long-term emission tendency of methane. The vulnerability of the methane production process with respect to soil temperature effects in methanogenic phase has been discussed and a feasible condition within a specified temperature range has defined for the nonvulnerability of the methane production process and also it has shown that under the same condition, zero-emission process of methane will be nonvulnerable with respect to the soil temperature effects in methanogenic phase. Lastly, condition for zero emission of methane is also obtained and it is interpreted through the emission indices.     

Wavelet analysis of nonstationary fluctuations of Monte Carlo-simulated excitatory postsynaptic currents

Tracking spectral changes of rapidly varying signals is a demanding task. In this study, we explore on Monte Carlo-simulated glutamate-activated AMPA patch and synaptic currents whether a wavelet analysis offers such a possibility. Unlike Fourier methods that determine only the frequency content of a signal, the wavelet analysis determines both the frequency and the time. This is owing to the nature of the basis functions, which are infinite for Fourier transforms (sines and cosines are infinite), but are finite for wavelet analysis (wavelets are localized waves). In agreement with previous reports, the frequency of the stationary patch current fluctuations is higher for larger currents, whereas the mean-variance plots are parabolic. The spectra of the current fluctuations and mean-variance plots are close to the theoretically predicted values. The median frequency of the synaptic and nonstationary patch currents is, however, time dependent, though at the peak of synaptic currents, the median frequency is insensitive to the number of glutamate molecules released. Such time dependence demonstrates that the "composite spectra" of the current fluctuations gathered over the whole duration of synaptic currents cannot be used to assess the mean open time or effective mean open time of AMPA channels. The current (patch or synaptic) versus median frequency plots show hysteresis. The median frequency is thus not a simple reflection of the overall receptor saturation levels and is greater during the rise phase for the same saturation level. The hysteresis is due to the higher occupancy of the doubly bound state during the rise phase and not due to the spatial spread of the saturation disk, which remains remarkably constant. Albeit time dependent, the variance of the synaptic and nonstationary patch currents can be accurately determined. Nevertheless the evaluation of the number of AMPA channels and their single current from the mean-variance plots of patch or synaptic currents is not highly accurate owing to the varying number of the activatable AMPA channels caused by desensitization. The spatial nonuniformity of open, bound, and desensitized AMPA channels, and the time dependence and spatial nonuniformity of the glutamate concentration in the synaptic cleft, further reduce the accuracy of estimates of the number of AMPA channels from synaptic currents. In conclusion, wavelet analysis of nonstationary fluctuations of patch and synaptic currents expands our ability to determine accurately the variance and frequency of current fluctuations, demonstrates the limits of applicability of techniques currently used to evaluate the single channel current and number of AMPA channels, and offers new insights into the mechanisms involved in the generation of unitary quantal events at excitatory central synapses.     

Optical Modeling of Plasmonic Nanoparticles Enhanced Light Emission of Silicon Light-Emitting Diodes

Significant enhancement of radiative efficiency of thin-film silicon light-emitting diodes achieved by placing the active layer in close proximity to silver (Ag) nanoparticles has been observed. In this paper, optical properties including transmission, reflection, and absorption of a random assembly of Ag nanoparticles are theoretically investigated using the effective medium model. Furthermore, the influence of Ag nanoparticles on light emission of silicon light-emitting diodes is studied by an improved effective mode volume model we propose here. The normalized line shape of dipole oscillation is calculated directly using Lorentz–Drude model without using any approximation. Thus, it results in more accurate calculation of the enhanced Purcell factor in comparison with the conventional approach. We show that an enhancement of radiative efficiency of silicon light-emitting diodes can be achieved by localized surface plasmons on metal nanoparticles. The calculated result of optimal Ag nanoparticle size to enhance light emission of silicon light-emitting diodes at 900 nm wavelength is in very good agreement with those obtained from the experimental result. The model is useful for the design of metallic nanoparticles enhanced light emitters.     

Daunomycin-polypeptide conjugates with antitumor activity

We have developed a group of water-soluble drug conjugates in which daunomycin (Dau) is coupled to cationic, amphoteric or anionic branched polypeptides and a new conjugate containing a cationic polypeptide carrier modified with a cell penetrating octaarginine. We investigated in vitro physiological activity of these conjugates in several aspects: in vitro cytotoxicity and cytostatic effect, adhesion and cellular uptake were examined on murine (J774 and L1210) and human (MonoMac6 and HL-60) leukemia cell lines and on murine bone marrow derived macrophages. We found that these processes are dependent on the properties of the carrier, on experimental conditions like concentration and incubation time. We found that attachment of polypeptide and cell penetrating peptide to the bioactive agent, depending on the cell line, could significantly improve the antitumor activity of the drug.     

The equilibrium concept and density dependence tests What does it all mean?

Summary Tests of density dependent regulation of population size depend on the concept of equilibrium population size. Such an equilibrium is a purely theoretical construct whose existence in the field is debatable and whose value cannot be measured. An equilibrium is supposed to fluctuate in time, but the extent of the fluctuations relative to those of the population size is unknowable. It is impossible to separate a fluctuating population size from a fluctuating equilibrium value and from fluctuating deviations from an equilibrium value. Because it cannot be determined whether a given population size is above, at, or below equilibrium, the course of population size in unpredictable and density dependence tests cannot be expected to produce useful results. Stabilization tests may provide a more useful alternative.     

Negative frequency‐dependent selection maintains coexisting genotypes during fluctuating selection

Natural environments are rarely static; rather selection can fluctuate on timescales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm‐regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency‐dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments, coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency‐dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments.     

Inorganic-pyrophosphate-dependent phosphorylation of spinach thylakoid proteins.

It has been shown for the first time that several photosystem-II thylakoid proteins and the main chlorophyll-a/b light-harvesting complex can be phosphorylated with inorganic pyrophosphate as phosphate donor. With pyrophosphate, as with ATP, the protein-kinase reaction is dependent on light or a strong reducing agent. The reaction which can be demonstrated in well-washed spinach thylakoids is dependent on electron transport and is controlled by the redox state of the plastoquinone pool. It is suggested that the pyrophosphate-dependent thylakoid protein phosphorylation is mediated by the same kinase which is responsible for the ATP-dependent protein phosphorylation. This pyrophosphate-dependent kinase activity may be derived from an evolutionary precursor from which ATP-dependent protein phosphorylation also developed.     

Conformations and interactions of excited states. II. Polystyrene, polypeptides, and proteins

Previous fluorescence and phosphorescence studies of aromatic model compounds have been extended to polymers: “atactic” and isotactic polystyrene, seven aromatic poly-(amino acids), and two proteins. We have confirmed previous observations that both forms of polystyrene exhibit strong excimer fluorescence emission at room temperature but not at 77°K. Of the poly(amino acids) (all observed in helix-supporting solvents), poly-L -phenylalanine, poly(α-benzyl-L -aspartic acid), and poly-1-benzyl-L -histidine likewise show excimer emission at room temperature but not at 77°K., while poly-L -tyrosine, poly-L -tryptophan, poly(γ-benzyl-L -glutamic acid), and poly-S-benzyl-L -cysteine exhibit no excimer emission at either temperature. The aromatic residues of bovine serum albumin exhibit only “normal” fluorescence, but, lysozyme appears to be unique among proteins in showing excimer-like tryptophan emission in the native state; its luminescence becomes “normal” upon denaturation. It appears very probable that none of these polymers has a ground-state conformation in which the aromatic groups have face-to-face orientations appropriate for excimer interaction. It is concluded that at room temperature absorption of light can cause local “melting” of regular (usually helical) structures and thus, in some polymers, permit the attainment of a face-to-face arrangement of aromatic rings within the radiative lifetime of their excited singlet states. In certain other polymers (for reasons not clear at present), and in all polymers at 77°K., this does not occur. This concept is extended to provide a bettor basis for understanding the mechanism of formation of the photodimer of thy mine in irradiated DNA.     

Rates of deactivation processes of indole derivatives in water-organic solvent mixtures--application to tryptophyl fluorescence of proteins.

The fluorescence quantum yield and the fluorescence decay of indole, 3-methylindole, 1-methylindole and N-acetyltryptophanamide have been measured in different water-dioxane mixtures. For the first three derivatives, the fluorescence decays were found independent of the emission wavelength and were analyzed as single exponential functions. In the case of N-methylindole the rate of the non radiative deactivation processes knr increased linearly with the molar fraction of dioxane whereas for indole and scatole the variation of knr was biphasic. This behaviour can be explained by two excited state deactivations of these non N-methylated compounds in water and high water content mixtures; one of these deactivation processes occuring through an hydrogen bond between the N-H group and a water molecule. The rate of non radiative deactivation of N-acetyltryptophanamide was dominated by the internal quenching involving the intramolecular carbonyl. The rate of the radiative deactivation process kF of these four compounds increased linearly with the wavenumber of the fluorescence spectrum maximum. Data relative to the three non N-methylated derivatives fell practically on the same straight line. Data from other works have been gathered in order to check if a similar relation between the intrinsic kF and vF values can exist for the tryptophyl fluorescence emission of proteins.     

Radiative decay engineering 7: Tamm state-coupled emission using a hybrid plasmonic–photonic structure

There is a continuing need to increase the brightness and photostability of fluorophores for use in biotechnology, medical diagnostics, and cell imaging. One approach developed during the past decade is to use metallic surfaces and nanostructures. It is now known that excited state fluorophores display interactions with surface plasmons, which can increase the radiative decay rates, modify the spatial distribution of emission, and result in directional emission. One important example is surface plasmon-coupled emission (SPCE). In this phenomenon, the fluorophores at close distances from a thin metal film, typically silver, display emission over a small range of angles into the substrate. A disadvantage of SPCE is that the emission occurs at large angles relative to the surface normal and at angles that are larger than the critical angle for the glass substrate. The large angles make it difficult to collect all of the coupled emission and have prevented the use of SPCE with high-throughput and/or array applications. In the current article, we describe a simple multilayer metal–dielectric structure that allows excitation with light that is perpendicular (normal) to the plane and provides emission within a narrow angular distribution that is normal to the plane. This structure consists of a thin silver film on top of a multilayer dielectric Bragg grating, with no nanoscale features except for the metal or dielectric layer thicknesses. Our structure is designed to support optical Tamm states, which are trapped electromagnetic modes between the metal film and the underlying Bragg grating. We used simulations with the transfer matrix method to understand the optical properties of Tamm states and localization of the modes or electric fields in the structure. Tamm states can exist with zero in-plane wavevector components and can be created without the use of a coupling prism. We show that fluorophores on top of the metal film can interact with the Tamm state under the metal film and display Tamm state-coupled emission (TSCE). In contrast to SPCE, the Tamm states can display either S or P polarization. The TSCE angle is highly sensitive to wavelength, which suggests the use of Tamm structures to provide both directional emission and wavelength dispersion. Metallic structures can modify fluorophore decay rates but also have high losses. Photonic crystals have low losses but may lack the enhanced light-induced fields near metals. The combination of plasmonic and photonic structures offers the opportunity for radiative decay engineering to design new formats for clinical testing and other fluorescence-based applications.     

Correlating Phase Behavior with Photophysical Properties in Mixed‐Cation Mixed‐Halide Perovskite Thin Films

Mixed cation perovskites currently achieve very promising efficiency and operational stability when used as the active semiconductor in thin‐film photovoltaic devices. However, an in‐depth understanding of the structural and photophysical properties that drive this enhanced performance is still lacking. Here the prototypical mixed‐cation mixed‐halide perovskite (FAPbI₃)_0.85(MAPbBr₃)_0.15 is explored, and temperature‐dependent X‐ray diffraction measurements that are correlated with steady state and time‐resolved photoluminescence data are presented. The measurements indicate that this material adopts a pseudocubic perovskite α phase at room temperature, with a transition to a pseudotetragonal β phase occurring at ≈260 K. It is found that the temperature dependence of the radiative recombination rates correlates with temperature‐dependent changes in the structural configuration, and observed phase transitions also mark changes in the gradient of the optical bandgap. The work illustrates that temperature‐dependent changes in the perovskite crystal structure alter the charge carrier recombination processes and photoluminescence properties within such hybrid organic–inorganic materials. The findings have significant implications for photovoltaic performance at different operating temperatures, as well as providing new insight on the effect of alloying cations and halides on the phase behavior of hybrid perovskite materials.     

Motility of the microtubular axostyle in Pyrsonympha

The rhythmic movement of the microtubular axostyle in the termite flagellate, Pyrsonympha vertens, was analyzed with polarization and electron microscopy. The protozoan axostyle is birefringent as a result of the semi-crystalline alignment of approximately 2,000 microtubules. The birefringence of the organelle permits analysis of the beat pattern in vivo. Modifications of the beat pattern were achieved with visible and UV microbeam irradiation. The beating axostyle is helically twisted and has two principal movements, one resembling ciliary and the other flagellar beating. The anterior portion of the beating axostyle has effective and recovery phases with each beat thereby simulating the flexural motion of a beating cilium. Undulations develop from the flexural flipping motion of the anterior segment and travel along the axostyle like flagellar waves. The shape of the waves differs from that of flagellar waves, however, and are described as sawtooth waves. The propagating sawtooth waves contain a sharp bend, approximately 3 micron in length, made up of two opposing flexures followed by a straight helical segment approximately 23 micron long. The average wavelength is approximately 25 micron, and three to four sawtooth waves travel along the axostyle at one time. The bends are nearly planar and can travel in either direction along the axostyle with equal velocity. At temperatures between 5 degrees and 30 degrees C, one sees a proportionate increase or decrease in wave propagation velocity as the temperature is raised or lowered. Beating stops below 5 degrees C but will resume if the preparation is warmed. A microbeam of visible light shone on a small segment of the axostyle causes the typical sawtooth waves to transform into short sine-like waves that accumulate in the area irradiated. Waves entering the affected region appear to stimulate waves already accumulated there to move, and waves that emerge take on the normal sawtooth wave pattern. The effective wavelengths of visible light capable of modifying the wave pattern is in the blue region of the spectrum. The axostyle is severed when irradiated with an intense microbeam of UV light. Short segments of axostyle produced by severing it at two places with a UV microbeam can curl upon themselves into shapes resembling lockwashers. We propose that the sawtooth waves in the axostyle of P. vertens are generated by interrow cross-bridges which are active in the straight regions.