The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

19 p.

Analysis of temporal structure in spike trains of visual cortical area MT

The temporal structure of neuronal spike trains in the visual cortex can provide detailed information about the stimulus and about the neuronal implementation of visual processing. Spike trains recorded from the macaque motion area MT in previous studies (Newsome et al., 1989a; Britten et al., 1992; Zohary et al., 1994) are analyzed here in the context of the dynamic random dot stimulus which was used to evoke them. If the stimulus is incoherent, the spike trains can be highly modulated and precisely locked in time to the stimulus. In contrast, the coherent motion stimulus creates little or no temporal modulation and allows us to study patterns in the spike train that may be intrinsic to the cortical circuitry in area MT. Long gaps in the spike train evoked by the preferred direction motion stimulus are found, and they appear to be symmetrical to bursts in the response to the anti-preferred direction of motion. A novel cross-correlation technique is used to establish that the gaps are correlated between pairs of neurons. Temporal modulation is also found in psychophysical experiments using a modified stimulus. A model is made that can account for the temporal modulation in terms of the computational theory of biological image motion processing. A frequency domain analysis of the stimulus reveals that it contains a repeated power spectrum that may account for psychophysical and electrophysiological observations.

Some neurons tend to fire bursts of action potentials while others avoid burst firing. Using numerical and analytical models of spike trains as Poisson processes with the addition of refractory periods and bursting, we are able to account for peaks in the power spectrum near 40 Hz without assuming the existence of an underlying oscillatory signal. A preliminary examination of the local field potential reveals that stimulus-locked oscillation appears briefly at the beginning of the trial.

Seismic structure above and below the core-mantle boundary

Seismic structure above and below the core-mantle boundary (CMB) has been studied through use of travel time and waveform analyses of several different seismic wave groups. Anomalous systematic trends in observables document mantle heterogeneity on both large and small scales. Analog and digital data has been utilized, and in many cases the analog data has been optically scanned and digitized prior to analysis.

Differential travel times of S - SKS are shown to be an excellent diagnostic of anomalous lower mantle shear velocity (V s) structure. Wavepath geometries beneath the central Pacific exhibit large S- SKS travel time residuals (up to 10 sec), and are consistent with a large scale 0(1000 km) slower than average V_s region (≥3%). S - SKS times for paths traversing this region exhibit smaller scale patterns and trends 0(100 km) indicating V_s perturbations on many scale lengths. These times are compared to predictions of three tomographically derived aspherical models: MDLSH of Tanimoto [1990], model SH12_WM13 of Suet al. [1992], and model SH.10c.17 of Masters et al. [1992]. Qualitative agreement between the tomographic model predictions and observations is encouraging, varying from fair to good. However, inconsistencies are present and suggest anomalies in the lower mantle of scale length smaller than the present 2000+ km scale resolution of tomographic models. 2-D wave propagation experiments show the importance of inhomogeneous raypaths when considering lateral heterogeneities in the lowermost mantle.

A dataset of waveforms and differential travel times of S, ScS, and the arrival from the D" layer, Scd, provides evidence for a laterally varying V_s velocity discontinuity at the base of the mantle. Two different localized D" regions beneath the central Pacific have been investigated. Predictions from a model having a V_s discontinuity 180 km above the CMB agree well with observations for an eastern mid-Pacific CMB region. This thickness differs from V_s discontinuity thicknesses found in other regions, such as a localized region beneath the western Pacific, which average near 280 km. The "sharpness" of the V_s jump at the top of D", i.e., the depth range over which the V_s increase occurs, is not resolved by our data, and our data can in fact may be modeled equally well by a lower mantle with the increase in V_s at the top of D" occurring over a 100 krn depth range. It is difficult at present to correlate D" thicknesses from this study to overall lower mantle heterogeneity, due to uncertainties in the 3-D models, as well as poor coverage in maps of D" discontinuity thicknesses.

P-wave velocity structure (V_p) at the base of the mantle is explored using the seismic phases SKS and SPdKS. SPdKS is formed when SKS waves at distances around 107° are incident upon the CMB with a slowness that allows for coupling with diffracted P-waves at the base of the mantle. The P-wave diffraction occurs at both the SKS entrance and exit locations of the outer core. SP_dKS arrives slightly later in time than SKS, having a wave path through the mantle and core very close to SKS. The difference time between SKS and SP_dKS strongly depends on V_p at the base of the mantle near SK Score entrance and exit points. Observations from deep focus Fiji-Tonga events recorded by North American stations, and South American events recorded by European and Eurasian stations exhibit anomalously large SP_dKS - SKS difference times. SKS and the later arriving SP_dKS phase are separated by several seconds more than predictions made by 1-D reference models, such as the global average PREM [Dziewonski and Anderson, 1981] model. Models having a pronounced low-velocity zone (5%) in V_p in the bottom 50-100 km of the mantle predict the size of the observed SP_dK S-SKS anomalies. Raypath perturbations from lower mantle V_s structure may also be contributing to the observed anomalies.

Outer core structure is investigated using the family of SmKS (m=2,3,4) seismic waves. SmKS are waves that travel as S-waves in the mantle, P-waves in the core, and reflect (m-1) times on the underside of the CMB, and are well-suited for constraining outermost core V_p structure. This is due to closeness of the mantle paths and also the shallow depth range these waves travel in the outermost core. S3KS - S2KS and S4KS - S3KS differential travel times were measured using the cross-correlation method and compared to those from reflectivity synthetics created from core models of past studies. High quality recordings from a deep focus Java Sea event which sample the outer core beneath the northern Pacific, the Arctic, and northwestern North America (spanning 1/8th of the core's surface area), have SmKS wavepaths that traverse regions where lower mantle heterogeneity is pre- dieted small, and are well-modeled by the PREM core model, with possibly a small V_p decrease (1.5%) in the outermost 50 km of the core. Such a reduction implies chemical stratification in this 50 km zone, though this model feature is not uniquely resolved. Data having wave paths through areas of known D" heterogeneity (±2% and greater), such as the source-side of SmKS lower mantle paths from Fiji-Tonga to Eurasia and Africa, exhibit systematic SmKS differential time anomalies of up to several seconds. 2-D wave propagation experiments demonstrate how large scale lower mantle velocity perturbations can explain long wavelength behavior of such anomalous SmKS times. When improperly accounted for, lower mantle heterogeneity maps directly into core structure. Raypaths departing from homogeneity play an important role in producing SmKS anomalies. The existence of outermost core heterogeneity is difficult to resolve at present due to uncertainties in global lower mantle structure. Resolving a one-dimensional chemically stratified outermost core also remains difficult due to the same uncertainties. Restricting study to higher multiples of SmKS (m=2,3,4) can help reduce the affect of mantle heterogeneity due to the closeness of the mantle legs of the wavepaths. SmKS waves are ideal in providing additional information on the details of lower mantle heterogeneity.

Effects of self energy of the ions on the double layer structure and properties at the dielectric interface

Although numerous theoretical efforts have been put forth, a systematic, unified and predictive theoretical framework that is able to capture all the essential physics of the interfacial behaviors of ions, such as the Hofmeister series effect, Jones-Ray effect and the salt effect on the bubble coalescence remain an outstanding challenge. The most common approach to treating electrostatic interactions in the presence of salt ions is the Poisson-Boltzmann (PB) theory. However, there are many systems for which the PB theory fails to offer even a qualitative explanation of the behavior, especially for ions distributed in the vicinity of an interface with dielectric contrast between the two media (like the water-vapor/oil interface). A key factor missing in the PB theory is the self energy of the ion.

In this thesis, we develop a self-consistent theory that treats the electrostatic self energy (including both the short-range Born solvation energy and the long-range image charge interactions), the nonelectrostatic contribution of the self energy, the ion-ion correlation and the screening effect systematically in a single framework. By assuming a finite charge spread of the ion instead of using the point-charge model, the self energy obtained by our theory is free of the divergence problems and gives a continuous self energy across the interface. This continuous feature allows ions on the water side and the vapor/oil side of the interface to be treated in a unified framework. The theory involves a minimum set of parameters of the ion, such as the valency, radius, polarizability of the ions, and the dielectric constants of the medium, that are both intrinsic and readily available. The general theory is first applied to study the thermodynamic property of the bulk electrolyte solution, which shows good agreement with the experiment result for predicting the activity coefficient and osmotic coefficient.

Next, we address the effect of local Born solvation energy on the bulk thermodynamics and interfacial properties of electrolyte solution mixtures. We show that difference in the solvation energy between the cations and anions naturally gives rise to local charge separation near the interface, and a finite Galvani potential between two coexisting solutions. The miscibility of the mixture can either increases or decreases depending on the competition between the solvation energy and translation entropy of the ions. The interfacial tension shows a non-monotonic dependence on the salt concentration: it increases linearly with the salt concentration at higher concentrations, and decreases approximately as the square root of the salt concentration for dilute solutions, which is in agreement with the Jones-Ray effect observed in experiment.

Next, we investigate the image effects on the double layer structure and interfacial properties near a single charged plate. We show that the image charge repulsion creates a depletion boundary layer that cannot be captured by a regular perturbation approach. The correct weak-coupling theory must include the self-energy of the ion due to the image charge interaction. The image force qualitatively alters the double layer structure and properties, and gives rise to many non-PB effects, such as nonmonotonic dependence of the surface energy on concentration and charge inversion. The image charge effect is then studied for electrolyte solutions between two plates. For two neutral plates, we show that depletion of the salt ions by the image charge repulsion results in short-range attractive and long-range repulsive forces. If cations and anions are of different valency, the asymmetric depletion leads to the formation of an induced electrical double layer. For two charged plates, the competition between the surface charge and the image charge effect can give rise to like- charge attraction.

Then, we study the inhomogeneous screening effect near the dielectric interface due to the anisotropic and nonuniform ion distribution. We show that the double layer structure and interfacial properties is drastically affected by the inhomogeneous screening if the bulk Debye screening length is comparable or smaller than the Bjerrum length. The width of the depletion layer is characterized by the Bjerrum length, independent of the salt concentration. We predict that the negative adsorption of ions at the interface increases linearly with the salt concentration, which cannot be captured by either the bulk screening approximation or the WKB approximation. For asymmetric salt, the inhomogeneous screening enhances the charge separation in the induced double layer and significantly increases the value of the surface potential.

Finally, to account for the ion specificity, we study the self energy of a single ion across the dielectric interface. The ion is considered to be polarizable: its charge distribution can be self-adjusted to the local dielectric environment to minimize the self energy. Using intrinsic parameters of the ions, such as the valency, radius, and polarizability, we predict the specific ion effect on the interfacial affinity of halogen anions at the water/air interface, and the strong adsorption of hydrophobic ions at the water/oil interface, in agreement with experiments and atomistic simulations.

The theory developed in this work represents the most systematic theoretical technique for weak-coupling electrolytes. We expect the theory to be more useful for studying a wide range of structural and dynamic properties in physicochemical, colloidal, soft-matter and biophysical systems.

Hyperfine interactions and nuclear structure

An automatic experimental apparatus for perturbed angular correlation measurements, capable of incorporating Ge(Li) detectors as well as scintillation counters, has been constructed.

The gamma-gamma perturbed angular correlation technique has been used to measure magnetic dipole moments of several nuclear excited states in the osmium transition region. In addition, the hyperfine magnetic fields, experienced by nuclei of 'impurity' atoms embedded in ferromagnetic host lattices, have been determined for several '4d' and '5d' impurity atoms.

The following magnetic dipole moments were obtained in the osmium transition region μ_2⁺(¹⁹⁰Os) = 0.54 ± 0.06 nm μ_4⁺(¹⁹⁰Os) = 0.88 ± 0.48 nm μ_2⁺(¹⁹²Os) = 0.56 ± 0.08 nm μ_2⁺(¹⁹²Pt) = 0.56 ± 0.06 nm μ_2^+’(¹⁹²Pt) = 0.62 ± 0.14 nm.

These results are discussed in terms of three collective nuclear models; the cranking model, the rotation-vibration model and the pairing-plus-quadrupole model. The measurements are found to be in satisfactory agreement with collective descriptions of low lying nuclear states in this region.

The following hyperfine magnetic fields of 'impurities' in ferromagnetic hosts were determined; H_int(Cd Ni) = - (64.0 ± 0.8)kG H_int(Hg Fe) = - (440 ± 105)kG H_int(Hg Co) = - (370 ± 78)kG H_int(Hg Ni) = - (86 ± 22)kG H_int(Tl Fe) = - (185 ± 70)kG H_int(Tl Co) = - (90 ± 35)kG H_int(Ra Fe) = - (105 ± 20)kG H_int(Ra Co) = - (80 ± 16)kG H_int(Ra Ni) = - (30 ± 10)kG, where in H_int(AB); A is the impurity atom embedded in the host lattice B. No quantitative theory is available for comparison. However, these results are found to obey the general systematics displayed by these fields. Several mechanisms which may be responsible for the appearance of these fields are mentioned.

Finally, a theoretical expression for time-differential perturbed angular correlation measurement, which duplicates experimental conditions is developed and its importance in data analysis is discussed.

The structure of liquid argon as determined by x-ray diffraction

X-ray diffraction measurements and subsequent data analyses have been carried out on liquid argon at five states in the density range of 0.91 to 1.135 gm/cc and temperature range of 127 to 143°K. Duplicate measurements were made on all states. These data yielded radial distribution and direct correlation functions which were then used to compute the pair potential using the Percus-Yevick equation. The potential minima are in the range of -105 to -120°K and appear to substantiate current theoretical estimates of the effective pair potential in the presence of a weak three-body force.

The data analysis procedure used was new and does not distinguish between the coherent and incoherent absorption factors for the cell scattering which were essentially equal. With this simplification, the argon scattering estimate was compared to the gas scattering estimate on the laboratory frame of reference and the two estimates coincided, indicating the data normalized. The argon scattering on the laboratory frame of reference was examined for the existence of the peaks in the structure factor and the existence of an observable third peak was considered doubtful.

Numerical studies of the effect of truncation, normalization, the subsidiary peak phenomenon in the radial distribution function, uncertainties in the low angle data relative to errors in the direct correlation function and the distortion phenomenon are presented.

The distortion phenomenon for this experiment explains why the Mikolaj-Pings argon data yielded pair potential well depths from the Percus-Yevick equation that were too shallow and an apparent slope with respect to density that was too steep compared to theoretical estimates.

The data presented for each measurement are: empty cell and cell plus argon intensity, absorption factors, argon intensity, smoothed argon intensity, smoothed argon intensity corrected for distortion, structure factor, radial distribution function, direct correlation function and the pair potential from the Percus-Yevick equation.

Anisotropic crystallographic properties, strain, and their effects on band structure of m -plane GaN on LiAlO2 (100)

The m-plane GaN films grown on LiAlO2(100) by metal-organic chemical vapor deposition exhibit anisotropic crystallographic properties. The Williamson-Hall plots point out they are due to the different tilts and lateral correlation lengths of mosaic blocks parallel and perpendicular to GaN[0001] in the growth plane. The symmetric and asymmetric reciprocal space maps reveal the strain of m-plane GaN to be biaxial in-plane compress epsilon(xx)=-0.79% and epsilon(zz)=-0.14% with an out-of-plane dilatation epsilon(yy)=0.38%. This anisotropic strain further separates the energy levels of top valence band at Gamma point. The energy splitting as 37 meV as well as in-plane polarization anisotropy for transitions are found by the polarized photoluminescence spectra at room temperature. (c) 2008 American Institute of Physics.

Survival and changes in the fine structure of selected tissues of Penaeus monodon Fabricius juveniles fed various carbohydrates

Penaeus monodon juveniles were reared on semipurified diets containing various carbohydrates (maltose, sucrose, dextrin, molasses, cassava starch, corn starch or sago palm starch). Significant differences were observed between the type as well as the level of carbohydrate in the diet on the survival of the juveniles. Results indicate that there does not seem to be any correlation between survival and the complexity of the carbohydrates.

Turbulent flow structure in experimental laboratory wind-generated gravity waves

This paper is the third part of a report on systematic measurements and analyses of wind-generated water waves in a laboratory environment. The results of the measurements of the turbulent flow on the water side are presented here, the details of which include the turbulence structure, the correlation functions, and the length and velocity scales. It shows that the mean turbulent velocity profiles are logarithmic, and the flows are hydraulically rough. The friction velocity in the water boundary layer is an order of magnitude smaller than that in the wind boundary layer. The level of turbulence is enhanced immediately beneath the water surface due to micro-breaking, which reflects that the Reynolds shear stress is of the order u *w 2. The vertical velocities of the turbulence are related to the relevant velocity scale at the still-water level. The autocorrelation function in the vertical direction shows features of typical anisotropic turbulence comprising a large range of wavelengths. The ratio between the microscale and macroscale can be expressed as λ/Λ=a Re Λ n, with the exponent n slightly different from -1/2, which is the value when turbulence production and dissipation are in balance. On the basis of the wavelength and turbulent velocity, the free-surface flows in the present experiments fall into the wavy free-surface flow regime. The integral turbulent scale on the water side alone underestimates the degree of disturbance at the free surface. © 2012 Elsevier B.V.

Influence of leaf tissue structure on host feeding selection by pea leaf miner Liriomyza huidobrensis (Diptera : Agromyzidae)

Host feeding selection by the female pea leafminer, Liriomyza huidobrensis, on 47 species of plants was studied. The leaves were sectioned by microtome, and 15 characteristics of the leaf tissue structure were measured under a microscope. Correlation analysis between host feeding selection and leaf tissue structure indicated that the preference of host feeding selection was positively correlated with the percentage of moisture content of leaves and negatively with thickness of the epidermis wall, and densities of the palisade and spongy tissues of leaves. Leaf tissue structure was influential in feeding and probing behavior of female L. huidobrensis. So, thickness of epidermis wall, densities of the palisade and spongy tissues can act as a physical barrier to female oviposition. Furthermore, higher densities of palisade and spongy tissues can be considered a resistant trait which affects mining of leaf miner larvae as well. As a result, plants with lower leaf moisture content may not be suitable for the development of L. huidobrensis.

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Population genetic structure of Carchesium polypinum (Ciliophora : Peritrichia) in four chinese lakes inferred from ISSR fingerprinting: High diversity but low differentiation

Although the peritrichous ciliate Carchesium polypinum is common in freshwater, its population genetic structure is largely unknown. We used inter-simple sequence repeat (ISSR) fingerprinting to analyze the genetic structure of 48 different isolates of the species from four lakes in Wuhan, central China. Using eight polymorphic primers, 81 discernible DNA fragments were detected, among which 76 (93.83%) were polymorphic, indicating high genetic diversity at the isolate level. Further, Nei's gene diversity (h) and Shannon's Information index (I) between the different isolates both revealed a remarkable genetic diversity, higher than previously indicated by their morphology. At the same time, substantial gene flow was found. So the main factors responsible for the high level of diversity within populations are probably due to conjugation (sexual reproduction) and wide distribution of swarmers. Analysis of molecular variance (AMOVA) showed that there was low genetic differentiation among the four populations probably due to common ancestry and flooding events. The cluster analysis and principal component analysis (PCA) suggested that genotypes isolated from the same lake displayed a higher genetic similarity than those from different lakes. Both analyses separated C. polypinum isolates into subgroups according to the geographical locations. However, there is only a weak positive correlation between the genetic distance and geographical distance, suggesting a minor effect of geographical distance on the distribution of genetic diversity between populations of C. polypinum at the local level. In conclusion, our studies clearly demonstrated that a single morphospecies may harbor high levels of genetic diversity, and that the degree of resolution offered by morphology as a marker for measuring distribution patterns of genetically distinct entities is too low.

Structure, magnetization, and low-temperature spin dynamic behavior of zincblende Mn-rich Mn(Ga)As nanoclusters embedded in GaAs

We have fabricated a set of samples of zincblende Mn-rich Mn(Ga)As clusters embedded in GaAs matrices by annealing (Ga,Mn)As films with different nominal Mn content at 650 degrees C. For the samples with Mn content no more than 4.5%, the Curie temperature reaches nearly 360 K. However, when Mn content is higher than 5.4%, the samples exhibit a spin-glass-like behavior. We suggest that these different magnetic properties are caused by the competing result of dipolar and Ruderman-Kittel-Kasuya-Yosida interaction among clusters. The low-temperature spin dynamic behavior, especially the relaxation effect, shows the extreme creeping effect which is reflected by the time constant tau of similar to 10(11) s at 10 K. We explain this phenomenon by the hierarchical model based on the mean-field approach. We also explain the memory effect by the relationship between the correlation function and the susceptibility.

Correlation between optical and electrical properties in In0.52Al0.48As/InxGa1-xAs metamorphic high-electron-mobility-transistor structures on GaAs substrates

4.2 K photoluminescence (PL) and 77 K standard Hall-effect measurements were performed for In0.52Al0.48As/InxGa1-xAs metamorphic high-electron-mobility-transistor (HEMT) structures grown on GaAs substrates with different indium contents in the InxGa1-xAs well or different Si delta-doping concentrations. It was found that electron concentrations increased with increasing PL intensity ratio of the "forbidden" transition (the second electron subband to the first heavy-hole subband) to the sum of the "allowed" transition (the first electron subband to the first heavy-hole subband) and the forbidden transition. And electron mobilities decreased with increasing product of the average full width at half maximum of allowed and forbidden transitions and the electron effective mass in the InxGa1-xAs quantum well. These results show that PL measurements are a good supplemental tool to Hall-effect measurements in optimization of the HEMT layer structure. (c) 2006 American Institute of Physics.

Raman evidence for atomic correlation between the two constituent tubes in double-walled carbon nanotubes

Four well-resolved peaks with very narrow linewidths were found in the D-band and G'-band features of double-walled carbon nanotubes (DWNTs). This fact implies the occurrence of additional van Hove singularities (vHSs) in the joint density of states (JDOS) of DWNTs, which is consistent with theoretical calculations. According to their peak frequencies and theoretical analysis, the two outer peaks can be deduced to originate from a strong coupling between the two constituent tubes of commensurate DWNTs and the two inner peaks were curvature-related and assigned to originate from the two tubes with a weak coupling. This observation and elucidation constitute the first Raman evidence for atomic correlation and the resulting electronic structure change of the two constituent tubes in DWNTs. This result opens the possibility of predicting and modifying the electronic properties of DWNTs for their electronic applications.