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At least 613 records · Page 34Linked to original sources

PubMed2005

N-K near-edge x-ray-absorption fine structures of acetonitrile in gas phase.

The dynamic processes of N(1s) core-hole excitation in gas-phase CH3CN molecule have been studied at both Hartree-Fock and hybrid density-functional theory levels. The vibrational structure is analyzed for fully optimized core-excited states. Frank-Condon factors are obtained using the linear coupling model for various potential surfaces. It is found that the vibrational profile of the N-K absorption can be largely described by a summation of two vibrational progressions: a structure-rich profile of nu(CN) stretching mode and a large envelope of congestioned vibrational levels related to the strong (-C-CN) terminal bending bond. Excellent agreement between theoretical and experimental spectra is obtained.

Journal Article↗

PubMed2005

Simulation of a complex spectrum: interplay of five electronic states and 21 vibrational degrees of freedom in C5H4 +.

Using a five-state, all-mode vibronic coupling model Hamiltonian derived in a previous publication [A. Markmann et al., J. Chem. Phys. 122, 144320 (2005)], we have calculated the photoelectron spectrum of the pentatetraene cation in the neighborhood of the B (2)E state, which can be represented with charge-localized components. To this end, quantum nuclear dynamics calculations were performed using the multiconfiguration time-dependent Hartree method, taking all 21 vibrational normal modes into account. Compared to experiment, the main features are reproduced but higher accuracy experiments are necessary to gauge the accuracy of the predictions for the vibronic progressions at the rising flank of the spectrum.

Journal Article↗

PubMed2006

Steady Marangoni flow traveling with chemical fronts.

When autocatalytic chemical fronts propagate in thin layers of solution in contact with air, they can induce capillary flows due to surface tension gradients across the front (Marangoni flows). We investigate here such an interplay between autocatalytic reactions, diffusion, and Marangoni effects with a theoretical model coupling the incompressible Navier-Stokes equations to a conservation equation for the autocatalytic product concentration in the absence of gravity and for isothermal conditions. The boundary condition at the open liquid/air interface takes the surface activity of this product into account and introduces the solutal Marangoni number M representing the intensity of the coupling between hydrodynamics and reaction-diffusion processes. Positive and negative Marangoni numbers correspond, respectively, to the cases where the product decreases or increases surface tension behind the front. We show that, in both cases, such coupled systems reach an asymptotic dynamics characterized by a steady fluid vortex traveling at a constant speed with the front and deforming it, with, however, an asymmetry between the results for positive and negative M. A parametric study shows that increased propagation speed, front deformation, and possible transient oscillating dynamics occur when the absolute value of M is increased.

Journal Article↗

PubMed2006

Primary and secondary relaxations in supercooled eugenol and isoeugenol at ambient and elevated pressures: dependence on chemical microstructure.

Dielectric loss spectra of two glass-forming isomers, eugenol and isoeugenol, measured at ambient and elevated pressures in the normal liquid, supercooled, and glassy states are presented. The isomeric chemical compounds studied differ only by the location of the double bond in the alkyl chain. Above the glass transition temperature T(g), the dielectric loss spectra of both isomers exhibit an excess wing on the high frequency flank of the loss peak of the alpha relaxation and an additional faster gamma process at the megahertz frequency range. By decreasing temperature below T(g) at ambient pressure or by elevating pressure above P(g), the glass transition pressure, at constant temperature, the excess wing of isoeugenol shifts to lower frequencies and is transformed into a secondary beta-loss peak, while in eugenol it becomes a shoulder. These spectral features enable the beta-relaxation time tau(beta) to be determined in the glassy state. These changes indicate that the excess wings in isoeugenol and eugenol are similar and both are secondary beta relaxations that are not resolved in the liquid state. While in both isoeugenol and eugenol the loss peak of the beta relaxation in the glassy state and the corresponding excess wing in the liquid state shifts to lower frequencies on elevating pressure, the locations of their gamma relaxation show little change with increasing pressure. The different pressure sensitivities of the excess wing and gamma relaxation are further demonstrated by the nearly perfect superposition of the alpha-loss peak together with excess wing from the data taken at ambient pressure and at elevated pressure (and higher temperature so as to have the same alpha-peak frequency), but not the gamma-loss peak in both isoeugenol and eugenol. On physical aging isoeugenol, the beta-loss peak shifts to lower frequencies, but not the gamma relaxation. Basing on these experimental facts, the faster gamma relaxation is a local intramolecular process involving a side group and the slower beta relaxation mimics the structural alpha relaxation in behavior, involves the entire molecule and satisfies the criteria for being the Johari-Goldstein beta relaxation. Analysis and interpretation of the spectra utilizing the coupling model further demonstrate that the excess wings seen in the equilibrium liquid states of these two isomers are their genuine Johari-Goldstein beta relaxation.

Journal Article↗

PubMed2006

Excluded volume effect on confined polymer translocation through a short nanochannel.

We simulated the translocation process of a polymer chain from a source container to a drain container through a short nanochannel. We utilized the bond fluctuation model coupled with Monte Carlo dynamics in our simulations. The calculation results show that the excluded volume effect significantly affects the polymer's translocation time tau. This time depends nonmonotonically on the polymer length N. For a fixed nanochannel length, tau decreases when the polymer length increases. tau, however, increases when the polymer length exceeds a certain threshold. This observation differs from those predicated for a Gaussian chain. In this paper, we will further present our findings to explain this phenomenon. The knowledge we gain from this research can enhance the understanding of complex transport processes in many biological systems.

Journal Article↗

PubMed2006

Femtosecond laser pulse control of multidimensional vibrational dynamics: Computational studies on the pyrazine molecule.

The multiconfiguration time-dependent Hartree (MCTDH) method is combined with the optimal control theory (OCT) to study femtosecond laser pulse control of multidimensional vibrational dynamics. Simulations are presented for the widely discussed three-electronic-level vibronic coupling model of pyrazine either in a three or four vibrational coordinate version. Thus, for the first time OCT is applied to a four-coordinate system. Different control tasks are investigated and also some general aspects of the OCT-MCTDH method combination are analyzed.

Journal Article↗

PubMed2006

Dielectric secondary relaxations in polypropylene glycols.

Broadband dielectric measurements of polypropylene glycol of molecular weight M(w)=400 g / mol (PPG 400) were carried out at ambient pressure over the wide temperature range from 123 to 353 K. Three relaxation processes were observed. Besides the structural alpha relaxation, two secondary relaxations, beta and gamma, were found. The beta process was identified as the true Johari-Goldstein relaxation by using a criterion based on the coupling model prediction. The faster gamma relaxation, well separated from the primary process, undoubtedly exhibits the anomalous behavior near the glass transition temperature (T(g)) which is reflected in the presence of a minimum of the temperature dependence of the gamma-relaxation time. We successfully applied the minimal model [Dyre and Olsen, Phys. Rev. Lett. 91, 155703 (2003)] to describe the entire temperature dependence of the gamma-relaxation time. The asymmetric double-well potential parameters obtained by Dyre and Olsen for the secondary relaxation of tripropylene glycol at ambient pressure were modified by fitting to the minimal model at lower temperatures. Moreover, we showed that the effect of the molecular weight of polypropylene glycol on the minimal model parameters is significantly larger than that of the high pressure. Such results can be explained by the smaller degree of hydrogen bonds formed by longer chain molecules of PPG at ambient pressure than that created by shorter chains of PPG at high pressure.

Journal Article↗

PubMed2006

Combined experimental-theoretical study of the lower excited singlet states of paravinyl phenol, an analog of the paracoumaric acid chromophore.

The low-lying excited singlet states of paravinyl phenol (pVP) are investigated experimentally and theoretically paying attention to their similarity to excited states of paracoumaric acid, the chromophore of the photoactive yellow protein (PYP). Resonance enhanced multiphoton ionization and laser induced fluorescence spectroscopic techniques are employed to obtain supersonically cooled, vibrationally resolved excitation and emission spectra related to the lowest (1)A'(V') excited state of pVP. Comprehensive analyses of the spectral structures are carried out by means of the equation-of-motion coupled cluster singles and doubles and time dependent density functional theory methods in combination with the linear vibronic coupling model and Franck-Condon calculations. The assignments of the spectral patterns are given, mostly in terms of excitations of totally symmetric modes. Weak activity of the non-totally-symmetric modes indicates low probability of photochemical processes in the Franck-Condon region of the (1)A'(V') state. The second (1)A'(V) and third (1)A" (Ryd) excited states of pVP are characterized with regard to their electronic structure, properties, and effects of geometry relaxations. The lengthening of the double bond relevant to the trans-cis isomerization of the PYP chromophore is found for the (1)A'(V) state. A possibility of photochemical processes and strong vibronic interactions in this state can be expected. The theoretical results for the (1)A"(Ryd) state predict that dissociation with respect to the O-H bond is possible.

Computer Simulation↗

PubMed2002

Low atmospheric CO(2) levels during the Permo- Carboniferous glaciation inferred from fossil lycopsids.

Earth history was punctuated during the Permo-Carboniferous [300-250 million years (Myr) ago] by the longest and most severe glaciation of the entire Phanerozoic Eon. But significant uncertainty surrounds the concentration of CO(2) in the atmosphere through this time interval and therefore its role in the evolution of this major prePleistocene glaciation. Here, I derive 24 Late Paleozoic CO(2) estimates from the fossil cuticle record of arborsecent lycopsids of the equatorial Carboniferous and Permian swamp communities. Quantitative calibration of Late Carboniferous (330-300 Myr ago) and Permian (270-260 Myr ago) lycopsid stomatal indices yield average atmospheric CO(2) concentrations of 344 ppm and 313 ppm, respectively. The reconstructions show a high degree of self-consistency and a degree of precision an order of magnitude greater than other approaches. Low CO(2) levels during the Permo-Carboniferous glaciation are in agreement with glaciological evidence for the presence of continental ice and coupled models of climate and ice-sheet growth on Pangea. Moreover, the Permian data indicate atmospheric CO(2) levels were low 260 Myr ago, by which time continental deglaciation was already underway. Positive biotic feedbacks on climate, and geotectonic events, therefore are implicated as mechanisms underlying deglaciation.

Atmosphere↗

PubMed1979

Geometric and electronic structure of oxyhemocyanin: spectral and chemical correlations to met apo, half met, met, and dimer active sites.

The chemical and spectral properties of a series of hemocyanin derivatives were systematically compared to provide insight into the geometric and electronic structure of the oxyhemocyanin active site. The binuclear copper site is characterized as two tetragonal Cu(II) atoms bridged by both an endogenous protein ligand and the exogenous ligand (i.e., peroxide), with the lack of an electron paramagnetic resonance signal being the result of antiferromagnetic exchange via the endogenous bridge. A transition dipole-vector coupling model is used to assign the unique absorption spectral properties of oxyhemocyanin: the bands at 570 and 486 nm are assigned as components of the peroxide pi v* to copper dx2-y2 charge transfer. The 345-nm band is one component of the pi sigma* leads to dx2-y2 charge transfer. The model also predicts an end-to-end bridging geometry for the peroxide in oxyhemocyanin.

Animals↗

PubMed1985

Purified hydrophobic proteins, chargerins, are essential for energy transduction in oxidative phosphorylation.

Studies on anisotropic inhibitors, a unique type of inhibitor of energy transduction in oxidative phosphorylation, suggested that redox reactions generate two kinds of negative charges on the outer surface of mitochondrial inner membranes, on redox complexes and on F0, and that the inhibitors inhibit energy transduction by binding to these negative charges. Recent experiments on photoaffinity labeling of mitochondria with monoazide ethidium, which is an anisotropic inhibitor, showed that the inhibitor specifically binds to a hydrophobic protein of the membranes. In the present work the mitochondrial components labeled with monoazide ethidium were further purified and two kinds of hydrophobic proteins (apparent molecular masses, 8 and 13 kDa) were found to be specifically labeled with the inhibitor. These proteins were named chargerin I and II, respectively. Redox reactions greatly increased the molar ratio of ethidium bound to chargerin I and II in mitochondria, reflecting a conformational change of the chargerins coupled with the redox reactions. It was also shown that antibody against chargerin II specifically inhibited ATP synthesis in mitoplasts (inner membranes plus matrix) prepared from rat liver mitochondria. Thus, the present findings show that chargerins have an essential role in energy transduction in oxidative phosphorylation in rat liver mitochondria, in good accord with the conformational coupling model of the H+ pumps and ATP synthesis.

Affinity Labels↗

PubMed1996

Secobarbital-mediated inactivation of cytochrome P450 2B1 and its active site mutants. Partitioning between heme and protein alkylation and epoxidation.

Secobarbital (SB) is a relatively selective mechanism-based inactivator of cytochrome P450 2B1, that partitions between epoxidation and heme and protein modification during its enzyme inactivation. The SB-2B1 heme adduct formed in situ in a functionally reconstituted system has been spectrally documented and structurally characterized as N-(5-(2-hydroxypropyl)-5-(1-methylbutyl)barbituric acid)protoporphyrin IX. The SB-protein modification has been localized to 2B1 peptide 277-323 corresponding to the active site helix I of cytochrome P450 101. The targeting of heme and this active site peptide suggests that the 2B1 active site topology could influence the course of its inactivation. To explore this possibility, the individual SB epoxidation, heme and protein modification, and corresponding molar partition ratios of the wild type and seven structural 2B1 mutants, site-directed at specific substrate recognition sites, and known to influence 2B1 catalysis were examined after Escherichia coli expression. These studies reveal that Thr-302 is critical for SB-mediated heme N-alkylation, whereas Val-367 is a critical determinant of 2B1 protein modification, and Val-363 is important for SB epoxidation. SB docking into a refined 2B1 homology model coupled with molecular dynamics analyses provide a logical rationale for these findings.

Alkylation↗

PubMed2002

Transcriptional activators differ in their abilities to control alternative splicing.

Promoter and enhancer elements can influence alternative splicing, but the basis for this phenomenon is not well understood. Here we investigated how different transcriptional activators affect the decision between inclusion and exclusion (skipping) of the fibronectin EDI exon. A mutant of the acidic VP16 activation domain called SW6 that preferentially inhibits polymerase II (pol II) elongation caused a reduction in EDI exon skipping. Exon skipping was fully restored in the presence of the SW6 mutant by either the SV40 enhancer in cis or the human immunodeficiency virus (HIV) Tat in trans, both of which specifically stimulate pol II elongation. HIV Tat also cooperated with the Sp1 and CTF activation domains to enhance transcript elongation and EDI skipping. The extent of exon skipping correlated with the efficiency with which pol II transcripts reach the 3' end of the gene but not with the overall fold increase in transcript levels caused by different activators. The ability of activators to enhance elongation by RNA polymerase II therefore correlates with their ability to enhance exon skipping. Consistent with this observation, the elongation inhibitor dichlororibofuranosylbenzimidazole (DRB) enhanced EDI inclusion. Conversely, the histone deacetylase inhibitor trichostatin A that is thought to stimulate elongation caused a modest inhibition of EDI inclusion. Together our results support a kinetic coupling model in which the rate of transcript elongation determines the outcome of two competing splicing reactions that occur co-transcriptionally. Rapid, highly processive transcription favors EDI exon skipping, whereas slower, less processive transcription favors inclusion.

Alternative Splicing↗

PubMed1979

Social skills training as an adjunct to sex therapy.

Many single men and women with sex problems lack the skills or confidence to meet potential partners and develop relationships. Social skills training is presented as a useful adjunct to sex therapy with such individuals. The relative strengths of group, workshop, and individual formats are discussed as well as screening procedures, important issues and methods in such training, and the results achieved by it. As more sex therapists break away from the couples model of treatment and work with men and women without partners, the need for social skills training will increase.

Behavior Therapy↗

PubMed2005

Adsorption of lipase on hollow fiber membrane chips.

The amount of lipase from Mucor miehei adsorption on ultrafiltration polysulfone hollow fiber membrane chips has been determined using different lipase concentrations at three different temperatures, namely 30, 35, and 40 degrees C. It was experimentally shown that adsorption of lipase increases with temperature. The results were used to evaluate the constants found in the Langmuir adsorption isotherm model coupled with the Van't Hoff's relationship. A temperature dependence correlation for the amount of adsorbed lipase activity, alip,ads, and that present in the supernatant solution, alip,free was determined. The effect of varying the concentration on a cross-linking agent, namely, glutaraldehyde, to the membrane chips was also tested. It was found that, under the same operating conditions, the amount of lipase adsorbed on polysulfone membranes was increased dramatically after pre-treating the membrane with 1% Glutaraldehyde. However, increasing the concentration of the cross-linking agent has a low effect on the amount of lipase adsorbed.

Adsorption↗

PubMed1995

GPI-anchored influenza hemagglutinin induces hemifusion to both red blood cell and planar bilayer membranes.

Under fusogenic conditions, fluorescent dye redistributed from the outer monolayer leaflet of red blood cells (RBCs) to cells expressing glycophosphatidylinositol-anchored influenza virus hemagglutinin (GPI-HA) without transfer of aqueous dye. This suggests that hemifusion, but not full fusion, occurred (Kemble, G. W., T. Danieli, and J. M. White. 1994. Cell. 76:383-391). We extended the evidence for hemifusion by labeling the inner monolayer leaflets of RBCs with FM4-64 and observing that these inner leaflets did not become continuous with GPI-HA-expressing cells. The region of hemifusion-separated aqueous contents, the hemifusion diaphragm, appeared to be extended and was long-lived. But when RBCs hemifused to GPI-HA-expressing cells were osmotically swollen, some diaphragms were disrupted, and spread of both inner leaflet and aqueous dyes was observed. This was characteristic of full fusion: inner leaflet and aqueous probes spread to cells expressing wild-type HA (wt-HA). By simultaneous video fluorescence microscopy and time-resolved electrical admittance measurements, we rigorously demonstrated that GPI-HA-expressing cells hemifuse to planar bilayer membranes: lipid continuity was established without formation of fusion pores. The hemifusion area became large. In contrast, for cells expressing wt-HA, before lipid dye spread, fusion pores were always observed, establishing that full fusion occurred. We present an elastic coupling model in which the ectodomain of wt-HA induces hemifusion and the transmembrane domain, absent in the GPI-HA-expressing cells, mediates full fusion.

Animals↗

PubMed1978

Initial conditions and the kinetics of the sodium conductance in Myxicola giant axons. I. effects on the time-course of the sodium conductance.

The effects of conditioning polarizations, ranging from--150 to 0 mV and of durations from 50 mus to 30 ms, on the time-course of GNa during test steps in potential were studied in Myxicola giant axons. Beyond the effects of conditioning polarizations on the amplitude of GNa, the only effect was to produce a translation of GNa(t) along the time axis without a change in shape. For depolarizing conditioning potentials, Hodgkin-Huxley kinetics predict time shifts about threefold greater than found experimentally, whereas the predictions of the coupled model of Goldman (1975. Biophys. J. 15:119--136) were in approximate agreement with our experiments. The time shifts developed over an exponential time-course as the conditioning pulse duration was increased. The time constant of development of the time shift was considerably faster than, and showed the opposite dependency on potential from, the values predicted by both models. It had a mean Q10 of 1/2.50. This fast activation process cannot account for the observed rise time behavior of GNa, suggesting that there is an additional activation process. All results are consistent with the idea that the gating structure displays more than three states, with state intermediate between rest and conducting.

Animals↗

PubMed2004

Antagonism of group I metabotropic glutamate receptors and PLC attenuates increases in inositol trisphosphate and reduces reactive gliosis in strain-injured astrocytes.

We have previously found that in vitro traumatic injury uncouples IP3-mediated intracellular free calcium ([Ca2+]i) signaling in astrocytes (Rzigalinski et al., 1998; Floyd et al., 2001). Since Group I metabotropic glutamate receptors (mGluRs) are coupled to IP3-mediated Ca2+ signaling, we investigated their role in the in vitro strain injury of cultured astrocytes. Astrocytes grown on Silastic membranes were labeled with 3H-myo-inositol and strain (stretch)-injured. Cells injured in the presence of LiCl to prevent inositol phosphate metabolism were acid extracted and inositol phosphates (IPx) isolated using anion exchange columns. Reactive gliosis was assessed as increased glial fibrillary acidic protein immunoreactivity (GFAP-IR). Pre- but not post-injury administration of (RS)-1-aminoindan-15-decarboxylic acid (AIDA) or (S)-4-carboxy-3-hydroxyphenylglycine (S4CH3HPG), both group I mGluR antagonists, attenuated injury-induced increases in IPx. Injury increased GFAP-IR in astrocytes at 24 and 48 h post injury, which was reduced or blocked by AIDA or inhibition of phospholipase C (PLC) with U73122. These findings suggest that strain injury activates Group I mGluRs, causing aberrant IPx production and uncoupling of the PLC signaling pathway. Changes in this signaling pathway may be related to induction of reactive gliosis. Additionally, our results suggest a complex physical coupling between G protein receptor, PLC, and IP3 receptor, in support of the conformational coupling model.

Animals↗