Transient photocurrent in molecular junctions: singlet switching on and triplet blocking.

PubMed

Petrov, E G; Leonov, V O; Snitsarev, V

2013-05-14

The kinetic approach adapted to describe charge transmission in molecular junctions, is used for the analysis of the photocurrent under conditions of moderate light intensity of the photochromic molecule. In the framework of the HOMO-LUMO model for the single electron molecular states, the analytic expressions describing the temporary behavior of the transient and steady state sequential (hopping) as well as direct (tunnel) current components have been derived. The conditions at which the current components achieve their maximal values are indicated. It is shown that if the rates of charge transmission in the unbiased molecular diode are much lower than the intramolecular singlet-singlet excitation/de-excitation rate, and the threefold degenerated triplet excited state of the molecule behaves like a trap blocking the charge transmission, a possibility of a large peak-like transient switch-on photocurrent arises.

Optimal energy growth in a stably stratified shear flow

NASA Astrophysics Data System (ADS)

Jose, Sharath; Roy, Anubhab; Bale, Rahul; Iyer, Krithika; Govindarajan, Rama

2018-02-01

Transient growth of perturbations by a linear non-modal evolution is studied here in a stably stratified bounded Couette flow. The density stratification is linear. Classical inviscid stability theory states that a parallel shear flow is stable to exponentially growing disturbances if the Richardson number (Ri) is greater than 1/4 everywhere in the flow. Experiments and numerical simulations at higher Ri show however that algebraically growing disturbances can lead to transient amplification. The complexity of a stably stratified shear flow stems from its ability to combine this transient amplification with propagating internal gravity waves (IGWs). The optimal perturbations associated with maximum energy amplification are numerically obtained at intermediate Reynolds numbers. It is shown that in this wall-bounded flow, the three-dimensional optimal perturbations are oblique, unlike in unstratified flow. A partitioning of energy into kinetic and potential helps in understanding the exchange of energies and how it modifies the transient growth. We show that the apportionment between potential and kinetic energy depends, in an interesting manner, on the Richardson number, and on time, as the transient growth proceeds from an optimal perturbation. The oft-quoted stabilizing role of stratification is also probed in the non-diffusive limit in the context of disturbance energy amplification.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

What can we learn from relaxation measurements of a laser-perturbed atmosphere? A modeling study

NASA Technical Reports Server (NTRS)

Clericetti, Agostino; Vandenbergh, Hubert; Rossi, Michel J.

1994-01-01

The chemical kinetic aspects of a transient increase in OH and HO2 by several orders of magnitude are explored in three model tropospheres. This chemical kinetic modeling effort was undertaken to support the operation of a pump-and-probe LIDAR instrument. A powerful excimer laser pulse perturbs the troposphere after which its relaxation back to steady state is examined by remote sensing, for example by DIAL or LIF. Instead of probing ambient levels of key free radicals, a study of the relaxation kinetics in real time enables chemical mechanistic studies in situ.

Spatial localization of excitons and charge carriers in hybrid perovskite thin films

DOE PAGES

Simpson, Mary Jane; Doughty, Benjamin; Yang, Bin; ...

2015-07-21

The fundamental photophysics underlying the remarkably high power conversion efficiency of organic-inorganic hybrid perovskite-based solar cells has been increasingly studied using complementary spectroscopic techniques. The spatially heterogeneous polycrystalline morphology of the photoactive layers owing to the presence of distinct crystalline grains has been generally neglected in optical measurements and therefore the reported results are typically averaged over hundreds or even thousands of such grains. Here, we apply femtosecond transient absorption microscopy to spatially and temporally probe ultrafast electronic excited-state dynamics in pristine methylammonium lead tri-iodide (CH 3NH 3PbI 3) thin films and composite structures. We found that the electronic excited-statemore » relaxation kinetics are extremely sensitive to the sample location probed, which was manifested by position-dependent decay timescales and transient signals. As a result, analysis of transient absorption kinetics acquired at distinct spatial positions enabled us to identify contributions of excitons and free charge carriers.« less

Transmission of a detonation across a density interface

NASA Astrophysics Data System (ADS)

Tang Yuk, K. C.; Mi, X. C.; Lee, J. H. S.; Ng, H. D.

2018-05-01

The present study investigates the transmission of a detonation wave across a density interface. The problem is first studied theoretically considering an incident Chapman-Jouguet (CJ) detonation wave, neglecting its detailed reaction-zone structure. It is found that, if there is a density decrease at the interface, a transmitted strong detonation wave and a reflected expansion wave would be formed; if there is a density increase, one would obtain a transmitted CJ detonation wave followed by an expansion wave and a reflected shock wave. Numerical simulations are then performed considering that the incident detonation has the Zel'dovich-von Neumann-Döring reaction-zone structure. The transient process that occurs subsequently to the detonation-interface interaction has been captured by the simulations. The effects of the magnitude of density change across the interface and different reaction kinetics (i.e., single-step Arrhenius kinetics vs. two-step induction-reaction kinetics) on the dynamics of the transmission process are explored. After the transient relaxation process, the transmitted wave reaches the final state in the new medium. For the cases with two-step induction-reaction kinetics, the transmitted wave fails to evolve to a steady detonation wave if the magnitude of density increase is greater than a critical value. For the cases wherein the transmitted wave can evolve to a steady detonation, the numerical results for both reaction models give final propagation states that agree with the theoretical solutions.

Investigations of the Controlling Factors for Air Emissions Associated With the Dredging of Indiana Harbor and Canal (IHC) and CDF Operations

DTIC Science & Technology

2008-04-01

concepts of a transient toxic constituent loss and transport model for both solids and chemical incorporating a kinetic approach rather than equilibrium...to air. A transient kinetic mass-transfer model was applied to the data and it was found that the TSS level was the most critical parameter for...measured (Thibodeaux et al. 2004). The transient behavior followed the expected theory of the mass-transfer kinetic, but the conventional LEA model

A Transient Kinetic Approach to Investigate Nucleoside Inhibitors of Mitochondrial DNA polymerase γ

PubMed Central

Anderson, Karen S.

2010-01-01

Nucleoside analogs play an essential role in treating human immunodeficiency virus (HIV) infection since the beginning of the AIDS epidemic and work by inhibition of HIV-1 reverse transcriptase (RT), a viral polymerase essential for DNA replication. Today, over 90% of all regimens for HIV treatment contain at least one nucleoside. Long-term use of nucleoside analogs has been associated with adverse effects including mitochondrial toxicity due to inhibition of the mitochondrial polymerase, DNA polymerase gamma (mtDNA pol ©). In this review, we describe our efforts to delineate the molecular mechanism of nucleoside inhibition of HIV-1 RT and mtDNA pol © based upon a transient kinetic approach using rapid chemical quench methodology. Using transient kinetic methods, the maximum rate of polymerization (kpol), the dissociation constant for the ground state binding (Kd), and the incorporation efficiency (kpol/Kd) can be determined for the nucleoside analogs and their natural substrates. This analysis allowed us to develop an understanding of the structure activity relationships that allow correlation between the structural and stereochemical features of the nucleoside analog drugs with their mechanistic behavior toward the viral polymerase, RT, and the host cell polymerase, mtDNA pol γ. An in-depth understanding of the mechanisms of inhibition of these enzymes is imperative in overcoming problems associated with toxicity. PMID:20573564

A Numerical Analysis of the Transient Response of an Ablation System Including Effects of Thermal Nonequilibrium, Mass Transfer and Chemical Kinetics. Ph.D Thesis - Virginia Polytechnic Inst. and State Univ.

NASA Technical Reports Server (NTRS)

Clark, R. K.

1972-01-01

The differential equations governing the transient response of a one-dimensional ablative thermal protection system undergoing stagnation ablation are derived. These equations are for thermal nonequilibrium effects between the pyrolysis gases and the char layer and kinetically controlled chemical reactions and mass transfer between the pyrolysis gases and the char layer. The boundary conditions are written for the particular case of stagnation heating with surface removal by oxidation or sublimation and pyrolysis of the uncharred layer occurring in a plane. The governing equations and boundary conditions are solved numerically using the modified implicit method (Crank-Nicolson method). Numerical results are compared with exact solutions for a number of simplified cases. The comparison is favorable in each instance.

Structural events in the photocycle of green fluorescent protein.

PubMed

van Thor, Jasper J; Zanetti, Giulia; Ronayne, Kate L; Towrie, Michael

2005-08-25

Picosecond time-resolved mid-infrared absorption changes of the wild type green fluorescent protein from Aequorea victoria are reported on structural events during the photocycle. Concomitant with rapid H/D transfer following excitation of the neutral A state at 400 nm, a transient signal at 1721/1711 cm(-1) (H/D) developed belonging to protonated glutamate 222, which was definitively assigned using the E222D mutant from the altered proton-transfer kinetics to aspartate in addition to the altered band position and intensity in the spectra. A transient at 1697 cm(-1), assigned to a structural perturbation of glutamine 69, had a H/D kinetic isotope effect of >32, showing the conformational dynamics to be sensitive to the active site H/D vibrations. The kinetic data up to 2 ns after excitation in the 1250-1800 cm(-1) region in D2O provided 10 and 75 ps time constants for the excited-state deuteron transfer and the associated A1* - A1 and A2* - A2 difference spectra and showed the radiative intermediate I state vibrations and the transient accumulation of the long-lived ground-state intermediate I2. Assignments of chromophore modes for the A1, A2, and I2 ground states are proposed on the basis of published model compound studies (Esposito, A. P.; Schellenberg, P.; Parson, W. W.; Reid, P. J. J. Mol. Struct. 2001, 569, 25 and He, X.; Bell, A. F.; Tonge, P. J. J. Phys. Chem. B 2002, 106, 6056). Tentative assignments for the singlet-state intermediates A1*, A2*, and I* are discussed. An unexpected and unassigned band that may be a C=C chromophore vibration was observed in the ground state (1665 cm(-1)) as well as in all photocycle intermediates. Optical dumping of the transient I population was achieved using an additional 532 nm pulse and the directly obtained I2 - I* difference spectrum was highly similar to the I2 - I* photocycle spectrum. The pump-dump-probe spectrum differed from the pump-probe photocycle difference spectrum with respect to the intensity of the phenol 1 mode at 1578 cm(-1), suggesting stronger delocalization of the negative charge onto the phenolic ring of the anionic chromophore in the dumped I2 state. Indication for structural heterogeneity of the chromophore, Glu 222, and the chromophore environment was found in the two parallel proton-transfer reactions and their distinct associated ground- and intermediate-state vibrations. Vibrational spectral markers at 1695 cm(-1) assigned to Gln 69, at 1631 cm(-1) belonging to a C=C mode, and at 1354 cm(-1) belonging to a phenolate vibration further indicated the I2 and I* states to be unrelaxed.

VO2 kinetics of constant-load exercise following bed-rest-induced deconditioning

NASA Technical Reports Server (NTRS)

Convertino, V. A.; Goldwater, D. J.; Sandler, H.

1984-01-01

Previous studies have shown that the oxygen uptake kinetics during exercise and recovery may be changed by alterations in work intensity, prior exercise, muscle group involvement, ambient conditions, posture, disease state, and level of physical conditioning. However, the effects of detraining on oxygen uptake kinetics have not been determined. The present investigation has the objective to determine the effects of deconditioning following seven days of continuous head-down bed rest on changes in steady-state oxygen uptake, O2 deficit, and recovery oxygen uptake during the performance of constant-load exercise. The obtained results may provide support for previous proposals that submaximal oxygen uptake was significantly reduced following bed rest. The major finding was that bed-rest deconditioning resulted in a reduction of total O2 transport/utilization capacity during the transient phase of upright but not supine exercise.

Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics

PubMed Central

Bongini, Lorenzo; Melli, Luca; Lombardi, Vincenzo; Bianco, Pasquale

2014-01-01

Under a tension of ∼65 pN, double-stranded DNA undergoes an overstretching transition from its basic (B-form) conformation to a 1.7 times longer conformation whose nature is only recently starting to be understood. Here we provide a structural and thermodynamic characterization of the transition by recording the length transient following force steps imposed on the λ-phage DNA with different melting degrees and temperatures (10–25°C). The shortening transient following a 20–35 pN force drop from the overstretching force shows a sequence of fast shortenings of double-stranded extended (S-form) segments and pauses owing to reannealing of melted segments. The lengthening transients following a 2–35 pN stretch to the overstretching force show the kinetics of a two-state reaction and indicate that the whole 70% extension is a B-S transition that precedes and is independent of melting. The temperature dependence of the lengthening transient shows that the entropic contribution to the B-S transition is one-third of the entropy change of thermal melting, reinforcing the evidence for a double-stranded S-form that maintains a significant fraction of the interstrand bonds. The cooperativity of the unitary elongation (22 bp) is independent of temperature, suggesting that structural factors, such as the nucleic acid sequence, control the transition. PMID:24353317

Insights into the Importance of Hydrogen Bonding in the [gamma]-Phosphate Binding Pocket of Myosin: Structural and Functional Studies of Serine 236

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frye, Jeremiah J.; Klenchin, Vadim A.; Bagshaw, Clive R.

2010-09-22

The active site of myosin contains a group of highly conserved amino acid residues whose roles in nucleotide hydrolysis and energy transduction might appear to be obvious from the initial structural and kinetic analyses but become less clear on deeper investigation. One such residue is Ser236 (Dictyostelium discoideum myosin II numbering) which was proposed to be involved in a hydrogen transfer network during {gamma}-phosphate hydrolysis of ATP, which would imply a critical function in ATP hydrolysis and motility. The S236A mutant protein shows a comparatively small decrease in hydrolytic activity and motility, and thus this residue does not appear tomore » be essential. To understand better the contribution of Ser236 to the function of myosin, structural and kinetic studies have been performed on the S236A mutant protein. The structures of the D. discoideum motor domain (S1dC) S236A mutant protein in complex with magnesium pyrophosphate, MgAMPPNP, and MgADP{center_dot}vanadate have been determined. In contrast to the previous structure of wild-type S1dC, the S236A{center_dot}MgAMPPNP complex crystallized in the closed state. Furthermore, transient-state kinetics showed a 4-fold reduction of the nucleotide release step, suggesting that the mutation stabilizes a closed active site. The structures show that a water molecule approximately adopts the location of the missing hydroxyl of Ser236 in the magnesium pyrophosphate and MgAMPPNP structures. This study suggests that the S236A mutant myosin proceeds via a different structural mechanism than wild-type myosin, where the alternate mechanism is able to maintain near normal transient-state kinetic values.« less

The Impact of ENSO on Extratropical Low Frequency Noise in Seasonal Forecasts

NASA Technical Reports Server (NTRS)

Schubert, Siegfried D.; Suarez, Max J.; Chang, Yehui; Branstator, Grant

2000-01-01

This study examines the uncertainty in forecasts of the January-February-March (JFM) mean extratropical circulation, and how that uncertainty is modulated by the El Nino/Southern Oscillation (ENSO). The analysis is based on ensembles of hindcasts made with an Atmospheric General Circulation Model (AGCM) forced with sea surface temperatures observed during; the 1983 El Nino and 1989 La Nina events. The AGCM produces pronounced interannual differences in the magnitude of the extratropical seasonal mean noise (intra-ensemble variability). The North Pacific, in particular, shows extensive regions where the 1989 seasonal mean noise kinetic energy (SKE), which is dominated by a "PNA-like" spatial structure, is more than twice that of the 1983 forecasts. The larger SKE in 1989 is associated with a larger than normal barotropic conversion of kinetic energy from the mean Pacific jet to the seasonal mean noise. The generation of SKE due to sub-monthly transients also shows substantial interannual differences, though these are much smaller than the differences in the mean flow conversions. An analysis of the Generation of monthly mean noise kinetic energy (NIKE) and its variability suggests that the seasonal mean noise is predominantly a statistical residue of variability resulting from dynamical processes operating on monthly and shorter times scales. A stochastically-forced barotropic model (linearized about the AGCM's 1983 and 1989 base states) is used to further assess the role of the basic state, submonthly transients, and tropical forcing, in modulating the uncertainties in the seasonal AGCM forecasts. When forced globally with spatially-white noise, the linear model generates much larger variance for the 1989 base state, consistent with the AGCM results. The extratropical variability for the 1989 base state is dominanted by a single eigenmode, and is strongly coupled with forcing over tropical western Pacific and the Indian Ocean, again consistent with the AGCM results. Linear calculations that include forcing from the AGCM variance of the tropical forcing and submonthly transients show a small impact on the variability over the Pacific/North American region compared with that of the base state differences.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984

Dynamics of intramolecular electron transfer reaction of FAD studied by magnetic field effects on transient absorption spectra.

PubMed

Murakami, Masaaki; Maeda, Kiminori; Arai, Tatsuo

2005-07-07

The kinetics of intermediates generated from intramolecular electron-transfer reaction by photo irradiation of the flavin adenine dinucleotide (FAD) molecule was studied by a magnetic field effect (MFE) on transient absorption (TA) spectra. Existence time of MFE and MFE action spectra have a strong dependence on the pH of solutions. The MFE action spectra have indicated the existence of interconversion between the radical pair and the cation form of the triplet excited state of flavin part. All rate constants of the triplet and the radical pair were determined by analysis of the MFE action spectra and decay kinetics of TA. The obtained values for the interconversion indicate that the formation of cation radical promotes the back electron-transfer reaction to the triplet excited state. Further, rate constants of spin relaxation and recombination have been studied by the time profiles of MFE at various pH. The drastic change of those two factors has been obtained and can be explained by SOC (spin-orbit coupling) induced back electron-transfer promoted by the formation of a stacking conformation at pH > 2.5.

Dynamics of vibrational relaxation in the S 1 state of carotenoids having 11 conjugated CC bonds

NASA Astrophysics Data System (ADS)

Hörvin Billsten, Helena; Zigmantas, Donatas; Sundström, Villy; Polívka, Tomáš

2002-04-01

Transient absorption spectra and kinetics in the 470-650 nm region were recorded for lycopene, β-carotene and zeaxanthin, all carotenoids with 11 conjugated double bonds, in two solvents with different polarity. Analysis of the red wing of the carotenoid S 1-S n transition revealed presence of a pronounced shoulder at early delay times. The kinetics recorded at this low-energy shoulder of the S 1-S n transition yields an additional decay component of 500-800 fs in addition to the main S 1 decay. This dynamics is ascribed to a vibrational relaxation in the S 1 state of the carotenoids.

Atomic-Scale Design of Iron Fischer-Tropsch Catalysts; A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manos Mavrikakis; James Dumesic; Rahul Nabar

2008-09-29

This work focuses on (1) searching/summarizing published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) preparation and characterization of unsupported iron catalysts with/without potassium/platinum promoters; (3) measurement of H{sub 2} and CO adsorption/dissociation kinetics on iron catalysts using transient methods; (3) analysis of the transient rate data to calculate kinetic parameters of early elementary steps in FTS; (4) construction of a microkinetic model of FTS on iron, and (5) validation of the model from collection of steady-state rate data for FTS on iron catalysts. Three unsupported iron catalysts and three alumina-supported iron catalysts weremore » prepared by non-aqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, temperature-programmed reduction (TPR), extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2} and thus ideal for kinetic and mechanistic studies. Kinetic parameters for CO adsorption, CO dissociation, and surface carbon hydrogenation on these catalysts were determined from temperature-programmed desorption (TPD) of CO and temperature programmed surface hydrogenation (TPSR), temperature-programmed hydrogenation (TPH), and isothermal, transient hydrogenation (ITH). A microkinetic model was constructed for the early steps in FTS on polycrystalline iron from the kinetic parameters of elementary steps determined experimentally in this work and from literature values. Steady-state rate data were collected in a Berty reactor and used for validation of the microkinetic model. These rate data were fitted to 'smart' Langmuir-Hinshelwood rate expressions derived from a sequence of elementary steps and using a combination of fitted steady-state parameters and parameters specified from the transient measurements. The results provide a platform for further development of microkinetic models of FTS on Fe and a basis for more precise modeling of FTS activity of Fe catalysts. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on various realistic models of industrial, Fe-based FTS catalysts. Close-packed, most stable Fe(110) facet was analyzed and subsequently carbide formation was found to be facile leading to the choice of the FeC(110) model representing a Fe facet with a sub-surface C atom. The Pt adatom (Fe{sup Pt}(110)) was found to be the most stable model for our studies into Pt promotion and finally the role of steps was elucidated by recourse to the defected Fe(211) facet. Binding Energies(BEs), preferred adsorption sites and geometries for all FTS relevant stable species and intermediates were evaluated on each model catalyst facet. A mechanistic model (comprising of 32 elementary steps involving 19 species) was constructed and each elementary step therein was fully characterized with respect to its thermochemistry and kinetics. Kinetic calculations involved evaluation of the Minimum Energy Pathways (MEPs) and activation energies (barriers) for each step. Vibrational frequencies were evaluated for the preferred adsorption configuration of each species with the aim of evaluating entropy-changes, pre exponential factors and serving as a useful connection with experimental surface science techniques. Comparative analysis among these four facets revealed important trends in their relative behavior and roles in FTS catalysis. Overall the First Principles Calculations afforded us a new insight into FTS catalysis on Fe and modified-Fe catalysts.« less

Anisotropic kinetic energy release and gyroscopic behavior of CO2 super rotors from an optical centrifuge.

PubMed

Murray, Matthew J; Ogden, Hannah M; Mullin, Amy S

2017-10-21

An optical centrifuge is used to generate an ensemble of CO 2 super rotors with oriented angular momentum. The collision dynamics and energy transfer behavior of the super rotor molecules are investigated using high-resolution transient IR absorption spectroscopy. New multipass IR detection provides improved sensitivity to perform polarization-dependent transient studies for rotational states with 76 ≤ J ≤ 100. Polarization-dependent measurements show that the collision-induced kinetic energy release is spatially anisotropic and results from both near-resonant energy transfer between super rotor molecules and non-resonant energy transfer between super rotors and thermal molecules. J-dependent studies show that the extent and duration of the orientational anisotropy increase with rotational angular momentum. The super rotors exhibit behavior akin to molecular gyroscopes, wherein molecules with larger amounts of angular momentum are less likely to change their angular momentum orientation through collisions.

Anisotropic kinetic energy release and gyroscopic behavior of CO2 super rotors from an optical centrifuge

NASA Astrophysics Data System (ADS)

Murray, Matthew J.; Ogden, Hannah M.; Mullin, Amy S.

2017-10-01

An optical centrifuge is used to generate an ensemble of CO2 super rotors with oriented angular momentum. The collision dynamics and energy transfer behavior of the super rotor molecules are investigated using high-resolution transient IR absorption spectroscopy. New multipass IR detection provides improved sensitivity to perform polarization-dependent transient studies for rotational states with 76 ≤ J ≤ 100. Polarization-dependent measurements show that the collision-induced kinetic energy release is spatially anisotropic and results from both near-resonant energy transfer between super rotor molecules and non-resonant energy transfer between super rotors and thermal molecules. J-dependent studies show that the extent and duration of the orientational anisotropy increase with rotational angular momentum. The super rotors exhibit behavior akin to molecular gyroscopes, wherein molecules with larger amounts of angular momentum are less likely to change their angular momentum orientation through collisions.

Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion.

PubMed

Oyen, David; Fenwick, R Bryn; Aoto, Phillip C; Stanfield, Robyn L; Wilson, Ian A; Dyson, H Jane; Wright, Peter E

2017-08-16

The rate-determining step in the catalytic cycle of E. coli dihydrofolate reductase is tetrahydrofolate (THF) product release, which can occur via an allosteric or an intrinsic pathway. The allosteric pathway, which becomes accessible when the reduced cofactor NADPH is bound, involves transient sampling of a higher energy conformational state, greatly increasing the product dissociation rate as compared to the intrinsic pathway that obtains when NADPH is absent. Although the kinetics of this process are known, the enzyme structure and the THF product conformation in the transiently formed excited state remain elusive. Here, we use side-chain proton NMR relaxation dispersion measurements, X-ray crystallography, and structure-based chemical shift predictions to explore the structural basis of allosteric product release. In the excited state of the E:THF:NADPH product release complex, the reduced nicotinamide ring of the cofactor transiently enters the active site where it displaces the pterin ring of the THF product. The p-aminobenzoyl-l-glutamate tail of THF remains weakly bound in a widened binding cleft. Thus, through transient entry of the nicotinamide ring into the active site, the NADPH cofactor remodels the enzyme structure and the conformation of the THF to form a weakly populated excited state that is poised for rapid product release.

Instrumental, theoretical, and experimental aspects of determining thermodynamic and kinetic parameters from steady-state and non-steady-state cyclic voltammetry at microelectrodes in high-resistance solvents: Application to the fac/mer-[Cr(CO){sub 3}({eta}{sup 3}-Ph{sub 2}PCH{sub 2}CH{sub 2}P(Ph)CH{sub 2}CH{sub 2}PPh{sub 2})]{sup +/0} square reaction sheme in dichloromethane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bond, A.M.; Feldberg, S.W.; Greenhill, H.B.

1992-05-01

Instrumental, experimental and theoretical approaches required to quantify the thermodynamic and kinetic aspects of the square reaction scheme relating the fac{sup +/0} and mer{sup +/0} redox couples in the high-resistance solvent dichloromethane, at microelectrodes, under both steady-state and fast scan rate (transient) conditions, are presented. fac{sup +}, mer{sup +}, fac{sup 0}, and mer{sup 0} represent the facial and meridional isomers of Cr-(CO){sub 3}({eta}{sup 3}-Ph{sub 2}PCH{sub 2}CH{sub 2}P(Ph)CH{sub 2}CH{sub 2}PPh{sub 2}) in the oxidized 17 electron (fac{sup +}, mer{sup +}) and reduced 18 electron (fac{sup 0}, mer{sup 0}) configurations, respectively. A computationally efficient simulation method based on the DuFort-Frankel algorithm ismore » readily applied to microelectrodes and enables simulations to be undertaken for both steady-state and transient voltammetry at electrodes of microdisk geometry. The minimal ohmic drop present under steady-state conditions enables a limited set of parameters to be calculated for the square scheme. However, data relevant to species generated as a product of electron transfer have to be determined from the transient voltammetry at fast scans rates. For the latter experiments, a newly designed electrochemical cell was developed along with relevant electronic circuitry to minimize the background current and uncompensated resistance. The cell contains two matched working microelectrodes (one in the test solution and one in the separated electrolyte solution) and a common quasi-reference electrode which passes through both compartments of the cell. It is concluded that a judicious choice of steady-state and transient techniques, such as those described in this work, are necessary to characterize complex reaction schemes in high-resistance solvents. 46 refs., 7 figs., 3 tabs.« less

Kinetic and Thermodynamic Rationale for SAHA Being a Preferential Human HDAC8 Inhibitor as Compared to the Structurally Similar Ligand, TSA

PubMed Central

Singh, Raushan K.; Lall, Naveena; Leedahl, Travis S.; McGillivray, Abigail; Mandal, Tanmay; Haldar, Manas; Mallik, Sanku; Cook, Gregory; Srivastava, D.K.

2013-01-01

Of the different hydroxamate-based histone deacetylase (HDAC) inhibitors, Suberoylanilide hydroxamic acid (SAHA) has been approved by the FDA for treatment of T-cell lymphoma. Interestingly, a structurally similar inhibitor, Trichostatin A (TSA), which has a higher in vitro inhibitory-potency against HDAC8, reportedly shows a poor efficacy in clinical settings. In order to gain the molecular insight into the above discriminatory feature, we performed transient kinetic and isothermal titration calorimetric studies for the interaction of SAHA and TSA to the recombinant form of human HDAC8. The transient kinetic data revealed that the binding of both the inhibitors to the enzyme showed the biphasic profiles, which represented an initial encounter of enzyme with the inhibitor followed by the isomerization of the transient enzyme-inhibitor complexes. The temperature-dependent transient kinetic studies with the above inhibitors revealed that the bimolecular process is primarily dominated by favorable enthalpic changes, as opposed to the isomerization step; which is solely contributed by entropic changes. The standard binding-enthalpy (ΔH0) of SAHA, deduced from the transient kinetic as well as the isothermal titration calorimetric experiments, was 2–3 kcal/mol higher as compared to TSA. The experimental data presented herein suggests that SAHA serves as a preferential (target-specific/selective) HDAC8 inhibitor as compared to TSA. Arguments are presented that the detailed kinetic and thermodynamic studies may guide in the rational design of HDAC inhibitors as therapeutic agents. PMID:24079912

Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion

PubMed Central

Meinhold, Derrick W.; Wright, Peter E.

2011-01-01

Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use 15N, , and 13CO NMR R2 relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which is invisible in NMR spectra. Measurements of R2 dispersion for residues contacted by the F-helix region in the native (N) structure reveal a transient state formed by local unfolding of helix F and undocking from the protein core. A similar state was detected at pH 4.75–4.95 and determined to be an on-pathway intermediate (I1) in a linear three-state unfolding scheme (N⇆I1⇆MG) leading to a transiently populated molten globule (MG) state. The slowest steps in unfolding and refolding are N → I1 (36 s-1) and MG → I1 (26 s-1), respectively. Differences in chemical shift between N and I1 are very small, except in regions adjacent to helix F, showing that their core structures are similar. Chemical shift changes between the N and MG states, obtained from R2 dispersion, reveal that the transient MG state is structurally similar to the equilibrium MG observed previously at high temperature and low pH. Analysis of MG state chemical shifts shows the location of residual helical structure in the transient intermediate and identifies regions that unfold or rearrange into nonnative structure during the N → MG transition. The experiments also identify regions of energetic frustration that “crack” during unfolding and impede the refolding process. PMID:21562212

Kinetic modeling and transient DRIFTS–MS studies of CO 2 methanation over Ru/Al 2O 3 catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiang; Hong, Yongchun; Shi, Hui

CO 2 methanation was investigated on 5% and 0.5% Ru/Al 2O 3 catalysts (Ru dispersions: ~18% and ~40%, respectively) by steady-state kinetic measurements and transient DRIFTS–MS. Methanation rates were higher over 5% Ru/Al 2O 3 than over 0.5% Ru/Al 2O 3. The measured activation energies, however, were lower on 0.5% Ru/Al 2O 3 than on 5% Ru/Al 2O 3. Transient DRIFTS–MS results demonstrated that direct CO 2 dissociation was negligible over Ru. CO 2 has to first react with surface hydroxyls on Al 2O 3 to form bicarbonates, which, in turn, react with adsorbed H on Ru to produce adsorbed formate species. Formates, most likely at the metal/oxide interface, can react rapidly with adsorbed H forming adsorbed CO, only a portion of which is reactive toward adsorbed H, ultimately leading to CH4 formation. The measured kinetics are fully consistent with a Langmuir–Hinshelwood type mechanism in which the H-assisted dissociation of the reactive CO* is the rate-determining step (RDS). The similar empirical rate expressions (r CH4 = kPmore » $$0.1\\atop{CO2}$$P$$0.3-0.5\\atop{H2}$$) and DRIFTS–MS results on the two catalysts under both transient and steady-state conditions suggest that the mechanism for CO 2 methanation does not change with Ru particle size under the studied experimental conditions. Kinetic modeling results further indicate that the intrinsic activation barrier for the RDS is slightly lower on 0.5% Ru/Al 2O 3 than on 5% Ru/Al 2O 3. Due to the presence of unreactive adsorbed CO under reaction conditions, the larger fraction of such surface sites that bind CO too strongly on 0.5% Ru/Al 2O 3 than on 5% Ru/Al 2O 3, as revealed by FTIR measurements, is regarded as the main reason for the lower rates for CO 2 methanation on 0.5% Ru/Al 2O 3. The catalyst preparation and catalytic measurements were supported by a Laboratory Directed Research and Development (LDRD) project. The authors gratefully acknowledge the financial support of this work by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.« less

Equilibrium and kinetic models for colloid release under transient solution chemistry conditions

USDA-ARS?s Scientific Manuscript database

We present continuum models to describe colloid release in the subsurface during transient physicochemical conditions. Our modeling approach relates the amount of colloid release to changes in the fraction of the solid surface area that contributes to retention. Equilibrium, kinetic, equilibrium and...

A study of the kinetic energy generation with general circulation models

NASA Technical Reports Server (NTRS)

Chen, T.-C.; Lee, Y.-H.

1983-01-01

The history data of winter simulation by the GLAS climate model and the NCAR community climate model are used to examine the generation of atmospheric kinetic energy. The contrast between the geographic distributions of the generation of kinetic energy and divergence of kinetic energy flux shows that kinetic energy is generated in the upstream side of jets, transported to the downstream side and destroyed there. The contributions from the time-mean and transient modes to the counterbalance between generation of kinetic energy and divergence of kinetic energy flux are also investigated. It is observed that the kinetic energy generated by the time-mean mode is essentially redistributed by the time-mean flow, while that generated by the transient flow is mainly responsible for the maintenance of the kinetic energy of the entire atmospheric flow.

VO2 Off Transient Kinetics in Extreme Intensity Swimming.

PubMed

Sousa, Ana; Figueiredo, Pedro; Keskinen, Kari L; Rodríguez, Ferran A; Machado, Leandro; Vilas-Boas, João P; Fernandes, Ricardo J

2011-01-01

Inconsistencies about dynamic asymmetry between the on- and off- transient responses in oxygen uptake are found in the literature. Therefore, the purpose of this study was to characterize the oxygen uptake off-transient kinetics during a maximal 200-m front crawl effort, as examining the degree to which the on/off regularity of the oxygen uptake kinetics response was preserved. Eight high level male swimmers performed a 200-m front crawl at maximal speed during which oxygen uptake was directly measured through breath-by-breath oxymetry (averaged every 5 s). This apparatus was connected to the swimmer by a low hydrodynamic resistance respiratory snorkel and valve system. The on- and off-transient phases were symmetrical in shape (mirror image) once they were adequately fitted by a single-exponential regression models, and no slow component for the oxygen uptake response was developed. Mean (± SD) peak oxygen uptake was 69.0 (± 6.3) mL·kg(-1)·min(-1), significantly correlated with time constant of the off- transient period (r = 0.76, p < 0.05) but not with any of the other oxygen off-transient kinetic parameters studied. A direct relationship between time constant of the off-transient period and mean swimming speed of the 200-m (r = 0.77, p < 0.05), and with the amplitude of the fast component of the effort period (r = 0.72, p < 0.05) were observed. The mean amplitude and time constant of the off-transient period values were significantly greater than the respective on- transient. In conclusion, although an asymmetry between the on- and off kinetic parameters was verified, both the 200-m effort and the respectively recovery period were better characterized by a single exponential regression model. Key pointsThe VO2 slow component was not observed in the recovery period of swimming extreme efforts;The on and off transient periods were better fitted by a single exponential function, and so, these effort and recovery periods of swimming extreme efforts are symmetrical;The rate of VO2 decline during the recovery period may be due to not only the magnitude of oxygen debt but also the VO2peak obtained during the effort period.

Differential equation methods for simulation of GFP kinetics in non-steady state experiments.

PubMed

Phair, Robert D

2018-03-15

Genetically encoded fluorescent proteins, combined with fluorescence microscopy, are widely used in cell biology to collect kinetic data on intracellular trafficking. Methods for extraction of quantitative information from these data are based on the mathematics of diffusion and tracer kinetics. Current methods, although useful and powerful, depend on the assumption that the cellular system being studied is in a steady state, that is, the assumption that all the molecular concentrations and fluxes are constant for the duration of the experiment. Here, we derive new tracer kinetic analytical methods for non-steady state biological systems by constructing mechanistic nonlinear differential equation models of the underlying cell biological processes and linking them to a separate set of differential equations governing the kinetics of the fluorescent tracer. Linking the two sets of equations is based on a new application of the fundamental tracer principle of indistinguishability and, unlike current methods, supports correct dependence of tracer kinetics on cellular dynamics. This approach thus provides a general mathematical framework for applications of GFP fluorescence microscopy (including photobleaching [FRAP, FLIP] and photoactivation to frequently encountered experimental protocols involving physiological or pharmacological perturbations (e.g., growth factors, neurotransmitters, acute knockouts, inhibitors, hormones, cytokines, and metabolites) that initiate mechanistically informative intracellular transients. When a new steady state is achieved, these methods automatically reduce to classical steady state tracer kinetic analysis. © 2018 Phair. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Ultrafast photophysics of pi-conjugated polymers for organic light emitting diode applications

NASA Astrophysics Data System (ADS)

Olejnik, Ella

In this work we used the pump-probe photomodulation (PM) spectroscopy technique to measure the transient PM spectrum and decay kinetics in various pi -- conjugated polymers (PCPs) films and blends. Using two ultrafast laser systems, we covered a broad spectral range from 0.25 -- 2.5 eV in the time domain from 200 fs to 1 ns with 150 fs time resolution. We also used continuous wave (CW) photomodulation spectroscopy, photoluminescence (PL), electro-absorption and doping-induced absorption to study the photoexcitations and other optical properties of PCPs and guest/ host blends. In particular we studied two different types of Poly(thienylenevinylene) polymer derivatives. One polymer type is the ordered regio-regular (RR) and regio-random (RRa) -- PTV in which the dark exciton, 2Ag is the lowest excited state. In these polymers the photoexcited exciton shows very fast decay kinetics due to the internal conversion to the dark exciton, which results in weak PL emission; thus these two polymers are non-luminescent. The other PTV derivative is the imide -- PTV which is more luminescent due to the proximity of 1Bu and 2Ag states, that results in longer decay kinetics and a difference between the calculated value of the QEPL (9%) and the measured one (1%). We also demonstrate transient strain spectroscopy in RR -- PTV thin films, where the ultrafast energy release associated with the exciton decay gives rise to substantial static and dynamic strains in the film that dramatically influences the film's transient PM response. We also study the photophysics of poly(dioctyloxy) phenylenevinylene polymer with different isotopes, where we substituted hydrogen (H-polymer) by deuterium (D-polymer), and 12C by 13C isotopes. From the transient decay kinetics measurements we found that the exciton recombination in DOO -- PPV consists of two processes. These are: intrinsic monomolecular, and exciton-exciton annihilation (bimolecular). In the D -- polymer, different probe frequencies of the main exciton photoinduced absorption band (PA1) show a variety of decay kinetics that result from various photoexcitations that contribute to the spectrum. Comparing the transient PM spectrum at 1 ns time delay to the CW PM shows the formation of triplet excitons, which is possible due to singlet fission of mAg (at 2.9 eV) into two triplets (2 X 1.4 eV). In the last part of this thesis we summarize our studies of organic light emitting diodes (OLED) devices based on a host/guest blend of Polyfluorene polymer that is mixed with various percentages of Ir(btp)2acac molecules. In this mixture the PFO (host) shows blue fluorescence, whereas the Ir-complex (guest) has red phosphorescence emission; thus OLED based on this mixture can serve as a `white OLED'. Since the PFO emission spectrum perfectly matches the absorption band of the Ir-complex, it induces an efficient energy transfer from the PFO host to the Ir-complex guest molecules, which we tried to time resolve by the transient PM method.

Ultrafast studies of the excited-state dynamics of copper and nickel phthalocyanine tetrasulfonates: potential sensitizers for the two-photon photodynamic therapy of tumors.

PubMed

Fournier, Michel; Pépin, Claude; Houde, Daniel; Ouellet, René; van Lier, Johan E

2004-01-01

In order to evaluate the potential of copper and nickel phthalocyanine tetrasulfonates as sensitizers for two-photon photodynamic therapy, we conducted kinetic femtosecond measurements of transient absorption and bleaching of their excited state dynamics in aqueous solution. Samples were pumped with 620 nm and 310 nm laser light, which allowed us to study relaxation processes from both the first and second singlet (or doublet for the copper phthalocyanine) excited states. A second excitation from the first excited triplet state, approximately 685 and 105 ps after the first excitation for copper and nickel phthalocyanine tetrasulfonate respectively, was the most efficient way to bring the molecules to an upper triplet state. Presumably this highest triplet state can inflict molecular damage on adjacent biomolecules int eh absence of oxygen, resulting in the desired cytotoxic cellular response. Transient absorption spectra at different fixed delays indicate that optimum efficiency would require that the second photon has a wavelength of approximately 750 nm.

Studies in electron phenomena in MOS structures: The pulsed C-V method. M.S. Thesis. Abstract Only

NASA Technical Reports Server (NTRS)

Kaplan, G.

1983-01-01

The pulse hysteresis capacitance voltage (C-V) provides a straight forward technique for measuring the change of various charges in MOS structures and a tool for investigating the kinetics of various electron phenomena is developed and described. The method can be used for measuring the energy distribution and kinetics of surface states with the resolution of about 1/5 x 10 to the -9 power cm eV. Some transients in an MOS structure, particularly, the thermal generation of minority charge carriers via surface states and the relaxation of minority charge carriers supplied from the inversion layer outside the MOS structure are theoretically investigated. Analytical expressions which clearly present the physics of those electron phenomena are derived.

Impulsive Collision Dynamics of CO Super Rotors from an Optical Centrifuge.

PubMed

Murray, Matthew J; Ogden, Hannah M; Toro, Carlos; Liu, Qingnan; Mullin, Amy S

2016-11-18

We report state-resolved collision dynamics for CO molecules prepared in an optical centrifuge and measured with high-resolution transient IR absorption spectroscopy. Time-resolved polarization-sensitive measurements of excited CO molecules in the J=29 rotational state reveal that the oriented angular momentum of CO rotors is relaxed by impulsive collisions. The translational energy gains for molecules in the initial plane of rotation are threefold larger than for randomized angular momentum orientations, indicating the presence of anisotropic kinetic energy. The transient data show enhanced population for CO molecules in the initial plane of rotation immediately following the optical centrifuge pulse. A comparison with previous CO 2 super rotor studies illustrates the behavior of molecular gyroscopes; spatial reorientation of CO 2 J=76 rotors takes substantially longer than that for CO J=29 rotors, despite similarities in classical rotational period and rotational energy gap. High-resolution transient IR absorption measurements of the CO J=29-39 rotational states show that the collisional depopulation rates increase with J quantum number. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A cross-bridge based model of force depression: Can a single modification address both transient and steady-state behaviors?

PubMed

Corr, David T; Herzog, Walter

2016-03-21

Force depression (FD), the reduction of isometric force following active shortening, is a phenomenon of skeletal muscle that has received significant attention in biomechanical and physiological literature, yet the mechanisms underlying FD remain unknown. Recent experiments identified a slower rate of force redevelopment with increasing amounts of steady-state FD, suggesting that FD may be caused, at least in part, by a decrease in cross-bridge binding rate (Corr and Herzog, 2005; Koppes et al., 2014). Herein, we develop a cross-bridge based model of FD in which the binding rate function, f, decreases with the mechanical work performed during shortening. This modification incorporates a direct relationship between steady-state FD and muscle mechanical work (Corr and Herzog, 2005; Herzog et al., 2000; Kosterina et al., 2008), and is consistent with a proposed mechanism attributing FD to stress-induced inhibition of cross-bridge attachments (Herzog, 1998; Maréchal and Plaghki, 1979). Thus, for an increase in mechanical work, the model should predict a slower force redevelopment (decreased attachment rate) to a more depressed steady-state force (fewer attached cross-bridges), and a reduction in contractile element stiffness (Ford et al., 1981). We hypothesized that since this modification affects the cross-bridge kinetics, a corresponding model would be able to account for both transient and steady-state FD behaviors. Comparisons to prior experiments (Corr and Herzog, 2005; Herzog et al., 2000; Kosterina et al., 2008) show that both steady-state and transient aspects of FD, as well as the relationship of FD with respect to speed and amplitude of shortening, are well captured by this model. Thus, this relatively simple cross-bridge based model of FD lends support to a mechanism involving the inhibition of cross-bridge binding, and indicates that cross-bridge kinetics may play a critical role in FD. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

DOE PAGES

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

2016-12-02

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Kinetic: A system code for analyzing nuclear thermal propulsion rocket engine transients

NASA Astrophysics Data System (ADS)

Schmidt, Eldon; Lazareth, Otto; Ludewig, Hans

The topics are presented in viewgraph form and include the following: outline of kinetic code; a kinetic information flow diagram; kinetic neutronic equations; turbopump/nozzle algorithm; kinetic heat transfer equations per node; and test problem diagram.

Dissociation of Calcium Transients and Force Development following a Change in Stimulation Frequency in Isolated Rabbit Myocardium.

PubMed

Haizlip, Kaylan M; Milani-Nejad, Nima; Brunello, Lucia; Varian, Kenneth D; Slabaugh, Jessica L; Walton, Shane D; Gyorke, Sandor; Davis, Jonathan P; Biesiadecki, Brandon J; Janssen, Paul M L

2015-01-01

As the heart transitions from one exercise intensity to another, changes in cardiac output occur, which are modulated by alterations in force development and calcium handling. Although the steady-state force-calcium relationship at various heart rates is well investigated, regulation of these processes during transitions in heart rate is poorly understood. In isolated right ventricular muscle preparations from the rabbit, we investigated the beat-to-beat alterations in force and calcium during the transition from one stimulation frequency to another, using contractile assessments and confocal microscopy. We show that a change in steady-state conditions occurs in multiple phases: a rapid phase, which is characterized by a fast change in force production mirrored by a change in calcium transient amplitude, and a slow phase, which follows the rapid phase and occurs as the muscle proceeds to stabilize at the new frequency. This second/late phase is characterized by a quantitative dissociation between the calcium transient amplitude and developed force. Twitch timing kinetics, such as time to peak tension and 50% relaxation rate, reached steady-state well before force development and calcium transient amplitude. The dynamic relationship between force and calcium upon a switch in stimulation frequency unveils the dynamic involvement of myofilament-based properties in frequency-dependent activation.

Interaction of Alpha-Chymotrypsin with a Strained Cyclic Ester: An Undergraduate Experiment in Transient State Kinetics on a Slow Time Scale.

ERIC Educational Resources Information Center

Nitta, Yasunori; And Others

1984-01-01

Describes a set of experiments (for senior-level biochemistry students) which permit evaluation and estimation of rate and equilibrium constants involving an intermediate in the alpha-chymotrypsin mediated hydrolysis of ortho-hydroxy-alpha-toluenesulfonic acid (I). The only equipment required for the experiments is a well-thermostated double beam…

Kinetic Monte Carlo simulations for transient thermal fields: Computational methodology and application to the submicrosecond laser processes in implanted silicon.

PubMed

Fisicaro, G; Pelaz, L; Lopez, P; La Magna, A

2012-09-01

Pulsed laser irradiation of damaged solids promotes ultrafast nonequilibrium kinetics, on the submicrosecond scale, leading to microscopic modifications of the material state. Reliable theoretical predictions of this evolution can be achieved only by simulating particle interactions in the presence of large and transient gradients of the thermal field. We propose a kinetic Monte Carlo (KMC) method for the simulation of damaged systems in the extremely far-from-equilibrium conditions caused by the laser irradiation. The reference systems are nonideal crystals containing point defect excesses, an order of magnitude larger than the equilibrium density, due to a preirradiation ion implantation process. The thermal and, eventual, melting problem is solved within the phase-field methodology, and the numerical solutions for the space- and time-dependent thermal field were then dynamically coupled to the KMC code. The formalism, implementation, and related tests of our computational code are discussed in detail. As an application example we analyze the evolution of the defect system caused by P ion implantation in Si under nanosecond pulsed irradiation. The simulation results suggest a significant annihilation of the implantation damage which can be well controlled by the laser fluence.

Ultrafast Dynamics in DNA and RNA Derivatives Monitored by Broadband Transient Absorption Spectrscopy

NASA Astrophysics Data System (ADS)

Brister, Matthew M.; Crespo-Hernández, Carlos E.

2015-06-01

The ultrafast dynamics of nucleic acids have been under scrutiny for the past couple of decades because of the role that the high-energy electronic states play in mutagenesis and carcinogenesis. Kinetic models have been proposed, based on both experimental and theoretical discoveries. Direct experimental evidence of the intersystem crossing rate and population of the triplet state for most nucleic acid bases has yet to be reported, even though the triplet state is thought to be the most reactive species. Utilizing broadband femtosecond transient absorption spectroscopy, we reveal the time scale at which singlet-to-triplet population transfer occurs in several nucleic acid derivatives in the condensed phase. The implication of these results to the current understanding of the DNA and RNA photochemistry will be discussed. The authors acknowledge the CAREER program of the National Science Foundation (Grant No. CHE-1255084) for financial support.

Analysis of stochastic crystallization in micron-sized droplets of undercooled liquid l-arabitol.

PubMed

Guinet, Yannick; Carpentier, Laurent; Paccou, Laurent; Derollez, Patrick; Hédoux, Alain

2016-11-29

Kinetics of isothermal crystallization of l-arabitol were analyzed from the undercooled liquid state within micron-sized droplets from micro-Raman spectroscopy. This study reveals that crystallization slightly above T g is controlled by stochastic heterogeneous nucleation inherent to the droplet size. Microscopic Raman investigations performed in droplets give the unique opportunity to analyze the pure metastable Form II of l-arabitol. It was found that Form II is characterized by a molecular packing more compact than that of the stable Form I, inherent to strong intermolecular hydrogen bonding. Kinetics laws obtained by analyzing several droplets at different temperatures, reveal the transient character of Form II, quasi systematically detected during the crystallization process of form I. Form II appears as the first step of crystallization prior to successive short-living metastable states which is necessary to achieve a complete crystallization in Form I. It was found that the kinetics of conversion between the metastable states (Form II) into Form I is dependent on the amount of strong hydrogen bonding distinctive of Form II. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessment of the stability of a multimachine power system by the transient energy margin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stanton, S.E.

1982-01-01

This reasearch develops a tool for the direct assessment of the transient stability of a multimachine electric power system that is subject to a large disturbance. The tool is the Transient Energy Margin. The transient of interest is the first swing (or inertial) transient. The Transient Energy Margin is computed by evaluating an energy function using the relevant unstable equilibrium point and the system states at the instant the disturbance is removed. In evaluating the function, a significant portion of the fault kinetic energy is identified as not contributing to system instability. The resulting energy value is a measure ofmore » the margin-of-safety for the disturbed system. A distinction is proposed between assessing system stability and assessing system security. The Transient Energy Margin is used first to assess the stability of the system. This profile ranks various distrubances to display the strengths and weaknesses of the system. A modified Transient Energy Margin is then proposed as an assessment of security; the transient energy margin profile is repeated to evaluate the system response in terms of the local minimum energy conditions approached by the critical trajectories. Both techniques are applied to a practical, 17 generator test system.« less

Transient atomic behavior and surface kinetics of GaN

NASA Astrophysics Data System (ADS)

Moseley, Michael; Billingsley, Daniel; Henderson, Walter; Trybus, Elaissa; Doolittle, W. Alan

2009-07-01

An in-depth model for the transient behavior of metal atoms adsorbed on the surface of GaN is developed. This model is developed by qualitatively analyzing transient reflection high energy electron diffraction (RHEED) signals, which were recorded for a variety of growth conditions of GaN grown by molecular-beam epitaxy (MBE) using metal-modulated epitaxy (MME). Details such as the initial desorption of a nitrogen adlayer and the formation of the Ga monolayer, bilayer, and droplets are monitored using RHEED and related to Ga flux and shutter cycles. The suggested model increases the understanding of the surface kinetics of GaN, provides an indirect method of monitoring the kinetic evolution of these surfaces, and introduces a novel method of in situ growth rate determination.

Transient Numerical Modeling of Catalytic Channels

NASA Technical Reports Server (NTRS)

Struk, Peter M.; Dietrich, Daniel L.; Miller, Fletcher J.; T'ien, James S.

2007-01-01

This paper presents a transient model of catalytic combustion suitable for isolated channels and monolith reactors. The model is a lumped two-phase (gas and solid) model where the gas phase is quasi-steady relative to the transient solid. Axial diffusion is neglected in the gas phase; lateral diffusion, however, is accounted for using transfer coefficients. The solid phase includes axial heat conduction and external heat loss due to convection and radiation. The combustion process utilizes detailed gas and surface reaction models. The gas-phase model becomes a system of stiff ordinary differential equations while the solid phase reduces, after discretization, into a system of stiff ordinary differential-algebraic equations. The time evolution of the system came from alternating integrations of the quasi-steady gas and transient solid. This work outlines the numerical model and presents some sensitivity studies on important parameters including internal transfer coefficients, catalytic surface site density, and external heat-loss (if applicable). The model is compared to two experiments using CO fuel: (1) steady-state conversion through an isothermal platinum (Pt) tube and (2) transient propagation of a catalytic reaction inside a small Pt tube. The model requires internal mass-transfer resistance to match the experiments at lower residence times. Under mass-transport limited conditions, the model reasonably predicted exit conversion using global mass-transfer coefficients. Near light-off, the model results did not match the experiment precisely even after adjustment of mass-transfer coefficients. Agreement improved for the first case after adjusting the surface kinetics such that the net rate of CO adsorption increased compared to O2. The CO / O2 surface mechanism came from a sub-set of reactions in a popular CH4 / O2 mechanism. For the second case, predictions improved for lean conditions with increased external heat loss or adjustment of the kinetics as in the first case. Finally, the results show that different initial surface-species distribution leads to different steady-states under certain conditions. These results demonstrate the utility of a lumped two-phase model of a transient catalytic combustor with detailed chemistry.

Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

PubMed

Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; van Dijk, Chris N; Vreede, Jocelyne; Woutersen, Sander

2014-03-06

Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu - and Arg + are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations.

PubMed

Meral, Derya; Provasi, Davide; Prada-Gracia, Diego; Möller, Jan; Marino, Kristen; Lohse, Martin J; Filizola, Marta

2018-05-16

Various experimental and computational techniques have been employed over the past decade to provide structural and thermodynamic insights into G Protein-Coupled Receptor (GPCR) dimerization. Here, we use multiple microsecond-long, coarse-grained, biased and unbiased molecular dynamics simulations (a total of ~4 milliseconds) combined with multi-ensemble Markov state models to elucidate the kinetics of homodimerization of a prototypic GPCR, the µ-opioid receptor (MOR), embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol lipid bilayer. Analysis of these computations identifies kinetically distinct macrostates comprising several different short-lived dimeric configurations of either inactive or activated MOR. Calculated kinetic rates and fractions of dimers at different MOR concentrations suggest a negligible population of MOR homodimers at physiological concentrations, which is supported by acceptor photobleaching fluorescence resonance energy transfer (FRET) experiments. This study provides a rigorous, quantitative explanation for some conflicting experimental data on GPCR oligomerization.

Transient responses of phosphoric acid fuel cell power plant system. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Lu, Cheng-Yi

1983-01-01

An analytical and computerized study of the steady state and transient response of a phosphoric acid fuel cell (PAFC) system was completed. Parametric studies and sensitivity analyses of the PAFC system's operation were accomplished. Four non-linear dynamic models of the fuel cell stack, reformer, shift converters, and heat exchangers were developed based on nonhomogeneous non-linear partial differential equations, which include the material, component, energy balance, and electrochemical kinetic features. Due to a lack of experimental data for the dynamic response of the components only the steady state results were compared with data from other sources, indicating reasonably good agreement. A steady state simulation of the entire system was developed using, nonlinear ordinary differential equations. The finite difference method and trial-and-error procedures were used to obtain a solution. Using the model, a PAFC system, that was developed under NASA Grant, NCC3-17, was improved through the optimization of the heat exchanger network. Three types of cooling configurations for cell plates were evaluated to obtain the best current density and temperature distributions. The steady state solutions were used as the initial conditions in the dynamic model. The transient response of a simplified PAFC system, which included all of the major components, subjected to a load change was obtained. Due to the length of the computation time for the transient response calculations, analysis on a real-time computer was not possible. A simulation of the real-time calculations was developed on a batch type computer. The transient response characteristics are needed for the optimization of the design and control of the whole PAFC system. All of the models, procedures and simulations were programmed in Fortran and run on IBM 370 computers at Cleveland State University and the NASA Lewis Research Center.

[Quantum differences of ortho/para H2O2 spin-isomers as a factor of the femtosecond charge separation kinetics modulation in reaction centers of purple bacteria].

PubMed

Pishchal'nikov, R Iu; Pershin, S M; Bunkin, A F

2012-01-01

We have proposed the mechanism of coherent modulations of the P* state in the transient absorption spectra of the reaction center isolated from purple bacteria. Two water molecules, located between special pair, Ba, Bb chlorophylls and histidine L173 and M202, are supposed to be ortho-H2O and para-H2O isomers with different magnetic properties. The distinctive modulation frequencies were labeling as rotational resonances of ortho-H2O. According to our assumption, the interaction of rotational modes of water isomers with the charge-transfer states is a reason of coherent modulations of kinetics. We have modified a Hamiltonian system in order to take into account the rotational modes of ortho-H2O. Evolution of the density matrix was calculated in Liouville space. The Redfield relaxation theory for molecular aggregates was used to model kinetics up to 3 ps.

Transient state kinetic investigation of ferritin iron release

NASA Astrophysics Data System (ADS)

Ciasca, G.; Papi, M.; Chiarpotto, M.; Rodio, M.; Campi, G.; Rossi, C.; De Sole, P.; Bianconi, A.

2012-02-01

Increased iron concentration in tissues appears to be a factor in the genesis and development of inflammatory and degenerative diseases. By means of real-time small angle x-ray scattering measurements, we studied the kinetics of iron release from the ferritin inorganic core as a function of time and distance from the iron core centre. Accordingly, the iron release process follows a three step model: (i) a defect nucleation in the outer part of the mineral core, (ii) the diffusion of the reducing agent towards the inner part of the core, and (iii) the erosion of the core from the inner to the outer part.

Kinetic theory of coupled oscillators.

PubMed

Hildebrand, Eric J; Buice, Michael A; Chow, Carson C

2007-02-02

We present an approach for the description of fluctuations that are due to finite system size induced correlations in the Kuramoto model of coupled oscillators. We construct a hierarchy for the moments of the density of oscillators that is analogous to the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy in the kinetic theory of plasmas and gases. To calculate the lowest order system size effect, we truncate this hierarchy at second order and solve the resulting closed equations for the two-oscillator correlation function around the incoherent state. We use this correlation function to compute the fluctuations of the order parameter, including the effect of transients, and compare this computation with numerical simulations.

Microsecond Unfolding Kinetics of Sheep Prion Protein Reveals an Intermediate that Correlates with Susceptibility to Classical Scrapie

PubMed Central

Chen, Kai-Chun; Xu, Ming; Wedemeyer, William J.; Roder, Heinrich

2011-01-01

The microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94–233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfolding kinetics of ovPrP provides evidence for an intermediate species. However, in contrast to previous results for human PrP, there is no evidence for an intermediate under refolding conditions. Global analysis of the kinetic data, based on a sequential three-state mechanism, quantitatively accounts for all folding and unfolding data as a function of denaturant concentration. The simulations predict that an intermediate accumulates under both folding and unfolding conditions, but is observable only in unfolding experiments because the intermediate is optically indistinguishable from the native state. The relative population of intermediates in two ovPrP variants, both transiently and under destabilizing equilibrium conditions, correlates with their propensities for classical scrapie. The variant susceptible to classical scrapie has a larger population of the intermediate state than the resistant variant. Thus, the susceptible variant should be favored to undergo the PrPC to PrPSc conversion and oligomerization. PMID:21889460

FlashPhotol: Using a Flash Photolysis Apparatus Simulator to Introduce Students to the Kinetics of Transient Species and Fast Reactions

ERIC Educational Resources Information Center

Bigger, Stephen W.

2016-01-01

FlashPhotol is an educational software package that introduces students to the kinetics of transient species and fast reactions. This is achieved by means of a computer-simulated flash photolysis apparatus that comprises all major functional elements and that students can use to perform various experiments. The experimental interface presents a…

Kinetic features and non-stationary electron trapping in paraxial magnetic nozzles

NASA Astrophysics Data System (ADS)

Sánchez-Arriaga, G.; Zhou, J.; Ahedo, E.; Martínez-Sánchez, M.; Ramos, J. J.

2018-03-01

The paraxial expansion of a collisionless plasma jet into vacuum, guided by a magnetic nozzle, is studied with an Eulerian and non-stationary Vlasov-Poisson solver. Parametric analyzes varying the magnetic field expansion rate, the size of the simulation box, and the electrostatic potential fall are presented. After choosing the potential fall leading to a zero net current beam, the steady states of the simulations exhibit a quasi-neutral region followed by a downstream sheath. The latter, an unavoidable consequence of the finite size of the computational domain, does not affect the quasi-neutral region if the box size is chosen appropriately. The steady state presents a strong decay of the perpendicular temperature of the electrons, whose profile versus the inverse of the magnetic field does not depend on the expansion rate within the quasi-neutral region. As a consequence, the electron distribution function is highly anisotropic downstream. The simulations revealed that the ions reach a higher velocity during the transient than in the steady state and their distribution functions are not far from mono-energetic. The density percentage of the population of electrons trapped during the transient, which is computed self-consistently by the code, is up to 25% of the total electron density in the quasi-neutral region. It is demonstrated that the exact amount depends on the history of the system and the steady state is not unique. Nevertheless, the amount of trapped electrons is smaller than the one assumed heuristically by kinetic stationary theories.

Peroxyl radical reactions with carotenoids in microemulsions: Influence of microemulsion composition and the nature of peroxyl radical precursor.

PubMed

El-Agamey, Ali; McGarvey, David J

2016-01-01

The reactions of acetylperoxyl radicals with different carotenoids (7,7'-dihydro-β-carotene and ζ-carotene) in SDS and CTAC microemulsions of different compositions were investigated using laser flash photolysis (LFP) coupled with kinetic absorption spectroscopy. The primary objective of this study was to explore the influence of microemulsion composition and the type of surfactant used on the yields and kinetics of various transients formed from the reaction of acetylperoxyl radicals with carotenoids. Also, the influence of the site (hydrocarbon phases or aqueous phase) of generation of the peroxyl radical precursor was examined by using 4-acetyl-4-phenylpiperidine hydrochloride (APPHCl) and 1,1-diphenylacetone (11DPA) as water-soluble and lipid-soluble peroxyl radical precursors, respectively. LFP of peroxyl radical precursors with 7,7'-dihydro-β-carotene (77DH) in different microemulsions gives rise to the formation of three distinct transients namely addition radical (λmax=460 nm), near infrared transient1 (NIR, λmax=700 nm) and 7,7'-dihydro-β-carotene radical cation (77DH(•+), λmax=770 nm). In addition, for ζ-carotene (ZETA) two transients (near infrared transient1 (NIR1, λmax=660 nm) and ζ-carotene radical cation (ZETA(•+), λmax=730-740 nm)) are generated following LFP of peroxyl radical precursors in the presence of ζ-carotene (ZETA) in different microemulsions. The results show that the composition of the microemulsion strongly influences the observed yield and kinetics of the transients formed from the reactions of peroxyl radicals (acetylperoxyl radicals) with carotenoids (77DH and ZETA). Also, the type of surfactant used in the microemulsions influences the yield of the transients formed. The dependence of the transient yields and kinetics on microemulsion composition (or the type of surfactant used in the microemulsion) can be attributed to the change of the polarity of the microenvironment of the carotenoid. Furthermore, the nature of the peroxyl radical precursor used (water-soluble or lipid-soluble peroxyl radical precursors) has little influence on the yields and kinetics of the transients formed from the reaction of peroxyl radicals with carotenoids. In the context of the interest in carotenoids as radical scavenging antioxidants, the fates of the addition radicals (formed from the reaction of carotenoid with peroxyl radicals) and carotenoid radical cations are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Kinetics of proton uptake and dye binding by photoactive yellow protein in wild type and in the E46Q and E46A mutants.

PubMed

Borucki, Berthold; Devanathan, Savitha; Otto, Harald; Cusanovich, Michael A; Tollin, Gordon; Heyn, Maarten P

2002-08-06

We studied the kinetics of proton uptake and release by photoactive yellow protein (PYP) from Ectothiorhodospira halophila in wild type and the E46Q and E46A mutants by transient absorption spectroscopy with the pH-indicator dyes bromocresol purple or cresol red in unbuffered solution. In parallel, we investigated the kinetics of chromophore protonation as monitored by the rise and decay of the blue-shifted state I(2) (lambda(max) = 355 nm). For wild type the proton uptake kinetics is synchronized with the fast phase of I(2) formation (tau = 500 micros at pH 6.2). The transient absorption signal from the dye also contains a slower component which is not due to dye deprotonation but is caused by dye binding to a hydrophobic patch that is transiently exposed in the structurally changed and partially unfolded I(2) intermediate. This conclusion is based on the wavelength, pH, and concentration dependence of the dye signal and on dye measurements in the presence of buffer. SVD analysis, moreover, indicates the presence of two components in the dye signal: protonation and dye binding. The dye binding has a rise time of about 4 ms and is coupled kinetically with a transition between two I(2) intermediates. In the mutant E46Q, which lacks the putative internal proton donor E46, the formation of I(2) is accelerated, but the proton uptake kinetics remains kinetically coupled to the fast phase of I(2) formation (tau = 100 micros at pH 6.3). For this mutant the protein conformational change, as monitored by the dye binding, occurs with about the same time constant as in wild type but with reduced amplitude. In the alkaline form of the mutant E46A the formation of the I(2)-like intermediate is even faster as is the proton uptake (tau = 20 micros at pH 8.3). No dye binding occurred in E46A, suggesting the absence of a conformational change. In all of the systems proton release is synchronized with the decay of I(2). Our results support mechanisms in which the chromophore of PYP is protonated directly from the external medium rather than by the internal donor E46.

Dependence of cross-bridge kinetics on myosin light chain isoforms in rabbit and rat skeletal muscle fibres.

PubMed

Andruchov, Oleg; Andruchova, Olena; Wang, Yishu; Galler, Stefan

2006-02-15

Cross-bridge kinetics underlying stretch-induced force transients was studied in fibres with different myosin light chain (MLC) isoforms from skeletal muscles of rabbit and rat. The force transients were induced by stepwise stretches (< 0.3% of fibre length) applied on maximally Ca2+-activated skinned fibres. Fast fibre types IIB, IID (or IIX) and IIA and the slow fibre type I containing the myosin heavy chain isoforms MHC-IIb, MHC-IId (or MHC-IIx), MHC-IIa and MHC-I, respectively, were investigated. The MLC isoform content varied within fibre types. Fast fibre types contained the fast regulatory MLC isoform MLC2f and different proportions of the fast alkali MLC isoforms MLC1f and MLC3f. Type I fibres contained the slow regulatory MLC isoform MLC2s and the slow alkali MLC isoform MLC1s. Slow MLC isoforms were also present in several type IIA fibres. The kinetics of force transients differed by a factor of about 30 between fibre types (order from fastest to slowest kinetics: IIB > IID > IIA > I). The kinetics of the force transients was not dependent on the relative content of MLC1f and MLC3f. Type IIA fibres containing fast and slow MLC isoforms were about 1.2 times slower than type IIA fibres containing only fast MLC isoforms. We conclude that while the cross-bridge kinetics is mainly determined by the MHC isoforms present, it is affected by fast and slow MLC isoforms but not by the relative content of MLC1f and MLC3f. Thus, the physiological role of fast and slow MLC isoforms in type IIA fibres is a fine-tuning of the cross-bridge kinetics.

Simultaneous recording of t-tubular electrical activity and Ca2+-release in heart failure

NASA Astrophysics Data System (ADS)

Crocini, C.; Coppini, R.; Ferrantini, C.; Yan, P.; Loew, L.; Tesi, C.; Poggesi, C.; Cerbai, E.; Pavone, F. S.; Sacconi, L.

2014-05-01

T-tubules (TT) are invaginations of the surface sarcolemma (SS) that mediate the rapid propagation of the action potential (AP) to the cardiomyocyte core. We employed the advantages of an ultrafast random access multi-photon (RAMP) microscope (Sacconi et al., PNAS 2012) with a double staining approach to optically record t-tubular AP and, simultaneously, the corresponding local Ca2+-release in different positions across the cardiomyocytes. Despite a uniform AP between SS and TT at steady-state stimulation, in control cardiomyocytes we observed a non-negligible be variability of local Ca2+-transient amplitude and kinetics. This variability was significantly reduced by applying 0.1μM Isoproterenol, which increases the opening probability of Ca2+-release units. In the rat heart failure model (HF), we previously demonstrated that some tubular elements fail to propagate AP. We found that the tubules unable to propagate AP, displayed a reduced correspondent Ca2+-transient amplitude as well as a slower Ca2+ rise compared to electrically coupled tubules. Moreover variability of Ca2+-transient kinetics were increased in HF. Finally, TT that did not show AP, occasionally exhibited spontaneous depolarizations that were never accompanied by local Ca2+-release in the absence of any pro-arrhythmogenic stimulation. Simultaneous recording of AP and Ca2+-transient allows us to probe the spatio-temporal variability of Ca2+-release, whereas the investigation of Ca2+-transient in HF discloses an unexpected uncoupling between t-tubular depolarization and Ca2+-release in remodeled tubules. This work was funded by the European Union 7th Framework Program (FP7/2007- 2013) under grant agreement n° 284464, 241526, by the Italian Ministry of University and Research (NANOMAX), and by Telethon-Italy (GGP13162).

The importance of becoming double-stranded: Innate immunity and the kinetic model of HIV-1 central plus strand synthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poeschla, Eric, E-mail: poeschla.eric@mayo.edu

Central initiation of plus strand synthesis is a conserved feature of lentiviruses and certain other retroelements. This complication of the standard reverse transcription mechanism produces a transient “central DNA flap” in the viral cDNA, which has been proposed to mediate its subsequent nuclear import. This model has assumed that the important feature is the flapped DNA structure itself rather than the process that produces it. Recently, an alternative kinetic model was proposed. It posits that central plus strand synthesis functions to accelerate conversion to the double-stranded state, thereby helping HIV-1 to evade single-strand DNA-targeting antiviral restrictions such as APOBEC3 proteins,more » and perhaps to avoid innate immune sensor mechanisms. The model is consistent with evidence that lentiviruses must often synthesize their cDNAs when dNTP concentrations are limiting and with data linking reverse transcription and uncoating. There may be additional kinetic advantages for the artificial genomes of lentiviral gene therapy vectors. - Highlights: • Two main functional models for HIV central plus strand synthesis have been proposed. • In one, a transient central DNA flap in the viral cDNA mediates HIV-1 nuclear import. • In the other, multiple kinetic consequences are emphasized. • One is defense against APOBEC3G, which deaminates single-stranded DNA. • Future questions pertain to antiviral restriction, uncoating and nuclear import.« less

Time course of the uridylylation and adenylylation states in the glutamine synthetase bicyclic cascade.

PubMed Central

Varón-Castellanos, R; Havsteen, B H; García-Moreno, M; Valero-Ruiz, E; Molina-Alarcón, M; García-Cánovas, F

1993-01-01

A kinetic analysis of the glutamine synthetase bicyclic cascade is presented. It includes the dependence on time from the onset of the reaction of both the uridylylation of Shapiro's regulatory protein and the adenylylation of the glutamine synthetase. The transient phase equations obtained allow an estimation of the time elapsed until the states of uridylylation and adenylylation reach their steady-states, and therefore an evaluation of the effective sensitivity of the system. The contribution of the uridylylation cycle to the adenylylation cycle has been studied, and an equation relating the state of adenylylation at any time to the state of uridylylation at the same instant has been derived. PMID:8104399

Kinetic Monte Carlo simulations of nucleation and growth in electrodeposition.

PubMed

Guo, Lian; Radisic, Aleksandar; Searson, Peter C

2005-12-22

Nucleation and growth during bulk electrodeposition is studied using kinetic Monte Carlo (KMC) simulations. Ion transport in solution is modeled using Brownian dynamics, and the kinetics of nucleation and growth are dependent on the probabilities of metal-on-substrate and metal-on-metal deposition. Using this approach, we make no assumptions about the nucleation rate, island density, or island distribution. The influence of the attachment probabilities and concentration on the time-dependent island density and current transients is reported. Various models have been assessed by recovering the nucleation rate and island density from the current-time transients.

Modeling hypertrophic IP3 transients in the cardiac myocyte.

PubMed

Cooling, Michael; Hunter, Peter; Crampin, Edmund J

2007-11-15

Cardiac hypertrophy is a known risk factor for heart disease, and at the cellular level is caused by a complex interaction of signal transduction pathways. The IP3-calcineurin pathway plays an important role in stimulating the transcription factor NFAT which binds to DNA cooperatively with other hypertrophic transcription factors. Using available kinetic data, we construct a mathematical model of the IP3 signal production system after stimulation by a hypertrophic alpha-adrenergic agonist (endothelin-1) in the mouse atrial cardiac myocyte. We use a global sensitivity analysis to identify key controlling parameters with respect to the resultant IP3 transient, including the phosphorylation of cell-membrane receptors, the ligand strength and binding kinetics to precoupled (with G(alpha)GDP) receptor, and the kinetics associated with precoupling the receptors. We show that the kinetics associated with the receptor system contribute to the behavior of the system to a great extent, with precoupled receptors driving the response to extracellular ligand. Finally, by reparameterizing for a second hypertrophic alpha-adrenergic agonist, angiotensin-II, we show that differences in key receptor kinetic and membrane density parameters are sufficient to explain different observed IP3 transients in essentially the same pathway.

Tetanic Ca2+ transient differences between slow- and fast-twitch mouse skeletal muscle fibres: a comprehensive experimental approach.

PubMed

Calderón, Juan C; Bolaños, Pura; Caputo, Carlo

2014-12-01

One hundred and eighty six enzymatically dissociated murine muscle fibres were loaded with Mag-Fluo-4 AM, and adhered to laminin, to evaluate the effect of modulating cytosolic Ca(2+) buffers and sarcoendoplasmic reticulum Ca(2+) ATPase (SERCA), mitochondria, and Na(+)/Ca(2+) exchanger (NCX) on the differential tetanic Ca(2+) transient kinetics found in different fibre types. Tetanic Ca(2+) transients were classified as morphology type I (MT-I) or type II (MT-II) according to their shape. The first peak of the MT-I (n = 25) and MT-II (n = 23) tetanic Ca(2+) transients had an amplitude (∆F/F) of 0.41 ± 0.03 and 0.83 ± 0.05 and a rise time (ms) of 1.35 and 0.98, respectively. MT-I signals had a time constant of decay (τ1, ms) of 75.9 ± 4.2 while MT-II transients showed a double exponential decay with time constants of decay (τ1 and τ2, ms) of 18.3 ± 1.4 and 742.2 ± 130.3. Sarcoendoplasmic reticulum Ca(2+) ATPase inhibition demonstrated that the decay phase of the tetanic transients mostly rely on SERCA function. Adding Ca(2+) chelators in the AM form to MT-I fibres changed the morphology of the initial five peaks to a MT-II one, modifying the decay phase of the signal in a dose-dependent manner. Mitochondria and NCX function have a minor role in explaining differences in tetanic Ca(2+) transients among fibre types but still help in removing Ca(2+) from the cytosol in both MT-I and MT-II fibres. Cytoplasmic Ca(2+) buffering capacity and SERCA function explain most of the different kinetics found in tetanic Ca(2+) transients from different fibre types, but mitochondria and NCX have a measurable role in shaping tetanic Ca(2+) responses in both slow and fast-twitch muscle fibre types. We provided experimental evidence on the mechanisms that help understand the kinetics of tetanic Ca(2+) transients themselves and explain kinetic differences found among fibre types.

Au279(SR)84: The Smallest Gold Thiolate Nanocrystal That Is Metallic and the Birth of Plasmon.

PubMed

Sakthivel, Naga Arjun; Stener, Mauro; Sementa, Luca; Fortunelli, Alessandro; Ramakrishna, Guda; Dass, Amala

2018-03-15

We report a detailed study on the optical properties of Au 279 (SR) 84 using steady-state and transient absorption measurements to probe its metallic nature, time-dependent density functional theory (TDDFT) studies to correlate the optical spectra, and density of states (DOS) to reveal the factors governing the origin of the collective surface plasmon resonance (SPR) oscillation. Au 279 is the smallest identified gold nanocrystal to exhibit SPR. Its optical absorption exhibits SPR at 510 nm. Power-dependent bleach recovery kinetics of Au 279 suggests that electron dynamics dominates its relaxation and it can support plasmon oscillations. Interestingly, TDDFT and DOS studies with different tail group residues (-CH 3 and -Ph) revealed the important role played by the tail groups of ligands in collective oscillation. Also, steady-state and time-resolved absorption for Au 36 , Au 44 , and Au 133 were studied to reveal the molecule-to-metal evolution of aromatic AuNMs. The optical gap and transient decay lifetimes decrease as the size increases.

Internet-purchased ibogaine toxicity confirmed with serum, urine, and product content levels.

PubMed

O'Connell, Charles W; Gerona, Roy R; Friesen, Matthew W; Ly, Binh T

2015-07-01

Ibogaine, a psychotropic indole alkaloid, is gaining popularity among medical subcultures for its purported anti addictive properties. Its use has been associated with altered mental status, ataxia, gastrointestinal distress, ventricular arrhythmias, and sudden and unexplained deaths.Its pharmacokinetics in toxic states is not well understood. Case report:A 33-year-old man overdosed on ibogaine in an attempt to quit his use of heroin. He developed altered state of consciousness, tremor, ataxia,nausea, vomiting, and transient QT interval prolongation, which all remitted as he cleared the substance. Ibogaine was confirmed in his urine and serum with a peak serum concentration of 377 ng/mL. Nonlinear elimination kinetics and a formula match to its active metabolite noriobgaine were observed as well. This case presents the unique description of serial serum concentrations as well as urine and product-confirmed ibogaine toxicity with transient toxin-related QT interval prolongation.

Kinetically reduced local Navier-Stokes equations for simulation of incompressible viscous flows.

PubMed

Borok, S; Ansumali, S; Karlin, I V

2007-12-01

Recently, another approach to study incompressible fluid flow was suggested [S. Ansumali, I. Karlin, and H. Ottinger, Phys. Rev. Lett. 94, 080602 (2005)]-the kinetically reduced local Navier-Stokes (KRLNS) equations. We consider a simplified two-dimensional KRLNS system and compare it with Chorin's artificial compressibility method. A comparison of the two methods for steady state computation of the flow in a lid-driven cavity at various Reynolds numbers shows that the results from both methods are in good agreement with each other. However, in the transient flow, it is demonstrated that the KRLNS equations correctly describe the time evolution of the velocity and of the pressure, unlike the artificial compressibility method.

Structure-Kinetics Correlations in Isostructural Crystals of α-(ortho-Tolyl)-acetophenones: Pinning Down Electronic Effects Using Laser-Flash Photolysis in the Solid State.

PubMed

Ayitou, Anoklase J-L; Flynn, Kristen; Jockusch, Steffen; Khan, Saeed I; Garcia-Garibay, Miguel A

2016-03-02

Aqueous suspensions of nanocrystals in the 200-500 nm size range of isostructural α-(ortho-tolyl)-acetophenone (1a) and α-(ortho-tolyl)-para-methylacetophenone (1b) displayed good absorption characteristics for flash photolysis experiments in a flow system, with transient spectra and decay kinetics with a quality that is similar to that recorded in solution. In contrast to solution measurements, reactions in the solid state were characterized by a rate limiting hydrogen transfer reaction from the triplet excited state and a very short-lived biradical intermediate, which does not accumulate. Notably, the rate for δ-hydrogen atom transfer of 1a (2.7 × 10(7) s(-1)) in the crystalline phase is 18-fold larger than that of 1b (1.5 × 10(6) s(-1)). With nearly identical molecular and crystal structures, this decrease in the rate of δ-hydrogen abstraction can be assigned unambiguously to an electronic effect by the para-methyl group in 1b, which increases the contribution of the (3)π,π* configuration relative to the reactive (3)n,π* configuration in the lowest triplet excited state. These results highlight the potential of relating single crystal X-ray structural data with absolute kinetics from laser flash photolysis.

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine.

PubMed

Lu, Wenchao; Liu, Jianbo

2016-02-24

The chemistry of singlet O2 toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels-Alder cycloaddition of singlet O2 to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at -100 °C. Herein, gas-phase ion-molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O2 at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O2 induced guanine oxidation, which is missing from conventional condensed-phase studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetic mechanism of non-muscle myosin IIB: functional adaptations for tension generation and maintenance.

PubMed

Wang, Fei; Kovacs, Mihaly; Hu, Aihua; Limouze, John; Harvey, Estelle V; Sellers, James R

2003-07-25

Besides driving contraction of various types of muscle tissue, conventional (class II) myosins serve essential cellular functions and are ubiquitously expressed in eukaryotic cells. Three different isoforms in the human myosin complement have been identified as non-muscle class II myosins. Here we report the kinetic characterization of a human non-muscle myosin IIB subfragment-1 construct produced in the baculovirus expression system. Transient kinetic data show that most steps of the actomyosin ATPase cycle are slowed down compared with other class II myosins. The ADP affinity of subfragment-1 is unusually high even in the presence of actin filaments, and the rate of ADP release is close to the steady-state ATPase rate. Thus, non-muscle myosin IIB subfragment-1 spends a significantly higher proportion of its kinetic cycle strongly attached to actin than do the muscle myosins. This feature is even more pronounced at slightly elevated ADP levels, and it may be important in carrying out the cellular functions of this isoform working in small filamentous assemblies.

Characterization of High-Frequency Excitation of a Wake by Simulation

NASA Technical Reports Server (NTRS)

Cain, Alan B.; Rogers, Michael M.; Kibens, Valdis; Mansour, Nagi (Technical Monitor)

2003-01-01

Insights into the effects of high-frequency forcing on free shear layer evolution are gained through analysis of several direct numerical simulations. High-frequency forcing of a fully turbulent plane wake results in only a weak transient effect. On the other hand, significant changes in the developed turbulent state may result when high-frequency forcing is applied to a transitional wake. The impacts of varying the characteristics of the high-frequency forcing are examined, particularly, the streamwise wavenumber band in which forcing is applied and the initial amplitude of the forcing. The high-frequency excitation is found to increase the dissipation rate of turbulent kinetic energy, to reduce the turbulent kinetic energy production rate, and to reduce the turbulent kinetic energy suppression increases with forcing amplitude once a threshold level has been reached. For a given initial forcing energy, the largest reduction in turbulent kinetic energy density was achieved by forcing wavenumbers that are about two to three times the neutral wavenumber determined from linear stability theory.

New approach to the study of transient protein conformations: the formation of a semiburied salt link in the folding pathway of barnase.

PubMed

Oliveberg, M; Fersht, A R

1996-05-28

We use in this study a novel kinetic approach to determine the H+ titration properties of a semiburied salt link in the transition state for unfolding of barnase. The approach is based on changes in the pH dependence of the kinetics upon mutation of a target residue. This makes it relatively insensitive to the absolute value of the stability and, thereby, to artifacts caused by structural rearrangements around the site of mutation. The semiburied salt bridge studied here is between Asp93 and Arg69. Mutation of either residue significantly destabilized the protein, and the pKa value of Asp93 is severely lowered in the native state to below 1 because of the ionic interaction with Arg69. The Asp93-Arg69 salt link appears to be formed early in the folding process; the pKa value of Asp93 in the transition state (approximately 1) is similar to that in the native state, and deletion of the ionic interaction with Arg69 substantially destabilizes the folding intermediate and changes the kinetic behavior from multistate to two-state or close to two-state, depending on the conditions. The results suggest that the formation of ionic interactions within clusters of hydrophobic residues can be important for early folding events and can control kinetically the folding pathway. This is not because of the inherent stability of the salt link but because the presence of two unpaired charges is very unfavorable. The data reveal also that fractional phi values are consistent with a uniformly expanded transition state or one with closely spaced energy levels and not with parallel folding pathways.

Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape

PubMed Central

Street, Timothy O; Barrick, Doug

2009-01-01

The Notch ankyrin domain is a repeat protein whose folding has been characterized through equilibrium and kinetic measurements. In previous work, equilibrium folding free energies of truncated constructs were used to generate an experimentally determined folding energy landscape (Mello and Barrick, Proc Natl Acad Sci USA 2004;101:14102–14107). Here, this folding energy landscape is used to parameterize a kinetic model in which local transition probabilities between partly folded states are based on energy values from the landscape. The landscape-based model correctly predicts highly diverse experimentally determined folding kinetics of the Notch ankyrin domain and sequence variants. These predictions include monophasic folding and biphasic unfolding, curvature in the unfolding limb of the chevron plot, population of a transient unfolding intermediate, relative folding rates of 19 variants spanning three orders of magnitude, and a change in the folding pathway that results from C-terminal stabilization. These findings indicate that the folding pathway(s) of the Notch ankyrin domain are thermodynamically selected: the primary determinants of kinetic behavior can be simply deduced from the local stability of individual repeats. PMID:19177351

Kinetic Folding Mechanism of Erythropoietin

PubMed Central

Banks, Douglas D.; Scavezze, Joanna L.; Siska, Christine C.

2009-01-01

This report describes what to our knowledge is the first kinetic folding studies of erythropoietin, a glycosylated four-helical bundle cytokine responsible for the regulation of red blood cell production. Kinetic responses for folding and unfolding reactions initiated by manual mixing were monitored by far-ultraviolet circular dichroism and fluorescence spectroscopy, and folding reactions initiated by stopped-flow mixing were monitored by fluorescence. The urea concentration dependence of the observed kinetics were best described by a three-state model with a transiently populated intermediate species that is on-pathway and obligatory. This folding scheme was further supported by the excellent agreement between the free energy of unfolding and m-value calculated from the microscopic rate constants derived from this model and these parameters determined from separate equilibrium unfolding experiments. Compared to the kinetics of other members of the four-helical bundle cytokine family, erythropoietin folding and unfolding reactions were slower and less susceptible to aggregation. We tentatively attribute these slower rates and protection from association events to the large amount of carbohydrate attached to erythropoietin at four sites. PMID:19450492

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid

PubMed Central

Castillo, Juan P.; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C.; Rosenthal, Joshua J. C.; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-01-01

The Na+/K+ pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na+ from the cell and import 2K+ per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na+/K+ pump that represent the kinetics of extracellular Na+ binding/release and Na+ occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na+ from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site. PMID:22143771

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid.

PubMed

Castillo, Juan P; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C; Rosenthal, Joshua J C; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-12-20

The Na(+)/K(+) pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na(+) from the cell and import 2K(+) per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na(+)/K(+) pump that represent the kinetics of extracellular Na(+) binding/release and Na(+) occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na(+) from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site.

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

DOE PAGES

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; ...

2017-06-09

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of “KMC stiffness” (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps / cpu-time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order tomore » achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events -- allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm designed for use in achieving and simulating steady-state conditions in KMC simulations. Lastly, as shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.« less

SQERTSS: Dynamic rank based throttling of transition probabilities in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Sutton, Jonathan E.; Hin, Céline; Savara, Aditya

2017-10-01

Lattice based Kinetic Monte Carlo (KMC) simulations offer a powerful simulation technique for investigating large reaction networks while retaining spatial configuration information, unlike ordinary differential equations. However, large chemical reaction networks can contain reaction processes with rates spanning multiple orders of magnitude. This can lead to the problem of "KMC stiffness" (similar to stiffness in differential equations), where the computational expense has the potential to be overwhelmed by very short time-steps during KMC simulations, with the simulation spending an inordinate amount of KMC steps/CPU time simulating fast frivolous processes (FFPs) without progressing the system (reaction network). In order to achieve simulation times that are experimentally relevant or desired for predictions, a dynamic throttling algorithm involving separation of the processes into speed-ranks based on event frequencies has been designed and implemented with the intent of decreasing the probability of FFP events, and increasing the probability of slow process events-allowing rate limiting events to become more likely to be observed in KMC simulations. This Staggered Quasi-Equilibrium Rank-based Throttling for Steady-state (SQERTSS) algorithm is designed for use in achieving and simulating steady-state conditions in KMC simulations. As shown in this work, the SQERTSS algorithm also works for transient conditions: the correct configuration space and final state will still be achieved if the required assumptions are not violated, with the caveat that the sizes of the time-steps may be distorted during the transient period.

Vibrational structure of the S 2 (1B u) excited state of diphenyloctatetraene observed by femtosecond stimulated Raman spectroscopy

NASA Astrophysics Data System (ADS)

Kukura, Philipp; McCamant, David W.; Davis, Paul H.; Mathies, Richard A.

2003-11-01

Femtosecond time-resolved stimulated Raman spectroscopy (FSRS) is used to study the vibrational structure and dynamics of the S 2 state of diphenyloctatetraene. Strong vibrational features at 1184, 1259 and 1578 cm -1 whose linewidths are determined by the S 2 electronic lifetime are observed at early times after photoexcitation at 397 nm. Kinetic analysis of the integrated Raman intensities as well as the transient absorption reveals an exponential decay of the S 2 state on the order of 100 fs. These results demonstrate the ability of FSRS to study the vibrational structure of excited state and chemical reaction dynamics on the femtosecond timescale.

Reversibility of red blood cell deformation

NASA Astrophysics Data System (ADS)

Zeitz, Maria; Sens, P.

2012-05-01

The ability of cells to undergo reversible shape changes is often crucial to their survival. For red blood cells (RBCs), irreversible alteration of the cell shape and flexibility often causes anemia. Here we show theoretically that RBCs may react irreversibly to mechanical perturbations because of tensile stress in their cytoskeleton. The transient polymerization of protein fibers inside the cell seen in sickle cell anemia or a transient external force can trigger the formation of a cytoskeleton-free membrane protrusion of μm dimensions. The complex relaxation kinetics of the cell shape is shown to be responsible for selecting the final state once the perturbation is removed, thereby controlling the reversibility of the deformation. In some case, tubular protrusion are expected to relax via a peculiar “pearling instability.”

Reversibility of red blood cell deformation.

PubMed

Zeitz, Maria; Sens, P

2012-05-01

The ability of cells to undergo reversible shape changes is often crucial to their survival. For red blood cells (RBCs), irreversible alteration of the cell shape and flexibility often causes anemia. Here we show theoretically that RBCs may react irreversibly to mechanical perturbations because of tensile stress in their cytoskeleton. The transient polymerization of protein fibers inside the cell seen in sickle cell anemia or a transient external force can trigger the formation of a cytoskeleton-free membrane protrusion of μm dimensions. The complex relaxation kinetics of the cell shape is shown to be responsible for selecting the final state once the perturbation is removed, thereby controlling the reversibility of the deformation. In some case, tubular protrusion are expected to relax via a peculiar "pearling instability."

Excitation Dynamics in Phycoerythrin 545: Modeling of Steady-State Spectra and Transient Absorption with Modified Redfield Theory

PubMed Central

Novoderezhkin, Vladimir I.; Doust, Alexander B.; Curutchet, Carles; Scholes, Gregory D.; van Grondelle, Rienk

2010-01-01

Abstract We model the spectra and excitation dynamics in the phycobiliprotein antenna complex PE545 isolated from the unicellular photosynthetic cryptophyte algae Rhodomonas CS24. The excitonic couplings between the eight bilins are calculated using the CIS/6-31G method. The site energies are extracted from a simultaneous fit of the absorption, circular dichroism, fluorescence, and excitation anisotropy spectra together with the transient absorption kinetics using the modified Redfield approach. Quantitative fit of the data enables us to assign the eight exciton components of the spectra and build up the energy transfer picture including pathways and timescales of energy relaxation, thus allowing a visualization of excitation dynamics within the complex. PMID:20643051

Relaxation rates of gene expression kinetics reveal the feedback signs of autoregulatory gene networks

NASA Astrophysics Data System (ADS)

Jia, Chen; Qian, Hong; Chen, Min; Zhang, Michael Q.

2018-03-01

The transient response to a stimulus and subsequent recovery to a steady state are the fundamental characteristics of a living organism. Here we study the relaxation kinetics of autoregulatory gene networks based on the chemical master equation model of single-cell stochastic gene expression with nonlinear feedback regulation. We report a novel relation between the rate of relaxation, characterized by the spectral gap of the Markov model, and the feedback sign of the underlying gene circuit. When a network has no feedback, the relaxation rate is exactly the decaying rate of the protein. We further show that positive feedback always slows down the relaxation kinetics while negative feedback always speeds it up. Numerical simulations demonstrate that this relation provides a possible method to infer the feedback topology of autoregulatory gene networks by using time-series data of gene expression.

A study of the applicability of nucleation theory to quasi-thermodynamic transformations of second and higher Ehrenfest-order

NASA Technical Reports Server (NTRS)

Barker, R. E., Jr.

1985-01-01

Transient and steady-state phenomena in temperature, stress, and electric, field intensity in ferroelectric polymers were investigated. The application and extension of the theory in the primary stage to the polarization domain nucleation and growth in ferroelectric polymers were developed. The kinetics of this growth were investigated. Expressions describing nucleation under the influence of an electric field were found through the expansion of the Gibbs' free energy in a Maclaurin series. The series was expanded in the electric field strength rather than the degree of undercooling. The resulting expressions were manipulated and applied to the case of nucleation of polarized domains in ferroelectric polymers. The kinetics of the nucleation and growth of polarized domains are also investigated. This was accomplished through the modification of the Johnson-Mehl-Avrami treatment of crystallization kinetics to be applicable to the growth of polarization domains in ferroelectric materials.

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

PubMed

Stoll, Gautier; Viara, Eric; Barillot, Emmanuel; Calzone, Laurence

2012-08-29

Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real numbers, mainly based on differential equations and chemical kinetics formalism; (2) and qualitative modeling, representing chemical species concentrations or activities by a finite set of discrete values. Both approaches answer particular (and often different) biological questions. Qualitative modeling approach permits a simple and less detailed description of the biological systems, efficiently describes stable state identification but remains inconvenient in describing the transient kinetics leading to these states. In this context, time is represented by discrete steps. Quantitative modeling, on the other hand, can describe more accurately the dynamical behavior of biological processes as it follows the evolution of concentration or activities of chemical species as a function of time, but requires an important amount of information on the parameters difficult to find in the literature. Here, we propose a modeling framework based on a qualitative approach that is intrinsically continuous in time. The algorithm presented in this article fills the gap between qualitative and quantitative modeling. It is based on continuous time Markov process applied on a Boolean state space. In order to describe the temporal evolution of the biological process we wish to model, we explicitly specify the transition rates for each node. For that purpose, we built a language that can be seen as a generalization of Boolean equations. Mathematically, this approach can be translated in a set of ordinary differential equations on probability distributions. We developed a C++ software, MaBoSS, that is able to simulate such a system by applying Kinetic Monte-Carlo (or Gillespie algorithm) on the Boolean state space. This software, parallelized and optimized, computes the temporal evolution of probability distributions and estimates stationary distributions. Applications of the Boolean Kinetic Monte-Carlo are demonstrated for three qualitative models: a toy model, a published model of p53/Mdm2 interaction and a published model of the mammalian cell cycle. Our approach allows to describe kinetic phenomena which were difficult to handle in the original models. In particular, transient effects are represented by time dependent probability distributions, interpretable in terms of cell populations.

Preliminary Results for the OECD/NEA Time Dependent Benchmark using Rattlesnake, Rattlesnake-IQS and TDKENO

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeHart, Mark D.; Mausolff, Zander; Weems, Zach

2016-08-01

One goal of the MAMMOTH M&S project is to validate the analysis capabilities within MAMMOTH. Historical data has shown limited value for validation of full three-dimensional (3D) multi-physics methods. Initial analysis considered the TREAT startup minimum critical core and one of the startup transient tests. At present, validation is focusing on measurements taken during the M8CAL test calibration series. These exercises will valuable in preliminary assessment of the ability of MAMMOTH to perform coupled multi-physics calculations; calculations performed to date are being used to validate the neutron transport solver Rattlesnake\\cite{Rattlesnake} and the fuels performance code BISON. Other validation projects outsidemore » of TREAT are available for single-physics benchmarking. Because the transient solution capability of Rattlesnake is one of the key attributes that makes it unique for TREAT transient simulations, validation of the transient solution of Rattlesnake using other time dependent kinetics benchmarks has considerable value. The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has recently developed a computational benchmark for transient simulations. This benchmark considered both two-dimensional (2D) and 3D configurations for a total number of 26 different transients. All are negative reactivity insertions, typically returning to the critical state after some time.« less

[Cardiopulmonary dynamics during a maximal exertion test in Mexican endurance athletes].

PubMed

Padilla, J; Martínez, E; Olvera, G; Ojeda Cruz, P; Caudillo Pérez, D

2000-01-01

To search for cardiopulmonary (CP) kinetic and dynamic differences between Mexican resistance athletes (RES = 10) and non athletes (NON = 19). From the expired volume (Ve), measured by an open circuit spirometry, we calculated both VO2 and VCO2 during stress test while the volunteer pedalled seated on an electronic cycloergometer that started at 50 W.2 min-1 followed by increments of 25 W.2 min-1 each, until VO2máx was reached. The exercise transient time course (min) response (VO2, VCO2, Ve and heart rate, HR; and also O2 pulse, PulO2) was transformed to seconds and modelled by computer using linear regression technique by the interactive minimum squares method, and the mean response time (MRT) was used as an overall kinetic CP parameter. The transient MRTs for VO2, VCO2 and Ve were slow in RES compared to NON. While the transient CP dynamics in NON lasted MRT_VO2 < (MRT_PulO2, MRT_FC) < MRT_VCO2 < MRT_Ve; the RES: both MRT_PulO2 and MRT_HR shifted to the right ((MRT_VO2, MRT_VCO2) < (MRT_PulO2, MRT_FC) < MRT_Ve). The relationships between the best sport profit mean velocity and both the MRT_VO2, MRT_VCO2 and MRT_PulO2 (GEK = gas exchange kinetics) showed fast_RES and slow_GEK, and slow_RES and fast_GEK. The transient CP kinetics was slow in RES compared NON. It is possible to distinguish cardiopulmonary kinetic differences among resistance athletes holding different sport profiles.

Exercise modality effect on oxygen uptake off-transient kinetics at maximal oxygen uptake intensity.

PubMed

Sousa, Ana; Rodríguez, Ferran A; Machado, Leandro; Vilas-Boas, J Paulo; Fernandes, Ricardo J

2015-06-01

What is the central question of this study? Do the mechanical differences between swimming, rowing, running and cycling have a potential effect on the oxygen uptake (V̇O2) off-kinetics after an exercise sustained until exhaustion at 100% of maximal oxygen uptake (V̇O2max) intensity? What is the main finding and its importance? The mechanical differences between exercise modes had a potential effect and contributed to distinct amplitude of the fast component (higher in running compared with cycling) and time constant (higher in swimming compared with rowing and cycling) in the V̇O2 off-kinetic patterns at 100% of V̇O2max intensity. This suggests that swimmers, unlike rowers and cyclists, would benefit more from a longer duration of training intervals after each set of exercise performed at V̇O2max intensity. The kinetics of oxygen uptake (V̇O2) during recovery (off-transient kinetics) for different exercise modes is largely unexplored, hampering the prescription of training and recovery to enhance performance. The purpose of this study was to compare the V̇O2 off-transient kinetics response between swimmers, rowers, runners and cyclists during their specific mode of exercise at 100% of maximal oxygen uptake (V̇O2max) intensity and to examine the on-off symmetry. Groups of swimmers, rowers, runners and cyclists (n = 8 per group) performed (i) an incremental exercise protocol to assess the velocity or power associated with V̇O2max (vV̇O2max or wV̇O2max, respectively) and (ii) a square-wave exercise transition from rest to vV̇O2max/vV̇O2maxwV̇O2maxwV̇O2max until volitional exhaustion. Pulmonary exchange parameters were measured using a telemetric portable gas analyser (K4b(2) ; Cosmed, Rome, Italy), and the on- and off-transient kinetics were analysed through a double-exponential approach. For all exercise modes, both transient periods were symmetrical in shape once they had both been adequately fitted by a double-exponential model. However, differences were found in the off-kinetic parameters between exercise modes; the amplitude of the fast component of the V̇O2 off-response was higher in running compared with cycling (48 ± 5 and 36 ± 7 ml kg(-1) min(-1) , respectively; P < 0.001), and the time constant of the same phase was higher in swimming compared with rowing and cycling (63 ± 5, 56 ± 5 and 55 ± 3 s, respectively; P < 0.001). Although both phases were well described by a double-exponential model, the differences between exercise modes had a potential effect and contributed to distinct V̇O2 off-transient kinetic patterns at 100% of V̇O2max intensity. © 2015 The Authors. Experimental Physiology © 2015 The Physiological Society.

Electrodiffusion kinetics of ionic transport in a simple membrane channel.

PubMed

Valent, Ivan; Petrovič, Pavol; Neogrády, Pavel; Schreiber, Igor; Marek, Miloš

2013-11-21

We employ numerical techniques for solving time-dependent full Poisson-Nernst-Planck (PNP) equations in 2D to analyze transient behavior of a simple ion channel subject to a sudden electric potential jump across the membrane (voltage clamp). Calculated spatiotemporal profiles of the ionic concentrations and electric potential show that two principal exponential processes can be distinguished in the electrodiffusion kinetics, in agreement with original Planck's predictions. The initial fast process corresponds to the dielectric relaxation, while the steady state is approached in a second slower exponential process attributed to the nonlinear ionic redistribution. Effects of the model parameters such as the channel length, height of the potential step, boundary concentrations, permittivity of the channel interior, and ionic mobilities on electrodiffusion kinetics are studied. Numerical solutions are used to determine spatiotemporal profiles of the electric field, ionic fluxes, and both the conductive and displacement currents. We demonstrate that the displacement current is a significant transient component of the total electric current through the channel. The presented results provide additional information about the classical voltage-clamp problem and offer further physical insights into the mechanism of electrodiffusion. The used numerical approach can be readily extended to multi-ionic models with a more structured domain geometry in 2D or 3D, and it is directly applicable to other systems, such as synthetic nanopores, nanofluidic channels, and nanopipettes.

A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB.

PubMed

Biedermannová, Lada; Prokop, Zbyněk; Gora, Artur; Chovancová, Eva; Kovács, Mihály; Damborsky, Jiří; Wade, Rebecca C

2012-08-17

Many enzymes have buried active sites. The properties of the tunnels connecting the active site with bulk solvent affect ligand binding and unbinding and also the catalytic properties. Here, we investigate ligand passage in the haloalkane dehalogenase enzyme LinB and the effect of replacing leucine by a bulky tryptophan at a tunnel-lining position. Transient kinetic experiments show that the mutation significantly slows down the rate of product release. Moreover, the mechanism of bromide ion release is changed from a one-step process in the wild type enzyme to a two-step process in the mutant. The rate constant of bromide ion release corresponds to the overall steady-state turnover rate constant, suggesting that product release became the rate-limiting step of catalysis in the mutant. We explain the experimental findings by investigating the molecular details of the process computationally. Analysis of trajectories from molecular dynamics simulations with a tunnel detection software reveals differences in the tunnels available for ligand egress. Corresponding differences are seen in simulations of product egress using a specialized enhanced sampling technique. The differences in the free energy barriers for egress of a bromide ion obtained using potential of mean force calculations are in good agreement with the differences in rates obtained from the transient kinetic experiments. Interactions of the bromide ion with the introduced tryptophan are shown to affect the free energy barrier for its passage. The study demonstrates how the mechanism of an enzymatic catalytic cycle and reaction kinetics can be engineered by modification of protein tunnels.

Broadening the cofactor specificity of a thermostable alcohol dehydrogenase using rational protein design introduces novel kinetic transient behavior.

PubMed

Campbell, Elliot; Wheeldon, Ian R; Banta, Scott

2010-12-01

Cofactor specificity in the aldo-keto reductase (AKR) superfamily has been well studied, and several groups have reported the rational alteration of cofactor specificity in these enzymes. Although most efforts have focused on mesostable AKRs, several putative AKRs have recently been identified from hyperthermophiles. The few that have been characterized exhibit a strong preference for NAD(H) as a cofactor, in contrast to the NADP(H) preference of the mesophilic AKRs. Using the design rules elucidated from mesostable AKRs, we introduced two site-directed mutations in the cofactor binding pocket to investigate cofactor specificity in a thermostable AKR, AdhD, which is an alcohol dehydrogenase from Pyrococcus furiosus. The resulting double mutant exhibited significantly improved activity and broadened cofactor specificity as compared to the wild-type. Results of previous pre-steady-state kinetic experiments suggest that the high affinity of the mesostable AKRs for NADP(H) stems from a conformational change upon cofactor binding which is mediated by interactions between a canonical arginine and the 2'-phosphate of the cofactor. Pre-steady-state kinetics with AdhD and the new mutants show a rich conformational behavior that is independent of the canonical arginine or the 2'-phosphate. Additionally, experiments with the highly active double mutant using NADPH as a cofactor demonstrate an unprecedented transient behavior where the binding mechanism appears to be dependent on cofactor concentration. These results suggest that the structural features involved in cofactor specificity in the AKRs are conserved within the superfamily, but the dynamic interactions of the enzyme with cofactors are unexpectedly complex. © 2010 Wiley Periodicals, Inc.

Kinetics of binary nucleation of vapors in size and composition space.

PubMed

Fisenko, Sergey P; Wilemski, Gerald

2004-11-01

We reformulate the kinetic description of binary nucleation in the gas phase using two natural independent variables: the total number of molecules g and the molar composition x of the cluster. The resulting kinetic equation can be viewed as a two-dimensional Fokker-Planck equation describing the simultaneous Brownian motion of the clusters in size and composition space. Explicit expressions for the Brownian diffusion coefficients in cluster size and composition space are obtained. For characterization of binary nucleation in gases three criteria are established. These criteria establish the relative importance of the rate processes in cluster size and composition space for different gas phase conditions and types of liquid mixtures. The equilibrium distribution function of the clusters is determined in terms of the variables g and x. We obtain an approximate analytical solution for the steady-state binary nucleation rate that has the correct limit in the transition to unary nucleation. To further illustrate our description, the nonequilibrium steady-state cluster concentrations are found by numerically solving the reformulated kinetic equation. For the reformulated transient problem, the relaxation or induction time for binary nucleation was calculated using Galerkin's method. This relaxation time is affected by processes in both size and composition space, but the contributions from each process can be separated only approximately.

Probing the cytochrome c' folding landscape.

PubMed

Pletneva, Ekaterina V; Zhao, Ziqing; Kimura, Tetsunari; Petrova, Krastina V; Gray, Harry B; Winkler, Jay R

2007-11-01

The folding kinetics of R. palustris cytochrome c' (cyt c') have been monitored by heme absorption and native Trp72 fluorescence at pH 5. The Trp72 fluorescence burst signal suggests early compaction of the polypeptide ensemble. Analysis of heme transient absorption spectra reveals deviations from two-state behavior, including a prominent slow phase that is accelerated by the prolyl isomerase cyclophilin. A nonnative proline configuration (Pro21) likely interferes with the formation of the helical bundle surrounding the heme.

Equilibrium and Kinetic Models for Colloid Release Under Transient Solution Chemistry Conditions

NASA Astrophysics Data System (ADS)

Bradford, S. A.; Torkzaban, S.; Leij, F. J.; Simunek, J.

2014-12-01

Colloid retention and release is well known to depend on a wide variety of physical, chemical, and microbiological factors that may vary temporally in the subsurface environment. We present equilibrium, kinetic, combined equilibrium and kinetic, and two-site kinetic models of colloid release during transient physicochemical conditions. Our mathematical modeling approach relates colloid release under transient conditions to changes in the fraction of the solid surface area that contributes to retention. The developed models were subsequently applied to experimental colloid release datasets to investigate the influence of variations in ionic strength (IS), pH, cation exchange, colloid size, and water velocity on release. Various combinations of equilibrium and/or kinetic release models were needed to describe the experimental data depending on the transient conditions and colloid type. Release of E. coli D21g was promoted by a decrease in solution IS and an increase in pH, similar to expected trends for a reduction in the secondary minimum and nanoscale chemical heterogeneity, respectively. The retention and release of 20 nm carboxyl modified latex nanoparticles (NPs) were demonstrated to be more sensitive to the presence of Ca2+ than D21g. Specifically, retention of NPs was greater than D21g in the presence of 2 mM CaCl2 solution, and release of NPs only occurred after exchange of Ca2+ by Na+ and then a reduction in the solution IS. These findings highlight the limitations of conventional interaction energy calculations to describe colloid retention and release, and point to the need to consider Born repulsion and nanoscale heterogeneity. Temporal changes in the water velocity did not have a large influence on the release of D21g. This insensitivity was likely due to factors that reduce the applied hydrodynamic torque and/or increase the resisting adhesive torque. Collectively, experimental and modeling results indicate that episodic colloid transport in the subsurface is expected because of transient conditions.

Kinetics of transient electroluminescence in organic light emitting diodes

NASA Astrophysics Data System (ADS)

Shukla, Manju; Kumar, Pankaj; Chand, Suresh; Brahme, Nameeta; Kher, R. S.; Khokhar, M. S. K.

2008-08-01

Mathematical simulation on the rise and decay kinetics of transient electroluminescence (EL) in organic light emitting diodes (OLEDs) is presented. The transient EL is studied with respect to a step voltage pulse. While rising, for lower values of time, the EL intensity shows a quadratic dependence on (t - tdel), where tdel is the time delay observed in the onset of EL, and finally attains saturation at a sufficiently large time. When the applied voltage is switched off, the initial EL decay shows an exponential dependence on (t - tdec), where tdec is the time when the voltage is switched off. The simulated results are compared with the transient EL performance of a bilayer OLED based on small molecular bis(2-methyl 8-hydroxyquinoline)(triphenyl siloxy) aluminium (SAlq). Transient EL studies have been carried out at different voltage pulse amplitudes. The simulated results show good agreement with experimental data. Using these simulated results the lifetime of the excitons in SAlq has also been calculated.

Device for data-acquisition from transient signals: kinetic considerations

PubMed Central

Sampedro, A. Sanchez; Vives, S. Sagrado

1990-01-01

This paper reports on the evaluation and testing of a home-made device. Data-acquisition, treatment of transient signals and the hardware and software involved are discussed. Some practical aspects are developed in order to power the autonomy of procedures using the device. Kinetic and multi-signal calculations are considered in order to cover the actual tendencies in continuous-flow analysis. Somepractical advantages versus the use of classical chart recorders or commercial computerized-instrument devices are pointed out. PMID:18925275

Kinetics of drug release from ointments: Role of transient-boundary layer.

PubMed

Xu, Xiaoming; Al-Ghabeish, Manar; Krishnaiah, Yellela S R; Rahman, Ziyaur; Khan, Mansoor A

2015-10-15

In the current work, an in vitro release testing method suitable for ointment formulations was developed using acyclovir as a model drug. Release studies were carried out using enhancer cells on acyclovir ointments prepared with oleaginous, absorption, and water-soluble bases. Kinetics and mechanism of drug release was found to be highly dependent on the type of ointment bases. In oleaginous bases, drug release followed a unique logarithmic-time dependent profile; in both absorption and water-soluble bases, drug release exhibited linearity with respect to square root of time (Higuchi model) albeit differences in the overall release profile. To help understand the underlying cause of logarithmic-time dependency of drug release, a novel transient-boundary hypothesis was proposed, verified, and compared to Higuchi theory. Furthermore, impact of drug solubility (under various pH conditions) and temperature on drug release were assessed. Additionally, conditions under which deviations from logarithmic-time drug release kinetics occur were determined using in situ UV fiber-optics. Overall, the results suggest that for oleaginous ointments containing dispersed drug particles, kinetics and mechanism of drug release is controlled by expansion of transient boundary layer, and drug release increases linearly with respect to logarithmic time. Published by Elsevier B.V.

Imaging ultrafast excited state pathways in transition metal complexes by X-ray transient absorption and scattering using X-ray free electron laser source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Lin X.; Shelby, Megan L.; Lestrange, Patrick J.

2016-01-01

This report will describe our recent studies of transition metal complex structural dynamics on the fs and ps time scales using an X-ray free electron laser source, Linac Coherent Light Source (LCLS). Ultrafast XANES spectra at the Ni K-edge of nickel(II) tetramesitylporphyrin (NiTMP) were successfully measured for optically excited state at a timescale from 100 fs to 50 ps, providing insight into its sub-ps electronic and structural relaxation processes. Importantly, a transient reduced state Ni(I) (π, 3dx2-y2) electronic state is captured through the interpretation of a short-lived excited state absorption on the low-energy shoulder of the edge, which is aidedmore » by the computation of X-ray transitions for postulated excited electronic states. The observed and computed inner shell to valence orbital transition energies demonstrate and quantify the influence of electronic configuration on specific metal orbital energies. A strong influence of the valence orbital occupation on the inner shell orbital energies indicates that one should not use the transition energy from 1s to other orbitals to draw conclusions about the d-orbital energies. For photocatalysis, a transient electronic configuration could influence d-orbital energies up to a few eV and any attempt to steer the reaction pathway should account for this to ensure that external energies can be used optimally in driving desirable processes. NiTMP structural evolution and the influence of the porphyrin macrocycle conformation on relaxation kinetics can be likewise inferred from this study.« less

Modelling of squall with the generalised kinetic equation

NASA Astrophysics Data System (ADS)

Annenkov, Sergei; Shrira, Victor

2014-05-01

We study the long-term evolution of random wind waves using the new generalised kinetic equation (GKE). The GKE derivation [1] does not assume the quasi-stationarity of a random wave field. In contrast with the Hasselmann kinetic equation, the GKE can describe fast spectral changes occurring when a wave field is driven out of a quasi-equilibrium state by a fast increase or decrease of wind, or by other factors. In these cases, a random wave field evolves on the dynamic timescale typical of coherent wave processes, rather than on the kinetic timescale predicted by the conventional statistical theory. Besides that, the generalised theory allows to trace the evolution of higher statistical moments of the field, notably the kurtosis, which is important for assessing the risk of freak waves and other applications. A new efficient and highly parallelised algorithm for the numerical simulation of the generalised kinetic equation is presented and discussed. Unlike in the case of the Hasselmann equation, the algorithm takes into account all (resonant and non-resonant) nonlinear wave interactions, but only approximately resonant interactions contribute to the spectral evolution. However, counter-intuitively, all interactions contribute to the kurtosis. Without forcing or dissipation, the algorithm is shown to conserve the relevant integrals. We show that under steady wind forcing the wave field evolution predicted by the GKE is close to the predictions of the conventional statistical theory, which is applicable in this case. In particular, we demonstrate the known long-term asymptotics for the evolution of the spectrum. When the wind forcing is not steady (in the simplest case, an instant increase or decrease of wind occurs), the generalised theory is the only way to study the spectral evolution, apart from the direct numerical simulation. The focus of the work is a detailed analysis of the fast evolution after an instant change of forcing, and of the subsequent transition to the new quasi-stationary state of a wave field. It is shown that both increase and decrease of wind lead to a significant transient increase of the dynamic kurtosis, although these changes remain small compared to the changes of the other component of the kurtosis, which is due to bound harmonics. A special consideration is given to the case of the squall, i.e. an instant and large (by a factor of 2-4) increase of wind, which lasts for O(102) characteristic wave periods. We show that fast adjustment processes lead to the formation of a transient spectrum, which has a considerably narrower peak than the spectra developed under a steady forcing. These transient spectra differ qualitatively from those predicted by the Hasselmann kinetic equation under the squall with the same parameters. 1. S.Annenkov, V.Shrira (2006) Role of non-resonant interactions in evolution of nonlinear random water wave fields, J. Fluid Mech. 561, 181-207.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehmann, C. S.; Picón, A.; Bostedt, C.

The availability at x-ray free electron lasers of generating two intense, femtosecond x-ray pulses with controlled time delay opens the possibility of performing time-resolved experiments for x-ray induced phenomena. We have applied this capability to molecular dynamics. In diatomic molecules composed of low-Z elements, K-shell ionization creates a core-hole state in which the main decay is an Auger process involving two electrons in the valence shell. After Auger decay, the nuclear wavepackets of the transient two-valence-hole states continue evolving on the femtosecond timescale, leading either to separated atomic ions or long-lived quasi-bound states. By using an x-ray pump and anmore » x-ray probe pulse tuned above the K-shell ionization threshold of the nitrogen molecule, we are able to observe ion dissociation in progress by measuring the time-dependent kinetic energy releases of different breakup channels. We simulated the measurements on N2 with a molecular dynamics model that accounts for K-shell ionization, Auger decay, and time evolution of the nuclear wavepackets. In addition to explaining the time-dependent feature in the measured kinetic energy release distributions from the dissociative states, the simulation also reveals the contributions of quasi-bound states.« less

Effect of strain on actomyosin kinetics in isometric muscle fibers.

PubMed

Siththanandan, V B; Donnelly, J L; Ferenczi, M A

2006-05-15

Investigations were conducted into the biochemical and mechanical states of cross-bridges during isometric muscle contraction. Rapid length steps (3 or 6 nm hs(-1)) were applied to rabbit psoas fibers, permeabilized and isometric, at either 12 degrees C or 20 degrees C. Fibers were activated by photolysis of P(3)-1-(2-nitrophenyl)-ethyl ester of ATP infused into rigor fibers at saturating Ca(2+). Sarcomere length, tension, and phosphate release were recorded-the latter using the MDCC-PBP fluorescent probe. A reduction in strain, induced by a rapid release step, produced a short-lived acceleration of phosphate release. Rates of the phosphate transient and that of phases 3 and 4 of tension recovery were unaffected by step size but were elevated at higher temperatures. In contrast the amplitude of the phosphate transient was smaller at 20 degrees C than 12 degrees C. The presence of 0.5 or 1.0 mM added ADP during a release step reduced both the rate of tension recovery and the poststep isometric tension. A kinetic scheme is presented to simulate the observed data and to precisely determine the rate constants for the elementary steps of the ATPase cycle.

Short relaxation times but long transient times in both simple and complex reaction networks

PubMed Central

Henry, Adrien; Martin, Olivier C.

2016-01-01

When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time τ, i.e. the inverse of the decay rate, is the longest characteristic time in the system. However, that need not be true, other times such as the lifetime of an infinitesimal perturbation can be much longer. In the present work, we demonstrate that this paradoxical property can arise even in quite simple systems such as a linear chain of reactions obeying mass action (MA) kinetics. By mathematical analysis of simple reaction networks, we pin-point the reason why the standard relaxation time does not provide relevant information on the potentially long transient times of typical infinitesimal perturbations. Overall, we consider four characteristic times and study their behaviour in both simple linear chains and in more complex reaction networks taken from the publicly available database ‘Biomodels’. In all these systems, whether involving MA rates, Michaelis–Menten reversible kinetics, or phenomenological laws for reaction rates, we find that the characteristic times corresponding to lifetimes of tracers and of concentration perturbations can be significantly longer than τ. PMID:27411726

Kinetics of Photoelectrochemical Oxidation of Methanol on Hematite Photoanodes

PubMed Central

2017-01-01

The kinetics of photoelectrochemical (PEC) oxidation of methanol, as a model organic substrate, on α-Fe2O3 photoanodes are studied using photoinduced absorption spectroscopy and transient photocurrent measurements. Methanol is oxidized on α-Fe2O3 to formaldehyde with near unity Faradaic efficiency. A rate law analysis under quasi-steady-state conditions of PEC methanol oxidation indicates that rate of reaction is second order in the density of surface holes on hematite and independent of the applied potential. Analogous data on anatase TiO2 photoanodes indicate similar second-order kinetics for methanol oxidation with a second-order rate constant 2 orders of magnitude higher than that on α-Fe2O3. Kinetic isotope effect studies determine that the rate constant for methanol oxidation on α-Fe2O3 is retarded ∼20-fold by H/D substitution. Employing these data, we propose a mechanism for methanol oxidation under 1 sun irradiation on these metal oxide surfaces and discuss the implications for the efficient PEC methanol oxidation to formaldehyde and concomitant hydrogen evolution. PMID:28735533

Adaptive Nodal Transport Methods for Reactor Transient Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas Downar; E. Lewis

2005-08-31

Develop methods for adaptively treating the angular, spatial, and time dependence of the neutron flux in reactor transient analysis. These methods were demonstrated in the DOE transport nodal code VARIANT and the US NRC spatial kinetics code, PARCS.

Multiphoton manipulations of enzymatic photoactivity in aspartate aminotransferase.

PubMed

Hill, Melissa P; Freer, Lucy H; Vang, Mai C; Carroll, Elizabeth C; Larsen, Delmar S

2011-04-21

The aspartate aminotransferase (AAT) enzyme utilizes the chromophoric pyridoxal 5'-phosphate (PLP) cofactor to facilitate the transamination of amino acids. Recently, we demonstrated that, upon exposure to blue light, PLP forms a reactive triplet state that rapidly (in microseconds) generates the high-energy quinonoid intermediate when bound to PLP-dependent enzymes [J. Am. Chem. Soc.2010, 132 (47), 16953-16961]. This increases the net catalytic activity (k(cat)) of AAT, since formation of the quinonoid is partially rate limiting via the thermally activated enzymatic pathway. The magnitude of observed photoenhancement initially scales linearly with pump fluence; however when a critical threshold is exceeded, the photoactivity saturates and is even suppressed at greater excitation fluences. The photodynamic mechanisms associated with this suppression behavior are characterized with the use of ultrafast multipulse pump-dump-probe and pump-repump-probe transient absorption techniques in combination with complementary two-color, steady-state excitation assays. Via multistate kinetic modeling of the transient ultrafast data and the steady-state assay data, the nonmonotonic incident power dependence of the photoactivty in AAT is decomposed into contributions from high-intensity dumping of the excited singlet state and repumping of the excited triplet state with induces the repopulation of the ground state via rapid intersystem crossing in the higher-lying triplet electronic manifold.

FeOx-TiO2 Film with Different Microstructures Leading to Femtosecond Transients with Different Properties: Biological Implications under Visible Light

PubMed Central

Rtimi, Sami; Pulgarin, Cesar; Nadtochenko, Victor A.; Gostev, Fedor E.; Shelaev, Ivan V.; Kiwi, John

2016-01-01

This study presents the first report addressing the effect of FeOx-TiO2 films microstructure on the transients detected by fast spectroscopy related to the long-range bacterial inactivation performance. The different fast kinetic femtosecond transient spectroscopy is reported for each FeOx+TiO2 microstructure. The lifetime of the short transient-species and the oxidative intermediate radicals generated under light were identified. Co-sputtered FeOx-TiO2 on polyethylene films presenting random distribution for both oxides were compared with sequentially sputtered FeOx/TiO2 films made up only by FeOx in the topmost layers. The ratio FeOx:TiO2 was optimized to attain the highest photo-conversion. By X-ray fluorescence, the Fe:Ti ration was found to be ~1.4 in the film bulk and by XPS-etching a ratio of 4:1 was found on the photocatalyst top-most layers. For co-sputtered FeOx-TiO2-PE films, the FeOx-TiO2 heterojunction led to electron injection from the FeOx to lower-lying TiO2 trapping states. The film optical properties, particle size, roughness, hydrophobic-hydrophilic shift and temporal evolution of the transient redox states were characterized in detail. Films with different microstructure led to different antibacterial activity. This suggests that the FeOx-TiO2-PE microstructure and not the position of the potential energy level of the semiconductors FeOx and TiO2 control the charge transfer under light irradiation. PMID:27443505

FeOx-TiO2 Film with Different Microstructures Leading to Femtosecond Transients with Different Properties: Biological Implications under Visible Light.

PubMed

Rtimi, Sami; Pulgarin, Cesar; Nadtochenko, Victor A; Gostev, Fedor E; Shelaev, Ivan V; Kiwi, John

2016-07-22

This study presents the first report addressing the effect of FeOx-TiO2 films microstructure on the transients detected by fast spectroscopy related to the long-range bacterial inactivation performance. The different fast kinetic femtosecond transient spectroscopy is reported for each FeOx+TiO2 microstructure. The lifetime of the short transient-species and the oxidative intermediate radicals generated under light were identified. Co-sputtered FeOx-TiO2 on polyethylene films presenting random distribution for both oxides were compared with sequentially sputtered FeOx/TiO2 films made up only by FeOx in the topmost layers. The ratio FeOx:TiO2 was optimized to attain the highest photo-conversion. By X-ray fluorescence, the Fe:Ti ration was found to be ~1.4 in the film bulk and by XPS-etching a ratio of 4:1 was found on the photocatalyst top-most layers. For co-sputtered FeOx-TiO2-PE films, the FeOx-TiO2 heterojunction led to electron injection from the FeOx to lower-lying TiO2 trapping states. The film optical properties, particle size, roughness, hydrophobic-hydrophilic shift and temporal evolution of the transient redox states were characterized in detail. Films with different microstructure led to different antibacterial activity. This suggests that the FeOx-TiO2-PE microstructure and not the position of the potential energy level of the semiconductors FeOx and TiO2 control the charge transfer under light irradiation.

FeOx-TiO2 Film with Different Microstructures Leading to Femtosecond Transients with Different Properties: Biological Implications under Visible Light

NASA Astrophysics Data System (ADS)

Rtimi, Sami; Pulgarin, Cesar; Nadtochenko, Victor A.; Gostev, Fedor E.; Shelaev, Ivan V.; Kiwi, John

2016-07-01

This study presents the first report addressing the effect of FeOx-TiO2 films microstructure on the transients detected by fast spectroscopy related to the long-range bacterial inactivation performance. The different fast kinetic femtosecond transient spectroscopy is reported for each FeOx+TiO2 microstructure. The lifetime of the short transient-species and the oxidative intermediate radicals generated under light were identified. Co-sputtered FeOx-TiO2 on polyethylene films presenting random distribution for both oxides were compared with sequentially sputtered FeOx/TiO2 films made up only by FeOx in the topmost layers. The ratio FeOx:TiO2 was optimized to attain the highest photo-conversion. By X-ray fluorescence, the Fe:Ti ration was found to be ~1.4 in the film bulk and by XPS-etching a ratio of 4:1 was found on the photocatalyst top-most layers. For co-sputtered FeOx-TiO2-PE films, the FeOx-TiO2 heterojunction led to electron injection from the FeOx to lower-lying TiO2 trapping states. The film optical properties, particle size, roughness, hydrophobic-hydrophilic shift and temporal evolution of the transient redox states were characterized in detail. Films with different microstructure led to different antibacterial activity. This suggests that the FeOx-TiO2-PE microstructure and not the position of the potential energy level of the semiconductors FeOx and TiO2 control the charge transfer under light irradiation.

Contrast between the mechanisms for dissociative electron attachment to CH3SCN and CH3NCS.

PubMed

Miller, Thomas M; Viggiano, Albert A; Shuman, Nicholas S

2018-05-14

The kinetics of thermal electron attachment to methyl thiocyanate (CH 3 SCN), methyl isothiocyanate (CH 3 NCS), and ethyl thiocyanate (C 2 H 5 SCN) were measured using flowing afterglow-Langmuir probe apparatuses at temperatures between 300 and 1000 K. CH 3 SCN and C 2 H 5 SCN undergo inefficient dissociative attachment to yield primarily SCN - at 300 K (k = 2 × 10 -10 cm 3 s -1 ), with increasing efficiency as temperature increases. The increase is well described by activation energies of 0.17 eV (CH 3 SCN) and 0.14 eV (C 2 H 5 SCN). CN - product is formed at <1% branching at 300 K, increasing to ∼30% branching at 1000 K. Attachment to CH 3 NCS yields exclusively SCN - ionic product but at a rate at 300 K that is below our detection threshold (k < 10 -12 cm 3 s -1 ). The rate coefficient increases rapidly with increasing temperature (k = 6 × 10 -11 cm 3 s -1 at 600 K), in a manner well described by an activation energy of 0.51 eV. Calculations at the B3LYP/def2-TZVPPD level suggest that attachment to CH 3 SCN proceeds through a dissociative state of CH 3 SCN - , while attachment to CH 3 NCS initially forms a weakly bound transient anion CH 3 NCS -* that isomerizes over an energetic barrier to yield SCN - . Kinetic modeling of the two systems is performed in an attempt to identify a kinetic signature differentiating the two mechanisms. The kinetic modeling reproduces the CH 3 NCS data only if dissociation through the transient anion is considered.

Contrast between the mechanisms for dissociative electron attachment to CH3SCN and CH3NCS

NASA Astrophysics Data System (ADS)

Miller, Thomas M.; Viggiano, Albert A.; Shuman, Nicholas S.

2018-05-01

The kinetics of thermal electron attachment to methyl thiocyanate (CH3SCN), methyl isothiocyanate (CH3NCS), and ethyl thiocyanate (C2H5SCN) were measured using flowing afterglow-Langmuir probe apparatuses at temperatures between 300 and 1000 K. CH3SCN and C2H5SCN undergo inefficient dissociative attachment to yield primarily SCN- at 300 K (k = 2 × 10-10 cm3 s-1), with increasing efficiency as temperature increases. The increase is well described by activation energies of 0.17 eV (CH3SCN) and 0.14 eV (C2H5SCN). CN- product is formed at <1% branching at 300 K, increasing to ˜30% branching at 1000 K. Attachment to CH3NCS yields exclusively SCN- ionic product but at a rate at 300 K that is below our detection threshold (k < 10-12 cm3 s-1). The rate coefficient increases rapidly with increasing temperature (k = 6 × 10-11 cm3 s-1 at 600 K), in a manner well described by an activation energy of 0.51 eV. Calculations at the B3LYP/def2-TZVPPD level suggest that attachment to CH3SCN proceeds through a dissociative state of CH3SCN-, while attachment to CH3NCS initially forms a weakly bound transient anion CH3NCS-* that isomerizes over an energetic barrier to yield SCN-. Kinetic modeling of the two systems is performed in an attempt to identify a kinetic signature differentiating the two mechanisms. The kinetic modeling reproduces the CH3NCS data only if dissociation through the transient anion is considered.

A new class of accelerated kinetic Monte Carlo algorithms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bulatov, V V; Oppelstrup, T; Athenes, M

2011-11-30

Kinetic (aka dynamic) Monte Carlo (KMC) is a powerful method for numerical simulations of time dependent evolution applied in a wide range of contexts including biology, chemistry, physics, nuclear sciences, financial engineering, etc. Generally, in a KMC the time evolution takes place one event at a time, where the sequence of events and the time intervals between them are selected (or sampled) using random numbers. While details of the method implementation vary depending on the model and context, there exist certain common issues that limit KMC applicability in almost all applications. Among such is the notorious 'flicker problem' where themore » same states of the systems are repeatedly visited but otherwise no essential evolution is observed. In its simplest form the flicker problem arises when two states are connected to each other by transitions whose rates far exceed the rates of all other transitions out of the same two states. In such cases, the model will endlessly hop between the two states otherwise producing no meaningful evolution. In most situation of practical interest, the trapping cluster includes more than two states making the flicker somewhat more difficult to detect and to deal with. Several methods have been proposed to overcome or mitigate the flicker problem, exactly [1-3] or approximately [4,5]. Of the exact methods, the one proposed by Novotny [1] is perhaps most relevant to our research. Novotny formulates the problem of escaping from a trapping cluster as a Markov system with absorbing states. Given an initial state inside the cluster, it is in principle possible to solve the Master Equation for the time dependent probabilities to find the walker in a given state (transient or absorbing) of the cluster at any time in the future. Novotny then proceeds to demonstrate implementation of his general method to trapping clusters containing the initial state plus one or two transient states and all of their absorbing states. Similar methods have been subsequently proposed in [refs] but applied in a different context. The most serious deficiency of the earlier methods is that size of the trapping cluster size is fixed and often too small to bring substantial simulation speedup. Furthermore, the overhead associated with solving for the probability distribution on the trapping cluster sometimes makes such simulations less efficient than the standard KMC. Here we report on a general and exact accelerated kinetic Monte Carlo algorithm generally applicable to arbitrary Markov models1. Two different implementations are attempted both based on incremental expansion of trapping sub-set of Markov states: (1) numerical solution of the Master Equation with absorbing states and (2) incremental graph reduction followed by randomization. Of the two implementations, the 2nd one performs better allowing, for the first time, to overcome trapping basins spanning several million Markov states. The new method is used for simulations of anomalous diffusion on a 2D substrate and of the kinetics of diffusive 1st order phase transformations in binary alloys. Depending on temperature and (alloy) super-saturation conditions, speedups of 3 to 7 orders of magnitude are demonstrated, with no compromise of simulation accuracy.« less

Generic concept to program the time domain of self-assemblies with a self-regulation mechanism.

PubMed

Heuser, Thomas; Steppert, Ann-Kathrin; Lopez, Catalina Molano; Zhu, Baolei; Walther, Andreas

2015-04-08

Nature regulates complex structures in space and time via feedback loops, kinetically controlled transformations, and under energy dissipation to allow non-equilibrium processes. Although man-made static self-assemblies realize excellent control over hierarchical structures via molecular programming, managing their temporal destiny by self-regulation is a largely unsolved challenge. Herein, we introduce a generic concept to control the time domain by programming the lifetimes of switchable self-assemblies in closed systems. We conceive dormant deactivators that, in combination with fast promoters, enable a unique kinetic balance to establish an autonomously self-regulating, transient pH-state, whose duration can be programmed over orders of magnitude-from minutes to days. Coupling this non-equilibrium state to pH-switchable self-assemblies allows predicting their assembly/disassembly fate in time, similar to a precise self-destruction mechanism. We demonstrate a platform approach by programming self-assembly lifetimes of block copolymers, nanoparticles, and peptides, enabling dynamic materials with a self-regulation functionality.

Materials and processing approaches for foundry-compatible transient electronics.

PubMed

Chang, Jan-Kai; Fang, Hui; Bower, Christopher A; Song, Enming; Yu, Xinge; Rogers, John A

2017-07-11

Foundry-based routes to transient silicon electronic devices have the potential to serve as the manufacturing basis for "green" electronic devices, biodegradable implants, hardware secure data storage systems, and unrecoverable remote devices. This article introduces materials and processing approaches that enable state-of-the-art silicon complementary metal-oxide-semiconductor (CMOS) foundries to be leveraged for high-performance, water-soluble forms of electronics. The key elements are ( i ) collections of biodegradable electronic materials (e.g., silicon, tungsten, silicon nitride, silicon dioxide) and device architectures that are compatible with manufacturing procedures currently used in the integrated circuit industry, ( ii ) release schemes and transfer printing methods for integration of multiple ultrathin components formed in this way onto biodegradable polymer substrates, and ( iii ) planarization and metallization techniques to yield interconnected and fully functional systems. Various CMOS devices and circuit elements created in this fashion and detailed measurements of their electrical characteristics highlight the capabilities. Accelerated dissolution studies in aqueous environments reveal the chemical kinetics associated with the underlying transient behaviors. The results demonstrate the technical feasibility for using foundry-based routes to sophisticated forms of transient electronic devices, with functional capabilities and cost structures that could support diverse applications in the biomedical, military, industrial, and consumer industries.

Materials and processing approaches for foundry-compatible transient electronics

NASA Astrophysics Data System (ADS)

Chang, Jan-Kai; Fang, Hui; Bower, Christopher A.; Song, Enming; Yu, Xinge; Rogers, John A.

2017-07-01

Foundry-based routes to transient silicon electronic devices have the potential to serve as the manufacturing basis for “green” electronic devices, biodegradable implants, hardware secure data storage systems, and unrecoverable remote devices. This article introduces materials and processing approaches that enable state-of-the-art silicon complementary metal-oxide-semiconductor (CMOS) foundries to be leveraged for high-performance, water-soluble forms of electronics. The key elements are (i) collections of biodegradable electronic materials (e.g., silicon, tungsten, silicon nitride, silicon dioxide) and device architectures that are compatible with manufacturing procedures currently used in the integrated circuit industry, (ii) release schemes and transfer printing methods for integration of multiple ultrathin components formed in this way onto biodegradable polymer substrates, and (iii) planarization and metallization techniques to yield interconnected and fully functional systems. Various CMOS devices and circuit elements created in this fashion and detailed measurements of their electrical characteristics highlight the capabilities. Accelerated dissolution studies in aqueous environments reveal the chemical kinetics associated with the underlying transient behaviors. The results demonstrate the technical feasibility for using foundry-based routes to sophisticated forms of transient electronic devices, with functional capabilities and cost structures that could support diverse applications in the biomedical, military, industrial, and consumer industries.

Most-Critical Transient Disturbances in an Incompressible Flat-Plate Boundary Layer

NASA Astrophysics Data System (ADS)

Monschke, Jason; White, Edward

2015-11-01

Transient growth is a linear disturbance growth mechanism that plays a key role in roughness-induced boundary-layer transition. It occurs when superposed stable, non-orthogonal continuous spectrum modes experience algebraic disturbance growth followed by exponential decay. Algebraic disturbance growth can modify the basic state making it susceptible to secondary instabilities rapidly leading to transition. Optimal disturbance theory was developed to model the most-dangerous disturbances. However, evidence suggests roughness-induced transient growth is sub-optimal yet leads to transition earlier than optimal theory suggests. This research computes initial disturbances most unstable to secondary instabilities to further develop the applicability of transient growth theory to surface roughness. The main approach is using nonlinear adjoint optimization with solutions of the parabolized Navier-Stokes and BiGlobal stability equations. Two objective functions were considered: disturbance kinetic energy growth and sinuous instability growth rate. The first objective function was used as validation of the optimization method. Counter-rotating streamwise vortices located low in the boundary layer maximize the sinuous instability growth rate. The authors would like to acknowledge NASA and the AFOSR for funding this work through AFOSR Grant FA9550-09-1-0341.

Quantitative Connection Between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryo-EM and smFRET Investigations of the Ribosome

PubMed Central

Frank, Joachim; Gonzalez, Ruben L.

2015-01-01

At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describes transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy and single-molecule fluorescence resonance energy transfer studies of the bacterial ribosomal pretranslocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pretranslocation complex, which are observed in a cryogenic electron microscopy study, may not be observed in several single-molecule fluorescence resonance energy transfer studies. PMID:25785884

Novel laser gain and time-resolved FTIR studies of photochemistry

NASA Technical Reports Server (NTRS)

Leone, Stephen R.

1990-01-01

Several techniques are discussed which can be used to explore laboratory photochemical processes and kinetics relevant to planetary atmospheres; these include time-resolved laser gain-versus-absorption spectroscopy and time-resolved Fourier transform infrared (FTIR) emission studies. The laser gain-versus-absorption method employed tunable diode and F-center lasers to determine the yields of excited photofragments and their kinetics. The time-resolved FTIR technique synchronizes the sweep of a commercial FTIR with a pulsed source of light to obtain emission spectra of novel transient species in the infrared. These methods are presently being employed to investigate molecular photodissociation, the yields of excited states of fragments, their subsequent reaction kinetics, Doppler velocity distributions, and velocity-changing collisions of translationally fast atoms. Such techniques may be employed in future investigations of planetary atmospheres, for example to study polycyclic aromatic hydrocarbons related to cometary emissions, to analyze acetylene decomposition products and reactions, and to determine spectral features in the near infrared and infrared wavelength regions for planetary molecules and clusters.

Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome.

PubMed

Thompson, Colin D Kinz; Sharma, Ajeet K; Frank, Joachim; Gonzalez, Ruben L; Chowdhury, Debashish

2015-08-27

At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describe transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies of the bacterial ribosomal pre-translocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pre-translocation complex, which are observed in a cryo-EM study, may not be observed in several smFRET studies.

The E. coli thioredoxin folding mechanism: the key role of the C-terminal helix.

PubMed

Vazquez, Diego S; Sánchez, Ignacio E; Garrote, Ana; Sica, Mauricio P; Santos, Javier

2015-02-01

In this work, the unfolding mechanism of oxidized Escherichia coli thioredoxin (EcTRX) was investigated experimentally and computationally. We characterized seven point mutants distributed along the C-terminal α-helix (CTH) and the preceding loop. The mutations destabilized the protein against global unfolding while leaving the native structure unchanged. Global analysis of the unfolding kinetics of all variants revealed a linear unfolding route with a high-energy on-pathway intermediate state flanked by two transition state ensembles TSE1 and TSE2. The experiments show that CTH is mainly unfolded in TSE1 and the intermediate and becomes structured in TSE2. Structure-based molecular dynamics are in agreement with these experiments and provide protein-wide structural information on transient states. In our model, EcTRX folding starts with structure formation in the β-sheet, while the protein helices coalesce later. As a whole, our results indicate that the CTH is a critical module in the folding process, restraining a heterogeneous intermediate ensemble into a biologically active native state and providing the native protein with thermodynamic and kinetic stability. Copyright © 2014 Elsevier B.V. All rights reserved.

Photooxidation of Diimine Dithiolate Platinium(II) Complexes Induced by Charge Transfer to Diimine Excitation.

PubMed

Zhang, Yin; Ley, Kevin D.; Schanze, Kirk S.

1996-11-20

A photochemical and photophysical investigation was carried out on (tbubpy)Pt(II)(dpdt) and (tbubpy)Pt(II)(edt) (1 and 2, respectively, where tbubpy = 4,4'-di-tert-butyl-2,2'-bipyridine, dpdt = meso-1,2-diphenyl-1,2-ethanedithiolate and edt = 1,2-ethanedithiolate). Luminescence and transient absorption studies reveal that these complexes feature a lowest excited state with Pt(S)(2) --> tbubpy charge transfer to diimine character. Both complexes are photostable in deoxygenated solution; however, photolysis into the visible charge transfer band in air-saturated solution induces moderately efficient photooxidation. Photooxidation of 1 produces the dehydrogenation product (tbubpy)Pt(II)(1,2-diphenyl-1,2-ethenedithiolate) (4). By contrast, photooxidation of 2 produces S-oxygenated complexes in which one or both thiolate ligands are converted to sulfinate (-SO(2)R) ligands. Mechanistic photochemical studies and transient absorption spectroscopy reveal that photooxidation occurs by (1) energy transfer from the charge transfer to diimine excited state of 1 to (3)O(2) to produce (1)O(2) and (2) reaction between (1)O(2) and the ground state 1. Kinetic data indicates that excited state 1 produces (1)O(2) efficiently and that reaction between ground state 1 and (1)O(2) occurs with k approximately 3 x 10(8) M(-)(1) s(-)(1).

A moment-convergence method for stochastic analysis of biochemical reaction networks.

PubMed

Zhang, Jiajun; Nie, Qing; Zhou, Tianshou

2016-05-21

Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in terms of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.

Computations of steady-state and transient premixed turbulent flames using pdf methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hulek, T.; Lindstedt, R.P.

1996-03-01

Premixed propagating turbulent flames are modeled using a one-point, single time, joint velocity-composition probability density function (pdf) closure. The pdf evolution equation is solved using a Monte Carlo method. The unclosed terms in the pdf equation are modeled using a modified version of the binomial Langevin model for scalar mixing of Valino and Dopazo, and the Haworth and Pope (HP) and Lagrangian Speziale-Sarkar-Gatski (LSSG) models for the viscous dissipation of velocity and the fluctuating pressure gradient. The source terms for the presumed one-step chemical reaction are extracted from the rate of fuel consumption in laminar premixed hydrocarbon flames, computed usingmore » a detailed chemical kinetic mechanism. Steady-state and transient solutions are obtained for planar turbulent methane-air and propane-air flames. The transient solution method features a coupling with a Finite Volume (FV) code to obtain the mean pressure field. The results are compared with the burning velocity measurements of Abdel-Gayed et al. and with velocity measurements obtained in freely propagating propane-air flames by Videto and Santavicca. The effects of different upstream turbulence fields, chemical source terms (different fuels and strained/unstrained laminar flames) and the influence of the velocity statistics models (HP and LSSG) are assessed.« less

Interpretation of energy deposition data from historical operation of the transient test facility (TREAT)

DOE PAGES

DeHart, Mark D.; Baker, Benjamin A.; Ortensi, Javier

2017-07-27

The Transient Test Reactor (TREAT) at Idaho National Laboratory will resume operations in late 2017 after a 23 year hiatus while maintained in a cold standby state. Over that time period, computational power and simulation capabilities have increased substantially and now allow for new multiphysics modeling possibilities that were not practical or feasible for most of TREAT's operational history. Hence the return of TREAT to operational service provides a unique opportunity to apply state-of-the-art software and associated methods in the modeling and simulation of general three-dimensional steady state and kinetic behavior for reactor operation, and for coupling of the coremore » power transient model to experiment simulations. However, measurements taken in previous operations were intended to predict power deposition in experimental samples, with little consideration of three-dimensional core power distributions. Hence, interpretation of data for the purpose of validation of modern methods can be challenging. For the research discussed herein, efforts are described for the process of proper interpretation of data from the most recent calibration experiments performed in the core, the M8 calibration series (M8-CAL). These measurements were taken between 1990 and 1993 using a set of fission wires and test fuel pins to estimate the power deposition that would be produced in fast reactor test fuel pins during the M8 experiment series. Because of the decision to place TREAT into a standby state in 1994, the M8 series of transients were never performed. However, potentially valuable information relevant for validation is available in the M8-CAL measurement data, if properly interpreted. This article describes the current state of the process of recovery of useful data from M8-CAL measurements and quantification of biases and uncertainties to potentially apply to the validation of multiphysics methods.« less

Interpretation of energy deposition data from historical operation of the transient test facility (TREAT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeHart, Mark D.; Baker, Benjamin A.; Ortensi, Javier

The Transient Test Reactor (TREAT) at Idaho National Laboratory will resume operations in late 2017 after a 23 year hiatus while maintained in a cold standby state. Over that time period, computational power and simulation capabilities have increased substantially and now allow for new multiphysics modeling possibilities that were not practical or feasible for most of TREAT's operational history. Hence the return of TREAT to operational service provides a unique opportunity to apply state-of-the-art software and associated methods in the modeling and simulation of general three-dimensional steady state and kinetic behavior for reactor operation, and for coupling of the coremore » power transient model to experiment simulations. However, measurements taken in previous operations were intended to predict power deposition in experimental samples, with little consideration of three-dimensional core power distributions. Hence, interpretation of data for the purpose of validation of modern methods can be challenging. For the research discussed herein, efforts are described for the process of proper interpretation of data from the most recent calibration experiments performed in the core, the M8 calibration series (M8-CAL). These measurements were taken between 1990 and 1993 using a set of fission wires and test fuel pins to estimate the power deposition that would be produced in fast reactor test fuel pins during the M8 experiment series. Because of the decision to place TREAT into a standby state in 1994, the M8 series of transients were never performed. However, potentially valuable information relevant for validation is available in the M8-CAL measurement data, if properly interpreted. This article describes the current state of the process of recovery of useful data from M8-CAL measurements and quantification of biases and uncertainties to potentially apply to the validation of multiphysics methods.« less

Reaction with cyanide of hydroxylamine oxidoreductase of Nitrosomonas europaea.

PubMed

Logan, M S; Balny, C; Hooper, A B

1995-07-18

Hydroxylamine oxidoreductase (HAO) catalyzes the reaction NH2OH+H2O-->HNO2+4e- + 4H+, a step in the energy-generating oxidation of ammonia to nitrite by the bacterium Nitrosomonas europaea. Each subunit of HAO contains 7 c-hemes and 1 heme P460. The latter, c-heme cross-linked from a methylene carbon to the ring of a protein tyrosine, forms part of the active site. The iron of heme P460 is probably linked by a bridging ligand to the iron of a c-heme. Here, the reaction of cyanide with ferric HAO was studied by optical, transient, and steady state kinetic techniques. The molecules, F-, Cl-, Br-, N3-, SCN-, and OCN- did not react with HAO. A single molecule of cyanide bound with high affinity to heme P460 of HAO. The optical and kinetic characteristics of formation of the monocyano complex of HAO resembled those of cyanide derivatives of other heme proteins. Cyanide, in the monocyano complex, was a noncompetitive inhibitor and remained bound during turnover. HAO was found in two forms. The most common form, HAO-A, formed only the monocyano derivative of heme P460, whereas the other, HAO-B, formed a mono- and dicyano complex. The optical properties and kinetics of formation of the mono- and dicyano complexes were different enough to easily allow independent analysis. The optical and kinetic characteristics of formation of the monocyano complex of heme P460 of HAO A and B were very similar. The dicyano complex of HAO-B appeared to result from the addition of a second molecule of cyanide to heme P460. The rate of conversion of the monocyano to the dicyano complex was stimulated 100-fold by the binding of substrate. Formation of the monoheme complex inhibited enzyme activity. The kinetic constants for the first-order formation of the monocyano derivative and the inhibition of substrate oxidation (under either transient or steady-state conditions) were different. The apparent discrepancy could be resolved by the hypothesis that HAO is functionally a dimer in which electrons rapidly equilibrate between the c-hemes of each subunit but not between oligomers. The results form the basis for the use of cyanide as a probe of the active site of HAO.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edgue, E.

The point kinetics approach is a classical useful method for a reactor transient analysis. It is helpful to known, however, when a more elaborate transient analysis, involving the space-dependence change of the flux through a given transient, should be considered. In this paper, the authors present a rather elegant and quick method to check the need for a space-dependent flux analysis through a control rod transient in a given nuclear reactor. The method is applied to a series of rod ejection experiments in the TRIGA MARK-II reactor of Istanbul Technical University (ITU).

Transient loading of CD34+ hematopoietic progenitor cells with polystyrene nanoparticles.

PubMed

Deville, Sarah; Hadiwikarta, Wahyu Wijaya; Smisdom, Nick; Wathiong, Bart; Ameloot, Marcel; Nelissen, Inge; Hooyberghs, Jef

2017-01-01

CD34 + hematopoietic progenitor cells (HPCs) offer great opportunities to develop new treatments for numerous malignant and non-malignant diseases. Nanoparticle (NP)-based strategies can further enhance this potential, and therefore a thorough understanding of the loading behavior of HPCs towards NPs is essential for a successful application. The present study focusses on the interaction kinetics of 40 nm sized carboxylated polystyrene (PS) NPs with HPCs. Interestingly, a transient association of the NPs with HPCs is observed, reaching a maximum within 1 hour and declining afterwards. This behavior is not seen in dendritic cells (CD34-DCs) differentiated from HPCs, which display a monotonic increase in NP load. We demonstrate that this transient interaction requires an energy-dependent cellular process, suggesting active loading and release of NPs by HPCs. This novel observation offers a unique approach to transiently equip HPCs. A simple theoretical approach modeling the kinetics of NP loading and release is presented, contributing to a framework of describing this phenomenon.

Bounds on internal state variables in viscoplasticity

NASA Technical Reports Server (NTRS)

Freed, Alan D.

1993-01-01

A typical viscoplastic model will introduce up to three types of internal state variables in order to properly describe transient material behavior; they are as follows: the back stress, the yield stress, and the drag strength. Different models employ different combinations of these internal variables--their selection and description of evolution being largely dependent on application and material selection. Under steady-state conditions, the internal variables cease to evolve and therefore become related to the external variables (stress and temperature) through simple functional relationships. A physically motivated hypothesis is presented that links the kinetic equation of viscoplasticity with that of creep under steady-state conditions. From this hypothesis one determines how the internal variables relate to one another at steady state, but most importantly, one obtains bounds on the magnitudes of stress and back stress, and on the yield stress and drag strength.

Free energy landscape of activation in a signaling protein at atomic resolution

PubMed Central

Pontiggia, F.; Pachov, D.V.; Clarkson, M.W.; Villali, J.; Hagan, M.F.; Pande, V.S.; Kern, D.

2015-01-01

The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signaling. However, how folded states interconvert is largely unknown due to the inability to experimentally observe transition pathways. Here we explore the free energy landscape of the bacterial response regulator NtrC by combining computation and NMR, and discover unexpected features underlying efficient signaling. We find that functional states are defined purely in kinetic and not structural terms. The need of a well-defined conformer, crucial to the active state, is absent in the inactive state, which comprises a heterogeneous collection of conformers. The transition between active and inactive states occurs through multiple pathways, facilitated by a number of nonnative transient hydrogen bonds, thus lowering the transition barrier through both entropic and enthalpic contributions. These findings may represent general features for functional conformational transitions within the folded state. PMID:26073309

Infrared Absorption Spectroscopy and Chemical Kinetics of Free Radicals. Final Performance Report, August 1, 1985--July 31, 1994

DOE R&D Accomplishments Database

Curl, R. F.; Glass, G. P.

1995-06-01

This research was directed at the detection, monitoring, and study (by infrared absorption spectroscopy) of the chemical kinetic behavior of small free radical species thought to be important intermediates in combustion. The work typically progressed from the detection and analysis of the infrared spectrum of combustion radical to the utilization of the infrared spectrum thus obtained in the investigation of chemical kinetics of the radical species. The methodology employed was infrared kinetic spectroscopy. In this technique the radical is produced by UV flash photolysis using an excimer laser and then its transient infrared absorption is observed using a single frequency cw laser as the source of the infrared probe light. When the probe laser frequency is near the center of an absorption line of the radical produced by the flash, the transient infrared absorption rises rapidly and then decays as the radical reacts with the precursor or with substances introduced for the purpose of studying the reaction kinetics or with itself. The decay times observed in these studies varied from less than one microsecond to more than one millisecond. By choosing appropriate time windows after the flash and the average infrared detector signal in a window as data channels, the infrared spectrum of the radical may be obtained. By locking the infrared probe laser to the center of the absorption line and measuring the rate of decay of the transient infrared absorption signal as the chemical composition of the gas mixture is varied, the chemical kinetics of the radical may be investigated. In what follows the systems investigated and the results obtained are outlined.

Understanding the Broad Substrate Repertoire of Nitroreductase Based on Its Kinetic Mechanism*

PubMed Central

Pitsawong, Warintra; Hoben, John P.; Miller, Anne-Frances

2014-01-01

The oxygen-insensitive nitroreductase from Enterobacter cloacae (NR) catalyzes two-electron reduction of nitroaromatics to the corresponding nitroso compounds and, subsequently, to hydroxylamine products. NR has an unusually broad substrate repertoire, which may be related to protein dynamics (flexibility) and/or a simple non-selective kinetic mechanism. To investigate the possible role of mechanism in the broad substrate repertoire of NR, the kinetics of oxidation of NR by para-nitrobenzoic acid (p-NBA) were investigated using stopped-flow techniques at 4 °C. The results revealed a hyperbolic dependence on the p-NBA concentration with a limiting rate of 1.90 ± 0.09 s−1, indicating one-step binding before the flavin oxidation step. There is no evidence for a distinct binding step in which specificity might be enforced. The reduction of p-NBA is rate-limiting in steady-state turnover (1.7 ± 0.3 s−1). The pre-steady-state reduction kinetics of NR by NADH indicate that NADH reduces the enzyme with a rate constant of 700 ± 20 s−1 and a dissociation constant of 0.51 ± 0.04 mm. Thus, we demonstrate simple transient kinetics in both the reductive and oxidative half-reactions that help to explain the broad substrate repertoire of NR. Finally, we tested the ability of NR to reduce para-hydroxylaminobenzoic acid, demonstrating that the corresponding amine does not accumulate to significant levels even under anaerobic conditions. Thus E. cloacae NR is not a good candidate for enzymatic production of aromatic amines. PMID:24706760

Application of ATHLET/DYN3D coupled codes system for fast liquid metal cooled reactor steady state simulation

NASA Astrophysics Data System (ADS)

Ivanov, V.; Samokhin, A.; Danicheva, I.; Khrennikov, N.; Bouscuet, J.; Velkov, K.; Pasichnyk, I.

2017-01-01

In this paper the approaches used for developing of the BN-800 reactor test model and for validation of coupled neutron-physic and thermohydraulic calculations are described. Coupled codes ATHLET 3.0 (code for thermohydraulic calculations of reactor transients) and DYN3D (3-dimensional code of neutron kinetics) are used for calculations. The main calculation results of reactor steady state condition are provided. 3-D model used for neutron calculations was developed for start reactor BN-800 load. The homogeneous approach is used for description of reactor assemblies. Along with main simplifications, the main reactor BN-800 core zones are described (LEZ, MEZ, HEZ, MOX, blankets). The 3D neutron physics calculations were provided with 28-group library, which is based on estimated nuclear data ENDF/B-7.0. Neutron SCALE code was used for preparation of group constants. Nodalization hydraulic model has boundary conditions by coolant mass-flow rate for core inlet part, by pressure and enthalpy for core outlet part, which can be chosen depending on reactor state. Core inlet and outlet temperatures were chosen according to reactor nominal state. The coolant mass flow rate profiling through the core is based on reactor power distribution. The test thermohydraulic calculations made with using of developed model showed acceptable results in coolant mass flow rate distribution through the reactor core and in axial temperature and pressure distribution. The developed model will be upgraded in future for different transient analysis in metal-cooled fast reactors of BN type including reactivity transients (control rods withdrawal, stop of the main circulation pump, etc.).

Catalytic conversion reactions mediated by single-file diffusion in linear nanopores: hydrodynamic versus stochastic behavior.

PubMed

Ackerman, David M; Wang, Jing; Wendel, Joseph H; Liu, Da-Jiang; Pruski, Marek; Evans, James W

2011-03-21

We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. Diffusion within the pores is subject to a strict single-file (no passing) constraint. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice-gas model for this reaction-diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction-diffusion type equations (mf-RDE). For slowly varying concentrations, we further develop coarse-grained continuum hydrodynamic reaction-diffusion equations (h-RDE) incorporating a precise treatment of single-file diffusion in this multispecies system. The h-RDE successfully describe nontrivial aspects of transient behavior, in contrast to the mf-RDE, and also correctly capture unreactive steady-state behavior in the pore interior. However, steady-state reactivity, which is localized near the pore ends when those regions are catalytic, is controlled by fluctuations not incorporated into the hydrodynamic treatment. The mf-RDE partly capture these fluctuation effects, but cannot describe scaling behavior of the reactivity.

Analytical Study of Gravity Effects on Laminar Diffusion Flames

NASA Technical Reports Server (NTRS)

Edelman, R. B.; Fortune, O.; Weilerstein, G.

1972-01-01

A mathematical model is presented for the description of axisymmetric laminar-jet diffusion flames. The analysis includes the effects of inertia, viscosity, diffusion, gravity and combustion. These mechanisms are coupled in a boundary layer type formulation and solutions are obtained by an explicit finite difference technique. A dimensional analysis shows that the maximum flame width radius, velocity and thermodynamic state characterize the flame structure. Comparisons with experimental data showed excellent agreement for normal gravity flames and fair agreement for steady state low Reynolds number zero gravity flames. Kinetics effects and radiation are shown to be the primary mechanisms responsible for this discrepancy. Additional factors are discussed including elipticity and transient effects.

The readily releasable pool of vesicles in chromaffin cells is replenished in a temperature-dependent manner and transiently overfills at 37 degrees C.

PubMed

Dinkelacker, V; Voets, T; Neher, E; Moser, T

2000-11-15

Maturation of exocytic vesicles to the release-ready state is regulated by several factors, including intracellular calcium concentration ([Ca(2+)](int)) and the state of protein phosphorylation. Here we investigated the effects of temperature on the recovery from depletion of the readily releasable pool (RRP) of vesicles in adrenal chromaffin cells. Exocytosis and [Ca(2+)](int) were monitored by combined membrane capacitance and fura-2 measurements. At higher temperatures, a faster pool refilling and a larger RRP size were observed. The time constants of the recovery from depletion ranged from 3.6 to 1.1 sec (22 and 37 degrees C, respectively) yielding a Q(10) of 2.3. The changes of the Ca(2+) signal between the different temperatures could not account for the differences in recovery kinetics. At 32 and 37 degrees C, we observed a transient overfilling of the RRP after pool depletion, which stands in clear contrast to the sustained secretory depression seen at lower temperatures. The overshoot in RRP size was very prominent in cells with lower basal [Ca(2+)](int), hence with a large difference between prestimulus and poststimulus [Ca(2+)](int). In cells with higher basal [Ca(2+)](int), the pool was larger under steady-state conditions but showed less overfilling on stimulation. We conclude that vesicle maturation is markedly accelerated at physiological temperature, thus allowing for a rapid adaptation of the pool size to the relatively short-lived Ca(2+) transient.

Recruiting at the Edge: Kinetic Energy Inhibits Anchovy Populations in the Western Mediterranean

PubMed Central

Ruiz, Javier; Macías, Diego; Rincón, Margarita M.; Pascual, Ananda; Catalán, Ignacio A.; Navarro, Gabriel

2013-01-01

The Strait of Gibraltar replenishes the Mediterranean with Atlantic waters through an intense eastward current known as the Atlantic Jet (AJ). The AJ fertilizes the southwestern Mediterranean and is considered to be the ultimate factor responsible for the comparatively high fish production of this region. Here, we perform an analysis of the available historical catches and catch per unit effort (CPUE), together with a long series of surface currents, kinetic energy and chlorophyll concentration. We show that the high kinetic energy of the AJ increases primary production but also negatively impacts the recruitment of anchovy. We contend that anchovy recruitment in the region is inhibited by the advection and dispersion of larvae and post-larvae during periods of strong advection by the AJ. The inhibitory impact of kinetic energy on anchovy landings is not a transient but rather a persistent state of the system. An exceptional combination of events creates an outbreak of this species in the Alboran Sea. These events depend on the Mediterranean-Atlantic exchange of water masses and, therefore, are highly sensitive to climate changes that are projected, though not always negatively, for fish landings. PMID:23451027

A sensitivity study of the effects of evaporation/condensation accommodation coefficients on transient heat pipe modeling

NASA Astrophysics Data System (ADS)

Hall, Michael L.; Doster, J. Michael

1990-03-01

The dynamic behavior of liquid metal heat pipe models is strongly influenced by the choice of evaporation and condensation modeling techniques. Classic kinetic theory descriptions of the evaporation and condensation processes are often inadequate for real situations; empirical accommodation coefficients are commonly utilized to reflect nonideal mass transfer rates. The complex geometries and flow fields found in proposed heat pipe systems cause considerable deviation from the classical models. the THROHPUT code, which has been described in previous works, was developed to model transient liquid metal heat pipe behavior from frozen startup conditions to steady state full power operation. It is used here to evaluate the sensitivity of transient liquid metal heat pipe models to the choice of evaporation and condensation accommodation coefficients. Comparisons are made with experimental liquid metal heat pipe data. It is found that heat pipe behavior can be predicted with the proper choice of the accommodation coefficients. However, the common assumption of spatially constant accommodation coefficients is found to be a limiting factor in the model.

TREAT Transient Analysis Benchmarking for the HEU Core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kontogeorgakos, D. C.; Connaway, H. M.; Wright, A. E.

2014-05-01

This work was performed to support the feasibility study on the potential conversion of the Transient Reactor Test Facility (TREAT) at Idaho National Laboratory from the use of high enriched uranium (HEU) fuel to the use of low enriched uranium (LEU) fuel. The analyses were performed by the GTRI Reactor Conversion staff at the Argonne National Laboratory (ANL). The objective of this study was to benchmark the transient calculations against temperature-limited transients performed in the final operating HEU TREAT core configuration. The MCNP code was used to evaluate steady-state neutronics behavior, and the point kinetics code TREKIN was used tomore » determine core power and energy during transients. The first part of the benchmarking process was to calculate with MCNP all the neutronic parameters required by TREKIN to simulate the transients: the transient rod-bank worth, the prompt neutron generation lifetime, the temperature reactivity feedback as a function of total core energy, and the core-average temperature and peak temperature as a functions of total core energy. The results of these calculations were compared against measurements or against reported values as documented in the available TREAT reports. The heating of the fuel was simulated as an adiabatic process. The reported values were extracted from ANL reports, intra-laboratory memos and experiment logsheets and in some cases it was not clear if the values were based on measurements, on calculations or a combination of both. Therefore, it was decided to use the term “reported” values when referring to such data. The methods and results from the HEU core transient analyses will be used for the potential LEU core configurations to predict the converted (LEU) core’s performance.« less

Transient Simulation of the Multi-SERTTA Experiment with MAMMOTH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortensi, Javier; Baker, Benjamin; Wang, Yaqi

This work details the MAMMOTH reactor physics simulations of the Static Environment Rodlet Transient Test Apparatus (SERTTA) conducted at Idaho National Laboratory in FY-2017. TREAT static-environment experiment vehicles are being developed to enable transient testing of Pressurized Water Reactor (PWR) type fuel specimens, including fuel concepts with enhanced accident tolerance (Accident Tolerant Fuels, ATF). The MAMMOTH simulations include point reactor kinetics as well as spatial dynamics for a temperature-limited transient. The strongly coupled multi-physics solutions of the neutron flux and temperature fields are second order accurate both in the spatial and temporal domains. MAMMOTH produces pellet stack powers that are within 1.5% of the Monte Carlo reference solutions. Some discrepancies between the MCNP model used in the design of the flux collars and the Serpent/MAMMOTH models lead to higher power and energy deposition values in Multi-SERTTA unit 1. The TREAT core results compare well with the safety case computed with point reactor kinetics in RELAP5-3D. The reactor period is 44 msec, which corresponds to a reactivity insertion of 2.685% delta k/kmore » $. The peak core power in the spatial dynamics simulation is 431 MW, which the point kinetics model over-predicts by 12%. The pulse width at half the maximum power is 0.177 sec. Subtle transient effects are apparent at the beginning insertion in the experimental samples due to the control rod removal. Additional difference due to transient effects are observed in the sample powers and enthalpy. The time dependence of the power coupling factor (PCF) is calculated for the various fuel stacks of the Multi-SERTTA vehicle. Sample temperatures in excess of 3100 K, the melting point UO$$_2$$, are computed with the adiabatic heat transfer model. The planned shaped-transient might introduce additional effects that cannot be predicted with PRK models. Future modeling will be focused on the shaped-transient by improving the control rod models in MAMMOTH and adding the BISON thermo-elastic models and thermal-fluids heat transfer.« less

Transiently disordered tails accelerate folding of globular proteins.

PubMed

Mallik, Saurav; Ray, Tanaya; Kundu, Sudip

2017-07-01

Numerous biological proteins exhibit intrinsic disorder at their termini, which are associated with multifarious functional roles. Here, we show the surprising result that an increased percentage of terminal short transiently disordered regions with enhanced flexibility (TstDREF) is associated with accelerated folding rates of globular proteins. Evolutionary conservation of predicted disorder at TstDREFs and drastic alteration of folding rates upon point-mutations suggest critical regulatory role(s) of TstDREFs in shaping the folding kinetics. TstDREFs are associated with long-range intramolecular interactions and the percentage of native secondary structural elements physically contacted by TstDREFs exhibit another surprising positive correlation with folding kinetics. These results allow us to infer probable molecular mechanisms behind the TstDREF-mediated regulation of folding kinetics that challenge protein biochemists to assess by direct experimental testing. © 2017 Federation of European Biochemical Societies.

Photochemical Kinetics of a Phosphine Oxide Free Radical Initiator from Femtosecond UV-Pump/Mid-IR-Probe Spectroscopy.

PubMed

Straub, Steffen; Lindner, Jörg; Vöhringer, Peter

2017-07-06

Femtosecond UV-pump/mid-infrared-probe spectroscopy was used to explore in detail the primary photochemical events of the free radical initiator, (2,4,6-trimethylbenzoyl)diphenylphosphine oxide, in liquid dichloromethane solution at room temperature. Following electronic excitation of its lowest excited singlet state, S 1 , the radical initiator undergoes an intersystem crossing to the triplet ground state, T 1 , with a time constant of 135 ps. A subsequent α-cleavage occurs from the triplet state with a time constant of 15 ps and yields a trimethylbenzoyl radical together with a diphenylphosphinoyl radical. Transient absorptions from the S 1 and T 1 states are observed that can be assigned to the P═O stretching mode and the symmetric in-plane deformation mode of the trimethylphenyl moiety of the radical initiator.

Dopamine alters glutamate receptor desensitization in retinal horizontal cells of the perch (Perca fluviatilis).

PubMed Central

Schmidt, K F; Kruse, M; Hatt, H

1994-01-01

The patch-clamp technique in combination with a fast liquid filament application system was used to study the effect of dopamine on the glutamate receptor desensitization in horizontal cells of the perch (Perca fluviatilis). Kinetics of ligand-gated ion channels in fish horizontal cells are modulated by dopamine. This modulation is presumably mediated by a cAMP-dependent protein phosphorylation. Before incubation with dopamine, the glutamate receptors of horizontal cells activate and desensitize with fast time constants. In the whole-cell recording mode, fast application of the agonists L-glutamate, quisqualate, or alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid prior to the dopamine incubation gives rise to fast transient currents with peak values of about 200 pA that desensitize within 100 ms. Kainate as agonist produced higher steady-state currents but no transient currents. After incubation of the cells with dopamine for 3 min, the desensitization was significantly reduced and the agonists L-glutamate, quisqualate, or alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid induced steady-state currents with amplitudes that were similar to the previously observed transient currents. Kainate-induced currents were only slightly affected. Fast desensitizing currents upon fast application of L-glutamate were also recorded from outside-out patches that were excised from horizontal cells before incubation with dopamine. The currents from excised patches desensitized to a steady-state level of about 0.2 of the peak amplitude with time constants of less than 2 ms. When the outside-out patches were excised from cells after dopamine incubation, steady-state currents were enhanced and no transient currents were observed. The results may indicate that the dopamine-dependent modulation of glutamate-induced currents, which is presumably mediated by a protein phosphorylation, is due to an alteration of the desensitization of the glutamate receptors. PMID:7520178

Femtosecond Heterodyne Transient Grating Detection of Conformational Dynamics in the S0 (11Ag-) State of Carotenoids After Nonradiative Decay of the S2 (11Bu+) State

NASA Astrophysics Data System (ADS)

Roscioli, Jerome D.; Ghosh, Soumen; Bishop, Michael M.; Lafountain, Amy M.; Frank, Harry A.; Beck, Warren F.

Transient grating spectroscopy was used to study the dynamics of nonradiative decay of the S1 (21Ag-) state in ß-carotene and peridinin after optical preparation of the S2) state. The kinetics of the recovery of the absorption and dispersion components of the third-order signal exhibit significantly different time constants. For β-carotene in benzonitrile, the absorption and dispersion recovery time constants are 11.6 and 10.2 ps. For peridinin in methanol, the time constants are 9.9 and 7.4 ps. These results indicate that the initial product of the decay of the S1 state is a conformationally displaced structure. The decay rate for the S1 state and the conformational relaxation rate are both slowed in peridinin as the polarity of the solvent decreases; in ethyl acetate, the conformational relaxation time constant is 45 ps, which rules out a dominant contribution from vibrational cooling. These results indicate that the S1 state develops intramolecular charge transfer character owing to distortions along torsional and out-of-plane coordinates, with a pyramidal structure favored as the most stable conformation. Recovery of the photoselected ground state conformation involves a reverse charge-transfer event followed by relaxation to a planar structure. Work supported by Photosynthetic Systems Program of the U.S. Department of Energy under Grant DE-SC0010847.

Passive films on magnesium anodes in primary batteries

NASA Technical Reports Server (NTRS)

Ratnakumar, B. V.

1988-01-01

The characteristics of the passive films over Mg anodes, which essentially govern the voltage delay of the latter, have been determined nondestructively from an analysis of the transient and steady-state response of the electrode potential to low amplitude galvanostatic polarization under various experimental conditions viz., with different corrosion inhibitor coatings on Mg, after various periods of ageing of anode in solutions containing corrosion inhibitors, at various low temperatures etc. Using these parameters, the kinetics of film build-up or dissolution under these conditions have been monitored. The morphology of the anode film has been verified with scanning electron microscopy. Similar transients at low temperatures point out a steep rise in the film resistivity which is essentially responsible for the severe voltage delay. Finally, possible application of this technique in secondary Li batteries to improve cycling characteristics of the Li anode has been pointed out.

Materials and processing approaches for foundry-compatible transient electronics

PubMed Central

Chang, Jan-Kai; Fang, Hui; Bower, Christopher A.; Song, Enming; Yu, Xinge; Rogers, John A.

2017-01-01

Foundry-based routes to transient silicon electronic devices have the potential to serve as the manufacturing basis for “green” electronic devices, biodegradable implants, hardware secure data storage systems, and unrecoverable remote devices. This article introduces materials and processing approaches that enable state-of-the-art silicon complementary metal-oxide-semiconductor (CMOS) foundries to be leveraged for high-performance, water-soluble forms of electronics. The key elements are (i) collections of biodegradable electronic materials (e.g., silicon, tungsten, silicon nitride, silicon dioxide) and device architectures that are compatible with manufacturing procedures currently used in the integrated circuit industry, (ii) release schemes and transfer printing methods for integration of multiple ultrathin components formed in this way onto biodegradable polymer substrates, and (iii) planarization and metallization techniques to yield interconnected and fully functional systems. Various CMOS devices and circuit elements created in this fashion and detailed measurements of their electrical characteristics highlight the capabilities. Accelerated dissolution studies in aqueous environments reveal the chemical kinetics associated with the underlying transient behaviors. The results demonstrate the technical feasibility for using foundry-based routes to sophisticated forms of transient electronic devices, with functional capabilities and cost structures that could support diverse applications in the biomedical, military, industrial, and consumer industries. PMID:28652373

Transient behavior of vertical scaling of mesoscale winds in the light of atmospheric turbulence transfer in and between synoptic and mesoscales

NASA Astrophysics Data System (ADS)

Barros, A. P.; Eghdami, M.

2017-12-01

High-resolution ( 1 km) numerical weather prediction models are capable of producing atmospheric spectra over synoptic and mesoscale ranges. Nogueira and Barros (2015) showed using high-resolution simulations in the Andes that the horizontal scale invariant behavior of atmospheric wind and water fields in the model is a process-dependent transient property that varies with the underlying dynamics. They found a sharp transition in the scaling parameters between non-convective and convective conditions. Spectral slopes around 2-2.3 arise under non-convective or very weak convective conditions, whereas in convective situations the transient scaling exponents remain under -5/3. Based on these results, Nogueira and Barros (2015) proposed a new sub-grid scale parameterization of clouds obtained from coarse resolution states alone. High Reynolds number direct numerical simulations of two-dimensional turbulence transfer shows that atmospheric flows involve concurrent direct (downscale) enstrophy transfer in the synoptic scales and inverse (upscale) kinetic energy transfer from the meso- to the synoptic-scales. In this study we use an analogy to investigate the transient behavior of kinetic energy spectra of winds over the Andes and Southern Appalachian Mountains representative of high and middle mountains, respectively. In the unstable conditions and particularly in the Planetary Boundary Layer (PBL) the spectral slopes approach -5/3 associated with the upscale KE turbulence transfer. However, in the stable conditions and above the planetary boundary layer, the spectra slopes approach steeper slopes about -3 associated with the downscale KE transfer. The underlying topography, surface roughness, diurnal heating and cooling and moist processes add to the complexity of the problem by introducing anisotropy and sources and sinks of energy. A comprehensive analysis and scaling of flow behavior conditional on stability regime for both KE and moist processes (total water, cloud water, rainfall) is necessary to elucidate scale-interactions among different processes.

A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP.

PubMed

Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T

2017-11-22

Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.

Neutronic safety parameters and transient analyses for Poland's MARIA research reactor.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bretscher, M. M.; Hanan, N. A.; Matos, J. E.

1999-09-27

Reactor kinetic parameters, reactivity feedback coefficients, and control rod reactivity worths have been calculated for the MARIA Research Reactor (Swierk, Poland) for M6-type fuel assemblies with {sup 235}U enrichments of 80% and 19.7%. Kinetic parameters were evaluated for family-dependent effective delayed neutron fractions, decay constants, and prompt neutron lifetimes and neutron generation times. Reactivity feedback coefficients were determined for fuel Doppler coefficients, coolant (H{sub 2}O) void and temperature coefficients, and for in-core and ex-core beryllium temperature coefficients. Total and differential control rod worths and safety rod worths were calculated for each fuel type. These parameters were used to calculate genericmore » transients for fast and slow reactivity insertions with both HEU and LEU fuels. The analyses show that the HEU and LEU cores have very similar responses to these transients.« less

Mapping transiently formed and sparsely populated conformations on a complex energy landscape.

PubMed

Wang, Yong; Papaleo, Elena; Lindorff-Larsen, Kresten

2016-08-23

Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally.

Effect of leaf incubation temperature profiles on Agrobacterium tumefaciens-mediated transient expression.

PubMed

Jung, Sang-Kyu; McDonald, Karen A; Dandekar, Abhaya M

2015-01-01

Agrobacterium tumefaciens-mediated transient expression is known to be highly dependent on incubation temperature. Compared with early studies that were conducted at constant temperature, we examined the effect of variable leaf incubation temperature on transient expression. As a model system, synthetic endoglucanase (E1) and endoxylanase (Xyn10A) genes were transiently expressed in detached whole sunflower leaves via vacuum infiltration for biofuel applications. We found that the kinetics of transient expression strongly depended on timing of the temperature change as well as leaf incubation temperature. Surprisingly, we found that high incubation temperature (27-30 °C) which is suboptimal for T-DNA transfer, significantly enhanced transient expression if the high temperature was applied during the late phase (Day 3-6) of leaf incubation whereas incubation temperature in a range of 20-25 °C for an early phase (Day 0-2) resulted in higher production. On the basis of these results, we propose that transient expression is governed by both T-DNA transfer and protein synthesis in plant cells that have different temperature dependent kinetics. Because the phases were separated in time and had different optimal temperatures, we were then able to develop a novel two phase optimization strategy for leaf incubation temperature. Applying the time-varying temperature profile, we were able to increase the protein accumulation by fivefold compared with the control at a constant temperature of 20 °C. From our knowledge, this is the first report illustrating the effect of variable temperature profiling for improved transient expression. © 2015 American Institute of Chemical Engineers.

New photocycle intermediates in the photoactive yellow protein from Ectothiorhodospira halophila: picosecond transient absorption spectroscopy.

PubMed

Ujj, L; Devanathan, S; Meyer, T E; Cusanovich, M A; Tollin, G; Atkinson, G H

1998-07-01

Previous studies have shown that the room temperature photocycle of the photoactive yellow protein (PYP) from Ectothiorhodospira halophila involves at least two intermediate species: I1, which forms in <10 ns and decays with a 200-micros lifetime to I2, which itself subsequently returns to the ground state with a 140-ms time constant at pH 7 (Genick et al. 1997. Biochemistry. 36:8-14). Picosecond transient absorption spectroscopy has been used here to reveal a photophysical relaxation process (stimulated emission) and photochemical intermediates in the PYP photocycle that have not been reported previously. The first new intermediate (I0) exhibits maximum absorption at approximately 510 nm and appears in

Simulation of photoreactive transients and of photochemical transformation of organic pollutants in sunlit boreal lakes across 14 degrees of latitude: A photochemical mapping of Sweden.

PubMed

Koehler, Birgit; Barsotti, Francesco; Minella, Marco; Landelius, Tomas; Minero, Claudio; Tranvik, Lars J; Vione, Davide

2018-02-01

Lake water constituents, such as chromophoric dissolved organic matter (CDOM) and nitrate, absorb sunlight which induces an array of photochemical reactions. Although these reactions are a substantial driver of pollutant degradation in lakes they are insufficiently understood, in particular on large scales. Here, we provide for the first time comprehensive photochemical maps covering a large geographic region. Using photochemical kinetics modeling for 1048 lakes across Sweden we simulated the steady-state concentrations of four photoreactive transient species, which are continuously produced and consumed in sunlit lake waters. We then simulated the transient-induced photochemical transformation of organic pollutants, to gain insight into the relevance of the different photoreaction pathways. We found that boreal lakes were often unfavorable environments for photoreactions mediated by hydroxyl radicals (OH) and carbonate radical anions (CO 3 - ), while photoreactions mediated by CDOM triplet states ( 3 CDOM*) and, to a lesser extent, singlet oxygen ( 1 O 2 ) were the most prevalent. These conditions promote the photodegradation of phenols, which are used as plastic, medical drug and herbicide precursors. When CDOM concentrations increase, as is currently commonly the case in boreal areas such as Sweden, 3 CDOM* will also increase, promoting its importance in photochemical pathways even more. Copyright © 2017 Elsevier Ltd. All rights reserved.

A moment-convergence method for stochastic analysis of biochemical reaction networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jiajun; Nie, Qing; Zhou, Tianshou, E-mail: mcszhtsh@mail.sysu.edu.cn

Traditional moment-closure methods need to assume that high-order cumulants of a probability distribution approximate to zero. However, this strong assumption is not satisfied for many biochemical reaction networks. Here, we introduce convergent moments (defined in mathematics as the coefficients in the Taylor expansion of the probability-generating function at some point) to overcome this drawback of the moment-closure methods. As such, we develop a new analysis method for stochastic chemical kinetics. This method provides an accurate approximation for the master probability equation (MPE). In particular, the connection between low-order convergent moments and rate constants can be more easily derived in termsmore » of explicit and analytical forms, allowing insights that would be difficult to obtain through direct simulation or manipulation of the MPE. In addition, it provides an accurate and efficient way to compute steady-state or transient probability distribution, avoiding the algorithmic difficulty associated with stiffness of the MPE due to large differences in sizes of rate constants. Applications of the method to several systems reveal nontrivial stochastic mechanisms of gene expression dynamics, e.g., intrinsic fluctuations can induce transient bimodality and amplify transient signals, and slow switching between promoter states can increase fluctuations in spatially heterogeneous signals. The overall approach has broad applications in modeling, analysis, and computation of complex biochemical networks with intrinsic noise.« less

Transient kinetics of the rapid shape change of unstirred human blood platelets stimulated with ADP.

PubMed Central

Deranleau, D A; Dubler, D; Rothen, C; Lüscher, E F

1982-01-01

Unstirred (isotropic) suspensions of human blood platelets stimulated with ADP in a stopped-flow laser turbidimeter exhibit a distinct extinction maximum during the course of the classical rapid conversion of initially smooth flat discoid cells to smaller-body spiny spheres. This implies the existence of a transient intermediate having a larger average light scattering cross section (extinction coefficient) than either the disc or the spiny sphere. Monophasic extinction increases reaching the same final value were observed when either discoid or spiny sphere platelets were converted to smooth spheres by treatment with chlorpromazine, and sphering of discoid cells was accompanied by a larger total extinction change than the retraction of pseudopods by already spherical cells. These and other results suggest that the ADP-induced transient state represents platelets that are approximately as "spherical" as the irregular spiny sphere but lack the characteristic long pseudopods and as a consequence are larger bodied. Fitting the ADP progress curves to the series reaction A leads to B leads to C by means of the light scattering equivalent of the Beer-Lambert law yielded scattering cross sections that are consistent with this explanation. The rate constants for the two reaction steps were identical, indicating that ADP activation corresponds to a continuous random (Poisson) process with successive apparent states "disc," "sphere," and "spiny sphere," whose individual probabilities are determined by a single rate-limiting step. PMID:6961409

Oxygen uptake kinetics of constant-load work - Upright vs. supine exercise

NASA Technical Reports Server (NTRS)

Convertino, V. A.; Goldwater, D. J.; Sandler, H.

1984-01-01

Supine and upright positions were used in a comparitive study of the effects of constant load exercise on oxygen uptake (VO2), O2 deficit, steady-state VO2 and VO2 following recovery from constant load work. Ten male subjects (36-40 yr.) performed one submaximal exercise test in the supine and one test in the upright position consisting of 5 min rest and 5 min cycle ergometer exercise at 700 kg/min followed by ten minutes of recovery. It is found that the significant difference in VO2 kinetics during exercise in the upright compared to supine position resulted from changes in oxygen transport and utilization mechanisms rather than changes in mechanical efficiency. To the extent that data measured in the supine position can be used to estimate physiological responses to zero gravity, it is suggested that limitation of systemic O2 consumption may be the result of slow rates of oxygen uptake during transient periods of muscular work. Significant reductions in the rate of steady-state VO2 attainment at submaximal work intensities may produce an onset of muscle fatigue and exhaustion.

Conformational Dynamics of Insulin

PubMed Central

Hua, Qing-Xin; Jia, Wenhua; Weiss, Michael A.

2011-01-01

We have exploited a prandial insulin analog to elucidate the underlying structure and dynamics of insulin as a monomer in solution. A model was provided by insulin lispro (the active component of Humalog®; Eli Lilly and Co.). Whereas NMR-based modeling recapitulated structural relationships of insulin crystals (T-state protomers), dynamic anomalies were revealed by amide-proton exchange kinetics in D2O. Surprisingly, the majority of hydrogen bonds observed in crystal structures are only transiently maintained in solution, including key T-state-specific inter-chain contacts. Long-lived hydrogen bonds (as defined by global exchange kinetics) exist only at a subset of four α-helical sites (two per chain) flanking an internal disulfide bridge (cystine A20–B19); these sites map within the proposed folding nucleus of proinsulin. The anomalous flexibility of insulin otherwise spans its active surface and may facilitate receptor binding. Because conformational fluctuations promote the degradation of pharmaceutical formulations, we envisage that “dynamic re-engineering” of insulin may enable design of ultra-stable formulations for humanitarian use in the developing world. PMID:22649374

Determination of cell metabolite VEGF₁₆₅ and dynamic analysis of protein-DNA interactions by combination of microfluidic technique and luminescent switch-on probe.

PubMed

Lin, Xuexia; Leung, Ka-Ho; Lin, Ling; Lin, Luyao; Lin, Sheng; Leung, Chung-Hang; Ma, Dik-Lung; Lin, Jin-Ming

2016-05-15

In this paper, we rationally design a novel G-quadruplex-selective luminescent iridium (III) complex for rapid detection of oligonucleotide and VEGF165 in microfluidics. This new probe is applied as a convenient biosensor for label-free quantitative analysis of VEGF165 protein from cell metabolism, as well as for studying the kinetics of the aptamer-protein interaction combination with a microfluidic platform. As a result, we have successfully established a quantitative analysis of VEGF165 from cell metabolism. Furthermore, based on the principles of hydrodynamic focusing and diffusive mixing, different transient states during kinetics process were monitored and recorded. Thus, the combination of microfluidic technique and G-quadruplex luminescent probe will be potentially applied in the studies of intramolecular interactions and molecule recognition in the future. Copyright © 2015 Elsevier B.V. All rights reserved.

Nanosecond laser photolysis studies of vitamin K 3 in aqueous solution

NASA Astrophysics Data System (ADS)

Chen, J. F.; Ge, X. W.; Chu, G. S.; Zhang, Z. C.; Zhang, M. W.; Yao, S. D.; Lin, N. Y.

1999-06-01

Vitamin K 3 in aqueous solution was investigated by 248 nm laser flash photolysis. Laser-induced transient species were characterized according to kinetic analysis and quenching experiments by Mn 2+ and O 2. In neutral solutions, the intermediates recorded were assigned to excited triplet states and dehydrogenated radicals of vitamin K 3. In comparison with the results of pulse radiolytical experiment, vitamin K 3 not only has strong electron affinity but could also could be photoionized by UV laser light. All this shows that vitamin K 3 acts as an effective electron carrier and electron transfer agent.

Coupling of TRAC-PF1/MOD2, Version 5.4.25, with NESTLE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knepper, P.L.; Hochreiter, L.E.; Ivanov, K.N.

1999-09-01

A three-dimensional (3-D) spatial kinetics capability within a thermal-hydraulics system code provides a more correct description of the core physics during reactor transients that involve significant variations in the neutron flux distribution. Coupled codes provide the ability to forecast safety margins in a best-estimate manner. The behavior of a reactor core and the feedback to the plant dynamics can be accurately simulated. For each time step, coupled codes are capable of resolving system interaction effects on neutronics feedback and are capable of describing local neutronics effects caused by the thermal hydraulics and neutronics coupling. With the improvements in computational technology,more » modeling complex reactor behaviors with coupled thermal hydraulics and spatial kinetics is feasible. Previously, reactor analysis codes were limited to either a detailed thermal-hydraulics model with simplified kinetics or multidimensional neutron kinetics with a simplified thermal-hydraulics model. The authors discuss the coupling of the Transient Reactor Analysis Code (TRAC)-PF1/MOD2, Version 5.4.25, with the NESTLE code.« less

Large-Scale Experiments in Microbially Induced Calcite Precipitation (MICP): Reactive Transport Model Development and Prediction

NASA Astrophysics Data System (ADS)

Nassar, Mohamed K.; Gurung, Deviyani; Bastani, Mehrdad; Ginn, Timothy R.; Shafei, Babak; Gomez, Michael G.; Graddy, Charles M. R.; Nelson, Doug C.; DeJong, Jason T.

2018-01-01

Design of in situ microbially induced calcite precipitation (MICP) strategies relies on a predictive capability. To date much of the mathematical modeling of MICP has focused on small-scale experiments and/or one-dimensional flow in porous media, and successful parameterizations of models in these settings may not pertain to larger scales or to nonuniform, transient flows. Our objective in this article is to report on modeling to test our ability to predict behavior of MICP under controlled conditions in a meter-scale tank experiment with transient nonuniform transport in a natural soil, using independently determined parameters. Flow in the tank was controlled by three wells, via a complex cycle of injection/withdrawals followed by no-flow intervals. Different injection solution recipes were used in sequence for transport characterization, biostimulation, cementation, and groundwater rinse phases of the 17 day experiment. Reaction kinetics were calibrated using separate column experiments designed with a similar sequence of phases. This allowed for a parsimonious modeling approach with zero fitting parameters for the tank experiment. These experiments and data were simulated using PHT3-D, involving transient nonuniform flow, alternating low and high Damköhler reactive transport, and combined equilibrium and kinetically controlled biogeochemical reactions. The assumption that microbes mediating the reaction were exclusively sessile, and with constant activity, in conjunction with the foregoing treatment of the reaction network, provided for efficient and accurate modeling of the entire process leading to nonuniform calcite precipitation. This analysis suggests that under the biostimulation conditions applied here the assumption of steady state sessile biocatalyst suffices to describe the microbially mediated calcite precipitation.

Sensitized photooxidation of phenols by fulvic acid and in natural waters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faust, B.C.; Hoigne, J.

1987-10-01

In addition to singlet oxygen, irradiation of fulvic acid solutions and lake water with UV and visible light (lambda > 315 nm) produces another transient oxidant species. This transient oxidant (probably an organic peroxy radical) is derived from natural dissolved organic material (DOM) and controls DOM-sensitized photooxidations of various alkylphenols. On the basis of kinetic data for the transient oxidant, DOM-sensitized photooxidation half-lives of alkylphenols are estimated to range from 1 day to several months in middle-latitude shallow surface waters.

Reordering transitions during annealing of block copolymer cylinder phases

DOE PAGES

Majewski, Pawel W.; Yager, Kevin G.

2015-10-06

While equilibrium block-copolymer morphologies are dictated by energy-minimization effects, the semi-ordered states observed experimentally often depend on the details of ordering pathways and kinetics. In this study, we explore reordering transitions in thin films of block-copolymer cylinder-forming polystyrene- block-poly(methyl methacrylate). We observe several transient states as films order towards horizontally-aligned cylinders. In particular, there is an early-stage reorganization from randomly-packed cylinders into hexagonally-packed vertically-aligned cylinders; followed by a reorientation transition from vertical to horizontal cylinder states. These transitions are thermally activated. The growth of horizontal grains within an otherwise vertical morphology proceeds anisotropically, resulting in anisotropic grains in the finalmore » horizontal state. The size, shape, and anisotropy of grains are influenced by ordering history; for instance, faster heating rates reduce grain anisotropy. These results help elucidate aspects of pathway-dependent ordering in block-copolymer thin films.« less

Dynamics of Re(2,2'-bipyridine)(CO)3Cl MLCT formation and decay after picosecond pulsed X-ray excitation and femtosecond UV excitation.

PubMed

Zhao, Liyan; Odaka, Hideho; Ono, Hiroshi; Kajimoto, Shinji; Hatanaka, Koji; Hobley, Jonathan; Fukumura, Hiroshi

2005-01-01

The dynamics of Re(2,2'-bipyridine)(CO)3Cl MLCT state formation and decay were determined after femtosecond UV laser excitation and picosecond pulsed X-ray excitation, in an N,N-dimethylformamide (DMF) solution as well as in its solid form. At room temperature, after UV excitation, this MLCT excited state emits both in DMF solution and in the solid form. Transient absorption spectra were measured in solution at various delay times following excitation by a 160 fs, 390 nm laser pulse. There was a prompt absorption increase at around 460 nm occurring within the pump probe convolution (<1 ps), which was assigned to the formation of the 3MLCT state. This transient absorbance was constant over 100 ps. In contrast to the solution state, in the solid state, the emission maximum slightly red-shifts with increasing time after laser excitation. In both solid and solution the emission rises within the system response time. The solid sample exhibited a 1.4 ns emission decay that was not observed for the solution sample. The emission rise from a solid sample after 20 ps pulsed X-ray excitation was significantly slower than the system's time resolution. It is proposed that kinetically energetic electrons are ejected following X-ray induced ionisation, creating ionised tracks in which energetic cations and electrons take time to recombine yielding delayed 3MLCT states that emit.

Equilibrium and kinetic models for colloid release under transient solution chemistry conditions.

PubMed

Bradford, Scott A; Torkzaban, Saeed; Leij, Feike; Simunek, Jiri

2015-10-01

We present continuum models to describe colloid release in the subsurface during transient physicochemical conditions. Our modeling approach relates the amount of colloid release to changes in the fraction of the solid surface area that contributes to retention. Equilibrium, kinetic, equilibrium and kinetic, and two-site kinetic models were developed to describe various rates of colloid release. These models were subsequently applied to experimental colloid release datasets to investigate the influence of variations in ionic strength (IS), pH, cation exchange, colloid size, and water velocity on release. Various combinations of equilibrium and/or kinetic release models were needed to describe the experimental data depending on the transient conditions and colloid type. Release of Escherichia coli D21g was promoted by a decrease in solution IS and an increase in pH, similar to expected trends for a reduction in the secondary minimum and nanoscale chemical heterogeneity. The retention and release of 20nm carboxyl modified latex nanoparticles (NPs) were demonstrated to be more sensitive to the presence of Ca(2+) than D21g. Specifically, retention of NPs was greater than D21g in the presence of 2mM CaCl2 solution, and release of NPs only occurred after exchange of Ca(2+) by Na(+) and then a reduction in the solution IS. These findings highlight the limitations of conventional interaction energy calculations to describe colloid retention and release, and point to the need to consider other interactions (e.g., Born, steric, and/or hydration forces) and/or nanoscale heterogeneity. Temporal changes in the water velocity did not have a large influence on the release of D21g for the examined conditions. This insensitivity was likely due to factors that reduce the applied hydrodynamic torque and/or increase the resisting adhesive torque; e.g., macroscopic roughness and grain-grain contacts. Our analysis and models improve our understanding and ability to describe the amounts and rates of colloid release and indicate that episodic colloid transport is expected under transient physicochemical conditions. Published by Elsevier B.V.

Transient Kinetics and Quantum Yield Studies of Nanocrystalline α-Phenyl-Substituted Ketones: Sorting Out Reactions from Singlet and Triplet Excited States.

PubMed

Park, Jin H; Chung, Tim S; Hipwell, Vince M; Rivera, Edris A; Garcia-Garibay, Miguel A

2018-06-11

Recent work has shown that diarylmethyl radicals generated by pulsed laser excitation in nanocrystalline (NC) suspensions of tetraarylacetones constitute a valuable probe for the detailed mechanistic analysis of the solid-state photodecarbonylation reaction. Using a combination of reaction quantum yields and laser flash photolysis in nanocrystalline suspensions of ketones with different substituents on one of the α-carbons we are able to suggest with confidence that a significant fraction of the initial α-cleavage reaction takes place from the ketone singlet excited state, that the originally formed diarylmethyl-acyl radical pair loses CO in the crystal with time constants in the sub-nanosecond regime, and that the secondary bis(diarylmethyl) triplet radical pair has a lifetime limited by the rate of intersystem crossing of ca. 70 ns.

Quantitative analysis of the Ca2+ -dependent regulation of delayed rectifier K+ current IKs in rabbit ventricular myocytes.

PubMed

Bartos, Daniel C; Morotti, Stefano; Ginsburg, Kenneth S; Grandi, Eleonora; Bers, Donald M

2017-04-01

[Ca 2+ ] i enhanced rabbit ventricular slowly activating delayed rectifier K + current (I Ks ) by negatively shifting the voltage dependence of activation and slowing deactivation, similar to perfusion of isoproterenol. Rabbit ventricular rapidly activating delayed rectifier K + current (I Kr ) amplitude and voltage dependence were unaffected by high [Ca 2+ ] i . When measuring or simulating I Ks during an action potential, I Ks was not different during a physiological Ca 2+ transient or when [Ca 2+ ] i was buffered to 500 nm. The slowly activating delayed rectifier K + current (I Ks ) contributes to repolarization of the cardiac action potential (AP). Intracellular Ca 2+ ([Ca 2+ ] i ) and β-adrenergic receptor (β-AR) stimulation modulate I Ks amplitude and kinetics, but details of these important I Ks regulators and their interaction are limited. We assessed the [Ca 2+ ] i dependence of I Ks in steady-state conditions and with dynamically changing membrane potential and [Ca 2+ ] i during an AP. I Ks was recorded from freshly isolated rabbit ventricular myocytes using whole-cell patch clamp. With intracellular pipette solutions that controlled free [Ca 2+ ] i , we found that raising [Ca 2+ ] i from 100 to 600 nm produced similar increases in I Ks as did β-AR activation, and the effects appeared additive. Both β-AR activation and high [Ca 2+ ] i increased maximally activated tail I Ks , negatively shifted the voltage dependence of activation, and slowed deactivation kinetics. These data informed changes in our well-established mathematical model of the rabbit myocyte. In both AP-clamp experiments and simulations, I Ks recorded during a normal physiological Ca 2+ transient was similar to I Ks measured with [Ca 2+ ] i clamped at 500-600 nm. Thus, our study provides novel quantitative data as to how physiological [Ca 2+ ] i regulates I Ks amplitude and kinetics during the normal rabbit AP. Our results suggest that micromolar [Ca 2+ ] i , in the submembrane or junctional cleft space, is not required to maximize [Ca 2+ ] i -dependent I Ks activation during normal Ca 2+ transients. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Quantitative analysis of the Ca2+‐dependent regulation of delayed rectifier K+ current I Ks in rabbit ventricular myocytes

PubMed Central

Bartos, Daniel C.; Morotti, Stefano; Ginsburg, Kenneth S.; Grandi, Eleonora

2017-01-01

Key points [Ca2+]i enhanced rabbit ventricular slowly activating delayed rectifier K+ current (I Ks) by negatively shifting the voltage dependence of activation and slowing deactivation, similar to perfusion of isoproterenol.Rabbit ventricular rapidly activating delayed rectifier K+ current (I Kr) amplitude and voltage dependence were unaffected by high [Ca2+]i.When measuring or simulating I Ks during an action potential, I Ks was not different during a physiological Ca2+ transient or when [Ca2+]i was buffered to 500 nm. Abstract The slowly activating delayed rectifier K+ current (I Ks) contributes to repolarization of the cardiac action potential (AP). Intracellular Ca2+ ([Ca2+]i) and β‐adrenergic receptor (β‐AR) stimulation modulate I Ks amplitude and kinetics, but details of these important I Ks regulators and their interaction are limited. We assessed the [Ca2+]i dependence of I Ks in steady‐state conditions and with dynamically changing membrane potential and [Ca2+]i during an AP. I Ks was recorded from freshly isolated rabbit ventricular myocytes using whole‐cell patch clamp. With intracellular pipette solutions that controlled free [Ca2+]i, we found that raising [Ca2+]i from 100 to 600 nm produced similar increases in I Ks as did β‐AR activation, and the effects appeared additive. Both β‐AR activation and high [Ca2+]i increased maximally activated tail I Ks, negatively shifted the voltage dependence of activation, and slowed deactivation kinetics. These data informed changes in our well‐established mathematical model of the rabbit myocyte. In both AP‐clamp experiments and simulations, I Ks recorded during a normal physiological Ca2+ transient was similar to I Ks measured with [Ca2+]i clamped at 500–600 nm. Thus, our study provides novel quantitative data as to how physiological [Ca2+]i regulates I Ks amplitude and kinetics during the normal rabbit AP. Our results suggest that micromolar [Ca2+]i, in the submembrane or junctional cleft space, is not required to maximize [Ca2+]i‐dependent I Ks activation during normal Ca2+ transients. PMID:28008618

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.

PubMed

Jamsen, Joonas A; Beard, William A; Pedersen, Lars C; Shock, David D; Moon, Andrea F; Krahn, Juno M; Bebenek, Katarzyna; Kunkel, Thomas A; Wilson, Samuel H

2017-08-15

DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PP i . The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol μ is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) μ functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol µ during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.

A coupled theory for chemically active and deformable solids with mass diffusion and heat conduction

NASA Astrophysics Data System (ADS)

Zhang, Xiaolong; Zhong, Zheng

2017-10-01

To analyse the frequently encountered thermo-chemo-mechanical problems in chemically active material applications, we develop a thermodynamically-consistent continuum theory of coupled deformation, mass diffusion, heat conduction and chemical reaction. Basic balance equations of force, mass and energy are presented at first, and then fully coupled constitutive laws interpreting multi-field interactions and evolving equations governing irreversible fluxes are constructed according to the energy dissipation inequality and the chemical kinetics. To consider the essential distinction between mass diffusion and chemical reactions in affecting free energy and dissipations of a highly coupled system, we regard both the concentrations of diffusive species and the extent of reaction as independent state variables. This new formulation then distinguishes between the energy contribution from the diffusive species entering the solid and that from the subsequent chemical reactions occurring among these species and the host solid, which not only interact with stresses or strains in different manners and on different time scales, but also induce different variations of solid microstructures and material properties. Taking advantage of this new description, we further establish a specialized isothermal model to predict precisely the transient chemo-mechanical response of a swelling solid with a proposed volumetric constraint that accounts for material incompressibility. Coupled kinetics is incorporated to capture the volumetric swelling of the solid caused by imbibition of external species and the simultaneous dilation arised from chemical reactions between the diffusing species and the solid. The model is then exemplified with two numerical examples of transient swelling accompanied by chemical reaction. Various ratios of characteristic times of diffusion and chemical reaction are taken into account to shed light on the dependency on kinetic time scales of evolution patterns for a diffusion-reaction controlled deformable solid.

Nucleation and growth in cluster dynamics: A quantitative test of the classical kinetic approach

NASA Astrophysics Data System (ADS)

Gránásy, László; James, Peter F.

2000-12-01

Nucleation and size dependent growth of nanometer sized crystalline particles in glassy media have been studied by numerically solving the Turnbull-Fisher master equations that describe the time evolution of cluster population. Time dependencies of the formation rate and number density are determined for large clusters (built of up to 2×105 formula units, containing 1.8×106 atoms). We demonstrate that the formation rate and number density of such clusters are well approximated by Shneidman's asymptotically exact analytical solution. A quantitative test of the kinetic Turnbull-Fisher model has been performed: Evaluating the kinetic coefficients and interfacial parameters from the transient time and steady-state nucleation rates measured on six stoichiometric oxide glass compositions (lithium-disilicate, barium-disilicate, lithium-diborate, wollastonite, 1:2:3 and 2:1:3 soda-lime-silica glass compositions), we calculated the macroscopic growth rates and compared with experiments. For wollastonite, lithium-diborate and the 1:2:3 soda-lime-silica glass, differences of 2 to 4 orders of magnitude have been observed between theory and experiment. This inadequacy of the microscopic kinetic parameters in describing macroscopic growth cannot be explained by either the curvature effect on the interfacial free energy or the self-consistency correction for the cluster free energy. The origin of the discrepancy is discussed.

Single-Molecule Counting of Point Mutations by Transient DNA Binding

NASA Astrophysics Data System (ADS)

Su, Xin; Li, Lidan; Wang, Shanshan; Hao, Dandan; Wang, Lei; Yu, Changyuan

2017-03-01

High-confidence detection of point mutations is important for disease diagnosis and clinical practice. Hybridization probes are extensively used, but are hindered by their poor single-nucleotide selectivity. Shortening the length of DNA hybridization probes weakens the stability of the probe-target duplex, leading to transient binding between complementary sequences. The kinetics of probe-target binding events are highly dependent on the number of complementary base pairs. Here, we present a single-molecule assay for point mutation detection based on transient DNA binding and use of total internal reflection fluorescence microscopy. Statistical analysis of single-molecule kinetics enabled us to effectively discriminate between wild type DNA sequences and single-nucleotide variants at the single-molecule level. A higher single-nucleotide discrimination is achieved than in our previous work by optimizing the assay conditions, which is guided by statistical modeling of kinetics with a gamma distribution. The KRAS c.34 A mutation can be clearly differentiated from the wild type sequence (KRAS c.34 G) at a relative abundance as low as 0.01% mutant to WT. To demonstrate the feasibility of this method for analysis of clinically relevant biological samples, we used this technology to detect mutations in single-stranded DNA generated from asymmetric RT-PCR of mRNA from two cancer cell lines.

Repassivation Investigations on Aluminium: Physical Chemistry of the Passive State

NASA Astrophysics Data System (ADS)

Nagy, Tristan Oliver; Weimerskirch, Morris Jhängi Joseph; Pacher, Ulrich; Kautek, Wolfgang

2016-09-01

We show the temporal change in repassivation mechanism as a time-dependent linear combination of a high-field model of oxide growth (HFM) and the point defect model (PDM). The observed switch in transient repassivation current-decrease under potentiostatic control occurs independently of the active electrode size and effective repassivation time for all applied overpotentials. For that, in situ depassivation of plasma electrolytically oxidized (PEO) coatings on aluminium was performed with nanosecond laser pulses at 266 nm and the repassivation current transients were recorded as a function of pulse number. A mathematical model combines the well established theories of oxide-film formation and growth kinetics, giving insight in the non linear transient behaviour of micro-defect passivation. According to our findings, the repassivation process can be described as a charge consumption via two concurrent channels. While the major current-decay at the very beginning of the fast healing oxide follows a point-defect type exponential damping, the HFM mechanism supersedes gradually, the longer the repassivation evolves. Furthermore, the material seems to reminisce former laser treatments via defects built-in during depassivation, leading to a higher charge contribution of the PDM mechanism at higher pulse numbers.

Temperature dependence of the hydrated electron's excited-state relaxation. II. Elucidating the relaxation mechanism through ultrafast transient absorption and stimulated emission spectroscopy

NASA Astrophysics Data System (ADS)

Farr, Erik P.; Zho, Chen-Chen; Challa, Jagannadha R.; Schwartz, Benjamin J.

2017-08-01

The structure of the hydrated electron, particularly whether it exists primarily within a cavity or encompasses interior water molecules, has been the subject of much recent debate. In Paper I [C.-C. Zho et al., J. Chem. Phys. 147, 074503 (2017)], we found that mixed quantum/classical simulations with cavity and non-cavity pseudopotentials gave different predictions for the temperature dependence of the rate of the photoexcited hydrated electron's relaxation back to the ground state. In this paper, we measure the ultrafast transient absorption spectroscopy of the photoexcited hydrated electron as a function of temperature to confront the predictions of our simulations. The ultrafast spectroscopy clearly shows faster relaxation dynamics at higher temperatures. In particular, the transient absorption data show a clear excess bleach beyond that of the equilibrium hydrated electron's ground-state absorption that can only be explained by stimulated emission. This stimulated emission component, which is consistent with the experimentally known fluorescence spectrum of the hydrated electron, decreases in both amplitude and lifetime as the temperature is increased. We use a kinetic model to globally fit the temperature-dependent transient absorption data at multiple temperatures ranging from 0 to 45 °C. We find the room-temperature lifetime of the excited-state hydrated electron to be 137 ±40 fs, in close agreement with recent time-resolved photoelectron spectroscopy (TRPES) experiments and in strong support of the "non-adiabatic" picture of the hydrated electron's excited-state relaxation. Moreover, we find that the excited-state lifetime is strongly temperature dependent, changing by slightly more than a factor of two over the 45 °C temperature range explored. This temperature dependence of the lifetime, along with a faster rate of ground-state cooling with increasing bulk temperature, should be directly observable by future TRPES experiments. Our data also suggest that the red side of the hydrated electron's fluorescence spectrum should significantly decrease with increasing temperature. Overall, our results are not consistent with the nearly complete lack of temperature dependence predicted by traditional cavity models of the hydrated electron but instead agree qualitatively and nearly quantitatively with the temperature-dependent structural changes predicted by the non-cavity hydrated electron model.

Surface acceptor states in MBE-grown CdTe layers

NASA Astrophysics Data System (ADS)

Wichrowska, Karolina; Wosinski, Tadeusz; Tkaczyk, Zbigniew; Kolkovsky, Valery; Karczewski, Grzegorz

2018-04-01

A deep-level hole trap associated with surface defect states has been revealed with deep-level transient spectroscopy investigations of metal-semiconductor junctions fabricated on nitrogen doped p-type CdTe layers grown by the molecular-beam epitaxy technique. The trap displayed the hole-emission activation energy of 0.33 eV and the logarithmic capture kinetics indicating its relation to extended defect states at the metal-semiconductor interface. Strong electric-field-induced enhancement of the thermal emission rate of holes from the trap has been attributed to the phonon-assisted tunneling effect from defect states involving very large lattice relaxation around the defect and metastability of its occupied state. Passivation with ammonium sulfide of the CdTe surface, prior to metallization, results in a significant decrease in the trap density. It also results in a distinct reduction in the width of the surface-acceptor-state-induced hysteresis loops in the capacitance vs. voltage characteristics of the metal-semiconductor junctions.

Pre-Steady-State Kinetics of Ba-Ca Exchange Reveals a Second Electrogenic Step Involved in Ca2+ Translocation by the Na-Ca Exchanger

PubMed Central

Haase, Andreas; Hartung, Klaus

2009-01-01

Kinetic properties of the Na-Ca exchanger (guinea pig NCX1) expressed in Xenopus oocytes were investigated with excised membrane patches in the inside-out configuration and photolytic Ca2+ concentration jumps with either 5 mM extracellular Sr2+ or Ba2+. After a Ca2+ concentration jump on the cytoplasmic side, the exchanger performed Sr-Ca or Ba-Ca exchange. In the Sr-Ca mode, currents are transient and decay in a monoexponential manner similar to that of currents in the Ca-Ca exchange mode described before. Currents recorded in the Ba-Ca mode are also transient, but the decay is biphasic. In the Sr-Ca mode the amount of charge translocated increases at negative potentials in agreement with experiments performed in the Ca-Ca mode. In the Ba-Ca mode the total amount of charge translocated after a Ca2+ concentration jump is ∼4 to 5 times that in Ca-Ca or Sr-Ca mode. In the Ba-Ca mode the voltage dependence of charge translocation depends on the Ca2+ concentration on the cytosolic side before the Ca2+ concentration jump. At low initial Ca2+ levels (∼0.5 μM), charge translocation is voltage independent. At a higher initial concentration (1 μM Ca2+), the amount of charge translocated increases at positive potentials. Biphasic relaxation of the current was also observed in the Ca-Ca mode if the external Ca2+ concentration was reduced to ≤0.5 mM. The results reported here and in previous publications can be described by using a 6-state model with two voltage-dependent conformational transitions. PMID:19486679

Transient-Absorption Spectroscopy of Cis-Trans Isomerization of N,N-dimethyl-4,4'-Azodianiline with 3D-Printed Temperature-Controlled Sample Holder

ERIC Educational Resources Information Center

Kosenkov, Dmytro; Shaw, James; Zuczek, Jennifer; Kholod, Yana

2016-01-01

The laboratory unit demonstrates a project based approach to teaching physical chemistry laboratory where upper-division undergraduates carry out a transient-absorption experiment investigating the kinetics of cis-trans isomerization of N,N-dimethyl-4,4'-azodianiline. Students participate in modification of a standard flash-photolysis spectrometer…

Light-water-reactor safety research program. Quarterly progress report, July--September 1975

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1975-01-01

Progress is summarized in the following research and development areas: (1) loss-of-coolant accident research; heat transfer and fluid dynamics; (2) transient fuel response and fission-product release; and (3) mechanical properties of Zircaloy containing oxygen. Also included is an appendix on Kinetics of Fission Gas and Volatile Fission-product Behavior under Transient Conditions in LWR Fuel.

Superluminous Transients at AGN Centers from Interaction between Black Hole Disk Winds and Broad-line Region Clouds

NASA Astrophysics Data System (ADS)

Moriya, Takashi J.; Tanaka, Masaomi; Morokuma, Tomoki; Ohsuga, Ken

2017-07-01

We propose that superluminous transients that appear at central regions of active galactic nuclei (AGNs) such as CSS100217:102913+404220 (CSS100217) and PS16dtm, which reach near- or super-Eddington luminosities of the central black holes, are powered by the interaction between accretion-disk winds and clouds in broad-line regions (BLRs) surrounding them. If the disk luminosity temporarily increases by, e.g., limit-cycle oscillations, leading to a powerful radiatively driven wind, strong shock waves propagate in the BLR. Because the dense clouds in the AGN BLRs typically have similar densities to those found in SNe IIn, strong radiative shocks emerge and efficiently convert the ejecta kinetic energy to radiation. As a result, transients similar to SNe IIn can be observed at AGN central regions. Since a typical black hole disk-wind velocity is ≃0.1c, where c is the speed of light, the ejecta kinetic energy is expected to be ≃1052 erg when ≃1 M ⊙ is ejected. This kinetic energy is transformed to radiation energy in a timescale for the wind to sweep up a similar mass to itself in the BLR, which is a few hundred days. Therefore, both luminosities (˜1044 erg s-1) and timescales (˜100 days) of the superluminous transients from AGN central regions match those expected in our interaction model. If CSS100217 and PS16dtm are related to the AGN activities triggered by limit-cycle oscillations, they become bright again in coming years or decades.

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

PubMed Central

Wang, Yong; Papaleo, Elena; Lindorff-Larsen, Kresten

2016-01-01

Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally. DOI: http://dx.doi.org/10.7554/eLife.17505.001 PMID:27552057

Analysis of a general circulation model. II - Distribution of kinetic energy in the South Atlantic and Kuroshio/Oyashio systems

NASA Technical Reports Server (NTRS)

Garraffo, Zulema; Garzoli, Silvia L.; Haxby, William; Olson, Donald

1992-01-01

It was found (Garzoli et al., 1992) that the general circulation model of Semtner and Chervin (1992) provides accurate descriptions of the Brazil-Malvinas and the Kuroshio/Oyashio confluence systems, except for the fact that the model prediction shows less variability than that present in observations. This paper investigates the problem of model variability by analyzing the mean and the eddy kinetic energy from the model and comparing the values with the Geosat altimeter observations for the South Atlantic Ocean and for the Kuroshio system. It is found that, while the model shows transient eddy activity in the areas that overlap the Geosat observations, the energy level of the model transient motions is considerably smaller following an arch along the bottom topography. The same was found from the comparisons made with values obtained from FGGE and surface drifters. It is suggested that the model is poorly resolving instabilities in the confluence front, and is not resolving other transients appearing in regions of marked topography.

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule

PubMed Central

Rosen, Laura E.; Connell, Katelyn B.; Marqusee, Susan

2014-01-01

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates. PMID:25258414

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

PubMed

Rosen, Laura E; Connell, Katelyn B; Marqusee, Susan

2014-10-14

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.

Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.

PubMed

Bernstein, Rachel; Schmidt, Kierstin L; Harbury, Pehr B; Marqusee, Susan

2011-06-28

Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.

Structural and kinetic mapping of side-chain exposure onto the protein energy landscape

PubMed Central

Bernstein, Rachel; Schmidt, Kierstin L.; Harbury, Pehr B.; Marqusee, Susan

2011-01-01

Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated. PMID:21670244

Trapping Dynamics in Photosystem I-Light Harvesting Complex I of Higher Plants Is Governed by the Competition Between Excited State Diffusion from Low Energy States and Photochemical Charge Separation.

PubMed

Molotokaite, Egle; Remelli, William; Casazza, Anna Paola; Zucchelli, Giuseppe; Polli, Dario; Cerullo, Giulio; Santabarbara, Stefano

2017-10-26

The dynamics of excited state equilibration and primary photochemical trapping have been investigated in the photosystem I-light harvesting complex I isolated from spinach, by the complementary time-resolved fluorescence and transient absorption approaches. The combined analysis of the experimental data indicates that the excited state decay is described by lifetimes in the ranges of 12-16 ps, 32-36 ps, and 64-77 ps, for both detection methods, whereas faster components, having lifetimes of 550-780 fs and 4.2-5.2 ps, are resolved only by transient absorption. A unified model capable of describing both the fluorescence and the absorption dynamics has been developed. From this model it appears that the majority of excited state equilibration between the bulk of the antenna pigments and the reaction center occurs in less than 2 ps, that the primary charge separated state is populated in ∼4 ps, and that the charge stabilization by electron transfer is completed in ∼70 ps. Energy equilibration dynamics associated with the long wavelength absorbing/emitting forms harbored by the PSI external antenna are also characterized by a time mean lifetime of ∼75 ps, thus overlapping with radical pair charge stabilization reactions. Even in the presence of a kinetic bottleneck for energy equilibration, the excited state dynamics are shown to be principally trap-limited. However, direct excitation of the low energy chlorophyll forms is predicted to lengthen significantly (∼2-folds) the average trapping time.

Transient oscillation of shape and membrane conductivity changes by field pulse-induced electroporation in nano-sized phospholipid vesicles.

PubMed

Dimitrov, Vasil; Kakorin, Sergej; Neumann, Eberhard

2013-05-07

The results of electrooptical and conductometrical measurements on unilamellar lipid vesicles (of mean radius a = 90 nm), filled with 0.2 M NaCl solution, suspended in 0.33 M sucrose solution of 0.2 mM NaCl, and exposed to a stepwise decaying electric field (time constant τE = 154 μs) in the range 10 ≤ E0 (kV cm(-1)) ≤ 90, are analyzed in terms of cyclic changes in vesicle shape and vesicle membrane conductivity. The two peaks in the dichroitic turbidity relaxations reflect two cycles of rapid membrane electroporation and slower resealing of long-lived electropores. The field-induced changes reflect structural transitions between closed (C) and porated (P) membrane states, qualified by pores of type P1 and of type P2, respectively. The transient change in the membrane conductivity and the transient shape oscillation are based on changes in the pore density of the (larger) P2-pores along a hysteresis cycle. The P2-pore formation leads to transient net ion flows across the P2-pores and to transient changes in the membrane field. The kinetic data are numerically processed in terms of coupled structural relaxation modes. Using the torus-hole pore model, the mean inner pore radii are estimated to be r1 = 0.38 (±0.05) nm and r2 = 1.7 (±0.1) nm, respectively. The observation of a transient oscillation of membrane electroporation and of shape changes in a longer lasting external field pulse is suggestive of potential resonance enhancement, for instance, of electro-uptake by, and of electro-release of biogenic molecules from, biological cells in trains of long-lasting low-intensity voltage pulses.

Electronic and atomic kinetics in solids irradiated with free-electron lasers or swift-heavy ions

NASA Astrophysics Data System (ADS)

Medvedev, N.; Volkov, A. E.; Ziaja, B.

2015-12-01

In this brief review we discuss the transient processes in solids under irradiation with femtosecond X-ray free-electron-laser (FEL) pulses and swift-heavy ions (SHI). Both kinds of irradiation produce highly excited electrons in a target on extremely short timescales. Transfer of the excess electronic energy into the lattice may lead to observable target modifications such as phase transitions and damage formation. Transient kinetics of material excitation and relaxation under FEL or SHI irradiation are comparatively discussed. The same origin for the electronic and atomic relaxation in both cases is demonstrated. Differences in these kinetics introduced by the geometrical effects (μm-size of a laser spot vs nm-size of an ion track) and initial irradiation (photoabsorption vs an ion impact) are analyzed. The basic mechanisms of electron transport and electron-lattice coupling are addressed. Appropriate models and their limitations are presented. Possibilities of thermal and nonthermal melting of materials under FEL and SHI irradiation are discussed.

Charge Carriers Modulate the Bonding of Semiconductor Nanoparticle Dopants As Revealed by Time-Resolved X-ray Spectroscopy

DOE PAGES

Hassan, Asra; Zhang, Xiaoyi; Liu, Xiaohan; ...

2017-08-28

Understanding the electronic structure of doped semiconductors is essential to realize advancements in electronics and in the rational design of nanoscale devices. Here, we report the results of time-resolved X-ray absorption studies on copper-doped cadmium sulfide nanoparticles that provide an explicit description of the electronic dynamics of the dopants. The interaction of a dopant ion and an excess charge carrier is unambiguously observed via monitoring the oxidation state. The experimental data combined with DFT calculations demonstrate that dopant bonding to the host matrix is modulated by its interaction with charge carriers. Additionally, the transient photoluminescence and the kinetics of dopantmore » oxidation reveal the presence of two types of surface-bound ions that create mid-gap states.« less

Charge Carriers Modulate the Bonding of Semiconductor Nanoparticle Dopants As Revealed by Time-Resolved X-ray Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hassan, Asra; Zhang, Xiaoyi; Liu, Xiaohan

Understanding the electronic structure of doped semiconductors is essential to realize advancements in electronics and in the rational design of nanoscale devices. Here, we report the results of time-resolved X-ray absorption studies on copper-doped cadmium sulfide nanoparticles that provide an explicit description of the electronic dynamics of the dopants. The interaction of a dopant ion and an excess charge carrier is unambiguously observed via monitoring the oxidation state. The experimental data combined with DFT calculations demonstrate that dopant bonding to the host matrix is modulated by its interaction with charge carriers. Additionally, the transient photoluminescence and the kinetics of dopantmore » oxidation reveal the presence of two types of surface-bound ions that create mid-gap states.« less

Kinetic and functional analysis of transient, persistent and resurgent sodium currents in rat cerebellar granule cells in situ: an electrophysiological and modelling study

PubMed Central

Magistretti, Jacopo; Castelli, Loretta; Forti, Lia; D'Angelo, Egidio

2006-01-01

Cerebellar neurones show complex and differentiated mechanisms of action potential generation that have been proposed to depend on peculiar properties of their voltage-dependent Na+ currents. In this study we analysed voltage-dependent Na+ currents of rat cerebellar granule cells (GCs) by performing whole-cell, patch-clamp experiments in acute rat cerebellar slices. A transient Na+ current (INaT) was always present and had the properties of a typical fast-activating/inactivating Na+ current. In addition to INaT, robust persistent (INaP) and resurgent (INaR) Na+ currents were observed. INaP peaked at ∼−40 mV, showed half-maximal activation at ∼−55 mV, and its maximal amplitude was about 1.5% of that of INaT. INaR was elicited by repolarizing pulses applied following step depolarizations able to activate/inactivate INaT, and showed voltage- and time-dependent activation and voltage-dependent decay kinetics. The conductance underlying INaR showed a bell-shaped voltage dependence, with peak at −35 mV. A significant correlation was found between GC INaR and INaT peak amplitudes; however, GCs expressing INaT of similar size showed marked variability in terms of INaR amplitude, and in a fraction of cells INaR was undetectable. INaT, INaP and INaR could be accounted for by a 13-state kinetic scheme comprising closed, open, inactivated and blocked states. Current-clamp experiments carried out to identify possible functional correlates of INaP and/or INaR revealed that in GCs single action potentials were followed by depolarizing afterpotentials (DAPs). In a majority of cells, DAPs showed properties consistent with INaR playing a role in their generation. Computer modelling showed that INaR promotes DAP generation and enhances high-frequency firing, whereas INaP boosts near-threshold firing activity. Our findings suggest that special properties of voltage-dependent Na+ currents provides GCs with mechanisms suitable for shaping activity patterns, with potentially important consequences for cerebellar information transfer and computation. PMID:16527854

Charge Carrier Dynamics of Quantum Confined Semiconductor Nanoparticles Analyzed via Transient Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Thibert, Arthur Joseph, III

Semiconductor nanoparticles are tiny crystalline structures (typically range from 1 - 100 nm) whose shape in many cases can be dictated through tailored chemical synthesis with atomic scale precision. The small size of these nanoparticles often results in quantum confinement (spatial confinement of wave functions), which imparts the ability to manipulate band-gap energies thus allowing them to be optimally engineered for different applications (i.e., photovoltaics, photocatalysis, imaging). However, charge carriers excited within these nanoparticles are often involved in many different processes: trapping, trap migration, Auger recombination, non-radiative relaxation, radiative relaxation, oxidation / reduction, or multiple exciton generation. Broadband ultrafast transient absorption laser spectroscopy is used to spectrally resolve the fate of excited charge carriers in both wavelength and time, providing insight as to what synthetic developments or operating conditions will be necessary to optimize their efficiency for certain applications. This thesis outlines the effort of resolving the dynamics of excited charge carriers for several Cd and Si based nanoparticle systems using this experimental technique. The thesis is organized into five chapters and two appendices as indicated below. Chapter 1 provides a brief introduction to the photophysics of semiconductor nanoparticles. It begins by defining what nanoparticles, semiconductors, charge carriers, and quantum confinement are. From there it details how the study of charge carrier dynamics within nanoparticles can lead to increased efficiency in applications such as photocatalysis. Finally, the experimental methodology associated with ultrafast transient absorption spectroscopy is introduced and its power in mapping charge carrier dynamics is established. Chapter 2 (JPCC, 19647, 2011) introduces the first of the studied samples: water-solubilized 2D CdSe nanoribbons (NRs), which were synthesized in the Osterloh laboratory (UCD). The measured signals were decomposed into the constituent dynamics of three transient populations: hot tightly bound excitons, relaxed tightly bound excitons, and separated trapped carriers (holes and electrons). The influenes of three external factors affecting the observed dynamics were explored: (1) excitation wavelength, (2) excitation fluence, and (3) presence of the hole scavenger HS -. Both higher-energy excitation photons and higher-intensity excitation induce slower relaxation of charge carriers to the band edge due to the need to dissipate excess excitation energy. Nonlinear decay kinetics of the relaxed exciton population is observed and demonstrated to arise from bimolecular trapping of excitons with low-density trap sites located at CdSe NR surface sites instead of the commonly resolved multiparticle Auger recombination mechanism. This is supported by the observed linear excitation-fluence dependence of the trapped-carrier population that is n umerically simulated and found to deviate from the excitation fluence dependence expected of Auger recombination kinetics. Introducing hole scavenging HS- has a negligible effect on the exciton kinetics, including migration and dissociation, and instead passivates surface trap states to induce the rapid elimination of holes after exciton dissociation. This increases the lifetime of the reactive electron population and increases measured photocatalytic H2 generation activity. A broad (200 nm) and persistent (20 ps) stimulated emission observed in the tightly bound excitons suggests their potential use as broadband microlasers. In chapter 3 (JPCL, 2688, 2011), the photocatalytic H2O splitting activities of CdSe and CdSe/CdS core/shell quantum dots, which were also synthesized in the Osterloh laboratory (UCD) are contrasted. CdSe/CdS core/shell quantum dots constructed from 4.0 nm CdSe quantum dots are shown to be strongly active for visible-light-driven photocatalytic H2 evolution in 0.1M Na 2S/Na2SO3 solution with a turnover number of 9.94 after 5 h at 103.9 μmol/h. CdSe quantum dots themselves are only marginally active in 0.1 M Na2S/Na2SO3 solution with a turnover number of 1.10 after 5 h at 11.53 μmol/h, while CdSe quantum dots in pure H2O are found to be completely inactive. Broad-band transient absorption spectroscopy is used to elucidate the mechanisms that facilitate the enhancement in the CdSe core/shell quantum dots, which is attributed to passivation of surface-deep trap states with energies lying below the reduction potential necessary for H2O reduction. Thus, it is shown that surface trapping dynamics and energetics can be manipulated to dictate the photocatalytic activities of novel CdSe quantum dot based photocatalytic materials. Chapter 4 builds upon this work examining the differences in dynamics that occur upon passivation of water soluble CdZnS alloy cores with ZnS shells, which were produced in the Snee laboratory (UI Chicago), via 400 nm pump broadband probe ultrafast transient absorption spectroscopy, and global analysis modeling. We also examine the perturbation invoked on charge carrier dynamics caused by growing Pd nanoparticles on the CdZnS/ZnS shell surface in-situ and note the cyclical charge carrier transfer that takes place. Both the CdZnS core and CdZnS/ZnS core/shell quantum dots exhibit unusually long lived excited states (much > 8 ns) while the CdZnS/ZnS.Pd tandem core/shell quantum dots recover much quicker (~3 ns). Additionally, ultrafast excitation fluence dependencies are used to characterize Auger recombination and the presence of two different trap state populations observable in the visible spectrum. In chapter 5 (JACS, 20664, 2011), we switch from examining direct band-gap chalcogenide based quantum dots to Si quantum dots synthesized in the Kauzlarich laboratory (UCD), which exhibit an indirect band-gap. Here a microwave-assisted reaction to produce hydrogen-terminated silicon quantum dots is discussed. The Si quantum dots were passivated for water solubility via two different methods: hydrosilylation produced 3-aminopropenyl-terminated Si quantum dots, and a modified Stöber process produced silica-encapsulated Si quantum dots. Both methods produce water-soluble quantum dots with maximum emission at 414 nm, and after purification, the quantum dots exhibit intrinsic fluorescence quantum yield efficiencies of 15 and 23%, respectively. Even though the quantum dots have different surfaces, they exhibit nearly identical absorption and fluorescence spectra. Femtosecond transient absorption spectroscopy was used for temporal resolution of the photoexcited carrier dynamics between the quantum dots and ligand. The transient dynamics of the 3-aminopropenyl-terminated Si quantum dots is interpreted as a formation and decay of a charge-transfer excited state between the delocalized π electrons of the carbon linker and the Si core excitons. This charge transfer state is stable for ~4 ns before reverting back to a more stable, long-living species. The silica-encapsulated Si QDs show a simpler spectrum without charge transfer dynamics. Appendix I (Chem. Mat., 1220, 2010), addresses the long-time (μs) transient kinetics associated with TiO2 and layered titanates (TBA2 2Ti4O9), which were synthesized in the Osterloh laboratory (UCD). Transient absorption data reveal that photogenerated electrons become trapped in mid band-gap states, from which they decay exponentially with a time-constant of 43.67 + 0.28 ms in titanates, which is much slower than the 68 + 1 ns observed for TiO2 nanocrystals. The slower kinetics observed for the TBA 2Ti4O9 nanosheets originates either from the presence of deeper trap sites on the sheets vs. the nanoparticles, more trap sites, or from more effective electron-hole separation because of the micrometer dimensions of the 2D lattice. Appendix II, depicts the visible solar spectrum at sea level detailing the percentage of photons and energy that exist within certain wavelength ranges.

N-terminal splicing extensions of the human MYO1C gene fine-tune the kinetics of the three full-length myosin IC isoforms.

PubMed

Zattelman, Lilach; Regev, Ronit; Ušaj, Marko; Reinke, Patrick Y A; Giese, Sven; Samson, Abraham O; Taft, Manuel H; Manstein, Dietmar J; Henn, Arnon

2017-10-27

The MYO1C gene produces three alternatively spliced isoforms, differing only in their N-terminal regions (NTRs). These isoforms, which exhibit both specific and overlapping nuclear and cytoplasmic functions, have different expression levels and nuclear-cytoplasmic partitioning. To investigate the effect of NTR extensions on the enzymatic behavior of individual isoforms, we overexpressed and purified the three full-length human isoforms from suspension-adapted HEK cells. MYO1C C favored the actomyosin closed state (AM C ), MYO1C 16 populated the actomyosin open state (AM O ) and AM C equally, and MYO1C 35 favored the AM O state. Moreover, the full-length constructs isomerized before ADP release, which has not been observed previously in truncated MYO1C C constructs. Furthermore, global numerical simulation analysis predicted that MYO1C 35 populated the actomyosin·ADP closed state (AMD C ) 5-fold more than the actomyosin·ADP open state (AMD O ) and to a greater degree than MYO1C C and MYO1C 16 (4- and 2-fold, respectively). On the basis of a homology model of the 35-amino acid NTR of MYO1C 35 (NTR 35 ) docked to the X-ray structure of MYO1C C , we predicted that MYO1C 35 NTR residue Arg-21 would engage in a specific interaction with post-relay helix residue Glu-469, which affects the mechanics of the myosin power stroke. In addition, we found that adding the NTR 35 peptide to MYO1C C yielded a protein that transiently mimics MYO1C 35 kinetic behavior. By contrast, NTR 35 , which harbors the R21G mutation, was unable to confer MYO1C 35 -like kinetic behavior. Thus, the NTRs affect the specific nucleotide-binding properties of MYO1C isoforms, adding to their kinetic diversity. We propose that this level of fine-tuning within MYO1C broadens its adaptability within cells. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

A versatile fiber-optic coupled system for sensitive optical spectroscopy in strong ambient light

NASA Astrophysics Data System (ADS)

Sinha, Sudarson Sekhar; Verma, Pramod Kumar; Makhal, Abhinandan; Pal, Samir Kumar

2009-05-01

In this work we describe design and use of a fiber-optic based optical system for the spectroscopic studies on the samples under the presence of strong ambient light. The system is tested to monitor absorption, emission, and picosecond-resolved fluorescence transients simultaneously with a time interval of 500 ms for several hours on a biologically important sample (vitamin B2) under strong UV light. An efficient stray-light rejection ratio of the setup is achieved by the confocal geometry of the excitation and detection channels. It is demonstrated using this setup that even low optical signal from a liquid sample under strong UV-exposure for the picosecond-resolved fluorescence transient measurement can reliably be detected by ultrasensitive microchannel plate photomultiplier tube solid state detector. The kinetics of photodeterioration of vitamin B2 measured using our setup is consistent with that reported in the literature. Our present studies also justify the usage of tungsten light than the fluorescent light for the healthy preservation of food with vitamin B2.

Doppler-resolved kinetics of saturation recovery

DOE PAGES

Forthomme, Damien; Hause, Michael L.; Yu, Hua -Gen; ...

2015-04-08

Frequency modulated laser transient absorption has been used to monitor the ground state rotational energy transfer rates of CN radicals in a double-resonance, depletion recovery experiment. When a pulsed laser is used to burn a hole in the equilibrium ground state population of one rotational state without velocity selection, the population recovery rate is found to depend strongly on the Doppler detuning of a narrow-band probe laser. Similar effects should be apparent for any relaxation rate process that competes effectively with velocity randomization. Alternative methods of extracting thermal rate constants in the presence of these non-thermal conditions are evaluated. Totalmore » recovery rate constants, analogous to total removal rate constants in an experiment preparing a single initial rotational level, are in good agreement with quantum scattering calculations, but are slower than previously reported experiments and show qualitatively different rotational state dependence between Ar and He collision partners. As a result, quasi-classical trajectory studies confirm that the differing rotational state dependence is primarily a kinematic effect.« less

Episodic fluid flow in the Nankai accretionary complex: Timescale, geochemistry, flow rates, and fluid budget

USGS Publications Warehouse

Saffer, D.M.; Bekins, B.A.

1998-01-01

Down-hole geochemical anomalies encountered in active accretionary systems can be used to constrain the timing, rates, and localization of fluid flow. Here we combine a coupled flow and solute transport model with a kinetic model for smectite dehydration to better understand and quantify fluid flow in the Nankai accretionary complex offshore of Japan. Compaction of sediments and clay dehydration provide fluid sources which drive the model flow system. We explicitly include the consolidation rate of underthrust sediments in our calculations to evaluate the impact that variations in this unknown quantity have on pressure and chloride distribution. Sensitivity analysis of steady state pressure solutions constrains bulk and flow conduit permeabilities. Steady state simulations with 30% smectite in the incoming sedimentary sequence result in minimum chloride concentrations at site 808 of 550 mM, but measured chlorinity is as low as 447 mM. We simulate the transient effects of hydrofracture or a strain event by assuming an instantaneous permeability increase of 3-4 orders of magnitude along a flow conduit (in this case the de??collement), using steady state results as initial conditions. Transient results with an increase in de??collement permeability from 10-16 m2 to 10-13 m2 and 20% smectite reproduce the observed chloride profile at site 808 after 80-160 kyr. Modeled chloride concentrations are highly sensitive to the consolidation rate of underthrust sediments, such that rapid compaction of underthrust material leads to increased freshening. Pressures within the de??collement during transient simulations rise rapidly to a significant fraction of lithostatic and remain high for at least 160 kyr, providing a mechanism for maintaining high permeability. Flow rates at the deformation front for transient simulations are in good agreement with direct measurements, but steady state flow rates are 2-3 orders of magnitude smaller than observed. Fluid budget calculations indicate that nearly 71% of the incoming water in the sediments leaves the accretionary wedge via diffuse flow out the seafloor, 0-5% escapes by focused flow along the de??collement, and roughly 1% is subducted. Copyright 1998 by the American Geophysical Union.

Non-equilibrium effects in high temperature chemical reactions

NASA Technical Reports Server (NTRS)

Johnson, Richard E.

1987-01-01

Reaction rate data were collected for chemical reactions occurring at high temperatures during reentry of space vehicles. The principle of detailed balancing is used in modeling kinetics of chemical reactions at high temperatures. Although this principle does not hold for certain transient or incubation times in the initial phase of the reaction, it does seem to be valid for the rates of internal energy transitions that occur within molecules and atoms. That is, for every rate of transition within the internal energy states of atoms or molecules, there is an inverse rate that is related through an equilibrium expression involving the energy difference of the transition.

Mechanisms creating transient and sustained photoresponses in mammalian retinal ganglion cells

PubMed Central

Zhao, Xiwu; Jaeckel, Elizabeth R.; Chervenak, Andrew P.

2017-01-01

Retinal neurons use sustained and transient light responses to encode visual stimuli of different frequency ranges, but the underlying mechanisms remain poorly understood. In particular, although earlier studies in retinal ganglion cells (RGCs) proposed seven potential mechanisms, all seven have since been disputed, and it remains unknown whether different RGC types use different mechanisms or how many mechanisms are used by each type. Here, we conduct a comprehensive survey in mice and rats of 12 candidate mechanisms that could conceivably produce tonic rod/cone-driven ON responses in intrinsically photosensitive RGCs (ipRGCs) and transient ON responses in three types of direction-selective RGCs (TRHR+, Hoxd10+ ON, and Hoxd10+ ON-OFF cells). We find that the tonic kinetics of ipRGCs arises from their substantially above-threshold resting potentials, input from sustained ON bipolar cells, absence of amacrine cell inhibition of presynaptic ON bipolar cells, and mGluR7-mediated maintenance of light-evoked glutamatergic input. All three types of direction-selective RGCs receive input from transient ON bipolar cells, and each type uses additional strategies to promote photoresponse transience: presynaptic inhibition and dopaminergic modulation for TRHR+ cells, center/surround antagonism and relatively negative resting potentials for Hoxd10+ ON cells, and presynaptic inhibition for Hoxd10+ ON-OFF cells. We find that the sustained nature of ipRGCs’ rod/cone-driven responses depends neither on melanopsin nor on N-methyl-d-aspartate (NMDA) receptors, whereas the transience of the direction-selective cells’ responses is influenced neither by α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/kainate receptor desensitization nor by glutamate uptake. For all cells, we further rule out spike frequency adaptation and intracellular Ca2+ as determinants of photoresponse kinetics. In conclusion, different RGC types use diverse mechanisms to produce sustained or transient light responses. Parenthetically, we find evidence in both mice and rats that the kinetics of light-induced mGluR6 deactivation determines whether an ON bipolar cell responds tonically or transiently to light. PMID:28153865

Kinetics of laser irradiated nanoparticles cloud

NASA Astrophysics Data System (ADS)

Mishra, S. K.; Upadhyay Kahaly, M.; Misra, Shikha

2018-02-01

A comprehensive kinetic model describing the complex kinetics of a laser irradiated nanoparticle ensemble has been developed. The absorbed laser radiation here serves dual purpose, viz., photoenhanced thermionic emission via rise in its temperature and direct photoemission of electrons. On the basis of mean charge theory along with the equations for particle (electron) and energy flux balance over the nanoparticles, the transient processes of charge/temperature evolution over its surface and mass diminution on account of the sublimation (phase change) process have been elucidated. Using this formulation phenomenon of nanoparticle charging, its temperature rise to the sublimation point, mass ablation, and cloud disintegration have been investigated; afterwards, typical timescales of disintegration, sublimation and complete evaporation in reference to a graphite nanoparticle cloud (as an illustrative case) have been parametrically investigated. Based on a numerical analysis, an adequate parameter space describing the nanoparticle operation below the sublimation temperature, in terms of laser intensity, wavelength and nanoparticle material work function, has been identified. The cloud disintegration is found to be sensitive to the nanoparticle charging through photoemission; as a consequence, it illustrates that radiation operating below the photoemission threshold causes disintegration in the phase change state, while above the threshold, it occurs with the onset of surface heating.

Coarsening in Solid-liquid Mixtures: Overview of Experiments on Shuttle and ISS

NASA Technical Reports Server (NTRS)

Duval, Walter M. B.; Hawersaat, Robert W.; Lorik, T.; Thompson, J.; Gulsoy, B.; Voorhees, P. W.

2013-01-01

The microgravity environment on the Shuttle and the International Space Station (ISS) provides the ideal condition to perform experiments on Coarsening in Solid-Liquid Mixtures (CSLM) as deleterious effects such as particle sedimentation and buoyancy-induced convection are suppressed. For an ideal system such as Lead-Tin in which all the thermophysical properties are known, the initial condition in microgravity of randomly dispersed particles with local clustering of solid Tin in eutectic liquid Lead-Tin matrix, permitted kinetic studies of competitive particle growth for a range of volume fractions. Verification that the quenching phase of the experiment had negligible effect of the spatial distribution of particles is shown through the computational solution of the dynamical equations of motion, thus insuring quench-free effects from the coarsened microstructure measurements. The low volume fraction experiments conducted on the Shuttle showed agreement with transient Ostwald ripening theory, and the steady-state requirement of LSW theory was not achieved. More recent experiments conducted on ISS with higher volume fractions have achieved steady-state condition and show that the kinetics follows the classical diffusion limited particle coarsening prediction and the measured 3D particle size distribution becomes broader as predicted from theory.

Synthesis, structure, and excited state kinetics of heteroleptic Cu(i) complexes with a new sterically demanding phenanthroline ligand

DOE PAGES

Kohler, Lars; Hadt, Ryan G.; Hayes, Dugan; ...

2017-09-25

In this paper we describe the synthesis of a new phenanthroline ligand, 2,9-di(2,4,6-tri-isopropyl-phenyl)-1,10-phenanthroline (bL2) and its use as the blocking ligand in the preparation of two new heteroleptic Cu(I)diimine complexes. Analysis of the CuHETPHEN single crystal structures shows a distinct distortion from an ideal tetrahedral geometry around the Cu(I) center, forced by the secondary phenanthroline ligand rotating to accommodate the isopropyl groups of bL2. The increased steric bulk of bL2 as compared to the more commonly used 2,9-dimesityl-1,10-phenanthroline blocking ligand prohibits intramolecular ligand–ligand interaction, which is unique among CuHETPHEN complexes. The ground state optical and redox properties of CuHETPHEN complexesmore » are responsive to the substitution on the blocking ligand even though the differences in structure are far removed from the Cu(I) center. Transient optical spectroscopy was used to understand the excited state kinetics in both coordinating and non-coordinating solvents following visible excitation. Substitution of the blocking phenanthroline ligand has a significant impact on the 3MLCT decay and can be used to increase the excited state lifetime by 50%. Electronic structure calculations established relationships between ground and excited state properties, and general entatic state concepts are discussed for copper photosensitizers. This work contributes to the growing library of CuHETPHEN complexes and broadens the fundamental understanding of their ground and excited state properties.« less

Excited-state dynamics of the medicinal pigment curcumin in a hydrogel.

PubMed

Harada, Takaaki; Lincoln, Stephen F; Kee, Tak W

2016-10-12

Curcumin is a yellow polyphenol with multiple medicinal effects. These effects, however, are limited due to its poor aqueous stability and solubility. A hydrogel of 3% octadecyl randomly substituted polyacrylate (PAAC18) has been shown to provide high aqueous stability for curcumin under physiological conditions, offering a route for photodynamic therapy. In this study, the excited-state photophysics of curcumin in the PAAC18 hydrogel is investigated using a combination of femtosecond transient absorption and fluorescence upconversion spectroscopy. The transient absorption results reveal a multiexponential decay in the excited-state kinetics with fast (1 ps & 15 ps) and slow (110 ps & ≈5 ns) components. The fast decay component exhibits a deuterium isotope effect with D 2 O in the hydrogel, indicating that the 15 ps decay component is attributable to excited-state intramolecular hydrogen atom transfer of curcumin in the PAAC18 hydrogel. In addition, solvent reorganisation of excited-state curcumin is investigated using multiwavelength femtosecond fluorescence upconversion spectroscopy. The results show that the dominant solvation response (τ = 0.08 ps) is a fast inertial motion owing to the presence of bulk-like water in the vicinity of the hydrophobic octadecyl substituents of the PAAC18 hydrogel. The results also show an additional response with longer time constants of 1 and 6 ps, which is attributable to translational diffusion of confined water molecules in the three-dimensional, cross-linking network of the octadecyl substituents of PAAC18. Overall, we show that excited-state intramolecular hydrogen atom transfer and solvent reorganisation are major photophysical events for curcumin in the PAAC18 hydrogel.

Cross-bridge elasticity in single smooth muscle cells

PubMed Central

1983-01-01

In smooth muscle, a cross-bridge mechanism is believed to be responsible for active force generation and fiber shortening. In the present studies, the viscoelastic and kinetic properties of the cross- bridge were probed by eliciting tension transients in response to small, rapid, step length changes (delta L = 0.3-1.0% Lcell in 2 ms). Tension transients were obtained in a single smooth muscle cell isolated from the toad (Bufo marinus) stomach muscularis, which was tied between a force transducer and a displacement device. To record the transients, which were of extremely small magnitude (0.1 microN), a high-frequency (400 Hz), ultrasensitive force transducer (18 mV/microN) was designed and built. The transients obtained during maximal force generation (Fmax = 2.26 microN) were characterized by a linear elastic response (Emax = 1.26 X 10(4) mN/mm2) coincident with the length step, which was followed by a biphasic tension recovery made up of two exponentials (tau fast = 5-20 ms, tau slow = 50-300 ms). During the development of force upon activation, transients were elicited. The relationship between stiffness and force was linear, which suggests that the transients originate within the cross-bridge and reflect the cross-bridge's viscoelastic and kinetic properties. The observed fiber elasticity suggests that the smooth muscle cross-bridge is considerably more compliant than in fast striated muscle. A thermodynamic model is presented that allows for an analysis of the factors contributing to the increased compliance of the smooth muscle cross-bridge. PMID:6413640

Hot Band Analysis and Kinetics Measurements for Ethynyl Radical, C_2H, in the 1.49 μm Region

NASA Astrophysics Data System (ADS)

Le, Anh T.; Hall, Gregory; Sears, Trevor

2017-06-01

Ethynyl, C_2H, is an important intermediate in combustion processes and has been widely observed in interstellar space. Spectroscopically, it is of particular interest because it possesses three low-lying electronic surfaces: a ground ^2Σ^+state, and a low-lying ^2Π excited electronic state, which splits due to the Renner-Teller effect. Vibronic coupling among these states leads to a complicated, mixed-character, energy level structure. We have previously reported work on three bands originating from the ˜{X}(0,0,0) ^2Σ ground state to excited vibronic states: two ^2Σ - ^2 Σ transitions at 6696 and 7088 \\wn and a ^2Π - ^2Σ transition at 7108 \\wn. In this work, the radicals were formed in a hot, non-thermal, population distribution by u.v. pulsed laser photolysis of a precursor. Kinetic measurements of the time-evolution of the ground state populations following collisional relaxation and reactive loss were also made, using some of the stronger rotational lines observed. Time-dependent signals in mixtures containing a variable concentration of precursor in argon suggested that vibronically hot C_2H radicals were less reactive than the relaxed, thermalized, radical. Two additional hot bands originating in states ˜{X}(0,1^1,0) ^2Π and ˜{X}(0,2^0,0) ^2Σ, have now been identified in the same spectral region. In a new series of experiments, we have measured the kinetics of formation and decay of representative levels involving all the assigned transitions, i.e. originating in ˜{X}(0,v_2,0), with v_2 =0 ,1, and 2, in various concentrations of mixtures of precursor, inert gas and hydrogen. The new spectra also show greatly improved signal-to-noise ratio in comparison to our previous work, due to the use of a transient FM detection scheme, and additional spectral assignments seem likely. Both kinetics and spectroscopic results will be described in the talk. Acknowledgments: Work at Brookhaven National Laboratory was carried out under Contract No. DE-SC0012704 with the U.S. Department of Energy, Office of Science, and supported by its Division of Chemical Sciences, Geosciences and Biosciences within the Office of Basic Energy Sciences. A. T. Le, G. E. Hall, T. J. Sears, J. Chem. Phys. 145 074306, 2016

Reactivity Initiated Accident Simulation to Inform Transient Testing of Candidate Advanced Cladding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Nicholas R; Wysocki, Aaron J; Terrani, Kurt A

2016-01-01

Abstract. Advanced cladding materials with potentially enhanced accident tolerance will yield different light water reactor performance and safety characteristics than the present zirconium-based cladding alloys. These differences are due to different cladding material properties and responses to the transient, and to some extent, reactor physics, thermal, and hydraulic characteristics. Some of the differences in reactors physics characteristics will be driven by the fundamental properties (e.g., absorption in iron for an iron-based cladding) and others will be driven by design modifications necessitated by the candidate cladding materials (e.g., a larger fuel pellet to compensate for parasitic absorption). Potential changes in thermalmore » hydraulic limits after transition from the current zirconium-based cladding to the advanced materials will also affect the transient response of the integral fuel. This paper leverages three-dimensional reactor core simulation capabilities to inform on appropriate experimental test conditions for candidate advanced cladding materials in a control rod ejection event. These test conditions are using three-dimensional nodal kinetics simulations of a reactivity initiated accident (RIA) in a representative state-of-the-art pressurized water reactor with both nuclear-grade iron-chromium-aluminum (FeCrAl) and silicon carbide based (SiC-SiC) cladding materials. The effort yields boundary conditions for experimental mechanical tests, specifically peak cladding strain during the power pulse following the rod ejection. The impact of candidate cladding materials on the reactor kinetics behavior of RIA progression versus reference zirconium cladding is predominantly due to differences in: (1) fuel mass/volume/specific power density, (2) spectral effects due to parasitic neutron absorption, (3) control rod worth due to hardened (or softened) spectrum, and (4) initial conditions due to power peaking and neutron transport cross sections in the equilibrium cycle cores due to hardened (or softened) spectrum. This study shows minimal impact of SiC-based cladding configurations on the transient response versus reference zirconium-based cladding. However, the FeCrAl cladding response indicates similar energy deposition, but with significantly shorter pulses of higher magnitude. Therefore the FeCrAl-based cases have a more rapid fuel thermal expansion rate and the resultant pellet-cladding interaction occurs more rapidly.« less

Electrochemically driven catalysis of Rhizobium sp. NT-26 arsenite oxidase with its native electron acceptor cytochrome c552.

PubMed

Kalimuthu, Palraj; Heath, Matthew D; Santini, Joanne M; Kappler, Ulrike; Bernhardt, Paul V

2014-01-01

We describe the catalytic voltammograms of the periplasmic arsenite oxidase (Aio) from the chemolithoautotrophic bacterium Rhizobium sp. str. NT-26 that oxidizes arsenite to arsenate. Electrochemistry of the enzyme was accomplished using its native electron transfer partner, cytochrome c552 (cyt c552), as a mediator. The protein cyt c552 adsorbed on a mercaptoundecanoic acid (MUA) modified Au electrode exhibited a stable, reversible one-electron voltammetric response at +275mV vs NHE (pH6). In the presence of arsenite and Aio the voltammetry of cyt c552 is transformed from a transient response to an amplified sigmoidal (steady state) wave consistent with an electro-catalytic system. Digital simulation was performed using a single set of parameters for all catalytic voltammetries obtained at different sweep rates and various substrate concentrations. The obtained kinetic constants from digital simulation provide new insight into the kinetics of the NT-26 Aio catalytic mechanism. © 2013.

Challenges in Understanding and Development of Predictive Models of Plasma Assisted Combustion

DTIC Science & Technology

2014-01-01

and electron temperature in transient plasmas sustained by nanosecond pulse duration discharges, and their comparison with modeling predictions, are...in nanosecond pulse discharge in nitrogen at 0.25 bar, using the kinetic model developed in Ref. [11]. Rapid electric field reduction during...discharge pulses with kinetic modeling calculations, using conventional hydrocarbon-air combustion mechanisms. Although modeling predictions for H2-air

Kinetics of liquid-mediated crystallization of amorphous Ge from multi-frame dynamic transmission electron microscopy

DOE PAGES

Santala, M. K.; Raoux, S.; Campbell, G. H.

2015-12-24

The kinetics of laser-induced, liquid-mediated crystallization of amorphous Ge thin films were studied using multi-frame dynamic transmission electron microscopy (DTEM), a nanosecond-scale photo-emission transmission electron microscopy technique. In these experiments, high temperature gradients are established in thin amorphous Ge films with a 12-ns laser pulse with a Gaussian spatial profile. The hottest region at the center of the laser spot crystallizes in ~100 ns and becomes nano-crystalline. Over the next several hundred nanoseconds crystallization continues radially outward from the nano-crystalline region forming elongated grains, some many microns long. The growth rate during the formation of these radial grains is measuredmore » with time-resolved imaging experiments. Crystal growth rates exceed 10 m/s, which are consistent with crystallization mediated by a very thin, undercooled transient liquid layer, rather than a purely solid-state transformation mechanism. The kinetics of this growth mode have been studied in detail under steady-state conditions, but here we provide a detailed study of liquid-mediated growth in high temperature gradients. Unexpectedly, the propagation rate of the crystallization front was observed to remain constant during this growth mode even when passing through large local temperature gradients, in stark contrast to other similar studies that suggested the growth rate changed dramatically. As a result, the high throughput of multi-frame DTEM provides gives a more complete picture of the role of temperature and temperature gradient on laser crystallization than previous DTEM experiments.« less

Kinetics of liquid-mediated crystallization of amorphous Ge from multi-frame dynamic transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santala, M. K., E-mail: melissa.santala@oregonstate.edu; Campbell, G. H.; Raoux, S.

2015-12-21

The kinetics of laser-induced, liquid-mediated crystallization of amorphous Ge thin films were studied using multi-frame dynamic transmission electron microscopy (DTEM), a nanosecond-scale photo-emission transmission electron microscopy technique. In these experiments, high temperature gradients are established in thin amorphous Ge films with a 12-ns laser pulse with a Gaussian spatial profile. The hottest region at the center of the laser spot crystallizes in ∼100 ns and becomes nano-crystalline. Over the next several hundred nanoseconds crystallization continues radially outward from the nano-crystalline region forming elongated grains, some many microns long. The growth rate during the formation of these radial grains is measured withmore » time-resolved imaging experiments. Crystal growth rates exceed 10 m/s, which are consistent with crystallization mediated by a very thin, undercooled transient liquid layer, rather than a purely solid-state transformation mechanism. The kinetics of this growth mode have been studied in detail under steady-state conditions, but here we provide a detailed study of liquid-mediated growth in high temperature gradients. Unexpectedly, the propagation rate of the crystallization front was observed to remain constant during this growth mode even when passing through large local temperature gradients, in stark contrast to other similar studies that suggested the growth rate changed dramatically. The high throughput of multi-frame DTEM provides gives a more complete picture of the role of temperature and temperature gradient on laser crystallization than previous DTEM experiments.« less

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

PubMed

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-04-26

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy.

PubMed

Hayes, Dugan; Kohler, Lars; Hadt, Ryan G; Zhang, Xiaoyi; Liu, Cunming; Mulfort, Karen L; Chen, Lin X

2018-01-28

The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(i) bis(phenanthroline)/ruthenium(ii) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(i)-Ru(ii) analogs of the homodinuclear Cu(i)-Cu(i) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

PubMed Central

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-01-01

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design. PMID:27128902

Ultrafast Transient Absorption Spectroscopy of Polymer-Based Organophotoredox Catalysts Mimicking Transition-Metal Complexes

NASA Astrophysics Data System (ADS)

Jamhawi, Abdelqader; Paul, Anam C.; Smith, Justin D.; Handa, Sachin; Liu, Jinjun

2017-06-01

Transition-metal complexes of rare earth metals including ruthenium and iridium are most commonly employed as visible-light photocatalysts. Despite their highly important and broad applications, they have many disadvantages including high cost associated with low abundance in earth crust, potential toxicity, requirement of specialized ligands for desired activity, and difficulty in recycling of metal contents as well as associated ligands. Polymer-based organophotoredox catalysts are promising alternatives and possess unique advantages such as easier synthesis from inexpensive starting material, longer excited state life time, broad range of activity, sustainability, and recyclability. In this research talk, time-resolved photoluminescence and femtosecond transient absorption (TA) spectroscopy measurements of three novel polymer-based organophotoredox catalysts will be presented. By our synthetic team, their catalytic activity has been proven in some highly valuable chemical transformations, that otherwise require transition metal complexes. Time-resolved spectroscopic investigations have demonstrated that photoinduced processes in these catalysts are similar to the transition metal complexes. Especially, intramolecular vibrational relaxation, internal conversion, and intersystem crossing from the S1 state to the T1 state all occur on a sub-picosecond timescale. The long lifetime of the T1 state ( 2-3 microsecond) renders these polymers potent oxidizing and reducing agents. A spectroscopic and kinetic model has been developed for global fitting of TA spectra in both the frequency and time domains. Implication of the current ultrafast spectroscopy studies of these novel molecules to their roles in photocatalysis will be discussed.

Three-dimensional time-dependent STAR reactor kinetics analyses coupled with RETRAN and MCPWR system response

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feltus, M.A.

1989-11-01

The operation of a nuclear power plant must be regularly supported by various reactor dynamics and thermal-hydraulic analyses, which may include final safety analysis report (FSAR) design-basis calculations, and conservative and best-estimate analyses. The development and improvement of computer codes and analysis methodologies provide many advantages, including the ability to evaluate the effect of modeling simplifications and assumptions made in previous reactor kinetics and thermal-hydraulic calculations. This paper describes the results of using the RETRAN, MCPWR, and STAR codes in a tandem, predictive-corrective manner for three pressurized water reactor (PWR) transients: (a) loss of feedwater (LOF) anticipated transient without scrammore » (ATWS), (b) station blackout ATWS, and (c) loss of total reactor coolant system (RCS) flow with a scram.« less

Surface Transient Binding-Based Fluorescence Correlation Spectroscopy (STB-FCS), a Simple and Easy-to-Implement Method to Extend the Upper Limit of the Time Window to Seconds.

PubMed

Peng, Sijia; Wang, Wenjuan; Chen, Chunlai

2018-05-10

Fluorescence correlation spectroscopy is a powerful single-molecule tool that is able to capture kinetic processes occurring at the nanosecond time scale. However, the upper limit of its time window is restricted by the dwell time of the molecule of interest in the confocal detection volume, which is usually around submilliseconds for a freely diffusing biomolecule. Here, we present a simple and easy-to-implement method, named surface transient binding-based fluorescence correlation spectroscopy (STB-FCS), which extends the upper limit of the time window to seconds. We further demonstrated that STB-FCS enables capture of both intramolecular and intermolecular kinetic processes whose time scales cross several orders of magnitude.

Neutrophil kinetics of recombinant human granulocyte colony-stimulating factor-induced neutropenia in rats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okada, Yuji; Kawagishi, Mayumi; Kusaka, Masaru

Single injection of recombinant human granulocyte colony-stimulating factor (rhG-CSF) immediately induced a decrease in the number of circulating neutrophils in rats. This neutropenia occurred 10 minutes after the injection but disappeared 40 minutes after injection. This transient neutropenia was dose-dependently induced by rhG-CSF and also induced by repeated injections. We studied the kinetics of circulating neutrophils in transient neutropenia. rhG-CSF markedly decreased the number of {sup 3}H-diisopropylfluorophosphate ({sup 3}H-DFP) labeled neutrophils in the circulation 10 minutes after injection but the labeled neutrophils recovered to near the control level 40 minutes after the injection. These results indicate that the neutrophil marginationmore » accounts for the neutrophenia and the marginated neutrophils return to the circulation.« less

Ca2+ transients in cardiac myocytes measured with high and low affinity Ca2+ indicators.

PubMed Central

Berlin, J R; Konishi, M

1993-01-01

Intracellular calcium ion ([Ca2+]i) transients were measured in voltage-clamped rat cardiac myocytes with fura-2 or furaptra to quantitate rapid changes in [Ca2+]i. Patch electrode solutions contained the K+ salt of fura-2 (50 microM) or furaptra (300 microM). With identical experimental conditions, peak amplitude of stimulated [Ca2+]i transients in furaptra-loaded myocytes was 4- to 6-fold greater than that in fura-2-loaded cells. To determine the reason for this discrepancy, intracellular fura-2 Ca2+ buffering, kinetics of Ca2+ binding, and optical properties were examined. Decreasing cellular fura-2 concentration by lowering electrode fura-2 concentration 5-fold, decreased the difference between the amplitudes of [Ca2+]i transients in fura-2 and furaptra-loaded myocytes by twofold. Thus, fura-2 buffers [Ca2+]i under these conditions; however, Ca2+ buffering is not the only factor that explains the different amplitudes of the [Ca2+]i transients measured with these indicators. From the temporal comparison of the [Ca2+]i transients measured with fura-2 and furaptra, the apparent reverse rate constant for Ca2+ binding of fura-2 was at least 65s-1, much faster than previously reported in skeletal muscle fibers. These binding kinetics do not explain the difference in the size of the [Ca2+]i transients reported by fura-2 and furaptra. Parameters for fura-2 calibration, Rmin, Rmax, and beta, were obtained in salt solutions (in vitro) and in myocytes exposed to the Ca2+ ionophore, 4-Br A23187, in EGTA-buffered solutions (in situ). Calibration of fura-2 fluorescence signals with these in situ parameters yielded [Ca2+]i transients whose peak amplitude was 50-100% larger than those calculated with in vitro parameters. Thus, in vitro calibration of fura-2 fluorescence significantly underestimates the amplitude of the [Ca2+]i transient. These data suggest that the difference in amplitude of [Ca2+]i transients in fura-2 and furaptra-loaded myocytes is due, in part, to Ca2+ buffering by fura-2 and use of in vitro calibration parameters. PMID:8274651

A comparative study of ethylene growth response kinetics in eudicots and monocots reveals a role for gibberellin in growth inhibition and recovery.

PubMed

Kim, Joonyup; Wilson, Rebecca L; Case, J Brett; Binder, Brad M

2012-11-01

Time-lapse imaging of dark-grown Arabidopsis (Arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. This study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. Although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. In contrast, with continued application of ethylene, white millet (Panicum miliaceum) seedlings had a rapid and transient growth inhibition response, rice (Oryza sativa 'Nipponbare') seedlings had a slow onset of growth stimulation, and barley (Hordeum vulgare) had a transient growth inhibition response followed, after a delay, by a prolonged inhibition response. Growth stimulation in rice correlated with a decrease in the levels of rice ETHYLENE INSENSTIVE3-LIKE2 (OsEIL2) and an increase in rice F-BOX DOMAIN AND LRR CONTAINING PROTEIN7 transcripts. The gibberellin (GA) biosynthesis inhibitor paclobutrazol caused millet seedlings to have a prolonged growth inhibition response when ethylene was applied. A transient ethylene growth inhibition response has previously been reported for Arabidopsis ethylene insensitive3-1 (ein3-1) eil1-1 double mutants. Paclobutrazol caused these mutants to have a prolonged response to ethylene, whereas constitutive GA signaling in this background eliminated ethylene responses. Sensitivity to paclobutrazol inversely correlated with the levels of EIN3 in Arabidopsis. Wild-type Arabidopsis seedlings treated with paclobutrazol and mutants deficient in GA levels or signaling had a delayed growth recovery after ethylene removal. It is interesting to note that ethylene caused alterations in gene expression that are predicted to increase GA levels in the ein3-1 eil1-1 seedlings. These results indicate that ethylene affects GA levels leading to modulation of ethylene growth inhibition kinetics.

Overview and Current Status of Analyses of Potential LEU Design Concepts for TREAT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Connaway, H. M.; Kontogeorgakos, D. C.; Papadias, D. D.

2015-10-01

Neutronic and thermal-hydraulic analyses have been performed to evaluate the performance of different low-enriched uranium (LEU) fuel design concepts for the conversion of the Transient Reactor Test Facility (TREAT) from its current high-enriched uranium (HEU) fuel. TREAT is an experimental reactor developed to generate high neutron flux transients for the testing of nuclear fuels. The goal of this work was to identify an LEU design which can maintain the performance of the existing HEU core while continuing to operate safely. A wide variety of design options were considered, with a focus on minimizing peak fuel temperatures and optimizing the powermore » coupling between the TREAT core and test samples. Designs were also evaluated to ensure that they provide sufficient reactivity and shutdown margin for each control rod bank. Analyses were performed using the core loading and experiment configuration of historic M8 Power Calibration experiments (M8CAL). The Monte Carlo code MCNP was utilized for steady-state analyses, and transient calculations were performed with the point kinetics code TREKIN. Thermal analyses were performed with the COMSOL multi-physics code. Using the results of this study, a new LEU Baseline design concept is being established, which will be evaluated in detail in a future report.« less

Application of Degenerately Doped Metal Oxides in the Study of Photoinduced Interfacial Electron Transfer.

PubMed

Farnum, Byron H; Morseth, Zachary A; Brennaman, M Kyle; Papanikolas, John M; Meyer, Thomas J

2015-06-18

Degenerately doped In2O3:Sn semiconductor nanoparticles (nanoITO) have been used to study the photoinduced interfacial electron-transfer reactivity of surface-bound [Ru(II)(bpy)2(4,4'-(PO3H2)2-bpy)](2+) (RuP(2+)) molecules as a function of driving force over a range of 1.8 eV. The metallic properties of the ITO nanoparticles, present within an interconnected mesoporous film, allowed for the driving force to be tuned by controlling their Fermi level with an external bias while their optical transparency allowed for transient absorption spectroscopy to be used to monitor electron-transfer kinetics. Photoinduced electron transfer from excited-state -RuP(2+*) molecules to nanoITO was found to be dependent on applied bias and competitive with nonradiative energy transfer to nanoITO. Back electron transfer from nanoITO to oxidized -RuP(3+) was also dependent on the applied bias but without complication from inter- or intraparticle electron diffusion in the oxide nanoparticles. Analysis of the electron injection kinetics as a function of driving force using Marcus-Gerischer theory resulted in an experimental estimate of the reorganization energy for the excited-state -RuP(3+/2+*) redox couple of λ* = 0.83 eV and an electronic coupling matrix element, arising from electronic wave function overlap between the donor orbital in the molecule and the acceptor orbital(s) in the nanoITO electrode, of Hab = 20-45 cm(-1). Similar analysis of the back electron-transfer kinetics yielded λ = 0.56 eV for the ground-state -RuP(3+/2+) redox couple and Hab = 2-4 cm(-1). The use of these wide band gap, degenerately doped materials provides a unique experimental approach for investigating single-site electron transfer at the surface of oxide nanoparticles.

Mathematical modeling of the relation between myosin phosphorylation and stress development in smooth muscles.

PubMed

Fajmut, Ales; Dobovisek, Andrej; Brumen, Milan

2005-01-01

In this paper the 4-state latch bridge model proposed by Rembold and Murphy is expanded; first by incorporation of the analytical expression of Ca2+ dependent MLCK activation from the work of Kato et al. and second, by inclusion of the myosin dephosphorylation based on the Michaelis-Menten kinetics. The analysis of the proposed model and the comparison with the original model results as well as with the experimental data is presented. The model is able to predict the steady-state isometric stress and the myosin phosphorylation in dependence on steady cytosolic [Ca2+] as well as the temporal evolution of the system in dependence on the input Ca2+ signal in the form of biphasic transient, whereby our model results are in several aspects in better agreement with experimental observations.

Relaxation dynamics and coherent energy exchange in coupled vibration-cavity polaritons (Conference Presentation)

NASA Astrophysics Data System (ADS)

Simpkins, Blake S.; Fears, Kenan P.; Dressick, Walter J.; Dunkelberger, Adam D.; Spann, Bryan T.; Owrutsky, Jeffrey C.

2016-09-01

Coherent coupling between an optical transition and confined optical mode have been investigated for electronic-state transitions, however, only very recently have vibrational transitions been considered. Here, we demonstrate both static and dynamic results for vibrational bands strongly coupled to optical cavities. We experimentally and numerically describe strong coupling between a Fabry-Pérot cavity and carbonyl stretch ( 1730 cm 1) in poly-methylmethacrylate and provide evidence that the mixed-states are immune to inhomogeneous broadening. We investigate strong and weak coupling regimes through examination of cavities loaded with varying concentrations of a urethane monomer. Rabi splittings are in excellent agreement with an analytical description using no fitting parameters. Ultrafast pump-probe measurements reveal transient absorption signals over a frequency range well-separated from the vibrational band, as well as drastically modified relaxation rates. We speculate these modified kinetics are a consequence of the energy proximity between the vibration-cavity polariton modes and excited state transitions and that polaritons offer an alternative relaxation path for vibrational excitations. Varying the polariton energies by angle-tuning yields transient results consistent with this hypothesis. Furthermore, Rabi oscillations, or quantum beats, are observed at early times and we see evidence that these coherent vibration-cavity polariton excitations impact excited state population through cavity losses. Together, these results indicate that cavity coupling may be used to influence both excitation and relaxation rates of vibrations. Opening the field of polaritonic coupling to vibrational species promises to be a rich arena amenable to a wide variety of infrared-active bonds that can be studied in steady state and dynamically.

Effects of premature stimulation on HERG K+ channels

PubMed Central

Lu, Yu; Mahaut-Smith, Martyn P; Varghese, Anthony; Huang, Christopher L-H; Kemp, Paul R; Vandenberg, Jamie I

2001-01-01

The unusual kinetics of human ether-à-go-go-related gene (HERG) K+ channels are consistent with a role in the suppression of arrhythmias initiated by premature beats. Action potential clamp protocols were used to investigate the effect of premature stimulation on HERG K+ channels, transfected in Chinese hamster ovary cells, at 37 °C. HERG K+ channel currents peaked during the terminal repolarization phase of normally paced action potential waveforms. However, the magnitude of the current and the time point at which conductance was maximal depended on the type of action potential waveform used (epicardial, endocardial, Purkinje fibre or atrial). HERG K+ channel currents recorded during premature action potentials consisted of an early transient outward current followed by a sustained outward current. The magnitude of the transient current component showed a biphasic dependence on the coupling interval between the normally paced and premature action potentials and was maximal at a coupling interval equivalent to 90% repolarization (APD90) for ventricular action potentials. The largest transient current response occurred at shorter coupling intervals for Purkinje fibre (APD90– 20 ms) and atrial (APD90– 30 ms) action potentials. The magnitude of the sustained current response following premature stimulation was similar to that recorded during the first action potential for ventricular action potential waveforms. However, for Purkinje and atrial action potentials the sustained current response was significantly larger during the premature action potential than during the normally paced action potential. A Markov model that included three closed states, one open and one inactivated state with transitions permitted between the pre-open closed state and the inactivated state, successfully reproduced our results for the effects of premature stimuli, both during square pulse and action potential clamp waveforms. These properties of HERG K+ channels may help to suppress arrhythmias initiated by early afterdepolarizations and premature beats in the ventricles, Purkinje fibres or atria. PMID:11744759

Singlet oxygen-sensitized delayed fluorescence of common water-soluble photosensitizers.

PubMed

Scholz, Marek; Dědic, Roman; Breitenbach, Thomas; Hála, Jan

2013-10-01

Six common water-soluble singlet oxygen ((1)O2) photosensitizers - 5,10,15,20-tetrakis(1-methyl-4-pyridinio) porphine (TMPyP), meso-tetrakis(4-sulfonathophenyl)porphine (TPPS4), Al(III) phthalocyanine chloride tetrasulfonic acid (AlPcS4), eosin Y, rose bengal, and methylene blue - were investigated in terms of their ability to produce delayed fluorescence (DF) in solutions at room temperature. All the photosensitizers dissolved in air-saturated phosphate buffered saline (PBS, pH 7.4) exhibit easily detectable DF, which can be nearly completely quenched by 10 mM NaN3, a specific (1)O2 quencher. The DF kinetics has a biexponential rise-decay character in a microsecond time domain. Therefore, we propose that singlet oxygen-sensitized delayed fluorescence (SOSDF), where the triplet state of a photosensitizer reacts with (1)O2 giving rise to an excited singlet state of the photosensitizer, is the prevailing mechanism. It was confirmed by additional evidence, such as a monoexponential decay of triplet-triplet transient absorption kinetics, dependence of SOSDF kinetics on oxygen concentration, absence of SOSDF in a nitrogen-saturated sample, or the effect of isotopic exchange H2O-D2O. Eosin Y and AlPcS4 show the largest SOSDF quantum yield among the selected photosensitizers, whereas rose bengal possesses the highest ratio of SOSDF intensity to prompt fluorescence intensity. The rate constant for the reaction of triplet state with (1)O2 giving rise to the excited singlet state of photosensitizer was estimated to be ~/>1 × 10(9) M(-1) s(-1). SOSDF kinetics contains information about both triplet and (1)O2 lifetimes and concentrations, which makes it a very useful alternative tool for monitoring photosensitizing and (1)O2 quenching processes, allowing its detection in the visible spectral region, utilizing the photosensitizer itself as a (1)O2 probe. Under our experimental conditions, SOSDF was up to three orders of magnitude more intense than the infrared (1)O2 phosphorescence and by far the most important pathway of DF. SOSDF was also detected in a suspension of 3T3 mouse fibroblast cells, which underlines the importance of SOSDF and its relevance for biological systems.

Nuclear reactor transient analysis via a quasi-static kinetics Monte Carlo method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jo, YuGwon; Cho, Bumhee; Cho, Nam Zin, E-mail: nzcho@kaist.ac.kr

2015-12-31

The predictor-corrector quasi-static (PCQS) method is applied to the Monte Carlo (MC) calculation for reactor transient analysis. To solve the transient fixed-source problem of the PCQS method, fission source iteration is used and a linear approximation of fission source distributions during a macro-time step is introduced to provide delayed neutron source. The conventional particle-tracking procedure is modified to solve the transient fixed-source problem via MC calculation. The PCQS method with MC calculation is compared with the direct time-dependent method of characteristics (MOC) on a TWIGL two-group problem for verification of the computer code. Then, the results on a continuous-energy problemmore » are presented.« less

Ischemia reperfusion dysfunction changes model-estimated kinetics of myofilament interaction due to inotropic drugs in isolated hearts

PubMed Central

Rhodes, Samhita S; Camara, Amadou KS; Ropella, Kristina M; Audi, Said H; Riess, Matthias L; Pagel, Paul S; Stowe, David F

2006-01-01

Background The phase-space relationship between simultaneously measured myoplasmic [Ca2+] and isovolumetric left ventricular pressure (LVP) in guinea pig intact hearts is altered by ischemic and inotropic interventions. Our objective was to mathematically model this phase-space relationship between [Ca2+] and LVP with a focus on the changes in cross-bridge kinetics and myofilament Ca2+ sensitivity responsible for alterations in Ca2+-contraction coupling due to inotropic drugs in the presence and absence of ischemia reperfusion (IR) injury. Methods We used a four state computational model to predict LVP using experimentally measured, averaged myoplasmic [Ca2+] transients from unpaced, isolated guinea pig hearts as the model input. Values of model parameters were estimated by minimizing the error between experimentally measured LVP and model-predicted LVP. Results We found that IR injury resulted in reduced myofilament Ca2+ sensitivity, and decreased cross-bridge association and dissociation rates. Dopamine (8 μM) reduced myofilament Ca2+ sensitivity before, but enhanced it after ischemia while improving cross-bridge kinetics before and after IR injury. Dobutamine (4 μM) reduced myofilament Ca2+ sensitivity while improving cross-bridge kinetics before and after ischemia. Digoxin (1 μM) increased myofilament Ca2+ sensitivity and cross-bridge kinetics after but not before ischemia. Levosimendan (1 μM) enhanced myofilament Ca2+ affinity and cross-bridge kinetics only after ischemia. Conclusion Estimated model parameters reveal mechanistic changes in Ca2+-contraction coupling due to IR injury, specifically the inefficient utilization of Ca2+ for contractile function with diastolic contracture (increase in resting diastolic LVP). The model parameters also reveal drug-induced improvements in Ca2+-contraction coupling before and after IR injury. PMID:16512898

Deciphering excited state evolution in halorhodopsin with stimulated emission pumping.

PubMed

Bismuth, Oshrat; Komm, Pavel; Friedman, Noga; Eliash, Tamar; Sheves, Mordechai; Ruhman, Sanford

2010-03-04

The primary photochemical dynamics of Hb. pharaonis Halorhodopsin (pHR) are investigated by femtosecond visible pump-near IR dump-hyperspectral probe spectroscopy. The efficiency of excited state depletion is deduced from transient changes in absorption, recorded with and without stimulated emission pumping (SEP), as a function of the dump delay. The concomitant reduction of photocycle population is assessed by probing the "K" intermediate difference spectrum. Results show that the cross section for stimulating emission is nearly constant throughout the fluorescent state lifetime. Probing "K" demonstrates that dumping produces a proportionate reduction in photocycle yields. We conclude that, despite its nonexponential internal conversion (IC) kinetics, the fluorescent state in pHR constitutes a single intermediate in the photocycle. This contrasts with conclusions drawn from the study of primary events in the related chloride pump from Hb. salinarum (sHR), believed to produce the "K" intermediate from a distinct short-lived subpopulation in the excited state. Our discoveries concerning internal conversion dynamics in pHR are discussed in light of recent expectations for similar excited state dynamics in both proteins.

Excited state dynamics of the astaxanthin radical cation

NASA Astrophysics Data System (ADS)

Amarie, Sergiu; Förster, Ute; Gildenhoff, Nina; Dreuw, Andreas; Wachtveitl, Josef

2010-07-01

Femtosecond transient absorption spectroscopy in the visible and NIR and ultrafast fluorescence spectroscopy were used to examine the excited state dynamics of astaxanthin and its radical cation. For neutral astaxanthin, two kinetic components corresponding to time constants of 130 fs (decay of the S 2 excited state) and 5.2 ps (nonradiative decay of the S 1 excited state) were sufficient to describe the data. The dynamics of the radical cation proved to be more complex. The main absorption band was shifted to 880 nm (D 0 → D 3 transition), showing a weak additional band at 1320 nm (D 0 → D 1 transition). We found, that D 3 decays to the lower-lying D 2 within 100 fs, followed by a decay to D 1 with a time constant of 0.9 ps. The D 1 state itself exhibited a dual behavior, the majority of the population is transferred to the ground state in 4.9 ps, while a small population decays on a longer timescale of 40 ps. Both transitions from D 1 were found to be fluorescent.

β-adrenergic effects on cardiac myofilaments and contraction in an integrated rabbit ventricular myocyte model

PubMed Central

Negroni, Jorge A.; Morotti, Stefano; Lascano, Elena C.; Gomes, Aldrin V.; Grandi, Eleonora; Puglisi, José L; Bers, Donald M.

2015-01-01

A five-state model of myofilament contraction was integrated into a well-established rabbit ventricular myocyte model of ion channels, Ca2+ transporters and kinase signaling to analyze the relative contribution of different phosphorylation targets to the overall mechanical response driven by β-adrenergic stimulation (β-AS). β-AS effect on sarcoplasmic reticulum Ca2+ handling, Ca2+, K+ and Cl− currents, and Na+/K+-ATPase properties were included based on experimental data. The inotropic effect on the myofilaments was represented as reduced myofilament Ca2+ sensitivity (XBCa) and titin stiffness, and increased cross-bridge (XB) cycling rate (XBcy). Assuming independent roles of XBCa and XBcy, the model reproduced experimental β-AS responses on action potentials and Ca2+ transient amplitude and kinetics. It also replicated the behavior of force-Ca2+, release-restretch, length-step, stiffness-frequency and force-velocity relationships, and increased force and shortening in isometric and isotonic twitch contractions. The β-AS effect was then switched off from individual targets to analyze their relative impact on contractility. Preventing β-AS effects on L-type Ca2+ channels or phospholamban limited Ca2+ transients and contractile responses in parallel, while blocking phospholemman and K+ channel (IKs) effects enhanced Ca2+ and inotropy. Removal of β-AS effects from XBCa enhanced contractile force while decreasing peak Ca2+ (due to greater Ca2+ buffering), but had less effect on shortening. Conversely, preventing β-AS effects on XBcy preserved Ca2+ transient effects, but blunted inotropy (both isometric force and especially shortening). Removal of titin effects had little impact on contraction. Finally, exclusion of β-AS from XBCa and XBcy while preserving effects on other targets resulted in preserved peak isometric force response (with slower kinetics) but nearly abolished enhanced shortening. β-AS effects on XBCa vs. XBcy have greater impact on isometric vs. isotonic contraction, respectively. PMID:25724724

A new code for predicting the thermo-mechanical and irradiation behavior of metallic fuels in sodium fast reactors

NASA Astrophysics Data System (ADS)

Karahan, Aydın; Buongiorno, Jacopo

2010-01-01

An engineering code to predict the irradiation behavior of U-Zr and U-Pu-Zr metallic alloy fuel pins and UO2-PuO2 mixed oxide fuel pins in sodium-cooled fast reactors was developed. The code was named Fuel Engineering and Structural analysis Tool (FEAST). FEAST has several modules working in coupled form with an explicit numerical algorithm. These modules describe fission gas release and fuel swelling, fuel chemistry and restructuring, temperature distribution, fuel-clad chemical interaction, and fuel and clad mechanical analysis including transient creep-fracture for the clad. Given the fuel pin geometry, composition and irradiation history, FEAST can analyze fuel and clad thermo-mechanical behavior at both steady-state and design-basis (non-disruptive) transient scenarios. FEAST was written in FORTRAN-90 and has a simple input file similar to that of the LWR fuel code FRAPCON. The metal-fuel version is called FEAST-METAL, and is described in this paper. The oxide-fuel version, FEAST-OXIDE is described in a companion paper. With respect to the old Argonne National Laboratory code LIFE-METAL and other same-generation codes, FEAST-METAL emphasizes more mechanistic, less empirical models, whenever available. Specifically, fission gas release and swelling are modeled with the GRSIS algorithm, which is based on detailed tracking of fission gas bubbles within the metal fuel. Migration of the fuel constituents is modeled by means of thermo-transport theory. Fuel-clad chemical interaction models based on precipitation kinetics were developed for steady-state operation and transients. Finally, a transient intergranular creep-fracture model for the clad, which tracks the nucleation and growth of the cavities at the grain boundaries, was developed for and implemented in the code. Reducing the empiricism in the constitutive models should make it more acceptable to extrapolate FEAST-METAL to new fuel compositions and higher burnup, as envisioned in advanced sodium reactors. FEAST-METAL was benchmarked against the open-literature EBR-II database for steady state and furnace tests (transients). The results show that the code is able to predict important phenomena such as clad strain, fission gas release, clad wastage, clad failure time, axial fuel slug deformation and fuel constituent redistribution, satisfactorily.

Exertional oxygen uptake kinetics: a stamen of stamina?

PubMed

Whipp, Brian J; Rossiter, H B; Ward, S A

2002-04-01

The fundamental pulmonary O(2) uptake (.VO(2)) response to moderate, constant-load exercise can be characterized as (d.VO(2)/dt)(tau)+Delta.VO(2) (t)=Delta.VO(2SS) where Delta.VO(2SS) is the steady-state response, and tau is the time constant, with the .VO(2) kinetics reflecting intramuscular O(2) uptake (.QO(2)) kinetics, to within 10%. The role of phosphocreatine (PCr) turnover in .QO(2) control can be explored using (31)P-MR spectroscopy, simultaneously with .VO(2). Although tau.VO(2) and tauPCr vary widely among subjects (approx. 20-65 s), they are not significantly different from each other, either at the on- or off-transient. A caveat to interpreting the "well-fit" exponential is that numerous units of similar Delta.VO(2SS) but with a wide tau distribution can also yield a .VO(2) response with an apparent single tau. This tau is, significantly, inversely correlated with lactate threshold and .VO(2max)(but is poorly predictive; a frail stamen, therefore), consistent with tau not characterizing a compartment with uniform kinetics. At higher intensities, the fundamental kinetics become supplemented with a slowly-developing phase, setting .VO(2)on a trajectory towards maximum .VO(2). This slow component is also demonstrable in Delta[PCr]: the decreased efficiency thereby reflecting a predominantly high phosphate-cost of force production rather than a high O(2)-cost of phosphate production. We also propose that the O(2)-deficit for the slow-component is more likely to reflect shifting Delta.VO(2SS) rather than a single one with a single tau.

Influence of fast and slow alkali myosin light chain isoforms on the kinetics of stretch-induced force transients of fast-twitch type IIA fibres of rat.

PubMed

Andruchov, Oleg; Galler, Stefan

2008-03-01

This study contributes to understand the physiological role of slow myosin light chain isoforms in fast-twitch type IIA fibres of skeletal muscle. These isoforms are often attached to the myosin necks of rat type IIA fibres, whereby the slow alkali myosin light chain isoform MLC1s is much more frequent and abundant than the slow regulatory myosin light chain isoform MLC2s. In the present study, single-skinned rat type IIA fibres were maximally Ca(2+) activated and subjected to stepwise stretches for causing a perturbation of myosin head pulling cycles. From the time course of the resulting force transients, myosin head kinetics was deduced. Fibres containing MLC1s exhibited slower kinetics independently of the presence or absence of MLC2s. At the maximal MLC1s concentration of about 75%, the slowing was about 40%. The slowing effect of MLC1s is possibly due to differences in the myosin heavy chain binding sites of the fast and slow alkali MLC isoforms, which changes the rigidity of the myosin neck. Compared with the impact of myosin heavy chain isoforms in various fast-twitch fibre types, the influence of MLC1s on myosin head kinetics of type IIA fibres is much smaller. In conclusion, the physiological role of fast and slow MLC isoforms in type IIA fibres is a fine-tuning of the myosin head kinetics.

Photo-induced changes of the surface band bending in GaN: Influence of growth technique, doping and polarity

NASA Astrophysics Data System (ADS)

Winnerl, Andrea; Pereira, Rui N.; Stutzmann, Martin

2017-05-01

In this work, we use conductance and contact potential difference photo-transient data to study the influence of the growth technique, doping, and crystal polarity on the kinetics of photo-generated charges in GaN. We found that the processes, and corresponding time scales, involved in the decay of charge carriers generated at and close to the GaN surface via photo-excitation are notably independent of the growth technique, doping (n- and p-types), and also crystal polarity. Hence, the transfer of photo-generated charges from band states back to surface states proceeds always by hopping via shallow defect states in the space-charge region (SCR) close to the surface. Concerning the charge carrier photo-generation kinetics, we observe considerable differences between samples grown with different techniques. While for GaN grown by metal-organic chemical vapor deposition, the accumulation of photo-conduction electrons results mainly from a combined trapping-hopping process (slow), where photo-generated electrons hop via shallow defect states to the conduction band (CB), in hydride vapor phase epitaxy and molecular beam epitaxy materials, a faster direct process involving electron transfer via CB states is also present. The time scales of both processes are quite insensitive to the doping level and crystal polarity. However, these processes become irrelevant for very high doping levels (both n- and p-types), where the width of the SCR is much smaller than the photon penetration depth, and therefore, most charge carriers are generated outside the SCR.

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.

PubMed

Harris, Michael E; Piccirilli, Joseph A; York, Darrin M

2015-11-01

The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

The influence of exercise duration at VO2 max on the off-transient pulmonary oxygen uptake phase during high intensity running activity.

PubMed

Billat, V L; Hamard, L; Koralsztein, J P

2002-12-01

The purpose of this study was to examine the influence of time run at maximal oxygen uptake (VO2 max) on the off-transient pulmonary oxygen uptake phase after supra-lactate threshold runs. We hypothesised: 1) that among the velocities eliciting VO2 max there is a velocity threshold from which there is a slow component in the VO2-off transient, and 2) that at this velocity the longer the duration of this time at VO2 max (associated with an accumulated oxygen kinetics since VO2 can not overlap VO2 max), the longer is the off-transient phase of oxygen uptake kinetics. Nine long-distance runners performed five maximal tests on a synthetic track (400 m) while breathing through the COSMED K4b2 portable, telemetric metabolic analyser: i) an incremental test which determined VO2 max, the minimal velocity associated with VO2 max (vVO2 max) and the velocity at the lactate threshold (vLT), ii) and in a random order, four supra-lactate threshold runs performed until exhaustion at vLT + 25, 50, 75 and 100% of the difference between vLT and vVO2 max (vdelta25, vdelta50, vdelta75, vdelta100). At vdelta25, vdelta50 (= 91.0 +/- 0.9% vVO2 max) and vdelta75, an asymmetry was found between the VO2 on (double exponential) and off-transient (mono exponential) phases. Only at vdelta75 there was at positive relationship between the time run at VO2 max (%tlimtot) and the VO2 recovery time constant (Z = 1.8, P = 0.05). In conclusion, this study showed that among the velocities eliciting VO2 max, vdelta75 is the velocity at which the longer the duration of the time at VO2 max, the longer is the off-transient phase of oxygen uptake kinetics. It may be possible that at vdelta50 there is not an accumulated oxygen deficit during the plateau of VO2 at VO2 max and that the duration of the time at VO2 max during the exhaustive runs at vdelta100, could be too short to induce an accumulating oxygen deficit affecting the oxygen recovery.

Origin of switching current transients in TIPS-pentacene based organic thin-film transistor with polymer dielectric

NASA Astrophysics Data System (ADS)

Singh, Subhash; Mohapatra, Y. N.

2017-06-01

We have investigated switch-on drain-source current transients in fully solution-processed thin film transistors based on 6,13-bis(triisopropylsilylethynyl) pentacene (TIPS-pentacene) using cross-linked poly-4-vinylphenol as a dielectric. We show that the nature of the transient (increasing or decreasing) depends on both the temperature and the amplitude of the switching pulse at the gate. The isothermal transients are analyzed spectroscopically in a time domain to extract the degree of non-exponentiality and its possible origin in trap kinetics. We propose a phenomenological model in which the exchange of electrons between interfacial ions and traps controls the nature of the drain current transients dictated by the Fermi level position. The origin of interfacial ions is attributed to the essential fabrication step of UV-ozone treatment of the dielectric prior to semiconductor deposition.

Formation and dissolution processes of the 6-thioguanine (6TG) self-assembled monolayer. A kinetic study.

PubMed

Madueño, Rafael; Pineda, Teresa; Sevilla, José Manuel; Blázquez, Manuel

2005-02-03

This is a report on the kinetics of the destruction and formation processes of the 6-thioguanine self-assembled monolayer (6TG SAM) on a mercury electrode from acid solutions by chronoamperometry. The destruction of the 6TG SAM that has been previously formed under open circuit potential conditions is carried out by stepping the potential from an initial value where the chemisorbed layer is stable up to potentials where the molecules are no longer chemisorbed. The destruction of the SAM has been described by a model that involves three types of contributions: (i) a Langmuir-type adsorption process, (ii) a 2D nucleation mechanism followed by a growth controlled by surface diffusion, and (iii) a 2D nucleation mechanism followed by a growth at a constant rate. The nonlinear fit of the experimental transients by using this procedure allows the quantitative determination of the individual contributions to the overall process. The kinetics of the formation process is studied under electrochemical conditions. The chronoamperometric experiment allows us to monitor the early stages of 6TG SAM formation. The implications of the physisorbed state at low potentials in the type of monolayer formation and destruction processes as well as the influence of temperature are also discussed.

Nucleation and evolution of spherical crystals with allowance for their unsteady-state growth rates

NASA Astrophysics Data System (ADS)

Alexandrov, D. V.

2018-02-01

The growth dynamics of a spherical crystal in a metastable liquid is analyzed theoretically. The unsteady-state contributions to the crystal radius and its growth rate are found as explicit functions of metastability level Δ and time t. It is shown that the fundamental contribution to the growth rate represents the time independent solution of a similar temperature conductivity problem (Alexandrov and Malygin 2013 J. Phys. A: Math. Theor. 46 455101) whereas the next unsteady-state contribution is proportional to Δ2 t . On the basis of these explicit unsteady-state solutions, the process of transient nucleation and growth of spherical crystals in a metastable system is theoretically studied at the intermediate stage of phase transformation. A complete analytical solution for the particle-radius distribution function and metastability level is constructed with allowance for the Weber-Volmer-Frenkel-Zel’dovich and Meirs kinetic mechanisms. It is shown that the obtained unsteady-state contribution to the crystal growth rate plays an important role in the nucleation process and drastically changes the particle-radius distribution function.

Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow.

PubMed

Das, Biswajit; Gangopadhyay, Gautam

2018-05-07

In the framework of large deviation theory, we have characterized nonequilibrium turnover statistics of enzyme catalysis in a chemiostatic flow with externally controllable parameters, like substrate injection rate and mechanical force. In the kinetics of the process, we have shown the fluctuation theorems in terms of the symmetry of the scaled cumulant generating function (SCGF) in the transient and steady state regime and a similar symmetry rule is reflected in a large deviation rate function (LDRF) as a property of the dissipation rate through boundaries. Large deviation theory also gives the thermodynamic force of a nonequilibrium steady state, as is usually recorded experimentally by a single molecule technique, which plays a key role responsible for the dynamical symmetry of the SCGF and LDRF. Using some special properties of the Legendre transformation, here, we have provided a relation between the fluctuations of fluxes and dissipation rates, and among them, the fluctuation of the turnover rate is routinely estimated but the fluctuation in the dissipation rate is yet to be characterized for small systems. Such an enzymatic reaction flow system can be a very good testing ground to systematically understand the rare events from the large deviation theory which is beyond fluctuation theorem and central limit theorem.

Large deviation theory for the kinetics and energetics of turnover of enzyme catalysis in a chemiostatic flow

NASA Astrophysics Data System (ADS)

Das, Biswajit; Gangopadhyay, Gautam

2018-05-01

In the framework of large deviation theory, we have characterized nonequilibrium turnover statistics of enzyme catalysis in a chemiostatic flow with externally controllable parameters, like substrate injection rate and mechanical force. In the kinetics of the process, we have shown the fluctuation theorems in terms of the symmetry of the scaled cumulant generating function (SCGF) in the transient and steady state regime and a similar symmetry rule is reflected in a large deviation rate function (LDRF) as a property of the dissipation rate through boundaries. Large deviation theory also gives the thermodynamic force of a nonequilibrium steady state, as is usually recorded experimentally by a single molecule technique, which plays a key role responsible for the dynamical symmetry of the SCGF and LDRF. Using some special properties of the Legendre transformation, here, we have provided a relation between the fluctuations of fluxes and dissipation rates, and among them, the fluctuation of the turnover rate is routinely estimated but the fluctuation in the dissipation rate is yet to be characterized for small systems. Such an enzymatic reaction flow system can be a very good testing ground to systematically understand the rare events from the large deviation theory which is beyond fluctuation theorem and central limit theorem.

Choreographing an enzyme’s dance

PubMed Central

Villali, Janice; Kern, Dorothee

2010-01-01

While ground state structures combined with chemical tools and enzyme kinetics deliver useful information on possible chemical mechanisms of enzyme catalysis, they do not unravel the finely balanced energy inventory to explain the impressive rate enhancement of enzymes. For this goal, a complete description of enzyme catalysis in the form of an energy landscape is needed. Since the rate of catalysis is determined by the climb over a sequence of energy barriers, we focus here on the critical question of transition pathways. A combination of time-resolved NMR and simulation deliver a glimpse into how proteins can so efficiently move within the ensemble of the native conformations while avoiding unfolding during that journey. The loss of energy due to breakage of native contacts is compensated by non-native transient hydrogen bonds during the transition thereby “holding on” to the energy until the new native contacts form that define the alternate functional state. The use of kinetic isotope effects (KIE) to study the chemical step show that coordinated atomic fluctuations of the protein component dictate the probability of “correct” distance and orientation, due to its extreme sensitivity to distance. The examples here stress the point that highly choreographed conformational sampling together with chemical integrity is a prerequisite for efficient enzyme catalysis. PMID:20822946

Two Components of Voltage-Dependent Inactivation in Cav1.2 Channels Revealed by Its Gating Currents

PubMed Central

Ferreira, Gonzalo; Ríos, Eduardo; Reyes, Nicolás

2003-01-01

Voltage-dependent inactivation (VDI) was studied through its effects on the voltage sensor in Cav1.2 channels expressed in tsA 201 cells. Two kinetically distinct phases of VDI in onset and recovery suggest the presence of dual VDI processes. Upon increasing duration of conditioning depolarizations, the half-distribution potential (V1/2) of intramembranous mobile charge was negatively shifted as a sum of two exponential terms, with time constants 0.5 s and 4 s, and relative amplitudes near 50% each. This kinetics behavior was consistent with that of increment of maximal charge related to inactivation (Qn). Recovery from inactivation was also accompanied by a reduction of Qn that varied with recovery time as a sum of two exponentials. The amplitudes of corresponding exponential terms were strongly correlated in onset and recovery, indicating that channels recover rapidly from fast VDI and slowly from slow VDI. Similar to charge “immobilization,” the charge moved in the repolarization (OFF) transient became slower during onset of fast VDI. Slow VDI had, instead, hallmarks of interconversion of charge. Confirming the mechanistic duality, fast VDI virtually disappeared when Li+ carried the current. A nine-state model with parallel fast and slow inactivation pathways from the open state reproduces most of the observations. PMID:12770874

Theory of parametrically amplified electron-phonon superconductivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Babadi, Mehrtash; Knap, Michael; Martin, Ivar

2017-07-01

Ultrafast optical manipulation of ordered phases in strongly correlated materials is a topic of significant theoretical, experimental, and technological interest. Inspired by a recent experiment on light-induced superconductivity in fullerenes [M. Mitrano et al., Nature (London) 530, 461 (2016)], we develop a comprehensive theory of light-induced superconductivity in driven electron-phonon systemswith lattice nonlinearities. In analogy with the operation of parametric amplifiers, we show how the interplay between the external drive and lattice nonlinearities lead to significantly enhanced effective electron-phonon couplings. We provide a detailed and unbiased study of the nonequilibrium dynamics of the driven system using the real-time Green's functionmore » technique. To this end, we develop a Floquet generalization of the Migdal-Eliashberg theory and derive a numerically tractable set of quantum Floquet-Boltzmann kinetic equations for the coupled electron-phonon system. We study the role of parametric phonon generation and electronic heating in destroying the transient superconducting state. Finally, we predict the transient formation of electronic Floquet bands in time-and angle-resolved photoemission spectroscopy experiments as a consequence of the proposed mechanism.« less

Transient luminescence induced by electrical refilling of charge carrier traps of dislocation network at hydrophilically bonded Si wafers interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bondarenko, Anton; Vyvenko, Oleg

2014-02-21

Dislocation network (DN) at hydrophilically bonded Si wafers interface is placed in space charge region (SCR) of a Schottky diode at a depth of about 150 nm from Schottky electrode for simultaneous investigation of its electrical and luminescent properties. Our recently proposed pulsed traps refilling enhanced luminescence (Pulsed-TREL) technique based on the effect of transient luminescence induced by refilling of charge carrier traps with electrical pulses is further developed and used as a tool to establish DN energy levels responsible for D1 band of dislocation-related luminescence in Si (DRL). In present work we do theoretical analysis and simulation of trapsmore » refilling kinetics dependence on refilling pulse magnitude (Vp) in two levels model: shallow and deep. The influence of initial charge state of deep level on shallow level occupation-Vp dependence is discussed. Characteristic features predicted by simulations are used for Pulsed-TREL experimental results interpretation. We conclude that only shallow (∼0.1 eV from conduction and valence band) energetic levels in the band gap participate in D1 DRL.« less

Modeling the heating and atomic kinetics of a photoionized neon plasma experiment

NASA Astrophysics Data System (ADS)

Lockard, Tom E.

Motivated by gas cell photoionized plasma experiments performed by our group at the Z facility of Sandia National Laboratories, we discuss in this dissertation a modeling study of the heating and ionization of the plasma for conditions characteristic of these experiments. Photoionized plasmas are non-equilibrium systems driven by a broadband x-ray radiation flux. They are commonly found in astrophysics but rarely seen in the laboratory. Several modeling tools have been employed: (1) a view-factor computer code constrained with side x-ray power and gated monochromatic image measurements of the z-pinch radiation, to model the time-history of the photon-energy resolved x-ray flux driving the photoionized plasma, (2) a Boltzmann self-consistent electron and atomic kinetics model to simulate the electron distribution function and configuration-averaged atomic kinetics, (3) a radiation-hydrodynamics code with inline non-equilibrium atomic kinetics to perform a comprehensive numerical simulation of the experiment and plasma heating, and (4) steady-state and time-dependent collisional-radiative atomic kinetics calculations with fine-structure energy level description to assess transient effects in the ionization and charge state distribution of the plasma. The results indicate that the photon-energy resolved x-ray flux impinging on the front window of the gas cell is very well approximated by a linear combination of three geometrically-diluted Planckian distributions. Knowledge of the spectral details of the x-ray drive turned out to be important for the heating and ionization of the plasma. The free electrons in the plasma thermalize quickly relative to the timescales associated with the time-history of the x-ray drive and the plasma atomic kinetics. Hence, electrons are well described by a Maxwellian energy distribution of a single temperature. This finding is important to support the application of a radiation-hydrodynamic model to simulate the experiment. It is found that the computed plasma heating compares well with experimental observation when the effects of the windows, hydrodynamics, and non-equilbirium neon emissivity and opacity are employed. The atomic kinetics shows significant time-dependent effects because the timescale of the x-ray drive is too short compared to that of the photoionization process. These modeling and simulation results are important to test theory and modeling assumptions and approximations, and also to provide guidance on data interpretation and analysis.

Topics in Diffusion Limited Reaction Processes

NASA Astrophysics Data System (ADS)

Lin, Jian-Cheng

We study, both theoretically and numerically, the macroscopic particle concentration in a class of simple diffusion-limited reactions: one species coagulation A + A to A, reversible coagulation A + A rightleftharpoons A, A + A to A with particle input, A + A rightleftharpoons A with particle input, single species annihilation A + A to inert, and two species annihilation A + B to inert. The main interest is in the asymptotic behavior of the particle concentration. We review the standard mean-field theory, mass-reaction kinetics and the associated nonlinear rate and diffusion-reaction equations. Theoretically we study the concentration using several closure schemes for truncating the infinite hierarchy of the kinetic equations for the joint density functions. Our goal is to evaluate the quality of some nonsystematic approximations by comparison with exact solutions. It is found that these approximations are very good at capturing the asymptotic behavior of the particle concentrations in the irreversible reactions, while they fail to predict the far-from-equilibrium dynamic phase transition in the one dimensional reversible coagulation reaction predicted by exact results. Numerically we use Monte Carlo simulation to study concentrations in the single species reversible coagulation process. In one dimension the numerical results are in excellent agreement with the exact analytic results. In two dimensions, our simulation data in the transient states suggest an interesting scaling for the deviation of the concentration from its equilibrium value, delta C(t) ~ exp( -beta(C_0)t^{alpha(C_0) }), where alpha(C_0) and beta(C_0) are functions of the initial concentration C_0. However, it seems unlikely to be able to answer the question of the existence of a dynamic phase transition in two dimensions by Monte Carlo simulation within a reasonable CPU time due to the long persistence of the transient states. In an appendix we solve exactly an annihilation-related percolation problem.

Heart failure drug changes the mechanoenzymology of the cardiac myosin powerstroke.

PubMed

Rohde, John A; Thomas, David D; Muretta, Joseph M

2017-03-07

Omecamtiv mecarbil (OM), a putative heart failure therapeutic, increases cardiac contractility. We hypothesize that it does this by changing the structural kinetics of the myosin powerstroke. We tested this directly by performing transient time-resolved FRET on a ventricular cardiac myosin biosensor. Our results demonstrate that OM stabilizes myosin's prepowerstroke structural state, supporting previous measurements showing that the drug shifts the equilibrium constant for myosin-catalyzed ATP hydrolysis toward the posthydrolysis biochemical state. OM slowed the actin-induced powerstroke, despite a twofold increase in the rate constant for actin-activated phosphate release, the biochemical step in myosin's ATPase cycle associated with force generation and the conversion of chemical energy into mechanical work. We conclude that OM alters the energetics of cardiac myosin's mechanical cycle, causing the powerstroke to occur after myosin weakly binds to actin and releases phosphate. We discuss the physiological implications for these changes.

Ultrafast Photoinduced Symmetry-Breaking Charge Separation and Electron Sharing in Perylenediimide Molecular Triangles.

PubMed

Wu, Yilei; Young, Ryan M; Frasconi, Marco; Schneebeli, Severin T; Spenst, Peter; Gardner, Daniel M; Brown, Kristen E; Würthner, Frank; Stoddart, J Fraser; Wasielewski, Michael R

2015-10-21

We report on a visible-light-absorbing chiral molecular triangle composed of three covalently linked 1,6,7,12-tetra(phenoxy)perylene-3,4:9,10-bis(dicarboximide) (PDI) units. The rigid triangular architecture reduces the electronic coupling between the PDIs, so ultrafast symmetry-breaking charge separation is kinetically favored over intramolecular excimer formation, as revealed by femtosecond transient absorption spectroscopy. Photoexcitation of the PDI triangle dissolved in CH2Cl2 gives PDI(+•)-PDI(-•) in τCS = 12.0 ± 0.2 ps. Fast subsequent intramolecular electron/hole hopping can equilibrate the six possible energetically degenerate ion-pair states, as suggested by electron paramagnetic resonance/electron-nuclear double resonance spectroscopy, which shows that one-electron reduction of the PDI triangle results in complete electron sharing among the three PDIs. Charge recombination of PDI(+•)-PDI(-•) to the ground state occurs in τCR = 1.12 ± 0.01 ns with no evidence of triplet excited state formation.

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy

DOE PAGES

Hayes, Dugan; Kohler, Lars; Hadt, Ryan G.; ...

2017-11-28

Here, the kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(I) bis(phenanthroline)/ruthenium(II) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(I)–Ru(II) analogs of the homodinuclear Cu(I)–Cu(I) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These resultsmore » suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.« less

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayes, Dugan; Kohler, Lars; Hadt, Ryan G.

Here, the kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(I) bis(phenanthroline)/ruthenium(II) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(I)–Ru(II) analogs of the homodinuclear Cu(I)–Cu(I) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These resultsmore » suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations.« less

Robustness of hydrological indicators for transient and stabilized climate states

NASA Astrophysics Data System (ADS)

Boulange, J. E.; Hanasaki, N.

2017-12-01

By signing the Paris agreement, countries have committed to pursue efforts to limit global warming to +1.5 °C relative to pre-industrial levels. Consequently, there is a growing interest in better understanding the impacts of a +1.5°C world. Previous analyses were conducted by considering a time slice period, centered on the year when the global mean temperature (GMT) crosses the +1.5°C threshold (Fig. 1). This time slice period is characterized by a transient state which may influence the reported results (transient climate state). Ideally, analyses should be carried under the condition the GMT is stabilized at +1.5°C (stabilized climate state) but, such targeted simulations do not exist for most GCMs.1A global hydrological model, the H08 model,2 and hydrological indicators (HI) obtained for the transient and stabilized states, are used to answer the following questions: (1) are there quantifiable differences between the HI computed for the transient and stabilized states? (2) can relations be derived between the HI computed for the transient and stabilized states? (3) what are the potential impacts induced by the differences in HI computed for the transient and stabilized states? Signal to noise ratios (S/N) obtained for the transient and stabilized states, in an identical warmer world (+1.7°C), are compared (Fig. 2). The S/N ratio computed for the stabilized state were significantly lower than those of the transient state for most regions and HI. However, at higher latitude, the S/N ratios computed for the two states were similar whereas for medium and low latitudes, the differences were more pronounced. For most regions and HI (except for surface temperature), the S/N ratios of the stabilized state were 10 to 20% weaker than those of the transient state. References:1 Knutti, R., Rogelj, J., Sedlacek, J. & Fischer, E. M. Nature Geosci (2016). 2 Hanasaki, N. et al. Hydrol. Earth Syst. Sci. (2008).

SUPPLY AND DEMAND IN CEREBRAL ENERGY METABOLISM: THE ROLE OF NUTRIENT TRANSPORTERS

PubMed Central

Simpson, Ian A.; Carruthers, Anthony; Vannucci, Susan J.

2007-01-01

Glucose is the obligate energetic fuel for the mammalian brain and most studies of cerebral energy metabolism assume that the vast majority of cerebral glucose utilization fuels neuronal activity via oxidative metabolism, both in the basal and activated state. Glucose transporter proteins (GLUTs) deliver glucose from the circulation to the brain: GLUT1 in the microvascular endothelial cells of the blood brain barrier (BBB) and glia; GLUT3 in neurons. Lactate, the glycolytic product of glucose metabolism, is transported into and out of neural cells by the monocarboxylate transporters: MCT1 in the BBB and astrocytes and MCT2 in neurons. The proposal of the astrocyte-neuron lactate shuttle hypothesis (Pellerin and Magistretti, 1994) suggested that astrocytes play the primary role in cerebral glucose utilization and generate lactate for neuronal energetics, especially during activation. Since the identification of the GLUTs and MCTs in brain, much has been learned about their transport properties, i.e. capacity and affinity for substrate, which must be considered in any model of cerebral glucose uptake and utilization. Using concentrations and kinetic parameters of GLUT1 and GLUT3 in BBB endothelial cells, astrocytes and neurons, along with the corresponding kinetic properties of the monocarboxylate transporters, we have successfully modeled brain glucose and lactate levels as well as lactate transients in response to neuronal stimulation. Simulations based on these parameters suggest that glucose readily diffuses through the basal lamina and interstitium to neurons, which are primarily responsible for glucose uptake, metabolism, and the generation of the lactate transients observed upon neuronal activation. PMID:17579656

Measuring the Influence of Pearlite Dissolution on the Transient Dynamic Strength of Rapidly Heated Plain Carbon Steels

NASA Astrophysics Data System (ADS)

Mates, Steven; Stoudt, Mark; Gangireddy, Sindhura

2016-07-01

Carbon steels containing ferrite-pearlite microstructures weaken dramatically when pearlite dissolves into austenite on heating. The kinetics of this phase transformation, while fast, can play a role during dynamic, high-temperature manufacturing processes, including high-speed machining, when the time scale of this transformation is on the order of the manufacturing process itself. In such a regime, the mechanical strength of carbon steel can become time dependent. The present work uses a rapidly heated, high-strain-rate mechanical test to study the effect of temperature and time on the amount of pearlite dissolved and on the resulting transient effect on dynamic strength of a low and a high carbon (eutectoid) steel. Measurements indicate that the transient effect occurs for heating times less than about 3 s. The 1075 steel loses about twice the strength compared to the 1018 steel (85 MPa to 45 MPa) owing to its higher initial pearlite volume fraction. Pearlite dissolution is confirmed by metallographic examination of tested samples. Despite the different starting pearlite fractions, the kinetics of dissolution are comparable for the two steels, owing to the similarity in their initial pearlite morphology.

The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wongnate, T.; Sliwa, D.; Ginovska, B.

2016-05-19

Methyl-coenzyme M reductase (MCR), the rate-limiting enzyme in methanogenesis and anaerobic methane oxidation, is responsible for the production of over one billion tons of methane per year. The mechanism of methane synthesis is unknown, with the two leading proposals involving either a methyl-nickel(III) (Mechanism I) or methyl radical/Ni(II)-thiolate (Mechanism II) intermediate(s). When the reaction between the active Ni(I) enzyme with substrates was studied by transient kinetic, spectroscopic and computational methods, formation of an EPR-silent Ni(II)-thiolate intermediate was positively identified by magnetic circular dichroism spectroscopy. There was no evidence for an EPR-active methyl-Ni(III) species. Temperature-dependent transient kinetic studies revealed that themore » activation energy for the initial catalytic step closely matched the value computed by density functional theory for Mechanism II. Thus, our results demonstrate that biological methane synthesis occurs by generation of a methyl radical.« less

Kinetics of a gas adsorption compressor

NASA Technical Reports Server (NTRS)

Chan, C. K.; Tward, E.; Elleman, D. D.

1984-01-01

Chan (1981) has suggested that a process based on gas adsorption could be used as a means to drive a Joule-Thomson (J-T) device. The resulting system has several advantages. It is heat powered, it has no sealing, there are no mechanical moving parts, and no active control is required. In the present investigation, a two-phase model is used to analyze the transients of a gas adsorption compressor. The modeling of the adsorption process is based on a consideration of complete thermal and mechanical equilibrium between the gaseous phase and the adsorbed gas phase. The experimental arrangement for two sets of kinetic tests is discussed, and data regarding the experimental results are presented in graphs. For a theoretical study, a two-phase model was developed to predict the transient behavior of the compressor. A computer code was written to solve the governing equations with the aid of a standard forward marching predictor-corrector method.

The Energetics of Transient Eddies in the Martian Northern Hemisphere

NASA Astrophysics Data System (ADS)

Battalio, Joseph Michael; Szunyogh, Istvan; Lemmon, Mark T.

2016-10-01

The energetics of northern hemisphere transient waves in the Mars Analysis Correction Data Assimilation is analyzed. Three periods between the fall and spring equinoxes (Ls=200°-230°, 255°-285°, and 330°-360°) during three Mars Years are selected to exemplify the fall, winter, and spring wave activity. Fall and spring eddy energetics is similar with some inter-annual and inter-seasonal variability, but winter eddy kinetic energy and its transport are strongly reduced in intensity as a result of the solsticial pause in eddy activity. Barotropic energy conversion acts as a sink of eddy kinetic energy throughout the northern hemisphere eddy period with little reduction in amplitude during the solsticial pause. Baroclinic energy conversion acts as a source in fall and spring but disappears during the winter period as a result of the stabilized vertical shear profile of the westerly jet around winter solstice.

Spatio-temporal kinetics of growth hormone receptor signaling in single cells using FRET microscopy.

PubMed

Biener-Ramanujan, Eva; Ramanujan, V Krishnan; Herman, Brian; Gertler, Arieh

2006-08-01

The growth hormone (GH) receptor (R)-mediated JAK2 (Janus kinase-2)-STAT5 (signaling transducer and activator of transcription-5) pathway involves a cascade of protein-protein interactions and tyrosine phosphorylations that occur in a spatially and temporally sensitive manner in cells. To study GHR dimerization or GH-induced conformational change of predimerized GHRs and STAT5 activation kinetics in intact cells, fluorescence resonance energy transfer (FRET) and live-cell imaging methods were employed. FRET measurements at the membrane of HEK-293T cells co-expressing GHRs tagged at the C-terminus with cyan (C) and yellow (Y) fluorescent proteins (FPs) revealed transient GHR dimerization lasting 2-3 min, with a maximum at 3 min after GH stimulation, which was sufficient to induce STAT5 activation. The transient nature of the dimerization or GH-induced conformational change of predimerized GHRs kinetics was not a result of GHR internalization, as neither potassium- nor cholesterol-depletion treatments prolonged the FRET signal. YFP-tagged STAT5 recruitment to the membrane, binding to GHR-CFP, and phosphorylation, occurred within minutes of GH stimulation. Activated STAT5a-YFP did not show nuclear accumulation, despite nuclear pSTAT5 increase, suggesting high turnover of STAT5 nuclear shuttling. Although GHR dimerization and STAT5 activation have been reported previously, this is the first spatially resolved demonstration of GHR-signaling kinetics in intact cells.

Energetic and metabolic transient response of Saccharomyces cerevisiae to benzoic acid.

PubMed

Kresnowati, M T A P; van Winden, W A; van Gulik, W M; Heijnen, J J

2008-11-01

Saccharomyces cerevisiae is known to be able to adapt to the presence of the commonly used food preservative benzoic acid with a large energy expenditure. Some mechanisms for the adaptation process have been suggested, but its quantitative energetic and metabolic aspects have rarely been discussed. This study discusses use of the stimulus response approach to quantitatively study the energetic and metabolic aspects of the transient adaptation of S. cerevisiae to a shift in benzoic acid concentration, from 0 to 0.8 mM. The information obtained also serves as the basis for further utilization of benzoic acid as a tool for targeted perturbation of the energy system, which is important in studying the kinetics and regulation of central carbon metabolism in S. cerevisiae. Using this experimental set-up, we found significant fast-transient (< 3000 s) increases in O(2) consumption and CO(2) production rates, of approximately 50%, which reflect a high energy requirement for the adaptation process. We also found that with a longer exposure time to benzoic acid, S. cerevisiae decreases the cell membrane permeability for this weak acid by a factor of 10 and decreases the cell size to approximately 80% of the initial value. The intracellular metabolite profile in the new steady-state indicates increases in the glycolytic and tricarboxylic acid cycle fluxes, which are in agreement with the observed increases in specific glucose and O(2) uptake rates.

Exploring exciton relaxation and multiexciton generation in PbSe nanocrystals using hyperspectral near-IR probing.

PubMed

Gdor, Itay; Sachs, Hanan; Roitblat, Avishy; Strasfeld, David B; Bawendi, Moungi G; Ruhman, Sanford

2012-04-24

Hyperspectral femtosecond transient absorption spectroscopy is employed to record exciton relaxation and recombination in colloidal lead selenide (PbSe) nanocrystals in unprecedented detail. Results obtained with different pump wavelengths and fluences are scrutinized with regard to three issues: (1) early subpicosecond spectral features due to "hot" excitons are analyzed in terms of suggested underlying mechanisms; (2) global kinetic analysis facilitates separation of the transient difference spectra into single, double, and triple exciton state contributions, from which individual band assignments can be tested; and (3) the transient spectra are screened for signatures of multiexciton generation (MEG) by comparing experiments with excitation pulses both below and well above the theoretical threshold for multiplication. For the latter, a recently devised ultrafast pump-probe spectroscopic approach is employed. Scaling sample concentrations and pump pulse intensities inversely with the extinction coefficient at each excitation wavelength overcomes ambiguities due to direct multiphoton excitation, uncertainties of absolute absorption cross sections, and low signal levels. As observed in a recent application of this method to InAs core/shell/shell nanodots, no sign of MEG was detected in this sample up to photon energy 3.7 times the band gap. Accordingly, numerous reports of efficient MEG in other samples of PbSe suggest that the efficiency of this process varies from sample to sample and depends on factors yet to be determined.

CREKID: A computer code for transient, gas-phase combustion of kinetics

NASA Technical Reports Server (NTRS)

Pratt, D. T.; Radhakrishnan, K.

1984-01-01

A new algorithm was developed for fast, automatic integration of chemical kinetic rate equations describing homogeneous, gas-phase combustion at constant pressure. Particular attention is paid to the distinguishing physical and computational characteristics of the induction, heat-release and equilibration regimes. The two-part predictor-corrector algorithm, based on an exponentially-fitted trapezoidal rule, includes filtering of ill-posed initial conditions, automatic selection of Newton-Jacobi or Newton iteration for convergence to achieve maximum computational efficiency while observing a prescribed error tolerance. The new algorithm was found to compare favorably with LSODE on two representative test problems drawn from combustion kinetics.

Numerical Solution of Moving Phase Boundary and Diffusion-Induced Stress of Sn Anode in the Lithium-Ion Battery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Chun-Hao; Chason, Eric; Guduru, Pradeep R.

Here, we have previously observed a large transient stress in Sn film anodes at the beginning of the Sn-Li 2Sn 5 phase transformation. To understand this behavior, we use numerical modeling to simulate the kinetics of the 1-D moving boundary and Li diffusion in the Sn anodes. A mixture of diffusion-controlled and interface-controlled kinetics is found. The Li concentration in the Li 2Sn 5 phase remains near a steady-state profile as the phase boundary propagates, whereas the Li diffusion in Sn is more complicated. Li continuously diffuses into the Sn layer and produces a supersaturation; the Li can then diffusemore » toward the Sn/Li 2Sn 5 interface and contribute to further phase transformation. Finally, the evolution of Li concentration in the Sn induces strain which involves rate-dependent plasticity and elastic unloading, resulting in the complex stress evolution that is observed. In the long term, the measured stress is dominated by the stress in the growing Li 2Sn 5 phase.« less

Mechanistic pathways of recognition of a solvent-inaccessible cavity of protein by a ligand

NASA Astrophysics Data System (ADS)

Mondal, Jagannath; Pandit, Subhendu; Dandekar, Bhupendra; Vallurupalli, Pramodh

One of the puzzling questions in the realm of protein-ligand recognition is how a solvent-inaccessible hydrophobic cavity of a protein gets recognized by a ligand. We address the topic by simulating, for the first time, the complete binding process of benzene from aqueous media to the well-known buried cavity of L99A T4 Lysozyme at an atomistic resolution. Our multiple unbiased microsecond-long trajectories, which were completely blind to the location of target binding site, are able to unequivocally identify the kinetic pathways along which benzene molecule meanders across the solvent and protein and ultimately spontaneously recognizes the deeply buried cavity of L99A T4 Lysozyme at an accurate precision. Our simulation, combined with analysis based on markov state model and free energy calculation, reveals that there are more than one distinct ligand binding pathways. Intriguingly, each of the identified pathways involves the transient opening of a channel of the protein prior to ligand binding. The work will also decipher rich mechanistic details on unbinding kinetics of the ligand as obtained from enhanced sampling techniques.

Numerical Solution of Moving Phase Boundary and Diffusion-Induced Stress of Sn Anode in the Lithium-Ion Battery

DOE PAGES

Chen, Chun-Hao; Chason, Eric; Guduru, Pradeep R.

2017-08-02

Here, we have previously observed a large transient stress in Sn film anodes at the beginning of the Sn-Li 2Sn 5 phase transformation. To understand this behavior, we use numerical modeling to simulate the kinetics of the 1-D moving boundary and Li diffusion in the Sn anodes. A mixture of diffusion-controlled and interface-controlled kinetics is found. The Li concentration in the Li 2Sn 5 phase remains near a steady-state profile as the phase boundary propagates, whereas the Li diffusion in Sn is more complicated. Li continuously diffuses into the Sn layer and produces a supersaturation; the Li can then diffusemore » toward the Sn/Li 2Sn 5 interface and contribute to further phase transformation. Finally, the evolution of Li concentration in the Sn induces strain which involves rate-dependent plasticity and elastic unloading, resulting in the complex stress evolution that is observed. In the long term, the measured stress is dominated by the stress in the growing Li 2Sn 5 phase.« less

Comparative Risks of Aldehyde Constituents in Cigarette Smoke Using Transient Computational Fluid Dynamics/Physiologically Based Pharmacokinetic Models of the Rat and Human Respiratory Tracts

PubMed Central

Corley, Richard A.; Kabilan, Senthil; Kuprat, Andrew P.; Carson, James P.; Jacob, Richard E.; Minard, Kevin R.; Teeguarden, Justin G.; Timchalk, Charles; Pipavath, Sudhakar; Glenny, Robb; Einstein, Daniel R.

2015-01-01

Computational fluid dynamics (CFD) modeling is well suited for addressing species-specific anatomy and physiology in calculating respiratory tissue exposures to inhaled materials. In this study, we overcame prior CFD model limitations to demonstrate the importance of realistic, transient breathing patterns for predicting site-specific tissue dose. Specifically, extended airway CFD models of the rat and human were coupled with airway region-specific physiologically based pharmacokinetic (PBPK) tissue models to describe the kinetics of 3 reactive constituents of cigarette smoke: acrolein, acetaldehyde and formaldehyde. Simulations of aldehyde no-observed-adverse-effect levels for nasal toxicity in the rat were conducted until breath-by-breath tissue concentration profiles reached steady state. Human oral breathing simulations were conducted using representative aldehyde yields from cigarette smoke, measured puff ventilation profiles and numbers of cigarettes smoked per day. As with prior steady-state CFD/PBPK simulations, the anterior respiratory nasal epithelial tissues received the greatest initial uptake rates for each aldehyde in the rat. However, integrated time- and tissue depth-dependent area under the curve (AUC) concentrations were typically greater in the anterior dorsal olfactory epithelium using the more realistic transient breathing profiles. For human simulations, oral and laryngeal tissues received the highest local tissue dose with greater penetration to pulmonary tissues than predicted in the rat. Based upon lifetime average daily dose comparisons of tissue hot-spot AUCs (top 2.5% of surface area-normalized AUCs in each region) and numbers of cigarettes smoked/day, the order of concern for human exposures was acrolein > formaldehyde > acetaldehyde even though acetaldehyde yields were 10-fold greater than formaldehyde and acrolein. PMID:25858911

Transient Kinetics Define a Complete Kinetic Model for Protein Arginine Methyltransferase 1*

PubMed Central

Hu, Hao; Luo, Cheng; Zheng, Y. George

2016-01-01

Protein arginine methyltransferases (PRMTs) are the enzymes responsible for posttranslational methylation of protein arginine residues in eukaryotic cells, particularly within the histone tails. A detailed mechanistic model of PRMT-catalyzed methylation is currently lacking, but it is essential for understanding the functions of PRMTs in various cellular pathways and for efficient design of PRMT inhibitors as potential treatments for a range of human diseases. In this work, we used stopped-flow fluorescence in combination with global kinetic simulation to dissect the transient kinetics of PRMT1, the predominant type I arginine methyltransferase. Several important mechanistic insights were revealed. The cofactor and the peptide substrate bound to PRMT1 in a random manner and then followed a kinetically preferred pathway to generate the catalytic enzyme-cofactor-substrate ternary complex. Product release proceeded in an ordered fashion, with peptide dissociation followed by release of the byproduct S-adenosylhomocysteine. Importantly, the dissociation rate of the monomethylated intermediate from the ternary complex was much faster than the methyl transfer. Such a result provided direct evidence for distributive arginine dimethylation, which means the monomethylated substrate has to be released to solution and rebind with PRMT1 before it undergoes further methylation. In addition, cofactor binding involved a conformational transition, likely an open-to-closed conversion of the active site pocket. Further, the histone H4 peptide bound to the two active sites of the PRMT1 homodimer with differential affinities, suggesting a negative cooperativity mechanism of substrate binding. These findings provide a new mechanistic understanding of how PRMTs interact with their substrates and transfer methyl groups. PMID:27834681

Oxidation of SiC Fiber-Reinforced SiC Matrix Composites with a BN Interphase

NASA Technical Reports Server (NTRS)

Opila, Elizabeth; Boyd, Meredith K.

2010-01-01

SiC-fiber reinforced SiC matrix composites with a BN interphase were oxidized in reduced oxygen partial pressures of oxygen to simulate the environment for hypersonic vehicle leading edge applications. The constituent fibers as well as composite coupons were oxidized in oxygen partial pressures ranging from 1000 ppm O2 to 5% O2 balance argon. Exposure temperatures ranged from 816 C to 1353 C (1500 F to 2450 F). The oxidation kinetics of the coated fibers were monitored by thermogravimetric analysis (TGA). An initial rapid transient weight gain was observed followed by parabolic kinetics. Possible mechanisms for the transient oxidation are discussed. One edge of the composite coupon seal coat was ground off to simulate damage to the composite which allowed oxygen ingress to the interior of the composite. Oxidation kinetics of the coupons were characterized by scanning electron microscopy since the weight changes were minimal. It was found that sealing of the coupon edge by silica formation occurred. Differences in the amount and morphology of the sealing silica as a function of time, temperature and oxygen partial pressure are discussed. Implications for use of these materials for hypersonic vehicle leading edge materials are summarized.

A Comparison of Martian Transient Wave Energetics in High and Low Optical Depth Environments

NASA Astrophysics Data System (ADS)

Battalio, J. M.; Szunyogh, I.; Lemmon, M. T.

2016-12-01

The local energetics of individual transient eddies from the Mars Analysis Correction Data Assimilation (MACDA) is compared between a year with a global-scale dust storm (MY 25) and two years of relatively low optical depth conditions. Eddies in each year are considered from a period of strong wave activity in the northern hemisphere before the winter solstice (Ls=170-240°). The local growth of eddies is typically triggered by geopotential flux convergence. While all waves exhibit some baroclinic growth, baroclinic energy conversion is weaker in the waves that occur during the global-scale dust storm. The weaker baroclinic energy conversion in these waves, however, is compensated by a more intense barotropic transfer of the kinetic energy from the mean flow to the waves: the contribution from barotropic energy conversion allows eddies during the global-scale dust storm to attain roughly the same maximum eddy kinetic energy as eddies during the low optical depth years. Individual eddies in the waves decay through a combination of barotropic conversion of the kinetic energy from the waves to the mean flow, geopotential flux divergence, and dissipation in both the high- and the low-optical-depth years.

Scanning Laser Ophthalmoscope Measurement of Local Fundus Reflectance and Autofluorescence Changes Arising from Rhodopsin Bleaching and Regeneration

PubMed Central

Morgan, Jessica I. W.; Pugh, Edward N.

2013-01-01

Purpose. We measured the bleaching and regeneration kinetics of rhodopsin in the living human eye with two-wavelength, wide-field scanning laser ophthalmoscopy (SLO), and investigated the effect of rhodopsin bleaching on autofluorescence intensity. Methods. The retina was imaged with an Optos P200C SLO by its reflectance of 532 and 633 nm light, and its autofluorescence excited by 532 nm light, before and after exposure to lights calibrated to bleach rhodopsin substantially. Bleaching was confined to circular retinal regions of 4.8° visual angle located approximately 16° superotemporal and superonasal to fixation. Images were captured as 12-bit tiff files and postprocessed to extract changes in reflectance and autofluorescence. Results. At the locus of bleaching transient increases in reflectance of the 532 nm, but not the 633 nm beam were observed readily and quantified. A transient increase in autofluorescence also occurred. The action spectrum, absolute sensitivity, and recovery of the 532 nm reflectance increase were consistent with previous measurements of human rhodopsin's spectral sensitivity, photosensitivity, and regeneration kinetics. The autofluorescence changes closely tracked the changes in rhodopsin density. Conclusions. The bleaching and regeneration kinetics of rhodopsin can be measured locally in the human retina with a widely available SLO. The increased autofluorescence excited by 532 nm light upon bleaching appears primarily due to transient elimination of rhodopsin's screening of autofluorescent fluorochromes in the RPE. The spatially localized measurement with a widely available SLO of rhodopsin, the most abundant protein in the retina, could be a valuable adjunct to retinal health assessment. PMID:23412087

Scanning laser ophthalmoscope measurement of local fundus reflectance and autofluorescence changes arising from rhodopsin bleaching and regeneration.

PubMed

Morgan, Jessica I W; Pugh, Edward N

2013-03-01

We measured the bleaching and regeneration kinetics of rhodopsin in the living human eye with two-wavelength, wide-field scanning laser ophthalmoscopy (SLO), and investigated the effect of rhodopsin bleaching on autofluorescence intensity. The retina was imaged with an Optos P200C SLO by its reflectance of 532 and 633 nm light, and its autofluorescence excited by 532 nm light, before and after exposure to lights calibrated to bleach rhodopsin substantially. Bleaching was confined to circular retinal regions of 4.8° visual angle located approximately 16° superotemporal and superonasal to fixation. Images were captured as 12-bit tiff files and postprocessed to extract changes in reflectance and autofluorescence. At the locus of bleaching transient increases in reflectance of the 532 nm, but not the 633 nm beam were observed readily and quantified. A transient increase in autofluorescence also occurred. The action spectrum, absolute sensitivity, and recovery of the 532 nm reflectance increase were consistent with previous measurements of human rhodopsin's spectral sensitivity, photosensitivity, and regeneration kinetics. The autofluorescence changes closely tracked the changes in rhodopsin density. The bleaching and regeneration kinetics of rhodopsin can be measured locally in the human retina with a widely available SLO. The increased autofluorescence excited by 532 nm light upon bleaching appears primarily due to transient elimination of rhodopsin's screening of autofluorescent fluorochromes in the RPE. The spatially localized measurement with a widely available SLO of rhodopsin, the most abundant protein in the retina, could be a valuable adjunct to retinal health assessment.

Deactivation kinetics of acid-sensing ion channel 1a are strongly pH-sensitive.

PubMed

MacLean, David M; Jayaraman, Vasanthi

2017-03-21

Acid-sensing ion channels (ASICs) are trimeric cation-selective ion channels activated by protons in the physiological range. Recent reports have revealed that postsynaptically localized ASICs contribute to the excitatory postsynaptic current by responding to the transient acidification of the synaptic cleft that accompanies neurotransmission. In response to such brief acidic transients, both recombinant and native ASICs show extremely rapid deactivation in outside-out patches when jumping from a pH 5 stimulus to a single resting pH of 8. Given that the resting pH of the synaptic cleft is highly dynamic and depends on recent synaptic activity, we explored the kinetics of ASIC1a and 1a/2a heteromers to such brief pH transients over a wider [H + ] range to approximate neuronal conditions better. Surprisingly, the deactivation of ASICs was steeply dependent on the pH, spanning nearly three orders of magnitude from extremely fast (<1 ms) at pH 8 to very slow (>300 ms) at pH 7. This study provides an example of a ligand-gated ion channel whose deactivation is sensitive to agonist concentrations that do not directly activate the receptor. Kinetic simulations and further mutagenesis provide evidence that ASICs show such steeply agonist-dependent deactivation because of strong cooperativity in proton binding. This capacity to signal across such a large synaptically relevant bandwidth enhances the response to small-amplitude acidifications likely to occur at the cleft and may provide ASICs with the ability to shape activity in response to the recent history of the synapse.

Dissolution chemistry and biocompatibility of single-crystalline silicon nanomembranes and associated materials for transient electronics.

PubMed

Hwang, Suk-Won; Park, Gayoung; Edwards, Chris; Corbin, Elise A; Kang, Seung-Kyun; Cheng, Huanyu; Song, Jun-Kyul; Kim, Jae-Hwan; Yu, Sooyoun; Ng, Joanne; Lee, Jung Eun; Kim, Jiyoung; Yee, Cassian; Bhaduri, Basanta; Su, Yewang; Omennetto, Fiorenzo G; Huang, Yonggang; Bashir, Rashid; Goddard, Lynford; Popescu, Gabriel; Lee, Kyung-Mi; Rogers, John A

2014-06-24

Single-crystalline silicon nanomembranes (Si NMs) represent a critically important class of material for high-performance forms of electronics that are capable of complete, controlled dissolution when immersed in water and/or biofluids, sometimes referred to as a type of "transient" electronics. The results reported here include the kinetics of hydrolysis of Si NMs in biofluids and various aqueous solutions through a range of relevant pH values, ionic concentrations and temperatures, and dependence on dopant types and concentrations. In vitro and in vivo investigations of Si NMs and other transient electronic materials demonstrate biocompatibility and bioresorption, thereby suggesting potential for envisioned applications in active, biodegradable electronic implants.

A Comparative Study of Ethylene Growth Response Kinetics in Eudicots and Monocots Reveals a Role for Gibberellin in Growth Inhibition and Recovery1[W][OA

PubMed Central

Kim, Joonyup; Wilson, Rebecca L.; Case, J. Brett; Binder, Brad M.

2012-01-01

Time-lapse imaging of dark-grown Arabidopsis (Arabidopsis thaliana) hypocotyls has revealed new aspects about ethylene signaling. This study expands upon these results by examining ethylene growth response kinetics of seedlings of several plant species. Although the response kinetics varied between the eudicots studied, all had prolonged growth inhibition for as long as ethylene was present. In contrast, with continued application of ethylene, white millet (Panicum miliaceum) seedlings had a rapid and transient growth inhibition response, rice (Oryza sativa ‘Nipponbare’) seedlings had a slow onset of growth stimulation, and barley (Hordeum vulgare) had a transient growth inhibition response followed, after a delay, by a prolonged inhibition response. Growth stimulation in rice correlated with a decrease in the levels of rice ETHYLENE INSENSTIVE3-LIKE2 (OsEIL2) and an increase in rice F-BOX DOMAIN AND LRR CONTAINING PROTEIN7 transcripts. The gibberellin (GA) biosynthesis inhibitor paclobutrazol caused millet seedlings to have a prolonged growth inhibition response when ethylene was applied. A transient ethylene growth inhibition response has previously been reported for Arabidopsis ethylene insensitive3-1 (ein3-1) eil1-1 double mutants. Paclobutrazol caused these mutants to have a prolonged response to ethylene, whereas constitutive GA signaling in this background eliminated ethylene responses. Sensitivity to paclobutrazol inversely correlated with the levels of EIN3 in Arabidopsis. Wild-type Arabidopsis seedlings treated with paclobutrazol and mutants deficient in GA levels or signaling had a delayed growth recovery after ethylene removal. It is interesting to note that ethylene caused alterations in gene expression that are predicted to increase GA levels in the ein3-1 eil1-1 seedlings. These results indicate that ethylene affects GA levels leading to modulation of ethylene growth inhibition kinetics. PMID:22977279

Equilibrium and kinetics of DNA overstretching modeled with a quartic energy landscape.

PubMed

Argudo, David; Purohit, Prashant K

2014-11-04

It is well known that the dsDNA molecule undergoes a phase transition from B-DNA into an overstretched state at high forces. For some time, the structure of the overstretched state remained unknown and highly debated, but recent advances in experimental techniques have presented evidence of more than one possible phase (or even a mixed phase) depending on ionic conditions, temperature, and basepair sequence. Here, we present a theoretical model to study the overstretching transition with the possibility that the overstretched state is a mixture of two phases: a structure with portions of inner strand separation (melted or M-DNA), and an extended phase that retains the basepair structure (S-DNA). We model the double-stranded DNA as a chain composed of n segments of length l, where the transition is studied by means of a Landau quartic potential with statistical fluctuations. The length l is a measure of cooperativity of the transition and is key to characterizing the overstretched phase. By analyzing the different values of l corresponding to a wide spectrum of experiments, we find that for a range of temperatures and ionic conditions, the overstretched form is likely to be a mix of M-DNA and S-DNA. For a transition close to a pure S-DNA state, where the change in extension is close to 1.7 times the original B-DNA length, we find l ? 25 basepairs regardless of temperature and ionic concentration. Our model is fully analytical, yet it accurately reproduces the force-extension curves, as well as the transient kinetic behavior, seen in DNA overstretching experiments.

Effects of hydrogen bonding on internal conversion of GFP-like chromophores. I. The para-amino systems.

PubMed

Huang, Guan-Jhih; Cheng, Chi-Wen; Hsu, Hung-Yu; Prabhakar, Ch; Lee, Yuan-Pern; Diau, Eric Wei-Guang; Yang, Jye-Shane

2013-03-07

To understand the effects of solvent-solute hydrogen bonding (SSHB) on the excited-state dynamics of two GFP-like chromophores, p-ABDI and p-CFABDI, we have determined the quantum yields for fluorescence (Φf) and the isomerization Z → E (ΦZE) and the femtosecond fluorescence and transient infrared absorption in selected solvents. The behavior that ΦZE ≅ 0.50 in aprotic solvents, such as CH3CN, indicates that the E-Z photoisomerization adopts a one-bond-flip mechanism through the torsion of the exocyclic C═C bond (the τ torsion) to form a perpendicular species (τ ∼90°) in the singlet excited state followed by internal conversion (IC) to the ground state and partition to form the E and Z isomers with equal probabilities. The observed ΦZE decreased from 0.50 to 0.15-0.28 when CH3CN was replaced with the protic solvents CH3OH and CF3CH2OH. In conjunction with the solvent-independent rapid (<1 ps) kinetics for the fluorescence decay and the solvent-dependent slow (7-20 ps) kinetics for the ground-state recovery, we conclude that the SSHB modifies the potential energy surface for the τ torsion in a way that the IC occurs also for the twisted intermediates with a τ-torsion angle smaller than 90°, which favors the formation of the Z isomers. The possibility of IC induced by torsion of the exocyclic C-C bond (the φ torsion) is also considered but excluded.

Directional charge transfer mediated by mid-gap states: A transient absorption spectroscopy study of CdSe quantum dot/β-Pb 0.33V 2O 5 heterostructures

DOE PAGES

Milleville, Christopher C.; Pelcher, Kate E.; Sfeir, Matthew Y.; ...

2016-02-15

For solar energy conversion, not only must a semiconductor absorb incident solar radiation efficiently but also its photoexcited electron—hole pairs must further be separated and transported across interfaces. Charge transfer across interfaces requires consideration of both thermodynamic driving forces as well as the competing kinetics of multiple possible transfer, cooling, and recombination pathways. In this work, we demonstrate a novel strategy for extracting holes from photoexcited CdSe quantum dots (QDs) based on interfacing with β-Pb 0.33V 2O 5 nanowires that have strategically positioned midgap states derived from the intercalating Pb 2+ ions. Unlike midgap states derived from defects or dopants,more » the states utilized here are derived from the intrinsic crystal structure and are thus homogeneously distributed across the material. CdSe/β-Pb 0.33V 2O 5 heterostructures were assembled using two distinct methods: successive ionic layer adsorption and reaction (SILAR) and linker-assisted assembly (LAA). Transient absorption spectroscopy measurements indicate that, for both types of heterostructures, photoexcitation of CdSe QDs was followed by the transfer of electrons to the conduction band of β-Pb 0.33V 2O 5 nanowires and holes to the midgap states of β-Pb 0.33V 2O 5 nanowires. Holes were transferred on time scales less than 1 ps, whereas electrons were transferred more slowly on time scales of ~2 ps. In contrast, for analogous heterostructures consisting of CdSe QDs interfaced with V 2O 5 nanowires (wherein midgap states are absent), only electron transfer was observed. Interestingly, electron transfer was readily achieved for CdSe QDs interfaced with V 2O 5 nanowires by the SILAR method; however, for interfaces incorporating molecular linkers, electron transfer was observed only upon excitation at energies substantially greater than the bandgap absorption threshold of CdSe. Furthermore, transient absorbance decay traces reveal longer excited-state lifetimes (1–3 μs) for CdSe/β-Pb 0.33V 2O 5 heterostructures relative to bare β-Pb 0.33V 2O 5 nanowires (0.2 to 0.6 μs); the difference is attributed to surface passivation of intrinsic surface defects in β-Pb 0.33V 2O 5 upon interfacing with CdSe.« less

Kinetic Characterization of Nonmuscle Myosin IIB at the Single Molecule Level*

PubMed Central

Nagy, Attila; Takagi, Yasuharu; Billington, Neil; Sun, Sara A.; Hong, Davin K. T.; Homsher, Earl; Wang, Aibing; Sellers, James R.

2013-01-01

Nonmuscle myosin IIB (NMIIB) is a cytoplasmic myosin, which plays an important role in cell motility by maintaining cortical tension. It forms bipolar thick filaments with ∼14 myosin molecule dimers on each side of the bare zone. Our previous studies showed that the NMIIB is a moderately high duty ratio (∼20–25%) motor. The ADP release step (∼0.35 s−1) of NMIIB is only ∼3 times faster than the rate-limiting phosphate release (0.13 ± 0.01 s−1). The aim of this study was to relate the known in vitro kinetic parameters to the results of single molecule experiments and to compare the kinetic and mechanical properties of single- and double-headed myosin fragments and nonmuscle IIB thick filaments. Examination of the kinetics of NMIIB interaction with actin at the single molecule level was accomplished using total internal reflection fluorescence (TIRF) with fluorescence imaging with 1-nm accuracy (FIONA) and dual-beam optical trapping. At a physiological ATP concentration (1 mm), the rate of detachment of the single-headed and double-headed molecules was similar (∼0.4 s−1). Using optical tweezers we found that the power stroke sizes of single- and double-headed heavy meromyosin (HMM) were each ∼6 nm. No signs of processive stepping at the single molecule level were observed in the case of NMIIB-HMM in optical tweezers or TIRF/in vitro motility experiments. In contrast, robust motility of individual fluorescently labeled thick filaments of full-length NMIIB was observed on actin filaments. Our results are in good agreement with the previous steady-state and transient kinetic studies and show that the individual nonprocessive nonmuscle myosin IIB molecules form a highly processive unit when polymerized into filaments. PMID:23148220

Note: Near infrared spectral and transient measurements of PbS quantum dots luminescence.

PubMed

Parfenov, P S; Litvin, A P; Ushakova, E V; Fedorov, A V; Baranov, A V; Berwick, K

2013-11-01

We describe an experimental setup for the characterization of luminescence from nanostructures. The setup is intended for steady-state and time-resolved luminescence measurements in the near-infrared region. The setup allows us to study spectral luminescence properties in the spectral range of 0.8-2.0 μm with high spectral resolution and kinetic luminescence properties between 0.8 and 1.7 μm with a time resolution of 3 ns. The capabilities of the system are illustrated by taking luminescence measurements from PbS quantum dots. We established the size dependencies of the optical properties of the PbS quantum dots over a wide spectral range. Finally, the energy transfer process was studied with a high temporal and spectral resolution.

Radiation induced decomposition of chlorinated phenols in water

NASA Astrophysics Data System (ADS)

Getoff, N.; Solar, S.

Experiments with 4-Cl-phenol as a model compound for pesticides were performed under steady-state conditions using deoxygenated solutions as well as such saturated with air, oxygen or oxygen mixed with ozone. The yield of Cl -ions serviced as an indicator for the degradation process. As main products of the first step of decomposition were identified: polyhydroxybenzenes, aldehydes and acids. The yield of aldehydes was studied as a function of the absorbed dose and substrate concentration. In the presence of ozone a chain-reaction of the oxidative pollutant degradation takes place. Transient absorption spectra and kinetics obtained by preliminary pulse radiolysis studies of 4-Cl-phenol in the presence of oxygen as well as probable reaction mechanisms are also presented.

Multiple trapping on a comb structure as a model of electron transport in disordered nanostructured semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sibatov, R. T., E-mail: ren-sib@bk.ru; Morozova, E. V., E-mail: kat-valezhanina@yandex.ru

2015-05-15

A model of dispersive transport in disordered nanostructured semiconductors has been proposed taking into account the percolation structure of a sample and joint action of several mechanisms. Topological and energy disorders have been simultaneously taken into account within the multiple trapping model on a comb structure modeling the percolation character of trajectories. The joint action of several mechanisms has been described within random walks with a mixture of waiting time distributions. Integral transport equations with fractional derivatives have been obtained for an arbitrary density of localized states. The kinetics of the transient current has been calculated within the proposed newmore » model in order to analyze time-of-flight experiments for nanostructured semiconductors.« less

The Volumetric Diversity of Misfolded Prion Protein Oligomers Revealed by Pressure Dissociation*

PubMed Central

Torrent, Joan; Lange, Reinhard; Rezaei, Human

2015-01-01

Protein oligomerization has been associated with a wide range of diseases. High pressure approaches offer a powerful tool for deciphering the underlying molecular mechanisms by revealing volume changes associated with the misfolding and assembly reactions. We applied high pressure to induce conformational changes in three distinct β-sheet-rich oligomers of the prion protein PrP, a protein characterized by a variety of infectious quaternary structures that can propagate stably and faithfully and cause diseases with specific phenotypic traits. We show that pressure induces dissociation of the oligomers and leads to a lower volume monomeric PrP state that refolds into the native conformation after pressure release. By measuring the different pressure and temperature sensitivity of the tested PrP oligomers, we demonstrate significantly different void volumes in their quaternary structure. In addition, by focusing on the kinetic and energetic behavior of the pressure-induced dissociation of one specific PrP oligomer, we reveal a large negative activation volume and an increase in both apparent activation enthalpy and entropy. This suggests a transition state ensemble that is less structured and significantly more hydrated than the oligomeric state. Finally, we found that site-specific fluorescent labeling allows monitoring of the transient population of a kinetic intermediate in the dissociation reaction. Our results indicate that defects in atomic packing may deserve consideration as a new factor that influences differences between PrP assemblies and that could be relevant also for explaining the origin of prion strains. PMID:26126829

Optical determination of charge transfer times from indoline dyes to ZnO in solid state dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Meyenburg, I.; Hofeditz, N.; Ruess, R.; Rudolph, M.; Schlettwein, D.; Heimbrodt, W.

2018-05-01

We studied the electron transfer at the interface of organic-inorganic hybrids consisting of indoline derivatives (D149 and D131) on ZnO substrates using a new optical method. We revealed the electron transfer times from the excited dye, e.g. the excitons formed in the dye aggregates to the ZnO substrate by analyzing the photoluminescence transients of the excitons after femtosecond excitation and applying kinetic model calculations. We reveal the changes of the electron transfer times by applying electrical bias. Pushing the Fermi energy of the ZnO substrate towards the excited dye level the transfer time gets longer and eventually the electron transfer is suppressed. The level alignment between the excited dye state and the ZnO Fermi-level is estimated. The excited state of D131 is about 100 meV higher than the respective state of D149 compared to the ZnO conduction band. This leads to shorter electron transfer times and eventually to higher quantum efficiencies of the solar cells.

SVD-aided pseudo principal-component analysis: A new method to speed up and improve determination of the optimum kinetic model from time-resolved data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oang, Key Young; Yang, Cheolhee; Muniyappan, Srinivasan

Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of themore » same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.« less

Analysis of transient fission gas behaviour in oxide fuel using BISON and TRANSURANUS

NASA Astrophysics Data System (ADS)

Barani, T.; Bruschi, E.; Pizzocri, D.; Pastore, G.; Van Uffelen, P.; Williamson, R. L.; Luzzi, L.

2017-04-01

The modelling of fission gas behaviour is a crucial aspect of nuclear fuel performance analysis in view of the related effects on the thermo-mechanical performance of the fuel rod, which can be particularly significant during transients. In particular, experimental observations indicate that substantial fission gas release (FGR) can occur on a small time scale during transients (burst release). To accurately reproduce the rapid kinetics of the burst release process in fuel performance calculations, a model that accounts for non-diffusional mechanisms such as fuel micro-cracking is needed. In this work, we present and assess a model for transient fission gas behaviour in oxide fuel, which is applied as an extension of conventional diffusion-based models to introduce the burst release effect. The concept and governing equations of the model are presented, and the sensitivity of results to the newly introduced parameters is evaluated through an analytic sensitivity analysis. The model is assessed for application to integral fuel rod analysis by implementation in two structurally different fuel performance codes: BISON (multi-dimensional finite element code) and TRANSURANUS (1.5D code). Model assessment is based on the analysis of 19 light water reactor fuel rod irradiation experiments from the OECD/NEA IFPE (International Fuel Performance Experiments) database, all of which are simulated with both codes. The results point out an improvement in both the quantitative predictions of integral fuel rod FGR and the qualitative representation of the FGR kinetics with the transient model relative to the canonical, purely diffusion-based models of the codes. The overall quantitative improvement of the integral FGR predictions in the two codes is comparable. Moreover, calculated radial profiles of xenon concentration after irradiation are investigated and compared to experimental data, illustrating the underlying representation of the physical mechanisms of burst release.

Features in chemical kinetics. I. Signatures of self-emerging dimensional reduction from a general format of the evolution law

NASA Astrophysics Data System (ADS)

Nicolini, Paolo; Frezzato, Diego

2013-06-01

Simplification of chemical kinetics description through dimensional reduction is particularly important to achieve an accurate numerical treatment of complex reacting systems, especially when stiff kinetics are considered and a comprehensive picture of the evolving system is required. To this aim several tools have been proposed in the past decades, such as sensitivity analysis, lumping approaches, and exploitation of time scales separation. In addition, there are methods based on the existence of the so-called slow manifolds, which are hyper-surfaces of lower dimension than the one of the whole phase-space and in whose neighborhood the slow evolution occurs after an initial fast transient. On the other hand, all tools contain to some extent a degree of subjectivity which seems to be irremovable. With reference to macroscopic and spatially homogeneous reacting systems under isothermal conditions, in this work we shall adopt a phenomenological approach to let self-emerge the dimensional reduction from the mathematical structure of the evolution law. By transforming the original system of polynomial differential equations, which describes the chemical evolution, into a universal quadratic format, and making a direct inspection of the high-order time-derivatives of the new dynamic variables, we then formulate a conjecture which leads to the concept of an "attractiveness" region in the phase-space where a well-defined state-dependent rate function ω has the simple evolution dot{ω }= - ω ^2 along any trajectory up to the stationary state. This constitutes, by itself, a drastic dimensional reduction from a system of N-dimensional equations (being N the number of chemical species) to a one-dimensional and universal evolution law for such a characteristic rate. Step-by-step numerical inspections on model kinetic schemes are presented. In the companion paper [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234102 (2013)], 10.1063/1.4809593 this outcome will be naturally related to the appearance (and hence, to the definition) of the slow manifolds.

Thermochemical Kinetics of H2O and HNO3 on crystalline Nitric Acid Hydrates (alpha-, beta-NAT, NAD) in the range 175-200 K

NASA Astrophysics Data System (ADS)

Rossi, Michel J.; Iannarelli, Riccardo

2015-04-01

The growth of NAT (Nitric Acid Trihydrate, HNO3x3H2O) and NAD (Nitric Acid Dihydrate, HNO3x2H2O) on an ice substrate, the evaporative lifetime of NAT and NAD as well as the interconversion of alpha- and beta-NAT competing with evaporation and growth under UT/LS conditions depends on the interfacial kinetics of H2O and HNO3 vapor on the condensed phase. Despite the existence of some literature results we have embarked on a systematic investigation of the kinetics using a multidiagnostic experimental approach enabled by the simultaneous observation of both the gas (residual gas mass spectrometry) as well as the condensed phase (FTIR absorption in transmission). We report on thermochemically consistent mass accommodation coefficients alpha and absolute evaporation rates Rev/molecule s-1cm-3 as a function of temperature which yields the corresponding vapor pressures of both H2O and HNO3 in equilibrium with the crystalline phases, hence the term thermochemical kinetics. These results have been obtained using a stirred flow reactor (SFR) using a macroscopic pure ice film of 1 micron or so thickness as a starting substrate mimicking atmospheric ice particles and are reported in a phase diagram specifically addressing UT (Upper Troposphere)/LS (Lower Stratosphere) conditions as far as temperature and partial pressures are concerned. The experiments have been performed either at steady-state flow conditions or in transient supersaturation using a pulsed solenoid valve in order to generate gas pulses whose decay were subsequently monitored in real time. Special attention has been given to the effect of the stainless-steel vessel walls in that Langmuir adsorption isotherms for H2O and HNO3 have been used to correct for wall-adsorption of both probe gases. Typically, the accommodation coefficients of H2O and HNO3 are similar throughout the temperature range whereas the rates of evaporation Rev of H2O are significantly larger than for HNO3 thus leading to the difference in vapor pressure revealed in the phase diagram. A noteworthy effect seems to be that the accommodation coefficients obtained in pulsed gas admission experiments (transient supersaturation) lead to significantly lower values owing to surface saturation, especially in the case of the thermodynamically stable beta-NAT substrate.

Fractal-like kinetics of intracellular enzymatic reactions: a chemical framework of endotoxin tolerance and a possible non-specific contribution of macromolecular crowding to cross-tolerance.

PubMed

Vasilescu, Catalin; Olteanu, Mircea; Flondor, Paul; Calin, George A

2013-09-14

The response to endotoxin (LPS), and subsequent signal transduction lead to the production of cytokines such as tumor necrosis factor-α (TNF-α) by innate immune cells. Cells or organisms pretreated with endotoxin enter into a transient state of hyporesponsiveness, referred to as endotoxin tolerance (ET) which represents a particular case of negative preconditioning. Despite recent progress in understanding the molecular basis of ET, there is no consensus yet on the primary mechanism responsible for ET and for the more complex cases of cross tolerance. In this study, we examined the consequences of the macromolecular crowding (MMC) and of fractal-like kinetics (FLK) of intracellular enzymatic reactions on the LPS signaling machinery. We hypothesized that this particular type of enzyme kinetics may explain the development of ET phenomenon. Our aim in the present study was to characterize the chemical kinetics framework in ET and determine whether fractal-like kinetics explains, at least in part, ET. We developed an ordinary differential equations (ODE) mathematical model that took into account the links between the MMC and the LPS signaling machinery leading to ET. We proposed that the intracellular fractal environment (MMC) contributes to ET and developed two mathematical models of enzyme kinetics: one based on Kopelman's fractal-like kinetics framework and the other based on Savageau's power law model. Kopelman's model provides a good image of the potential influence of a fractal intracellular environment (MMC) on ET. The Savageau power law model also partially explains ET. The computer simulations supported the hypothesis that MMC and FLK may play a role in ET. The model highlights the links between the organization of the intracellular environment, MMC and the LPS signaling machinery leading to ET. Our FLK-based model does not minimize the role of the numerous negative regulatory factors. It simply draws attention to the fact that macromolecular crowding can contribute significantly to the induction of ET by imposing geometric constrains and a particular chemical kinetic for the intracellular reactions.

Timing and efficacy of Ca2+ channel activation in hippocampal mossy fiber boutons.

PubMed

Bischofberger, Josef; Geiger, Jörg R P; Jonas, Peter

2002-12-15

The presynaptic Ca2+ signal is a key determinant of transmitter release at chemical synapses. In cortical synaptic terminals, however, little is known about the kinetic properties of the presynaptic Ca2+ channels. To investigate the timing and magnitude of the presynaptic Ca2+ inflow, we performed whole-cell patch-clamp recordings from mossy fiber boutons (MFBs) in rat hippocampus. MFBs showed large high-voltage-activated Ca(2+) currents, with a maximal amplitude of approximately 100 pA at a membrane potential of 0 mV. Both activation and deactivation were fast, with time constants in the submillisecond range at a temperature of approximately 23 degrees C. An MFB action potential (AP) applied as a voltage-clamp command evoked a transient Ca2+ current with an average amplitude of approximately 170 pA and a half-duration of 580 microsec. A prepulse to +40 mV had only minimal effects on the AP-evoked Ca2+ current, indicating that presynaptic APs open the voltage-gated Ca2+ channels very effectively. On the basis of the experimental data, we developed a kinetic model with four closed states and one open state, linked by voltage-dependent rate constants. Simulations of the Ca2+ current could reproduce the experimental data, including the large amplitude and rapid time course of the current evoked by MFB APs. Furthermore, the simulations indicate that the shape of the presynaptic AP and the gating kinetics of the Ca2+ channels are tuned to produce a maximal Ca2+ influx during a minimal period of time. The precise timing and high efficacy of Ca2+ channel activation at this cortical glutamatergic synapse may be important for synchronous transmitter release and temporal information processing.

Ultrafast carrier dynamics of titanic acid nanotubes investigated by transient absorption spectroscopy.

PubMed

Wang, Li; Zhao, Hui; Pan, Lin Yun; Weng, Yu Xiang; Nakato, Yoshihiro; Tamai, Naoto

2010-12-01

Carrier dynamics of titanic acid nanotubes (phase of H2Ti2O5.H2O) deposited on a quartz plate was examined by visible/near-IR transient absorption spectroscopy with an ultraviolet excitation. The carrier dynamics of titanic acid nanotubes follows the fast trapping process which attributed to the intrinsic tubular structure, the relaxation of shallow trapped carriers and the recombination as a second-order kinetic process. Transient absorption of titanic acid nanotubes was dominated by the absorption of surface-trapped holes in visible region around 500 nm, which was proved by the faster decay dynamics in the presence of polyvinyl alcohol as a hole-scavenger. However, the slow relaxation of free carriers was much more pronounced in the TiO2 single crystals, as compared with the transient absorption spectra of titanic acid nanotubes under the similar excitation.

Oxidation reactions of 1- and 2-naphthols: an experimental and theoretical study.

PubMed

Sreekanth, R; Prasanthkumar, Kavanal P; Sunil Paul, M M; Aravind, Usha K; Aravindakumar, C T

2013-11-07

The transients formed during the reactions of oxidizing radicals with 1-naphthol (1) and 2-naphthol (2) in aqueous medium have been investigated by pulse radiolysis with detection by absorption spectroscopy and density functional theory (DFT) calculations. The transient spectra formed on hydroxyl radical ((•)OH) reactions of 1 and 2 exhibited λ(max) at 340 and 350 nm at neutral pH. The rate constants of the (•)OH reactions of 1 (2) were determined from build-up kinetics at λ(max) of the transients as (9.63 ± 0.04) × 10(9) M(-1) s(-1) ((7.31 ± 0.11) × 10(9) M(-1) s(-1)). DFT calculations using the B3LYP/6-31+G(d,p) method have been performed to locate favorable reaction sites in both 1 and 2 and identification of the pertinent transients responsible for experimental results. Calculations demonstrated that (•)OH additions can occur mostly at C1 and C4 positions of 1, and at C1 and C8 positions of 2. Among several isomeric (•)OH adducts possible, the C1 adduct was found to be energetically most stable both in 1 and 2. Time-dependent density functional theory (TDDFT) calculations in the solution phase has shown that the experimental spectrum of 1 was mainly attributed by 1a4 (kinetically driven (•)OH-adduct) formed via the addition of (•)OH at the C4 position which was 0.73 kcal/mol endergonic compared to 1a1 (thermodynamic (•)OH adduct), whereas 2a1 (thermodynamic/kinetic (•)OH-adduct) was mainly responsible for the experimental spectrum of 2. Naphthoxyl radicals of 1 and 2 have been predicted as the transient formed in the reaction of (•)OH at basic pH. In addition, the same transient species resulted from the reactions of oxide radical ion (O(•-)) at pH ≈ 13 and azide radical (N3(•)) at pH 7 with 1 and 2. Further, UV photolysis of aqueous solutions of 1 and 2 containing H2O2 (UV/H2O2) were used for the (•)OH induced oxidation product formations up on 60% degradations of 1 and 2; profiling of the oxidation products were performed by using an ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) method. According to the UPLC-Q-TOF-MS analyses, the preliminary oxidation products are limited to dihydroxy naphthalenes and naphthoquinones with N2-saturation, while some additional products (mainly isomeric monohydroxy-naphthoquinones) have been observed in the degradations of 1 and 2 in the presence of O2. We postulate that dihydroxy naphthalenes are derived explicitly from the most favorable (•)OH-adducts speculated (preference is in terms of the kinetic/thermodynamic dominancy of transients) by using theoretical calculations which in turn substantiate the proposed reaction mechanisms. The observations of (•)OH-adducts for an aromatic phenol (herein for both 1 and 2 at pH 7) rather than phenoxyl type radical in the pulse radiolysis experiments is a distinct and unique illustration. The present study provides a meaningful basis for the early stages associated with the (•)OH initiated advanced oxidation processes of 1- and 2-naphthols.

Transient release kinetics of rod bipolar cells revealed by capacitance measurement of exocytosis from axon terminals in rat retinal slices.

PubMed

Oltedal, Leif; Hartveit, Espen

2010-05-01

Presynaptic transmitter release has mostly been studied through measurements of postsynaptic responses, but a few synapses offer direct access to the presynaptic terminal, thereby allowing capacitance measurements of exocytosis. For mammalian rod bipolar cells, synaptic transmission has been investigated in great detail by recording postsynaptic currents in AII amacrine cells. Presynaptic measurements of the dynamics of vesicular cycling have so far been limited to isolated rod bipolar cells in dissociated preparations. Here, we first used computer simulations of compartmental models of morphologically reconstructed rod bipolar cells to adapt the 'Sine + DC' technique for capacitance measurements of exocytosis at axon terminals of intact rod bipolar cells in retinal slices. In subsequent physiological recordings, voltage pulses that triggered presynaptic Ca(2+) influx evoked capacitance increases that were proportional to the pulse duration. With pulse durations 100 ms, the increase saturated at 10 fF, corresponding to the size of a readily releasable pool of vesicles. Pulse durations 400 ms evoked additional capacitance increases, probably reflecting recruitment from additional pools of vesicles. By using Ca(2+) tail current stimuli, we separated Ca(2+) influx from Ca(2+) channel activation kinetics, allowing us to estimate the intrinsic release kinetics of the readily releasable pool, yielding a time constant of 1.1 ms and a maximum release rate of 2-3 vesicles (release site)(1) ms(1). Following exocytosis, we observed endocytosis with time constants ranging from 0.7 to 17 s. Under physiological conditions, it is likely that release will be transient, with the kinetics limited by the activation kinetics of the voltage-gated Ca(2+) channels.

Development of an integrated thermal-hydraulics capability incorporating RELAP5 and PANTHER neutronics code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Page, R.; Jones, J.R.

1997-07-01

Ensuring that safety analysis needs are met in the future is likely to lead to the development of new codes and the further development of existing codes. It is therefore advantageous to define standards for data interfaces and to develop software interfacing techniques which can readily accommodate changes when they are made. Defining interface standards is beneficial but is necessarily restricted in application if future requirements are not known in detail. Code interfacing methods are of particular relevance with the move towards automatic grid frequency response operation where the integration of plant dynamic, core follow and fault study calculation toolsmore » is considered advantageous. This paper describes the background and features of a new code TALINK (Transient Analysis code LINKage program) used to provide a flexible interface to link the RELAP5 thermal hydraulics code with the PANTHER neutron kinetics and the SIBDYM whole plant dynamic modelling codes used by Nuclear Electric. The complete package enables the codes to be executed in parallel and provides an integrated whole plant thermal-hydraulics and neutron kinetics model. In addition the paper discusses the capabilities and pedigree of the component codes used to form the integrated transient analysis package and the details of the calculation of a postulated Sizewell `B` Loss of offsite power fault transient.« less

Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways.

PubMed

Rydzewski, J; Jakubowski, R; Nowak, W; Grubmüller, H

2018-06-12

The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase ( TcAChE) was investigated by 4 μs unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front door along the axis of the active-site gorge (pwf) and through a new transient side door (pws), i.e., formed by the Ω-loop (residues 67-94 of TcAChE). An analysis of the inhibitor unbinding along the RPs suggests that pws is opened transiently after hupA and the Ω-loop reach a low free-energy transition state characterized by the orientation of the pyridone group of the inhibitor directed toward the Ω-loop plane. Unlike pws, pwf does not require large structural changes in TcAChE to be accessible. The estimated free energies and rates agree well with available experimental data. The dissociation rates along the unbinding pathways are similar, suggesting that the dissociation of hupA along pws is likely to be relevant. This indicates that perturbations to hupA- TcAChE interactions could potentially induce pathway hopping. In summary, our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases for the rational design of the next-generation slow-onset inhibitors with optimized pharmacokinetic properties for the treatment of Alzheimer's disease.

Carrier multiplication and charge transport in artificial quantum-dot solids probed by ultrafast photocurrent spectroscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Klimov, Victor I.

2017-05-01

Understanding and controlling carrier transport and recombination dynamics in colloidal quantum dot films is key to their application in electronic and optoelectronic devices. Towards this end, we have conducted transient photocurrent measurements to monitor transport through quantum confined band edge states in lead selenide quantum dots films as a function of pump fluence, temperature, electrical bias, and surface treatment. Room temperature dynamics reveal two distinct timescales of intra-dot geminate processes followed by non-geminate inter-dot processes. The non-geminate kinetics is well described by the recombination of holes with photoinjected and pre-existing electrons residing in mid-gap states. We find the mobility of the quantum-confined states shows no temperature dependence down to 6 K, indicating a tunneling mechanism of early time photoconductance. We present evidence of the importance of the exciton fine structure in controlling the low temperature photoconductance, whereby the nanoscale enhanced exchange interaction between electrons and holes in quantum dots introduces a barrier to charge separation. Finally, side-by-side comparison of photocurrent transients using excitation with low- and high-photon energies (1.5 vs. 3.0 eV) reveals clear signatures of carrier multiplication (CM), that is, generation of multiple excitons by single photons. Based on photocurrent measurements of quantum dot solids and optical measurements of solution based samples, we conclude that the CM efficiency is unaffected by strong inter-dot coupling. Therefore, the results of previous numerous spectroscopic CM studies conducted on dilute quantum dot suspensions should, in principle, be reproducible in electronically coupled QD films used in devices.

Transient response of nonlinear polymer networks: A kinetic theory

NASA Astrophysics Data System (ADS)

Vernerey, Franck J.

2018-06-01

Dynamic networks are found in a majority of natural materials, but also in engineering materials, such as entangled polymers and physically cross-linked gels. Owing to their transient bond dynamics, these networks display a rich class of behaviors, from elasticity, rheology, self-healing, or growth. Although classical theories in rheology and mechanics have enabled us to characterize these materials, there is still a gap in our understanding on how individuals (i.e., the mechanics of each building blocks and its connection with others) affect the emerging response of the network. In this work, we introduce an alternative way to think about these networks from a statistical point of view. More specifically, a network is seen as a collection of individual polymer chains connected by weak bonds that can associate and dissociate over time. From the knowledge of these individual chains (elasticity, transient attachment, and detachment events), we construct a statistical description of the population and derive an evolution equation of their distribution based on applied deformation and their local interactions. We specifically concentrate on nonlinear elastic response that follows from the strain stiffening response of individual chains of finite size. Upon appropriate averaging operations and using a mean field approximation, we show that the distribution can be replaced by a so-called chain distribution tensor that is used to determine important macroscopic measures such as stress, energy storage and dissipation in the network. Prediction of the kinetic theory are then explored against known experimental measurement of polymer responses under uniaxial loading. It is found that even under the simplest assumptions of force-independent chain kinetics, the model is able to reproduce complex time-dependent behaviors of rubber and self-healing supramolecular polymers.

Kinetic changes in tetanic Ca2+ transients in enzymatically dissociated muscle fibres under repetitive stimulation

PubMed Central

Calderón, Juan C; Bolaños, Pura; Caputo, Carlo

2011-01-01

Abstract We used enzymatically dissociated flexor digitorum brevis (FDB) and soleus fibres loaded with the fast Ca2+ dye Magfluo-4 AM, and adhered to Laminin, to test whether repetitive stimulation induces progressive changes in the kinetics of Ca2+ release and reuptake in a fibre-type-dependent fashion. We applied a protocol of tetani of 350 ms, 100 Hz, every 4 s to reach a mean amplitude reduction of 25% of the first peak. Morphology type I (MT-I) and morphology type II (MT-II) fibres underwent a total of 96 and 52.8 tetani (P < 0.01 between groups), respectively. The MT-II fibres (n = 18) showed significant reductions of the amplitude (19%), an increase in rise time (8.5%) and a further reduction of the amplitude/rise time ratio (25.5%) of the first peak of the tetanic transient after 40 tetani, while MT-I fibres (n = 5) did not show any of these changes. However, both fibre types showed significant reductions in the maximum rate of rise of the first peak after 40 tetani. Two subpopulations among the MT-II fibres could be distinguished according to Ca2+ reuptake changes. Fast-fatigable MT-II fibres (fMT-II) showed an increase of 32.2% in the half-width value of the first peak, while for fatigue-resistant MT-II fibres (rMT-II), the increase amounted to 6.9%, both after 40 tetani. Significant and non-significant increases of 36.4% and 11.9% in the first time constant of decay (t1) values were seen after 40 tetani in fMT-II and rMT-II fibres, respectively. MT-I fibres did not show kinetic changes in any of the Ca2+ reuptake variables. All changes were reversed after an average recovery of 7.5 and 15.4 min for MT-I and MT-II fibres, respectively. Further experiments ruled out the possibility that the differences in the kinetic changes of the first peak of the Ca2+ transients between fibres MT-I and MT-II could be related to the inactivation of Ca2+ release mechanism. In conclusion, we established a model of enzymatically dissociated fibres, loaded with Magfluo-4 and adhered to Laminin, to study muscle fatigue and demonstrated fibre-type-dependent, fatigue-induced kinetic changes in both Ca2+ release and reuptake. PMID:21878526

Birefringence and incipient plastic deformation in elastically overdriven [100] CaF2 under shock compression

NASA Astrophysics Data System (ADS)

Li, Y.; Zhou, X. M.; Cai, Y.; Liu, C. L.; Luo, S. N.

2018-04-01

[100] CaF2 single crystals are shock-compressed via symmetric planar impact, and the flyer plate-target interface velocity histories are measured with a laser displacement interferometry. The shock loading is slightly above the Hugoniot elastic limit to investigate incipient plasticity and its kinetics, and its effects on optical properties and deformation inhomogeneity. Fringe patterns demonstrate different features in modulation of fringe amplitude, including birefringence and complicated modulations. The birefringence is attributed to local lattice rotation accompanying incipient plasticity. Spatially resolved measurements show inhomogeneity in deformation, birefringence, and fringe pattern evolutions, most likely caused by the inhomogeneity associated with lattice rotation and dislocation slip. Transiently overdriven elastic states are observed, and the incubation time for incipient plasticity decreases inversely with increasing overdrive by the elastic shock.

Further analytical study of hybrid rocket combustion

NASA Technical Reports Server (NTRS)

Hung, W. S. Y.; Chen, C. S.; Haviland, J. K.

1972-01-01

Analytical studies of the transient and steady-state combustion processes in a hybrid rocket system are discussed. The particular system chosen consists of a gaseous oxidizer flowing within a tube of solid fuel, resulting in a heterogeneous combustion. Finite rate chemical kinetics with appropriate reaction mechanisms were incorporated in the model. A temperature dependent Arrhenius type fuel surface regression rate equation was chosen for the current study. The governing mathematical equations employed for the reacting gas phase and for the solid phase are the general, two-dimensional, time-dependent conservation equations in a cylindrical coordinate system. Keeping the simplifying assumptions to a minimum, these basic equations were programmed for numerical computation, using two implicit finite-difference schemes, the Lax-Wendroff scheme for the gas phase, and, the Crank-Nicolson scheme for the solid phase.

Unsteady heat transfer performance of heat pipe with axially swallow-tailed microgrooves

NASA Astrophysics Data System (ADS)

Zhang, R. P.

2017-04-01

A mathematical model is developed for predicting the transient heat transfer and fluid flow of heat pipe with axially swallow-tailed microgrooves. The effects of liquid convective heat transfer in the microgrooves, liquid-vapor interfacial phase-change heat transfer and liquid-vapor interfacial shear stress are accounted for in the present model. The coupled non-linear control equations are solved numerically. Mass flow rate at the interface is obtained from the application of kinetic theory. Time variation of wall temperature is studied from the initial startup to steady state. The numerical results are verified by experiments. Time constants for startup and shutdown operation are defined to determine how fast a heat pipe responds to an applied input heat flux, which slightly decreases with increasing heat load.

Direct Observation of Insulin Association Dynamics with Time-Resolved X-ray Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rimmerman, Dolev; Leshchev, Denis; Hsu, Darren J.

Biological functions frequently require protein-protein interactions that involve secondary and tertiary structural perturbation. Here we study protein-protein dissociation and reassociation dynamics in insulin, a model system for protein oligomerization. Insulin dimer dissociation into monomers was induced by a nanosecond temperature-jump (T-jump) of ~8 °C in aqueous solution, and the resulting protein and solvent dynamics were tracked by time-resolved X-ray solution scattering (TRXSS) on time scales of 10 ns to 100 ms. The protein scattering signals revealed the formation of five distinguishable transient species during the association process that deviate from simple two state kinetics. Our results show that the combinationmore » of T-jump pump coupled to TRXSS probe allows for direct tracking of structural dynamics in nonphotoactive proteins.« less

Outflow-driven Transients from the Birth of Binary Black Holes. II. Primary-induced Accretion Transients

NASA Astrophysics Data System (ADS)

Kimura, Shigeo S.; Murase, Kohta; Mészáros, Peter

2017-12-01

We discuss the electromagnetic radiation from newborn binary black holes (BBHs). As a consequence of the evolution of massive stellar binaries, a binary consisting of a primary black hole (BH) and a secondary Wolf–Rayet star is expected as a BBH progenitor system. We investigate optical transients from the birth of BBHs powered by the Bondi–Hoyle–Lyttleton accretion onto the primary BH, which occur ∼1–10 Gyr earlier than gravitational-wave signals at the BH–BH merger. When the secondary massive star collapses into a BH, it may eject a fraction of its outer material and may form a disk around the primary BH and induces a powerful disk wind. These primary-induced winds can lead to optical transients with a kinetic energy of ∼1047–3 × 1048 erg, an ejecta velocity of 108–109 cm s‑1, a duration of a few days, and an absolute magnitude ranging from about ‑11 to ‑14. The light curves and late-time spectra of these transients are distinctive from those of ordinary supernovae, and detection of this type of transient is possible by future optical transient surveys if the event rate of this transient is comparable to the merger rate of BBHs. This paper focuses on the emissions from disk-driven transients induced by the primary BH, different from Paper I, which focuses on wind-driven transients from the tidally locked secondary massive star.

Pump-dump-probe and pump-repump-probe ultrafast spectroscopy resolves cross section of an early ground state intermediate and stimulated emission in the photoreactions of the Pr ground state of the cyanobacterial phytochrome Cph1.

PubMed

Fitzpatrick, Ann E; Lincoln, Craig N; van Wilderen, Luuk J G W; van Thor, Jasper J

2012-01-26

The primary photoreactions of the red absorbing ground state (Pr) of the cyanobacterial phytochrome Cph1 from Synechocystis PCC 6803 involve C15═C16 Z-E photoisomerization of its phycocyanobilin chromophore. The first observable product intermediate in pump-probe measurements of the photocycle, "Lumi-R", is formed with picosecond kinetics and involves excited state decay reactions that have 3 and 14 ps time constants. Here, we have studied the photochemical formation of the Lumi-R intermediate using multipulse picosecond visible spectroscopy. Pump-dump-probe (PDP) and pump-repump-probe (PRP) experiments were carried out by employing two femtosecond visible pulses with 1, 14, and 160 ps delays, together with a broadband dispersive visible probe. The time delays between the two excitation pulses have been selected to allow interaction with the dominant (3 and 14 ps) kinetic phases of Lumi-R formation. The frequency dependence of the PDP and PRP amplitudes was investigated at 620, 640, 660, and 680 nm, covering excited state absorption (λ(max) = 620 nm), ground state absorption (λ(max) = 660 nm), and stimulated emission (λ(max) = 680 nm) cross sections. Experimental double difference transient absorbance signals (ΔΔOD), from the PDP and PRP measurements, required corrections to remove contributions from ground state repumping. The sensitivity of the resulting ΔΔOD signals was systematically investigated for possible connectivity schemes and photochemical parameters. When applying a homogeneous (sequentially decaying) connectivity scheme in both the 3 and 14 ps kinetic phases, evidence for repumping of an intermediate that has an electronic ground state configuration (GSI) is taken from the dump-induced S1 formation with 620, 640, and 660 nm wavelengths and 1 and 14 ps repump delays. Evidence for repumping a GSI is also seen, for the same excitation wavelengths, when imposing a target connectivity scheme proposed in the literature for the 1 ps repump delay. In contrast, using a 680 nm dump pulse, ground state formation is observed for all models examined. The ΔΔOD signals were dominated by stimulated emission, at both 1 and 14 ps delays for the longer wavelength excitation. The GSI, which is revealed by the PRP measurements and not resolved from pump-probe measurements, is found to be directly formed from the excited state of Pr, and its formation is considered using heterogeneous, homogeneous, and target models to globally fit the data.

Shedding light into the detailed excited-state relaxation pathways and reaction mechanisms of thionaphthol isomers.

PubMed

Riyad, Yasser M; Naumov, Sergej; Hermann, Ralf; Abel, Bernd

2011-02-10

Nanosecond laser flash photolysis employing transient detection of emission and absorption in combination with pulse radiolysis and quantum theory has been employed to shed light into the kinetics, quantum yields, and mechanisms of the deactivation of the first excited singlet state of 1- and 2-thionaphthols (NpSH(S(1))). In contrast to thiophenols (ArSH(S(1))), the results revealed that the decay of the first excited singlet state of 1- and 2-thionaphthols (NpSH(S(1))) is governed by radiationless internal conversion (Φ(IC) = 0.29-0.46; 0.016-0.190) and intersystem crossing (Φ(ISC) = 0.14-0.15; 0.4-0.6), respectively, with pronounced S-H photodissociation (Φ(D) = 0.40-0.55; 0.35-0.40). Fluorescence as a deactivation channel plays a minor role (Φ(F) = 0.001-0.010; 0.010-0.034). Quantum chemical calculations helped in understanding the formation of naphthylthiyl radicals and rationalizing the differences in the efficiency of intersystem crossing of the 1- and 2-thionaphthol systems.

Solvent- and DNA-Controlled Phototriggered Linkage Isomerization in a Ruthenium Sulfoxide Complex Incorporating Dipyrido[3,2-a:2',3'-c]phenazine (dppz).

PubMed

Phapale, Daulat; Ghosh, Rajib; Das, Dipanwita

2017-06-05

A new tris-heteroleptic complex [Ru(bpy)(dppz)(OSO)](ClO 4 ), [1](ClO 4 ) (bpy = 2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine and OSO = 2-methylsulfinylbenzoate), was synthesized and characterized to control the photochromic Ru-S → Ru-O linkage isomerization. Details isomerization kinetics studied by UV-visible absorption spectroscopy and cyclic voltammetry revealed that efficient photochromic S → O isomerization and thermal O → S reversal take place in solvents like propylene carbonate (PC), methanol, and dichloromethane. Strikingly, photoisomerization of [1](ClO 4 ) is arrested in water although is active in the analogous compound [Ru(bpy) 2 (OSO)](ClO 4 ). Effective excited state deactivation through dark 3 MLCT state involving dppz ligand of [1](ClO 4 ) switches off photochromism in aqueous medium. Interestingly, the photochromism is activated in aqueous solution in the presence of DNA which shields the dppz localized dark state through intercalation. Ultrafast transient absorption spectroscopic measurement sheds light on the differential behavior of photochromism in aqueous and nonaqueous solvents.

Measurement of DNA translocation dynamics in a solid-state nanopore at 100-ns temporal resolution

PubMed Central

Shekar, Siddharth; Niedzwiecki, David J.; Chien, Chen-Chi; Ong, Peijie; Fleischer, Daniel A.; Lin, Jianxun; Rosenstein, Jacob K.; Drndic, Marija; Shepard, Kenneth L.

2017-01-01

Despite the potential for nanopores to be a platform for high-bandwidth study of single-molecule systems, ionic current measurements through nanopores have been limited in their temporal resolution by noise arising from poorly optimized measurement electronics and large parasitic capacitances in the nanopore membranes. Here, we present a complementary metal-oxide-semiconductor (CMOS) nanopore (CNP) amplifier capable of low noise recordings at an unprecedented 10 MHz bandwidth. When integrated with state-of-the-art solid-state nanopores in silicon nitride membranes, we achieve an SNR of greater than 10 for ssDNA translocations at a measurement bandwidth of 5 MHz, which represents the fastest ion current recordings through nanopores reported to date. We observe transient features in ssDNA translocation events that are as short as 200 ns, which are hidden even at bandwidths as high as 1 MHz. These features offer further insights into the translocation kinetics of molecules entering and exiting the pore. This platform highlights the advantages of high-bandwidth translocation measurements made possible by integrating nanopores and custom-designed electronics. PMID:27332998

PHISICS/RELAP5-3D RESULTS FOR EXERCISES II-1 AND II-2 OF THE OECD/NEA MHTGR-350 BENCHMARK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strydom, Gerhard

2016-03-01

The Idaho National Laboratory (INL) Advanced Reactor Technologies (ART) High-Temperature Gas-Cooled Reactor (HTGR) Methods group currently leads the Modular High-Temperature Gas-Cooled Reactor (MHTGR) 350 benchmark. The benchmark consists of a set of lattice-depletion, steady-state, and transient problems that can be used by HTGR simulation groups to assess the performance of their code suites. The paper summarizes the results obtained for the first two transient exercises defined for Phase II of the benchmark. The Parallel and Highly Innovative Simulation for INL Code System (PHISICS), coupled with the INL system code RELAP5-3D, was used to generate the results for the Depressurized Conductionmore » Cooldown (DCC) (exercise II-1a) and Pressurized Conduction Cooldown (PCC) (exercise II-2) transients. These exercises require the time-dependent simulation of coupled neutronics and thermal-hydraulics phenomena, and utilize the steady-state solution previously obtained for exercise I-3 of Phase I. This paper also includes a comparison of the benchmark results obtained with a traditional system code “ring” model against a more detailed “block” model that include kinetics feedback on an individual block level and thermal feedbacks on a triangular sub-mesh. The higher spatial fidelity that can be obtained by the block model is illustrated with comparisons of the maximum fuel temperatures, especially in the case of natural convection conditions that dominate the DCC and PCC events. Differences up to 125 K (or 10%) were observed between the ring and block model predictions of the DCC transient, mostly due to the block model’s capability of tracking individual block decay powers and more detailed helium flow distributions. In general, the block model only required DCC and PCC calculation times twice as long as the ring models, and it therefore seems that the additional development and calculation time required for the block model could be worth the gain that can be obtained in the spatial resolution« less

Novel fluorescence resonance energy transfer-based reporter reveals differential calcineurin activation in neonatal and adult cardiomyocytes

PubMed Central

Bazzazi, Hojjat; Sang, Lingjie; Dick, Ivy E; Joshi-Mukherjee, Rosy; Yang, Wanjun; Yue, David T

2015-01-01

Abstract The phosphatase calcineurin is a central component of many calcium signalling pathways, relaying calcium signals from the plasma membrane to the nucleus. It has critical functions in a multitude of systems, including immune, cardiac and neuronal. Given the widespread importance of calcineurin in both normal and pathological conditions, new tools that elucidate the spatiotemporal dynamics of calcineurin activity would be invaluable. Here we develop two separate genetically encoded fluorescence resonance energy transfer (FRET)-based sensors of calcineurin activation, DuoCaN and UniCaN. Both sensors showcase a large dynamic range and rapid response kinetics, differing primarily in the linker structure between the FRET pairs. Both sensors were calibrated in HEK293 cells and their responses correlated well with NFAT translocation to the nucleus, validating the biological relevance of the sensor readout. The sensors were subsequently expressed in neonatal rat ventricular myocytes and acutely isolated adult guinea pig ventricular myocytes. Both sensors demonstrated robust responses in myocytes and revealed kinetic differences in calcineurin activation during changes in pacing rate for neonatal versus adult myocytes. Finally, mathematical modelling combined with quantitative FRET measurements provided novel insights into the kinetics and integration of calcineurin activation in response to myocyte Ca transients. In all, DuoCaN and UniCaN stand as valuable new tools for understanding the role of calcineurin in normal and pathological signalling. Key points Novel fluorescence resonance energy transfer-based genetically encoded reporters of calcineurin are constructed by fusing the two subunits of calcineurin with P2A-based linkers retaining the expected native conformation of calcineurin. Calcineurin reporters display robust responses to calcium transients in HEK293 cells. The sensor responses are correlated with NFATc1 translocation dynamics in HEK293 cells. The sensors are uniformly distributed in neonatal myocytes and respond efficiently to single electrically evoked calcium transients and show cumulative activation at frequencies of 0.5 and 1 Hz. In adult myocytes, the calcineurin sensors appear to be localized to the cardiac z-lines, and respond to cumulative calcium transients at frequencies of 0.5 and 1 Hz. PMID:26096996

Electron-transfer dynamics of photosynthetic reaction centers in thermoresponsive soft materials.

PubMed

Laible, Philip D; Kelley, Richard F; Wasielewski, Michael R; Firestone, Millicent A

2005-12-15

Poly(ethylene glycol)-grafted, lipid-based, thermoresponsive, soft nanostructures are shown to serve as scaffolding into which reconstituted integral membrane proteins, such as the bacterial photosynthetic reaction centers (RCs) can be stabilized, and their packing arrangement, and hence photophysical properties, can be controlled. The self-assembled nanostructures exist in two distinct states: a liquid-crystalline gel phase at temperatures above 21 degrees C and a non-birefringent, reduced viscosity state at lower temperatures. Characterization of the effect of protein introduction on the mesoscopic structure of the materials by 31P NMR and small-angle X-ray scattering shows that the expanded lamellar structure of the protein-free material is retained. At reduced temperatures, however, the aggregate structure is found to convert from a two-dimensional normal hexagonal structure to a three-dimensional cubic phase upon introduction of the RCs. Structural and functional characteristics of the RCs were determined by ground-state and femtosecond transient absorption spectroscopy. Time-resolved results indicate that the kinetics of primary electron transfer for the RCs in the low-viscosity cold phase of the self-assembled nanostructures are identical to those observed in a detergent-solubilized state in buffered aqueous solutions (approximately 4 ps) over a wide range of protein concentrations and experimental conditions. This is also true for RCs held within the lamellar gel phase at low protein concentrations and at short sample storage times. In contrast are kinetics from samples that are prepared with high RC concentrations and stored for several hours, which display additional kinetic components with extended electron-transfer times (approximately 10-12 ps). This observation is tentatively attributed to energy transfer between RCs that have laterally (in-plane) organized within the lipid bilayers of the lamellar gel phase prior to charge separation. These results not only demonstrate the use of soft nanostructures as a matrix in which to stabilize and organize membrane proteins but also suggest the possibility of using them to control the interactions between proteins and thus to tune their collective optical/electronic properties.

Transient behavior of redox flow battery connected to circuit based on global phase structure

NASA Astrophysics Data System (ADS)

Mannari, Toko; Hikihara, Takashi

A Redox Flow Battery (RFB) is one of the promising energy storage systems in power grid. An RFB has many advantages such as a quick response, a large capacity, and a scalability. Due to these advantages, an RFB can operate in mixed time scale. Actually, it has been demonstrated that an RFB can be used for load leveling, compensating sag, and smoothing the output of the renewable sources. An analysis on transient behaviors of an RFB is a key issue for these applications. An RFB is governed by electrical, chemical, and fluid dynamics. The hybrid structure makes the analysis difficult. To analyze transient behaviors of an RFB, the exact model is necessary. In this paper, we focus on a change in a concentration of ions in the electrolyte, and simulate the change with a model which is mainly based on chemical kinetics. The simulation results introduces transient behaviors of an RFB in a response to a load variation. There are found three kinds of typical transient behaviors including oscillations. As results, it is clarified that the complex transient behaviors, due to slow and fast dynamics in the system, arise by the quick response to load.

On the transient dynamics of piezoelectric-based, state-switched systems

NASA Astrophysics Data System (ADS)

Lopp, Garrett K.; Kelley, Christopher R.; Kauffman, Jeffrey L.

2018-01-01

This letter reports on the induced mechanical transients for piezoelectric-based, state-switching approaches utilizing both experimental tests and a numerical model that more accurately captures the dynamics associated with a switch between stiffness states. Currently, switching models instantaneously dissipate the stored piezoelectric voltage, resulting in a discrete change in effective stiffness states and a discontinuity in the system dynamics during the switching event. The proposed model allows for a rapid but continuous voltage dissipation and the corresponding variation between stiffness states, as one sees in physical implementations. This rapid variation in system stiffness when switching at a point of non-zero strain leads to high-frequency, large-amplitude transients in the system acceleration response. Utilizing a fundamental piezoelectric bimorph, a comparison between the numerical and experimental results reveals that these mechanical transients are much stronger than originally anticipated and masked by measurement hardware limitations, thus highlighting the significance of an appropriate system model governing the switch dynamics. Such a model enables designers to analyze systems that incorporate piezoelectric-based state switching with greater accuracy to ensure that these transients do not degrade the intended performance. Finally, if the switching does create unacceptable transients, controlling the duration of voltage dissipation enables control over the frequency content and peak amplitudes associated with the switch-induced acceleration transients.

Fluorescein: a Photo-CIDNP Sensitizer Enabling Hyper-Sensitive NMR Data Collection in Liquids at Low Micromolar Concentration

PubMed Central

Okuno, Yusuke; Cavagnero, Silvia

2016-01-01

Photochemically induced dynamic nuclear polarization (photo-CIDNP) is a powerful approach for sensitivity enhancement in NMR spectroscopy. In liquids, inter-molecular photo-CIDNP depends on the transient bimolecular reaction between photoexcited dye and sample of interest. Hence the extent of polarization is sample-concentration dependent. This study introduces fluorescein (FL) as a photo-CIDNP dye whose performance is exquisitely tailored to data collection at extremely low sample concentrations. The photo-CIDNP resonance intensities of tryptophan in the presence of either FL or FMN (i.e., the routinely employed flavin mononucleotide photosensitizer) in the liquid state show that FL yields superior sensitivity and enables rapid data collection down to an unprecedented 1 micromolar concentration. This result was achieved on a conventional spectrometer operating at 14.1 Tesla, and equipped with a room-temperature probe (i.e., non-cryogenic). Kinetic simulations show that the excellent behavior of FL arises from its long excited-state triplet lifetime and superior photostability relative to conventional photo-CIDNP sensitizers. PMID:26744790

Charge Transfer Dynamics at Dye-Sensitized ZnO and TiO2 Interfaces Studied by Ultrafast XUV Photoelectron Spectroscopy

PubMed Central

Borgwardt, Mario; Wilke, Martin; Kampen, Thorsten; Mähl, Sven; Xiao, Manda; Spiccia, Leone; Lange, Kathrin M.; Kiyan, Igor Yu.; Aziz, Emad F.

2016-01-01

Interfacial charge transfer from photoexcited ruthenium-based N3 dye molecules into ZnO thin films received controversial interpretations. To identify the physical origin for the delayed electron transfer in ZnO compared to TiO2, we probe directly the electronic structure at both dye-semiconductor interfaces by applying ultrafast XUV photoemission spectroscopy. In the range of pump-probe time delays between 0.5 to 1.0 ps, the transient signal of the intermediate states was compared, revealing a distinct difference in their electron binding energies of 0.4 eV. This finding strongly indicates the nature of the charge injection at the ZnO interface associated with the formation of an interfacial electron-cation complex. It further highlights that the energetic alignment between the dye donor and semiconductor acceptor states appears to be of minor importance for the injection kinetics and that the injection efficiency is dominated by the electronic coupling. PMID:27073060

Bidirectionality and compartmentation of metabolic fluxes are revealed in the dynamics of isotopomer networks.

PubMed

Schryer, David W; Peterson, Pearu; Paalme, Toomas; Vendelin, Marko

2009-04-17

Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth.

Full Core TREAT Kinetics Demonstration Using Rattlesnake/BISON Coupling Within MAMMOTH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortensi, Javier; DeHart, Mark D.; Gleicher, Frederick N.

2015-08-01

This report summarizes key aspects of research in evaluation of modeling needs for TREAT transient simulation. Using a measured TREAT critical measurement and a transient for a small, experimentally simplified core, Rattlesnake and MAMMOTH simulations are performed building from simple infinite media to a full core model. Cross sections processing methods are evaluated, various homogenization approaches are assessed and the neutronic behavior of the core studied to determine key modeling aspects. The simulation of the minimum critical core with the diffusion solver shows very good agreement with the reference Monte Carlo simulation and the experiment. The full core transient simulationmore » with thermal feedback shows a significantly lower power peak compared to the documented experimental measurement, which is not unexpected in the early stages of model development.« less

Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range

PubMed Central

Ventura, Alejandra C.; Bush, Alan; Vasen, Gustavo; Goldín, Matías A.; Burkinshaw, Brianne; Bhattacharjee, Nirveek; Folch, Albert; Brent, Roger; Chernomoretz, Ariel; Colman-Lerner, Alejandro

2014-01-01

Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general “systems level” mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step. PMID:25172920

Fibrillization kinetics of insulin solution in an interfacial shearing flow

NASA Astrophysics Data System (ADS)

Balaraj, Vignesh; McBride, Samantha; Hirsa, Amir; Lopez, Juan

2015-11-01

Although the association of fibril plaques with neurodegenerative diseases like Alzheimer's and Parkinson's is well established, in-depth understanding of the roles played by various physical factors in seeding and growth of fibrils is far from well known. Of the numerous factors affecting this complex phenomenon, the effect of fluid flow and shear at interfaces is paramount as it is ubiquitous and the most varying factor in vivo. Many amyloidogenic proteins have been found to denature upon contact at hydrophobic interfaces due to the self-assembling nature of protein in its monomeric state. Here, fibrillization kinetics of insulin solution is studied in an interfacial shearing flow. The transient surface rheological response of the insulin solution to the flow and its effect on the bulk fibrillization process has been quantified. Minute differences in hydrophobic characteristics between two variants of insulin- Human recombinant and Bovine insulin are found to result in very different responses. Results presented will be in the form of fibrillization assays, images of fibril plaques formed, and changes in surface rheological properties of the insulin solution. The interfacial velocity field, measured from images (via Brewster Angle Microscopy), is compared with computations. Supported by NNX13AQ22G, National Aeronautics and Space Administration.

Absolute Steady-State Thermal Conductivity Measurements by Use of a Transient Hot-Wire System.

PubMed

Roder, H M; Perkins, R A; Laesecke, A; Nieto de Castro, C A

2000-01-01

A transient hot-wire apparatus was used to measure the thermal conductivity of argon with both steady-state and transient methods. The effects of wire diameter, eccentricity of the wire in the cavity, axial conduction, and natural convection were accounted for in the analysis of the steady-state measurements. Based on measurements on argon, the relative uncertainty at the 95 % level of confidence of the new steady-state measurements is 2 % at low densities. Using the same hot wires, the relative uncertainty of the transient measurements is 1 % at the 95 % level of confidence. This is the first report of thermal conductivity measurements made by two different methods in the same apparatus. The steady-state method is shown to complement normal transient measurements at low densities, particularly for fluids where the thermophysical properties at low densities are not known with high accuracy.

Lithographically fabricated silicon microreactor for operando QEXAFS studies in exhaust gas catalysis during simulation of a standard driving cycle

NASA Astrophysics Data System (ADS)

Doronkin, D. E.; Baier, S.; Sheppard, T.; Benzi, F.; Grunwaldt, J.-D.

2016-05-01

Selective catalytic reduction of NOx by ammonia over Cu-ZSM-5 was monitored by operando QEXAFS during simulation of the New European Driving Cycle. The required fast temperature transients were realized using a novel silicon microreactor, enabling simultaneous spectroscopic and kinetic analysis by X-ray absorption spectroscopy (XAS) and mass spectrometry (MS). Periods of high temperature were correlated to an increase in both N2 production and change of coordination of Cu sites. This operando approach using Si microreactors can be applied to other heterogeneous catalytic systems involving fast temperature transients.

Theory of passive proton conductance in lipid bilayers.

PubMed

Nagle, J F

1987-10-01

The large permeability of lipid bilayers to protons compared to other small ions calls for a special proton transport mechanism. At the present time, only mechanisms involving transient hydrogen-bonded chains of water can account for the experimental result that the conductance is nearly independent of pH. Three models involving transient hydrogen-bonded chains are discussed, including an outline of the kinetic calculations that lead to predictions of current versus voltage drop and current versus pH differences. These calculations can be compared to experiment to determine which, if any, of these models pertains to lipid bilayers.

Photochemistry of bromoacetylene - Formation of HBr and quenching of excited Br/4 2P 0 1/2/

NASA Technical Reports Server (NTRS)

Laufer, A. H.

1979-01-01

The photolysis of bromacetylene is examined by means of vacuum ultraviolet flash photolysis-kinetic spectroscopy, with attention given to the production of Br atoms in the 2P 0 3/2 and 2P 0 1/2 states, the production of HBr, and UV absorption attributable to the ethynyl radical. Although Br(2P 0 1/2) and Br(2P 0 3/2) were both directly observed at the shortest delay time after the flash, strongly indicating the presence of the ethynyl radical, transient absorption by C2H was not detected in the range 125 to 180 nm. Quenching rate constants for the decay of the 2P 0 1/2 state of Br, which is observed to form concurrently with the ground state, are derived for quenching by He, CH2Br, CF4, and D2 from the pseudo-first-order decay rates. HBr was observed as a secondary photolysis product, and a model of its formation by the exothermic reaction of ground-state atoms with C2HBR, coupled with the secondary production of Br atoms, is found to agree well with the experiment.

Action potentials and ion conductances in wild-type and CALHM1-knockout type II taste cells

PubMed Central

Saung, Wint Thu; Foskett, J. Kevin

2017-01-01

Taste bud type II cells fire action potentials in response to tastants, triggering nonvesicular ATP release to gustatory neurons via voltage-gated CALHM1-associated ion channels. Whereas CALHM1 regulates mouse cortical neuron excitability, its roles in regulating type II cell excitability are unknown. In this study, we compared membrane conductances and action potentials in single identified TRPM5-GFP-expressing circumvallate papillae type II cells acutely isolated from wild-type (WT) and Calhm1 knockout (KO) mice. The activation kinetics of large voltage-gated outward currents were accelerated in cells from Calhm1 KO mice, and their associated nonselective tail currents, previously shown to be highly correlated with ATP release, were completely absent in Calhm1 KO cells, suggesting that CALHM1 contributes to all of these currents. Calhm1 deletion did not significantly alter resting membrane potential or input resistance, the amplitudes and kinetics of Na+ currents either estimated from action potentials or recorded from steady-state voltage pulses, or action potential threshold, overshoot peak, afterhyperpolarization, and firing frequency. However, Calhm1 deletion reduced the half-widths of action potentials and accelerated the deactivation kinetics of transient outward currents, suggesting that the CALHM1-associated conductance becomes activated during the repolarization phase of action potentials. NEW & NOTEWORTHY CALHM1 is an essential ion channel component of the ATP neurotransmitter release mechanism in type II taste bud cells. Its contribution to type II cell resting membrane properties and excitability is unknown. Nonselective voltage-gated currents, previously associated with ATP release, were absent in cells lacking CALHM1. Calhm1 deletion was without effects on resting membrane properties or voltage-gated Na+ and K+ channels but contributed modestly to the kinetics of action potentials. PMID:28202574

Action potentials and ion conductances in wild-type and CALHM1-knockout type II taste cells.

PubMed

Ma, Zhongming; Saung, Wint Thu; Foskett, J Kevin

2017-05-01

Taste bud type II cells fire action potentials in response to tastants, triggering nonvesicular ATP release to gustatory neurons via voltage-gated CALHM1-associated ion channels. Whereas CALHM1 regulates mouse cortical neuron excitability, its roles in regulating type II cell excitability are unknown. In this study, we compared membrane conductances and action potentials in single identified TRPM5-GFP-expressing circumvallate papillae type II cells acutely isolated from wild-type (WT) and Calhm1 knockout (KO) mice. The activation kinetics of large voltage-gated outward currents were accelerated in cells from Calhm1 KO mice, and their associated nonselective tail currents, previously shown to be highly correlated with ATP release, were completely absent in Calhm1 KO cells, suggesting that CALHM1 contributes to all of these currents. Calhm1 deletion did not significantly alter resting membrane potential or input resistance, the amplitudes and kinetics of Na + currents either estimated from action potentials or recorded from steady-state voltage pulses, or action potential threshold, overshoot peak, afterhyperpolarization, and firing frequency. However, Calhm1 deletion reduced the half-widths of action potentials and accelerated the deactivation kinetics of transient outward currents, suggesting that the CALHM1-associated conductance becomes activated during the repolarization phase of action potentials. NEW & NOTEWORTHY CALHM1 is an essential ion channel component of the ATP neurotransmitter release mechanism in type II taste bud cells. Its contribution to type II cell resting membrane properties and excitability is unknown. Nonselective voltage-gated currents, previously associated with ATP release, were absent in cells lacking CALHM1. Calhm1 deletion was without effects on resting membrane properties or voltage-gated Na + and K + channels but contributed modestly to the kinetics of action potentials. Copyright © 2017 the American Physiological Society.

Transient state kinetics of transcription elongation by T7 RNA polymerase.

PubMed

Anand, Vasanti Subramanian; Patel, Smita S

2006-11-24

The single subunit DNA-dependent RNA polymerase (RNAP) from bacteriophage T7 catalyzes both promoter-dependent transcription initiation and promoter-independent elongation. Using a promoter-free substrate, we have dissected the kinetic pathway of single nucleotide incorporation during elongation. We show that T7 RNAP undergoes a slow conformational change (0.01-0.03 s(-1)) to form an elongation competent complex with the promoter-free substrate (dissociation constant (Kd) of 96 nM). The complex binds to a correct NTP (Kd of 80 microM) and incorporates the nucleoside monophosphate (NMP) into RNA primer very efficiently (220 s(-1) at 25 degrees C). An overall free energy change (-5.5 kcal/mol) and internal free energy change (-3.7 kcal/mol) of single NMP incorporation was calculated from the measured equilibrium constants. In the presence of inorganic pyrophosphate (PPi), the elongation complex catalyzes the reverse pyrophosphorolysis reaction at a maximum rate of 0.8 s(-1) with PPi Kd of 1.2 mM. Several experiments were designed to investigate the rate-limiting step in the pathway of single nucleotide addition. Acid-quench and pulse-chase kinetics indicated that an isomerization step before chemistry is rate-limiting. The very similar rate constants of sequential incorporation of two nucleotides indicated that the steps after chemistry are fast. Based on available data, we propose that the preinsertion to insertion isomerization of NTP observed in the crystallographic studies of T7 RNAP is a likely candidate for the rate-limiting step. The studies here provide a kinetic framework to investigate structure-function and fidelity of RNA synthesis and to further explore the role of the conformational change in nucleotide selection during RNA synthesis.

Kinetics of Ca2+ binding to parvalbumin in bovine chromaffin cells: implications for [Ca2+] transients of neuronal dendrites

PubMed Central

Lee, Suk-Ho; Schwaller, Beat; Neher, Erwin

2000-01-01

The effect of parvalbumin (PV) on [Ca2+] transients was investigated by perfusing adrenal chromaffin cells with fura-2 and fluorescein isothiocyanate (FITC)-labelled PV. As PV diffused into cells, the decay of [Ca2+] transients was transformed from monophasic into biphasic. The proportion of the initial fast decay phase increased in parallel with the fluorescence intensity of FITC, indicating that PV is responsible for the initial fast decay phase.The relationship between the fast decay phase and the [Ca2+] level was investigated using depolarizing trains of stimuli. Within a train the relative amplitude of the fast decay phase was inversely dependent on the [Ca2+] level preceding a given stimulus.Based on these observations, we estimated the Ca2+ binding ratio of PV (κP), the apparent dissociation constant of PV for Ca2+ (Kdc,app), and the unbinding rate constant of Ca2+ from PV (kc-) in the cytosol of chromaffin cells. Assuming free [Mg2+] to be 0.14 mm, we obtained values of 51.4 ± 2.0 nm (n = 3) and 0.95 ± 0.026 s−1 (n = 3), for Kdc,app and kc-, respectively.With the parameters obtained in the perfusion study, we simulated [Ca2+] transients, using two different Ca2+ extrusion rates (γ) – 20 and 300 s−1– which represent typical values for chromaffin cells and neuronal dendrites, respectively. The simulation indicated that Ca2+ is pumped out before it is equilibrated with PV, when γ is comparable to the equilibration rates between PV and Ca2+, resulting in the fast decay phase of a biexponential [Ca2+] transient.From these results we conclude that Ca2+ buffers with slow kinetics, such as PV, may cause biexponential decays in [Ca2+] transients, thereby complicating the analysis of endogenous Ca2+ binding ratios (κS) based on time constants. Nevertheless, estimates of κS based on Ca2+ increments provide reasonable estimates for Ca2+ binding ratios before equilibration with PV. PMID:10835044

Emergence of ion channel modal gating from independent subunit kinetics.

PubMed

Bicknell, Brendan A; Goodhill, Geoffrey J

2016-09-06

Many ion channels exhibit a slow stochastic switching between distinct modes of gating activity. This feature of channel behavior has pronounced implications for the dynamics of ionic currents and the signaling pathways that they regulate. A canonical example is the inositol 1,4,5-trisphosphate receptor (IP3R) channel, whose regulation of intracellular Ca(2+) concentration is essential for numerous cellular processes. However, the underlying biophysical mechanisms that give rise to modal gating in this and most other channels remain unknown. Although ion channels are composed of protein subunits, previous mathematical models of modal gating are coarse grained at the level of whole-channel states, limiting further dialogue between theory and experiment. Here we propose an origin for modal gating, by modeling the kinetics of ligand binding and conformational change in the IP3R at the subunit level. We find good agreement with experimental data over a wide range of ligand concentrations, accounting for equilibrium channel properties, transient responses to changing ligand conditions, and modal gating statistics. We show how this can be understood within a simple analytical framework and confirm our results with stochastic simulations. The model assumes that channel subunits are independent, demonstrating that cooperative binding or concerted conformational changes are not required for modal gating. Moreover, the model embodies a generally applicable principle: If a timescale separation exists in the kinetics of individual subunits, then modal gating can arise as an emergent property of channel behavior.

Transient Effects in Planar Solidification of Dilute Binary Alloys

NASA Technical Reports Server (NTRS)

Mazuruk, Konstantin; Volz, Martin P.

2008-01-01

The initial transient during planar solidification of dilute binary alloys is studied in the framework of the boundary integral method that leads to the non-linear Volterra integral governing equation. An analytical solution of this equation is obtained for the case of a constant growth rate which constitutes the well-known Tiller's formula for the solute transient. The more physically relevant, constant ramping down temperature case has been studied both numerically and analytically. In particular, an asymptotic analytical solution is obtained for the initial transient behavior. A numerical technique to solve the non-linear Volterra equation is developed and the solution is obtained for a family of the governing parameters. For the rapid solidification condition, growth rate spikes have been observed even for the infinite kinetics model. When recirculating fluid flow is included into the analysis, the spike feature is dramatically diminished. Finally, we have investigated planar solidification with a fluctuating temperature field as a possible mechanism for frequently observed solute trapping bands.

Communication: Appearance of undershoots in start-up shear: Experimental findings captured by tumbling-snake dynamics

NASA Astrophysics Data System (ADS)

Stephanou, Pavlos S.; Schweizer, Thomas; Kröger, Martin

2017-04-01

Our experimental data unambiguously show (i) a damping behavior (the appearance of an undershoot following the overshoot) in the transient shear viscosity of a concentrated polymeric solution, and (ii) the absence of a corresponding behavior in the transient normal stress coefficients. Both trends are shown to be quantitatively captured by the bead-link chain kinetic theory for concentrated polymer solutions and entangled polymer melts proposed by Curtiss and Bird, supplemented by a non-constant link tension coefficient that we relate to the nematic order parameter. The observed phenomena are attributed to the tumbling behavior of the links, triggered by rotational fluctuations, on top of reptation. Using model parameters deduced from stationary data, we calculate the transient behavior of the stress tensor for this "tumbling-snake" model after startup of shear flow efficiently via simple Brownian dynamics. The unaltered method is capable of handling arbitrary homogeneous flows and has the promising capacity to improve our understanding of the transient behavior of concentrated polymer solutions.

Dynamic simulation of coronal mass ejections

NASA Technical Reports Server (NTRS)

Steinolfson, R. S.; Wu, S. T.

1980-01-01

A model is developed for the formation and propagation through the lower corona of the loop-like coronal transients in which mass is ejected from near the solar surface to the outer corona. It is assumed that the initial state for the transient is a coronal streamer. The initial state for the streamer is a polytropic, hydrodynamic solution to the steady-state radial equation of motion coupled with a force-free dipole magnetic field. The numerical solution of the complete time-dependent equations then gradually approaches a stationary coronal streamer configuration. The streamer configuration becomes the initial state for the coronal transient. The streamer and transient simulations are performed completely independent of each other. The transient is created by a sudden increase in the pressure at the base of the closed-field region in the streamer configuration. Both coronal streamers and coronal transients are calculated for values of the plasma beta (the ratio of thermal to magnetic pressure) varying from 0.1 to 100.

Modeling of cryopreservation of engineered tissues with one-dimensional geometry.

PubMed

Cui, Z F; Dykhuizen, R C; Nerem, R M; Sembanis, A

2002-01-01

Long-term storage of engineered bio-artificial tissues is required to ensure the off-the-shelf availability to clinicians due to their long production cycle. Cryopreservation is likely the choice for long-term preservation. Although the cryopreservation of cells is well established for many cell types, cryopreservation of tissues is far more complicated. Cells at different locations in the tissue could experience very different local environmental changes, i.e., the change of concentration of cryoprotecting chemicals (CPA) and temperature, during the addition/removal of CPA and cooling/warming, which leads to nonuniformity in cell survival in the tissue. This is due to the limitation of mass and heat transfer within the tissue. A specific aim of cryopreservation of tissue is to ensure a maximum recovery of cells and their functionality throughout a tissue. Cells at all locations should be protected adequately by the CPA and frozen at rates conducive to survival. It is hence highly desirable to know the cell transient and final states during cryopreservation within the whole tissue, which can be best studied by mathematical modeling. In this work, a model framework for cryopreservation of one-dimensional artificial tissues is developed on the basis of solving the coupled equations to describe the mass and heat transfer within the tissue and osmotic transport through the cell membrane. Using an artificial pancreas as an example, we carried out a simulation to examine the temperature history, cell volume, solute redistribution, and other state parameters during the freezing of the spherical heterogeneous construct (a single bead). It is found that the parameters affecting the mass transfer of CPA in tissue and through the cell membrane and the freezing rate play dominant roles in affecting the cell volume transient and extracellular ice formation. Thermal conductivity and extracellular ice formation kinetics, on the other hand, have little effect on cell transient and final states, as the heat transfer rate is much faster than mass diffusion. The outcome of such a model study can be used to evaluate the construct design on its survivability during cryopreservation and to select a cryopreservation protocol to achieve maximum cell survival.

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy† †Electronic supplementary information (ESI) available: Synthesis schemes, experimental methods, NMR spectra, X-ray crystallographic information, emission spectra, cyclic voltammetry, electronic structure calculations, data analysis and numerical methods, and other additional figures. CCDC 1561879. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc04055e

PubMed Central

Kohler, Lars; Hadt, Ryan G.; Zhang, Xiaoyi; Liu, Cunming

2017-01-01

The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(i) bis(phenanthroline)/ruthenium(ii) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(i)–Ru(ii) analogs of the homodinuclear Cu(i)–Cu(i) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations. PMID:29629153

Exciton-Delocalizing Ligands Can Speed Up Energy Migration in Nanocrystal Solids.

PubMed

Azzaro, Michael S; Dodin, Amro; Zhang, Diana Y; Willard, Adam P; Roberts, Sean T

2018-05-09

Researchers have long sought to use surface ligands to enhance energy migration in nanocrystal solids by decreasing the physical separation between nanocrystals and strengthening their electronic coupling. Exciton-delocalizing ligands, which possess frontier molecular orbitals that strongly mix with nanocrystal band-edge states, are well-suited for this role because they can facilitate carrier-wave function extension beyond the nanocrystal core, reducing barriers for energy transfer. This report details the use of the exciton-delocalizing ligand phenyldithiocarbamate (PDTC) to tune the transport rate and diffusion length of excitons in CdSe nanocrystal solids. A film composed of oleate-terminated CdSe nanocrystals is subjected to a solid-state ligand exchange to replace oleate with PDTC. Exciton migration in the films is subsequently investigated by femtosecond transient absorption. Our experiments indicate that the treatment of nanocrystal films with PDTC leads to rapid (∼400 fs) downhill energy migration (∼80 meV), while no such migration occurs in oleate-capped films. Kinetic Monte Carlo simulations allow us to extract both rates and length scales for exciton diffusion in PDTC-treated films. These simulations reproduce dynamics observed in transient absorption measurements over a range of temperatures and confirm excitons hop via a Miller-Abrahams mechanism. Importantly, our experiments and simulations show PDTC treatment increases the exciton hopping rate to 200 fs, an improvement of 5 orders of magnitude relative to oleate-capped films. This exciton hopping rate stands as one of the fastest determined for CdSe solids. The facile, room-temperature processing and improved transport properties offered by the solid-state exchange of exciton-delocalizing ligands show they offer promise for the construction of strongly coupled nanocrystal arrays.

Vibrational cooling dynamics of a [FeFe]-hydrogenase mimic probed by time-resolved infrared spectroscopy.

PubMed

Caplins, Benjamin W; Lomont, Justin P; Nguyen, Son C; Harris, Charles B

2014-12-11

Picosecond time-resolved infrared spectroscopy (TRIR) was performed for the first time on a dithiolate bridged binuclear iron(I) hexacarbonyl complex ([Fe₂(μ-bdt)(CO)₆], bdt = benzene-1,2-dithiolate) which is a structural mimic of the active site of the [FeFe]-hydrogenase enzyme. As these model active sites are increasingly being studied for their potential in photocatalytic systems for hydrogen production, understanding their excited and ground state dynamics is critical. In n-heptane, absorption of 400 nm light causes carbonyl loss with low quantum yield (<10%), while the majority (ca. 90%) of the parent complex is regenerated with biexponential kinetics (τ₁ = 21 ps and τ₂ = 134 ps). In order to understand the mechanism of picosecond bleach recovery, a series of UV-pump TRIR experiments were performed in different solvents. The long time decay (τ₂) of the transient spectra is seen to change substantially as a function of solvent, from 95 ps in THF to 262 ps in CCl₄. Broadband IR-pump TRIR experiments were performed for comparison. The measured vibrational lifetimes (T₁(avg)) of the carbonyl stretches were found to be in excellent correspondence to the observed τ₂ decays in the UV-pump experiments, signifying that vibrationally excited carbonyl stretches are responsible for the observed longtime decays. The fast spectral evolution (τ₁) was determined to be due to vibrational cooling of low frequency modes anharmonically coupled to the carbonyl stretches that were excited after electronic internal conversion. The results show that cooling of both low and high frequency vibrational modes on the electronic ground state give rise to the observed picosecond TRIR transient spectra of this compound, without the need to invoke electronically excited states.

Multi-Dimensional, Non-Pyrolyzing Ablation Test Problems

NASA Technical Reports Server (NTRS)

Risch, Tim; Kostyk, Chris

2016-01-01

Non-pyrolyzingcarbonaceous materials represent a class of candidate material for hypersonic vehicle components providing both structural and thermal protection system capabilities. Two problems relevant to this technology are presented. The first considers the one-dimensional ablation of a carbon material subject to convective heating. The second considers two-dimensional conduction in a rectangular block subject to radiative heating. Surface thermochemistry for both problems includes finite-rate surface kinetics at low temperatures, diffusion limited ablation at intermediate temperatures, and vaporization at high temperatures. The first problem requires the solution of both the steady-state thermal profile with respect to the ablating surface and the transient thermal history for a one-dimensional ablating planar slab with temperature-dependent material properties. The slab front face is convectively heated and also reradiates to a room temperature environment. The back face is adiabatic. The steady-state temperature profile and steady-state mass loss rate should be predicted. Time-dependent front and back face temperature, surface recession and recession rate along with the final temperature profile should be predicted for the time-dependent solution. The second problem requires the solution for the transient temperature history for an ablating, two-dimensional rectangular solid with anisotropic, temperature-dependent thermal properties. The front face is radiatively heated, convectively cooled, and also reradiates to a room temperature environment. The back face and sidewalls are adiabatic. The solution should include the following 9 items: final surface recession profile, time-dependent temperature history of both the front face and back face at both the centerline and sidewall, as well as the time-dependent surface recession and recession rate on the front face at both the centerline and sidewall. The results of the problems from all submitters will be collected, summarized, and presented at a later conference.

Effect of silicate and phosphate additives on the kinetics of the oxygen evolution reaction in valve-regulated lead/acid batteries

NASA Astrophysics Data System (ADS)

Vinod, M. P.; Vijayamohanan, K.; Joshi, S. N.

Effect of sodium silicate and phosphoric acid additives on the kinetics of oxygen evolution on PbO 2 electrodes in sulfuric acid has been studied in gelled and flooded electrolytes with relevance to valve-regulated lead/acid batteries. A comparison of the open-circuit potential versus time transients, with and without these additives, indicates that the additives suppress self-discharge of the electrodes. Tafel polarization studies also suggest that the addition of phosphoric acid attenuates the rate of oxygen evolution reaction. These findings have been supported with cyclic voltammetric data.

Reducing the surface roughness beyond the pulsed-laser-deposition limit.

PubMed

Vasco, E; Polop, C; Sacedón, J L

2009-10-01

Here, we outline the theoretical fundamentals of a promising growth kinetics of films from the vapor phase, in which pulsed fluxes are combined with temperature transients to enable short-range surface relaxations (e.g., species rearrangements) and to inhibit long-range relaxations (atomic exchange between species). A group of physical techniques (fully pulsed thermal and/or laser depositions) based on this kinetics is developed that can be used to prepare films with roughnesses even lower than those obtained with pulsed-laser deposition, which is the physical vapor-phase deposition technique that has produced the flattest films reported so far.

Modeling biotic uptake by periphyton and transient hyporrheic storage of nitrate in a natural stream

USGS Publications Warehouse

Kim, Brian K.A.; Jackman, Alan P.; Triska, Frank J.

1992-01-01

To a convection-dispersion hydrologic transport model we coupled a transient storage submodel (Bencala, 1984) and a biotic uptake submodel based on Michaelis-Menten kinetics (Kim et al., 1990). Our purpose was threefold: (1) to simulate nitrate retention in response to change in load in a third-order stream, (2) to differentiate biotic versus hydrologie factors in nitrate retention, and (3) to produce a research tool whose properties are consistent with laboratory and field observations. Hydrodynamic parameters were fitted from chloride concentration during a 20-day chloride-nitrate coinjection (Bencala, 1984), and biotic uptake kinetics were based on flume studies by Kim et al. (1990) and Triska et al. (1983). Nitrate concentration from the 20-day coinjection experiment served as a base for model validation. The complete transport retention model reasonably predicted the observed nitrate concentration. However, simulations which lacked either the transient storage submodel or the biotic uptake submodel poorly predicted the observed nitrate concentration. Model simulations indicated that transient storage in channel and hyporrheic interstices dominated nitrate retention within the first 24 hours, whereas biotic uptake dominated thereafter. A sawtooth function for Vmax ranging from 0.10 to 0.17 μg NO3-N s−1 gAFDM−1 (grams ash free dry mass) slightly underpredicted nitrate retention in simulations of 2–7 days. This result was reasonable since uptake by other nitrate-demanding processes were not included. The model demonstrated how ecosystem retention is an interaction between physical and biotic processes and supports the validity of coupling separate hydrodynamic and reactive submodels to established solute transport models in biological studies of fluvial ecosystems.

Assay of Calcium Transients and Synapses in Rat Hippocampal Neurons by Kinetic Image Cytometry and High-Content Analysis: An In Vitro Model System for Postchemotherapy Cognitive Impairment.

PubMed

McDonough, Patrick M; Prigozhina, Natalie L; Basa, Ranor C B; Price, Jeffrey H

2017-07-01

Postchemotherapy cognitive impairment (PCCI) is commonly exhibited by cancer patients treated with a variety of chemotherapeutic agents, including the endocrine disruptor tamoxifen (TAM). The etiology of PCCI is poorly understood. Our goal was to develop high-throughput assay methods to test the effects of chemicals on neuronal function applicable to PCCI. Rat hippocampal neurons (RHNs) were plated in 96- or 384-well dishes and exposed to test compounds (forskolin [FSK], 17β-estradiol [ES]), TAM or fulvestrant [FUL], aka ICI 182,780) for 6-14 days. Kinetic Image Cytometry™ (KIC™) methods were developed to quantify spontaneously occurring intracellular calcium transients representing the activity of the neurons, and high-content analysis (HCA) methods were developed to quantify the expression, colocalization, and puncta formed by synaptic proteins (postsynaptic density protein-95 [PSD-95] and presynaptic protein Synapsin-1 [Syn-1]). As quantified by KIC, FSK increased the occurrence and synchronization of the calcium transients indicating stimulatory effects on RHN activity, whereas TAM had inhibitory effects. As quantified by HCA, FSK also increased PSD-95 puncta and PSD-95:Syn-1 colocalization, whereas ES increased the puncta of both PSD-95 and Syn-1 with little effect on colocalization. The estrogen receptor antagonist FUL also increased PSD-95 puncta. In contrast, TAM reduced Syn-1 and PSD-95:Syn-1 colocalization, consistent with its inhibitory effects on the calcium transients. Thus TAM reduced activity and synapse formation by the RHNs, which may relate to the ability of this agent to cause PCCI. The results illustrate that KIC and HCA can be used to quantify neurotoxic and neuroprotective effects of chemicals in RHNs to investigate mechanisms and potential therapeutics for PCCI.

Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry*

PubMed Central

Meneses, Erick; Mittermaier, Anthony

2014-01-01

Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr–Purcell–Meiboom–Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes. PMID:25122758

Hemoglobin Kinetics and Long-term Prognosis in Heart Failure.

PubMed

Díez-López, Carles; Lupón, Josep; de Antonio, Marta; Zamora, Elisabet; Domingo, Mar; Santesmases, Javier; Troya, Maria-Isabel; Boldó, Maria; Bayes-Genis, Antoni

2016-09-01

The influence of hemoglobin kinetics on outcomes in heart failure has been incompletely established. Hemoglobin was determined at the first visit and at 6 months. Anemia was defined according to World Health Organization criteria (hemoglobin < 13g/dL for men and hemoglobin < 12g/dL for women). Patients were classified relative to their hemoglobin values as nonanemic (both measurements normal), transiently anemic (anemic at the first visit but not at 6 months), newly anemic (nonanemic initially but anemic at 6 months), or permanently anemic (anemic in both measurements). A total of 1173 consecutive patients (71.9% men, mean age 66.8±12.2 years) were included in the study. In all, 476 patients (40.6%) were considered nonanemic, 170 (14.5%) had transient anemia, 147 (12.5%) developed new-onset anemia, and 380 (32.4%) were persistently anemic. During a follow-up of 3.7±2.8 years after the 6-month visit, 494 patients died. On comprehensive multivariable analyses, anemia (P < .001) and the type of anemia (P < .001) remained as independent predictors of all-cause mortality. Compared with patients without anemia, patients with persistent anemia (hazard ratio [HR] = 1.62; 95% confidence interval [95%CI], 1.30-2.03; P < .001) and new-onset anemia (HR = 1.39; 95%CI, 1.04-1.87, P = .03) had higher mortality, and even transient anemia showed a similar trend, although without reaching statistical significance (HR = 1.31; 95%CI, 0.97-1.77, P = .075). Anemia, especially persistent and of new-onset, and to a lesser degree, transient anemia, is deleterious in heart failure. Copyright © 2016 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Superluminous Transients at AGN Centers from Interaction between Black Hole Disk Winds and Broad-line Region Clouds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moriya, Takashi J.; Tanaka, Masaomi; Ohsuga, Ken

We propose that superluminous transients that appear at central regions of active galactic nuclei (AGNs) such as CSS100217:102913+404220 (CSS100217) and PS16dtm, which reach near- or super-Eddington luminosities of the central black holes, are powered by the interaction between accretion-disk winds and clouds in broad-line regions (BLRs) surrounding them. If the disk luminosity temporarily increases by, e.g., limit–cycle oscillations, leading to a powerful radiatively driven wind, strong shock waves propagate in the BLR. Because the dense clouds in the AGN BLRs typically have similar densities to those found in SNe IIn, strong radiative shocks emerge and efficiently convert the ejecta kineticmore » energy to radiation. As a result, transients similar to SNe IIn can be observed at AGN central regions. Since a typical black hole disk-wind velocity is ≃0.1 c , where c is the speed of light, the ejecta kinetic energy is expected to be ≃10{sup 52} erg when ≃1 M {sub ⊙} is ejected. This kinetic energy is transformed to radiation energy in a timescale for the wind to sweep up a similar mass to itself in the BLR, which is a few hundred days. Therefore, both luminosities (∼10{sup 44} erg s{sup −1}) and timescales (∼100 days) of the superluminous transients from AGN central regions match those expected in our interaction model. If CSS100217 and PS16dtm are related to the AGN activities triggered by limit–cycle oscillations, they become bright again in coming years or decades.« less

Ecotoxicity of two organophosphate pesticides chlorpyrifos and dichlorvos on non-targeting cyanobacteria Microcystis wesenbergii.

PubMed

Sun, Kai-Feng; Xu, Xiang-Rong; Duan, Shun-Shan; Wang, You-Shao; Cheng, Hao; Zhang, Zai-Wang; Zhou, Guang-Jie; Hong, Yi-Guo

2015-10-01

Organophosphate pesticides (OPs), as a replacement for the organochlorine pesticides, are generally considered non-toxic to plants and algae. Chlorpyrifos and dichlorvos are two OPs used for pest control all over the world. In this study, the dose-response of cyanobacteria Microcystis wesenbergii on OPs exposure and the stimulating effect of OPs with and without phosphorus source were investigated. The results showed that high concentrations of chlorpyrifos and dichlorvos caused significant decrease of chlorophyll a content. The median inhibitory concentrations (EC50) of chlorpyrifos and dichlorvos at 96 h were 15.40 and 261.16 μmol L(-1), respectively. Growth of M. wesenbergii under low concentration of OPs (ranged from 1/10,000 to 1/20 EC50), was increased by 35.85 % (chlorpyrifos) and 41.83 % (dichlorvos) at 120 h, respectively. Correspondingly, the highest enhancement on the maximum quantum yield (F v/F m) was 4.20 % (24 h) and 9.70 % (48 h), respectively. Chlorophyll fluorescence kinetics, known as O-J-I-P transients, showed significant enhancements in the O-J, J-I, and I-P transients under low concentrations of dichlorvos at 144 h, while enhancements of chlorophyll fluorescence kinetics induced by low concentrations of chlorpyrifos were only observed in the J-I transient at 144 h. Significant decreases of chlorophyll content, F v/F m and O-J-I-P transients with OPs as sole phosphorus source were found when they were compared with inorganic phosphate treatments. The results demonstrated an evidently hormetic dose-response of M. wesenbergii to both chlorpyrifos and dichlorvos, where high dose (far beyond environmental concentrations) exposure caused growth inhibition and low dose exposure induced enhancement on physiological processes. The stimulating effect of two OPs on growth of M. wesenbergii was negligible under phosphate limitation.

Real-Time Kinetic Modeling of Voltage-Gated Ion Channels Using Dynamic Clamp

PubMed Central

Milescu, Lorin S.; Yamanishi, Tadashi; Ptak, Krzysztof; Mogri, Murtaza Z.; Smith, Jeffrey C.

2008-01-01

We propose what to our knowledge is a new technique for modeling the kinetics of voltage-gated ion channels in a functional context, in neurons or other excitable cells. The principle is to pharmacologically block the studied channel type, and to functionally replace it with dynamic clamp, on the basis of a computational model. Then, the parameters of the model are modified in real time (manually or automatically), with the objective of matching the dynamical behavior of the cell (e.g., action potential shape and spiking frequency), but also the transient and steady-state properties of the model (e.g., those derived from voltage-clamp recordings). Through this approach, one may find a model and parameter values that explain both the observed cellular dynamics and the biophysical properties of the channel. We extensively tested the method, focusing on Nav models. Complex Markov models (10–12 states or more) could be accurately integrated in real time at >50 kHz using the transition probability matrix, but not the explicit Euler method. The practicality of the technique was tested with experiments in raphe pacemaker neurons. Through automated real-time fitting, a Hodgkin-Huxley model could be found that reproduced well the action potential shape and the spiking frequency. Adding a virtual axonal compartment with a high density of Nav channels further improved the action potential shape. The computational procedure was implemented in the free QuB software, running under Microsoft Windows and featuring a friendly graphical user interface. PMID:18375511

Electrical properties of grain boundaries and dislocations in crystalline silicon: Influence of impurity incorporation and hydrogenation

NASA Astrophysics Data System (ADS)

Park, Yongkook

This thesis examines the electrical properties of grain boundaries (GBs) and dislocations in crystalline silicon. The influence of impurity incorporation and hydrogenation on the electrical properties of grain boundaries , as well as the electrical activity of impurity decorated dislocations and the retention of impurities at dislocations at high temperatures have been investigated. The electrical properties of Si GB were examined by C-V, J-V , and capacitance transient methods using aluminum/Si(100)/Si(001) junctions. First, the density of states and the carrier capture cross-sections of the clean GB were evaluated by C-V/J-V analyses. The density of GB states was determined as 4.0x1012 cm-2eV -1. It was found that the states close to the valance band edge have relatively smaller hole capture cross sections than those at higher energy position, and electron capture cross sections are at least two or three orders larger than the corresponding hole capture cross sections. Secondly, the influence of iron contamination and hydrogenation following iron contamination on the electrical properties of (110)/(001) Si GB was characterized by a capacitance transient technique. Compared with the clean sample, iron contamination increased both the density of states by at least three times and the zero-bias barrier height by 70 meV, while reducing by two orders of magnitude the electron/hole capture cross-section ratio. Hydrogenation following iron contamination led to the reduction of the density of Fe-decorated GB states, which was increased to over 2x1013 cm-2eV-1 after iron contamination, to ˜1x1013 cm-2 eV-1 after hydrogenation treatment. The increased zero-bias GB energy barrier due to iron contamination was reversed as well by hydrogen treatment. The density of GB states before and after hydrogenation was evaluated by J-V, C-V and capacitance transient methods using gold/direct-silicon-bonded (DSB) (110) thin silicon top layer/(100) silicon substrate junctions. The GB potential energy barrier in thermal equilibrium was reduced by 70 meV. Whereas the clean sample had a density of GB states of ˜6x1012 cm-2eV-1 in the range of Ev+0.54˜0.64 eV, hydrogenation reduced the density of GB states to ˜9x1011 cm-2eV -1 in the range of Ev+0.56˜0.61 eV, which is about a seven-fold reduction from that of the clean sample. Segregation and thermal dissociation kinetics of hydrogen at a large-angle general GB in crystalline silicon have been investigated using deuterium as a readily identifiable isotope which duplicates hydrogen chemistry. Segregation or trapping of deuterium (hydrogen) introduced was found to take place at (110)/(001) Si GB. The segregation coefficient (k) of deuterium (hydrogen) at GB was determined as k≈24+/-3 at 100°C. Thermal dissociation of deuterium (hydrogen) from GB obeyed first-order kinetics with an activation energy of ˜1.62 eV. The electrical activities of dislocations in a SiGe/Si heterostructure were examined by deep level transient spectroscopy (DLTS) after iron contamination and phosphorous diffusion gettering. DLTS of iron contaminated samples revealed a peak at 210 K, which was assigned to individual iron atoms or very small (<2 nm) precipitates decorated along dislocations. Arrhenius plot of the 210 K peak yielded a hole capture cross section of 2.4x10-14 cm2 and an energy level of 0.42 eV above the valance band. DLTS of the iron contaminated sample revealed that 6x10 14 cm-3 of boron can more effectively trap interstitial iron at room temperature than the strain field/defect sites at 107 ˜108 cm-2 dislocations. Phosphorous diffusion experiments revealed that the gettering efficiency of iron impurities depends on the dislocation density. For regions of high dislocation density, phosphorous diffusion cannot remove all iron impurities decorated at dislocations, suggesting a strong binding of iron impurities at dislocation core defects.

Vibronic relaxation dynamics of o-dichlorobenzene in its lowest excited singlet state

NASA Astrophysics Data System (ADS)

Liu, Benkang; Zhao, Haiyan; Lin, Xiang; Li, Xinxin; Gao, Mengmeng; Wang, Li; Wang, Wei

2018-01-01

Vibronic dynamics of o-dichlorobenzene in its lowest excited singlet state, S1, is investigated in real time by using femtosecond pump-probe method, combined with time-of-flight mass spectroscopy and photoelectron velocity mapping technique. Relaxation processes for the excitation in the range of 276-252 nm can be fitted by single exponential decay model, while in the case of wavelength shorter than 252 nm two-exponential decay model must be adopted for simulating transient profiles. Lifetime constants of the vibrationally excited S1 states change from 651 ± 10 ps for 276 nm excitation to 61 ± 1 ps for 242 nm excitation. Both the internal conversion from the S1 to the highly vibrationally excited ground state S0 and the intersystem crossing from the S1 to the triplet state are supposed to play important roles in de-excitation processes. Exponential fitting of the de-excitation rates on the excitation energy implies such de-excitation process starts from the highly vibrationally excited S0 state, which is validated, by probing the relaxation following photoexcitation at 281 nm, below the S1 origin. Time-dependent photoelectron kinetic energy distributions have been obtained experimentally. As the excitation wavelength changes from 276 nm to 242 nm, different cationic vibronic vibrations can be populated, determined by the Franck-Condon factors between the large geometry distorted excited singlet states and final cationic states.

Developmental assessment of the Fort St. Vrain version of the Composite HTGR Analysis Program (CHAP-2)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stroh, K.R.

1980-01-01

The Composite HTGR Analysis Program (CHAP) consists of a model-independent systems analysis mainframe named LASAN and model-dependent linked code modules, each representing a component, subsystem, or phenomenon of an HTGR plant. The Fort St. Vrain (FSV) version (CHAP-2) includes 21 coded modules that model the neutron kinetics and thermal response of the core; the thermal-hydraulics of the reactor primary coolant system, secondary steam supply system, and balance-of-plant; the actions of the control system and plant protection system; the response of the reactor building; and the relative hazard resulting from fuel particle failure. FSV steady-state and transient plant data are beingmore » used to partially verify the component modeling and dynamic smulation techniques used to predict plant response to postulated accident sequences.« less

Effect of wall-mediated hydrodynamic fluctuations on the kinetics of a Brownian nanoparticle

NASA Astrophysics Data System (ADS)

Yu, Hsiu-Yu; Eckmann, David M.; Ayyaswamy, Portonovo S.; Radhakrishnan, Ravi

2016-12-01

The reactive flux formalism (Chandler 1978 J. Chem. Phys. 68, 2959-2970. (doi:10.1063/1.436049)) and the subsequent development of methods such as transition path sampling have laid the foundation for explicitly quantifying the rate process in terms of microscopic simulations. However, explicit methods to account for how the hydrodynamic correlations impact the transient reaction rate are missing in the colloidal literature. We show that the composite generalized Langevin equation (Yu et al. 2015 Phys. Rev. E 91, 052303. (doi:10.1103/PhysRevE.91.052303)) makes a significant step towards solving the coupled processes of molecular reactions and hydrodynamic relaxation by examining how the wall-mediated hydrodynamic memory impacts the two-stage temporal relaxation of the reaction rate for a nanoparticle transition between two bound states in the bulk, near-wall and lubrication regimes.

Onset of the radial electric field oscillations in the neoclassical plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, C.S.; Novakovskii, S.V.; Sagdeev, R.Z.

1996-12-31

It is shown that the relaxation of the radial electric field in the tokomak plasmas towards its neoclassical value is accompanied by the fast oscillations of the order of the ion transient frequency V{sub T}/qR. This happens during the transition from the Pfirsch-Schluter collisional regime to the plateau regime at v{sub c}qR/V{sub T} {le} c{sub cr} {le} 1. The investigation has been performed with the help of the specially developed numerical code for solution of the nonsteady-state drift kinetic equation with the exact collisional term in the Hirshman-Sigmar-Clarke form. Comparison with the analytical results, corresponding to the regime of themore » very low collisions as well as with previous approximate models for the plateau regime will also be reported.« less

Near shot-noise limited time-resolved circular dichroism pump-probe spectrometer

NASA Astrophysics Data System (ADS)

Stadnytskyi, Valentyn; Orf, Gregory S.; Blankenship, Robert E.; Savikhin, Sergei

2018-03-01

We describe an optical near shot-noise limited time-resolved circular dichroism (TRCD) pump-probe spectrometer capable of reliably measuring circular dichroism signals in the order of μdeg with nanosecond time resolution. Such sensitivity is achieved through a modification of existing TRCD designs and introduction of a new data processing protocol that eliminates approximations that have caused substantial nonlinearities in past measurements and allows the measurement of absorption and circular dichroism transients simultaneously with a single pump pulse. The exceptional signal-to-noise ratio of the described setup makes the TRCD technique applicable to a large range of non-biological and biological systems. The spectrometer was used to record, for the first time, weak TRCD kinetics associated with the triplet state energy transfer in the photosynthetic Fenna-Matthews-Olson antenna pigment-protein complex.

Cytostatica efficiency enhancement by vitamins C, E and β-carotene under irradiation. State of the art

NASA Astrophysics Data System (ADS)

Getoff, Nikola

2001-01-01

A review is presented on the enhancement of MMC (mitomycin C) efficiency by the vitamins C, E and β-carotene using E. coil bacteria (AB 1157) and leukemia cells (HL 60) as a model for experiments in vitro. New and previously published spectroscopic and kinetic data of transients obtained by pulse radiolysis of MMC and the above mentioned vitamins were also discussed. Based on all these results a possible cascade electron transfer process from vit. C→ vit. E→ β-car.→MMC or oxidants in the living cells is presented. By vit. C deficiency a cell mutation might occur, possibly leading to appearance of cancer. The presented radiation chemical and radiation biological characteristic data are of importance as a basis for the development of an improved chemo-radiation therapy of cancer.

NMR at Low and Ultra-Low Temperatures

PubMed Central

Tycko, Robert

2017-01-01

Conspectus Solid state nuclear magnetic resonance (NMR) measurements at low temperatures have been common in physical sciences for many years, and are becoming increasingly important in studies of biomolecular systems. This article reviews a diverse set of projects from my laboratory, dating back to the early 1990s, that illustrate the motivations for low-temperature solid state NMR, the types of information that are available from the measurements, and likely directions for future research. These projects include NMR studies of both physical and biological systems, performed at low (cooled with nitrogen, down to 77 K) and very low (cooled with helium, below 77 K) temperatures, and performed with and without magic-angle spinning (MAS). In NMR studies of physical systems, the main motivation is to study phenomena that occur only at low temperatures. Two examples from my laboratory are studies of molecular rotation and an orientational ordering in solid C60 at low temperatures and studies of unusual electronic states, called skyrmions, in two-dimensionally confined electron systems within semiconductor quantum wells. NMR measurements on quantum wells were facilitated by optical pumping of nuclear spin polarizations, a signal enhancement phenomenon that exists at very low temperatures. In studies of biomolecular systems, motivations for low-temperature NMR include suppression of molecular tumbling (thereby permitting solid state NMR measurements on soluble proteins), suppression of conformational exchange (thereby permitting quantitation of conformational distributions), and trapping of transient intermediate states in a non-equilibrium kinetic process (by rapid freeze-quenching). Solid state NMR measurements on AIDS-related peptide/antibody complexes, chemically denatured states of the model protein HP35, and a transient intermediate in the rapid folding pathway of HP35 illustrate these motivations. NMR sensitivity generally increases with decreasing sample temperature. It is therefore advantageous to go as cold as possible, particularly in studies of biomolecular systems in frozen solutions. However, solid state NMR studies of biomolecular systems generally require rapid MAS. A novel MAS NMR probe design that uses nitrogen gas for sample spinning and cold helium only for sample cooling allows a wide variety of solid state NMR measurements to be performed on biomolecular systems at 20-25 K, where signals are enhanced by factors of 12-15 relative to measurements at room temperature. MAS NMR at very low temperatures also facilitates dynamic nuclear polarization (DNP), allowing sizeable additional signal enhancements and large absolute NMR signal amplitudes to be achieved with relatively low microwave powers. Current research in my laboratory seeks to develop and exploit DNP-enhanced MAS NMR at very low temperatures, for example in studies of transient intermediates in protein folding and aggregation processes and studies of peptide/protein complexes that can be prepared only at low concentrations. PMID:23470028

Frequency-dependent, transient effects of subthalamic nucleus deep brain stimulation on methamphetamine-induced circling and neuronal activity in the hemiparkinsonian rat.

PubMed

So, Rosa Q; McConnell, George C; Grill, Warren M

2017-03-01

Methamphetamine-induced circling is used to quantify the behavioral effects of subthalamic nucleus (STN) deep brain stimulation (DBS) in hemiparkinsonian rats. We observed a frequency-dependent transient effect of DBS on circling, and quantified this effect to determine its neuronal basis. High frequency STN DBS (75-260Hz) resulted in transient circling contralateral to the lesion at the onset of stimulation, which was not sustained after the first several seconds of stimulation. Following the transient behavioral change, DBS resulted in a frequency-dependent steady-state reduction in pathological ipsilateral circling, but no change in overall movement. Recordings from single neurons in globus pallidus externa (GPe) and substantia nigra pars reticulata (SNr) revealed that high frequency, but not low frequency, STN DBS elicited transient changes in both firing rate and neuronal oscillatory power at the stimulation frequency in a subpopulation of GPe and SNr neurons. These transient changes were not sustained, and most neurons exhibited a different response during the steady-state phase of DBS. During the steady-state, DBS produced elevated neuronal oscillatory power at the stimulus frequency in a majority of GPe and SNr neurons, and the increase was more pronounced during high frequency DBS than during low frequency DBS. Changes in oscillatory power during both transient and steady-state DBS were highly correlated with changes in firing rates. These results suggest that distinct neural mechanisms were responsible for transient and sustained behavioral responses to STN DBS. The transient contralateral turning behavior following the onset of high frequency DBS was paralleled by transient changes in firing rate and oscillatory power in the GPe and SNr, while steady-state suppression of ipsilateral turning was paralleled by sustained increased synchronization of basal ganglia neurons to the stimulus pulses. Our analysis of distinct frequency-dependent transient and steady-state responses to DBS lays the foundation for future mechanistic studies of the immediate and persistent effects of DBS. Copyright © 2016 Elsevier B.V. All rights reserved.

An Intuitive Approach to Steady-State Kinetics.

ERIC Educational Resources Information Center

Raines, Ronald T.; Hansen, David E.

1988-01-01

Attempts to provide an intuitive understanding of steady state kinetics. Discusses the meaning of steady state and uses free energy profiles to illustrate and follow complex kinetic and thermodynamic relationships. Provides examples with explanations. (MVL)

Dynamic Optoelectronic Properties in Perovskite Oxide Thin Films Measured with Ultrafast Transient Absorption & Reflectance Spectroscopy

NASA Astrophysics Data System (ADS)

Smolin, Sergey Y.

Ultrafast transient absorption and reflectance spectroscopy are foundational techniques for studying photoexcited carrier recombination mechanisms, lifetimes, and charge transfer rates. Because quantifying photoexcited carrier dynamics is central to the intelligent design and improvement of many solid state devices, these transient optical techniques have been applied to a wide range of semiconductors. However, despite their promise, interpretation of transient absorption and reflectance data is not always straightforward and often relies on assumptions of physical processes, especially with respect to the influence of heating. Studying the material space of perovskite oxides, the careful collection, interpretation, and analysis of ultrafast data is presented here as a guide for future research into novel semiconductors. Perovskite oxides are a class of transition metal oxides with the chemical structure ABO3. Although traditionally studied for their diverse physical, electronic, and magnetic properties, perovskite oxides have gained recent research attention as novel candidates for light harvesting applications. Indeed, strong tunable absorption, unique interfacial properties, and vast chemical flexibility make perovskite oxides a promising photoactive material system. However, there is limited research characterizing dynamic optoelectronic properties, such as recombination lifetimes, which are critical to know in the design of any light-harvesting device. In this thesis, ultrafast transient absorption and reflectance spectroscopy was used to understand these dynamic optoelectronic properties in highquality, thin (<50 nm) perovskite oxide films grown by molecular beam epitaxy. Starting with epitaxial LaFeO3 (LFO) grown on (LaAlO 3)0.3(Sr2AlTaO6)0.7 (LSAT), transient absorption spectroscopy reveals two photoinduced absorption features at the band gap of LFO at 2.4 eV and at the higher energy absorption edge at 3.5 eV. Using a combination of temperature-dependent, variable-angle spectroscopic ellipsometry and time-resolved ultrafast optical spectroscopy on a type I heterostructure, we clarify thermal and electronic contributions to spectral transients in LaFeO3. Upon comparison to thermally-derived static spectra of LaFeO3, we find that thermal contributions dominate the transient absorption and reflectance spectra above the band gap. A transient photoinduced absorption feature below the band gap at 1.9 eV is not reproduced in the thermally derived spectra and has significantly longer decay kinetics from the thermallyinduced features; therefore, this long lived photoinduced absorption is likely derived, at least partially, from photoexcited carriers with lifetimes much longer than 3 nanoseconds. LaFeO3 has a wide band gap of 2.4 eV but its absorption can be decreased with chemical substitution of Sr for Fe to make it more suitable for various applications. This type of A-site substitution is a common route to change static optical absorption in perovskite oxides, but there are no systematic studies looking at how A-site substitution changes dynamic optoelectronic properties. To understand the relationship between composition and static and dynamic optical properties we worked with the model system of La1-xSrxFeO 3-delta epitaxial films grown on LSAT, uncovering the effects of A-site cation substitution and oxygen stoichiometry. Variable-angle spectroscopic ellipsometry was used to measure static optical properties, revealing a linear increase in absorption coefficient at 1.25 eV and a red-shifting of the optical absorption edge with increasing Sr fraction. The absorption spectra can be similarly tuned through the introduction of oxygen vacancies, indicating the critical role that nominal Fe valence plays in optical absorption. Dynamic optoelectronic properties were studied with ultrafast transient reflectance spectroscopy with broadband visible (1.6 eV to 4 eV) and near-infrared (0.9 eV to 1.5 eV) probes. The sign of the reflectance change in the near-infrared region in LSFO is indicative of carrier bandfilling of newly created electronic states by photoexcited carriers. Moreover, we find that similar transient spectral trends can be induced with A-site substitution or through oxygen vacancies, which is a surprising result. Probing the near-infrared region reveals similar nanosecond (1-3 ns) photoexcited carrier lifetimes for oxygen deficient and stoichiometric films. These results demonstrate that while the static optical absorption is strongly dependent on nominal Fe valence tuned through cation or anion stoichiometry, oxygen vacancies do not appear to play a significantly detrimental role in long lived recombination kinetics. Although this thesis represents one of the first comprehensive studies using broad band transient absorption and reflectance spectroscopy to study dynamic optoelectronic phenomena in perovskite oxides, it can also serve as a guide for the implementation and interpretation of ultrafast spectroscopy in other material systems. Moreover, the ultrafast work on perovskite oxides indicates that these materials have long nanosecond lifetimes required for light harvesting devices and should be investigated further.

Black Box Real-Time Transient Absorption Spectroscopy and Electron Correlation

NASA Astrophysics Data System (ADS)

Parkhill, John

2017-06-01

We introduce an atomistic, all-electron, black-box electronic structure code to simulate transient absorption (TA) spectra and apply it to simulate pyrazole and a GFP- chromophore derivative1. The method is an application of OSCF2, our dissipative exten- sion of time-dependent density-functional theory. We compare our simulated spectra directly with recent ultra-fast spectroscopic experiments. We identify features in the TA spectra to Pauli-blocking which may be missed without a first-principles model. An important ingredient in this method is the stationary-TDDFT correction scheme recently put forwards by Fischer, Govind, and Cramer which allows us to overcome a limitation of adiabatic TDDFT. We demonstrate that OSCF2 is able to reproduce the energies of bleaches and induced absorptions, as well as the decay of the transient spectrum, with only the molecular structure as input. We show that the treatment of electron correlation is the biggest hurdle for TA simulations, which motivates the second half of the talk a new method for realtime electron correlation. We continue to derive and propagate self-consistent electronic dynamics. Extending our derivation of OSCF2 to include electron correlation we obtain a non-linear correlated one-body equation of motion which corrects TDHF. Similar equations are known in quantum kinetic theory, but rare in electronic structure. We introduce approximations that stabilize the theory and reduce its computational cost. We compare the resulting dynamics with well-known exact and approximate theories showing improvements over TDHF. When propagated EE2 changes occupation numbers like exact theory, an important feature missing from TDHF or TDDFT. We introduce a rotating wave approximation to reduce the scaling of the model to O(N^4), and enable propagation on realistically large systems. The equation-of-motion does not rely on a pure-state model for the electronic state, and could be used to study the relationship between electron correlation and relaxation/dephasing or as a non-adiabatic kernel for TDDFT. We show that a quasi-thermal Fermi-Dirac population of one-particle states is a stationary state of the method reached as the endpoint of propagation in some limits. We discuss this 'thermalization' of an isolated quantum many-body system in the context of the eigenstate thermalization hypothesis.

Transition state region in the A-Band photodissociation of allyl iodide—A femtosecond extreme ultraviolet transient absorption study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhattacherjee, Aditi, E-mail: abhattacherjee@berkeley.edu, E-mail: andrewattar@berkeley.edu; Attar, Andrew R., E-mail: abhattacherjee@berkeley.edu, E-mail: andrewattar@berkeley.edu; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

2016-03-28

Femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy based on a high-harmonic generation source is used to study the 266 nm induced A-band photodissociation dynamics of allyl iodide (CH{sub 2} =CHCH{sub 2}I). The photolysis of the C—I bond at this wavelength produces iodine atoms both in the ground ({sup 2}P{sub 3/2}, I) and spin-orbit excited ({sup 2}P{sub 1/2}, I*) states, with the latter as the predominant channel. Using XUV absorption at the iodine N{sub 4/5} edge (45–60 eV), the experiments constitute a direct probe of not only the long-lived atomic iodine reaction products but also the fleeting transition state region ofmore » the repulsive n{sub I}σ{sup ∗}{sub C—I} excited states. Specifically, three distinct features are identified in the XUV transient absorption spectrum at 45.3 eV, 47.4 eV, and 48.4 eV (denoted transients A, B, and C, respectively), which arise from the repulsive valence-excited nσ{sup ∗} states and project onto the high-lying core-excited states of the dissociating molecule via excitation of 4d(I) core electrons. Transients A and B originate from 4d(I) → n(I) core-to-valence transitions, whereas transient C is best assigned to a 4d(I) →σ{sup ∗}(C—I) transition. The measured differential absorbance of these new features along with the I/I* branching ratios known from the literature is used to suggest a more definitive assignment, albeit provisional, of the transients to specific dissociative states within the A-band manifold. The transients are found to peak around 55 fs–65 fs and decay completely by 145 fs–185 fs, demonstrating the ability of XUV spectroscopy to map the evolution of reactants into products in real time. The similarity in the energies of transients A and B with analogous features observed in methyl iodide [Attar et al. J. Phys. Chem. Lett. 6, 5072, (2015)] together with the new observation of transient C in the present work provides a more complete picture of the valence electronic structure in the transition state region. The results provide a benchmark for theoretical calculations on the nature of core-excited states in halogenated hydrocarbons, especially in the transition state region along the C—I reaction coordinate.« less

A mechanical energy analysis of gait initiation

NASA Technical Reports Server (NTRS)

Miller, C. A.; Verstraete, M. C.

1999-01-01

The analysis of gait initiation (the transient state between standing and walking) is an important diagnostic tool to study pathologic gait and to evaluate prosthetic devices. While past studies have quantified mechanical energy of the body during steady-state gait, to date no one has computed the mechanical energy of the body during gait initiation. In this study, gait initiation in seven normal male subjects was studied using a mechanical energy analysis to compute total body energy. The data showed three separate states: quiet standing, gait initiation, and steady-state gait. During gait initiation, the trends in the energy data for the individual segments were similar to those seen during steady-state gait (and in Winter DA, Quanbury AO, Reimer GD. Analysis of instantaneous energy of normal gait. J Biochem 1976;9:253-257), but diminished in amplitude. However, these amplitudes increased to those seen in steady-state during the gait initiation event (GIE), with the greatest increase occurring in the second step due to the push-off of the foundation leg. The baseline level of mechanical energy was due to the potential energy of the individual segments, while the cyclic nature of the data was indicative of the kinetic energy of the particular leg in swing phase during that step. The data presented showed differences in energy trends during gait initiation from those of steady state, thereby demonstrating the importance of this event in the study of locomotion.

Chemistry, photophysics, and ultrafast kinetics of two structurally related Schiff bases containing the naphthalene or quinoline ring

NASA Astrophysics Data System (ADS)

Fita, P.; Luzina, E.; Dziembowska, T.; Radzewicz, Cz.; Grabowska, A.

2006-11-01

The two structurally related Schiff bases, 2-hydroxynaphthylidene-(8-aminoquinoline) (HNAQ) and 2-hydroxynaphthylidene-1'-naphthylamine (HNAN), were studied by means of steady-state and time resolved optical spectroscopies as well as time-dependent density functional theory (TDDFT) calculations. The first one, HNAQ, is stable as a keto tautomer in the ground state and in the excited state in solutions, therefore it was used as a model of a keto tautomer of HNAN which exists mainly in its enol form in the ground state at room temperature. Excited state intramolecular proton transfer in the HNAN molecule leads to a very weak (quantum yield of the order of 10-4) strongly Stokes-shifted fluorescence. The characteristic time of the proton transfer (about 30fs) was estimated from femtosecond transient absorption data supported by global analysis and deconvolution techniques. Approximately 35% of excited molecules create a photochromic form whose lifetime was beyond the time window of the experiment (2ns). The remaining ones reach the relaxed S1 state (of a lifetime of approximately 4ps), whose emission is present in the decay associated difference spectra. Some evidence for the back proton transfer from the ground state of the keto form with the characteristic time of approximately 13ps was also found. The energies and orbital characteristics of main electronic transitions in both molecules calculated by TDDFT method are also discussed.

Negative Cooperativity in the Interaction of Prostaglandin H Synthase-1 with the Competitive Inhibitor Naproxen Can Be Described as the Interaction of a Non-competitive Inhibitor with Heterogeneous Enzyme Preparation.

PubMed

Filimonov, I S; Berzova, A P; Barkhatov, V I; Krivoshey, A V; Trushkin, N A; Vrzheshch, P V

2018-02-01

The kinetic mechanism of the interaction of nonsteroidal anti-inflammatory drugs (NSAIDs) with their main pharmacological target, prostaglandin H synthase (PGHS), has not yet been established. We showed that inhibition of PGHS-1 from sheep vesicular glands by naproxen (a representative of NSAIDs) demonstrates a non-competitive character with respect to arachidonic acid and cannot be described within a framework of the commonly used kinetic schemes. However, it can be described by taking into account the negative cooperativity of naproxen binding to the cyclooxygenase active sites of the PGHS-1 homodimer (the first naproxen molecule forms a more stable complex (K 1 = 0.1 µM) with the enzyme than the second naproxen molecule (K 2 = 9.2 µM)). An apparent non-competitive interaction of PGHS-1 with naproxen is due to slow dissociation of the enzyme-inhibitor complexes. The same experimental data could also be described using commonly accepted kinetic schemes, assuming that naproxen interacts was a mixture of two enzyme species with the inhibition constants K α = 0.05 µM and K β = 18.3 µM. Theoretical analysis and numerical calculations show that the phenomenon of kinetic convergence of these two models has a general nature: when K 2 > K 1 , the kinetic patterns (for transient kinetics and equilibrium state) generated by the cooperative model could be described by a scheme assuming the presence of two enzyme forms with the inhibition constants K α = K 1 /2, K β = 2·K 2 . When K 2 < K 1 , the cooperative model can be presented as a scheme with two inhibitor molecules simultaneously binding to the enzyme with the observed inhibition constant K (K = K 1 ·K 2 ). The assumption on the heterogeneity of the enzyme preparation in relation to its affinity to the inhibitor can be used instead of the assumption on the negative cooperativity of the enzyme-inhibitor interactions for convenient and easy practical description of such phenomena in enzymology, biotechnology, pharmacology, and other fields of science.

One-dimensional Numerical Model of Transient Discharges in Air of a Spatial Plasma Ignition Device

NASA Astrophysics Data System (ADS)

Saceleanu, Florin N.

This thesis examines the modes of discharge of a plasma ignition device. Oscilloscope data of the discharge voltage and current are analyzed for various pressures in air at ambient temperature. It is determined that the discharge operates in 2 modes: a glow discharge and a postulated streamer discharge. Subsequently, a 1-dimensional fluid simulation of plasma using the finite volume method (FVM) is developed to gain insight into the particle kinetics. Transient results of the simulation agree with theories of electric discharges; however, quasi-steady state results were not reached due to high diffusion time of ions in air. Next, an ordinary differential equation (ODE) is derived to understand the discharge transition. Simulated results were used to estimate the voltage waveform, which describes the ODE's forcing function; additional simulated results were used to estimate the discharge current and the ODE's non-linearity. It is found that the ODE's non-linearity increases exponentially for capacitive discharges. It is postulated that the non-linearity defines the mode transition observed experimentally. The research is motivated by Spatial Plasma Discharge Ignition (SPDI), an innovative ignition system postulated to increase combustion efficiency in automobile engines for up to 9%. The research thus far can only hypothesize SPDI's benefits on combustion, based on the literature review and the modes of discharge.

Dynamics of singlet fission and electron injection in self-assembled acene monolayers on titanium dioxide† †Electronic supplementary information (ESI) available: Steady-state UV-VIS and PL, solution transient absorption, X-ray diffraction, decay associated spectra, and TIPS Tc COOH/Al2O3/TiO2 film kinetics. See DOI: 10.1039/c7sc04688j

PubMed Central

Pace, Natalie A.; Arias, Dylan H.; Granger, Devin B.; Christensen, Steven; Anthony, John E.

2018-01-01

We employ a combination of linear spectroscopy, electrochemistry, and transient absorption spectroscopy to characterize the interplay between electron transfer and singlet fission dynamics in polyacene-based dyes attached to nanostructured TiO2. For triisopropyl silylethynyl (TIPS)-pentacene, we find that the singlet fission time constant increases to 6.5 ps on a nanostructured TiO2 surface relative to a thin film time constant of 150 fs, and that triplets do not dissociate after they are formed. In contrast, TIPS-tetracene singlets quickly dissociate in 2 ps at the molecule/TiO2 interface, and this dissociation outcompetes the relatively slow singlet fission process. The addition of an alumina layer slows down electron injection, allowing the formation of triplets from singlet fission in 40 ps. However, the triplets do not inject electrons, which is likely due to a lack of sufficient driving force for triplet dissociation. These results point to the critical balance required between efficient singlet fission and appropriate energetics for interfacial charge transfer. PMID:29732084

Forty years of temporal analysis of products

DOE PAGES

Morgan, K.; Maguire, N.; Fushimi, R.; ...

2017-05-16

Detailed understanding of mechanisms and reaction kinetics are required in order to develop and optimize catalysts and catalytic processes. While steady state investigations are known to give a global view of the catalytic system, transient studies are invaluable since they can provide more detailed insight into elementary steps. For almost thirty years temporal analysis of products (TAP) has been successfully utilized for transient studies of gas phase heterogeneous catalysis, and there have been a number of advances in instrumentation and numerical modeling methods in that time. In the current work, the range of available TAP apparatus will be discussed whilemore » detailed explanations of the types of TAP experiment, the information that can be determined from these experiments and the analysis methods are also included. TAP is a complex methodology and is often viewed as a niche specialty. Here, part of the intention of this work is to highlight the significant contributions TAP can make to catalytic research, while also discussing the issues which will make TAP more relevant and approachable to a wider segment of the catalytic research community. With this in mind, an outlook is also disclosed for the technique in terms of what is needed to revitalize the field and make it more applicable to the recent advances in catalyst characterization (e.g. operando modes).« less

Forty years of temporal analysis of products

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morgan, K.; Maguire, N.; Fushimi, R.

Detailed understanding of mechanisms and reaction kinetics are required in order to develop and optimize catalysts and catalytic processes. While steady state investigations are known to give a global view of the catalytic system, transient studies are invaluable since they can provide more detailed insight into elementary steps. For almost thirty years temporal analysis of products (TAP) has been successfully utilized for transient studies of gas phase heterogeneous catalysis, and there have been a number of advances in instrumentation and numerical modeling methods in that time. In the current work, the range of available TAP apparatus will be discussed whilemore » detailed explanations of the types of TAP experiment, the information that can be determined from these experiments and the analysis methods are also included. TAP is a complex methodology and is often viewed as a niche specialty. Here, part of the intention of this work is to highlight the significant contributions TAP can make to catalytic research, while also discussing the issues which will make TAP more relevant and approachable to a wider segment of the catalytic research community. With this in mind, an outlook is also disclosed for the technique in terms of what is needed to revitalize the field and make it more applicable to the recent advances in catalyst characterization (e.g. operando modes).« less

Understanding Epileptiform After-Discharges as Rhythmic Oscillatory Transients.

PubMed

Baier, Gerold; Taylor, Peter N; Wang, Yujiang

2017-01-01

Electro-cortical activity in patients with epilepsy may show abnormal rhythmic transients in response to stimulation. Even when using the same stimulation parameters in the same patient, wide variability in the duration of transient response has been reported. These transients have long been considered important for the mapping of the excitability levels in the epileptic brain but their dynamic mechanism is still not well understood. To investigate the occurrence of abnormal transients dynamically, we use a thalamo-cortical neural population model of epileptic spike-wave activity and study the interaction between slow and fast subsystems. In a reduced version of the thalamo-cortical model, slow wave oscillations arise from a fold of cycles (FoC) bifurcation. This marks the onset of a region of bistability between a high amplitude oscillatory rhythm and the background state. In vicinity of the bistability in parameter space, the model has excitable dynamics, showing prolonged rhythmic transients in response to suprathreshold pulse stimulation. We analyse the state space geometry of the bistable and excitable states, and find that the rhythmic transient arises when the impending FoC bifurcation deforms the state space and creates an area of locally reduced attraction to the fixed point. This area essentially allows trajectories to dwell there before escaping to the stable steady state, thus creating rhythmic transients. In the full thalamo-cortical model, we find a similar FoC bifurcation structure. Based on the analysis, we propose an explanation of why stimulation induced epileptiform activity may vary between trials, and predict how the variability could be related to ongoing oscillatory background activity. We compare our dynamic mechanism with other mechanisms (such as a slow parameter change) to generate excitable transients, and we discuss the proposed excitability mechanism in the context of stimulation responses in the epileptic cortex.

Detonation onset following shock wave focusing

NASA Astrophysics Data System (ADS)

Smirnov, N. N.; Penyazkov, O. G.; Sevrouk, K. L.; Nikitin, V. F.; Stamov, L. I.; Tyurenkova, V. V.

2017-06-01

The aim of the present paper is to study detonation initiation due to focusing of a shock wave reflected inside a cone. Both numerical and experimental investigations were conducted. Comparison of results made it possible to validate the developed 3-d transient mathematical model of chemically reacting gas mixture flows incorporating hydrogen - air mixtures. The results of theoretical and numerical experiments made it possible improving kinetic schemes and turbulence models. Several different flow scenarios were detected in reflection of shock waves all being dependent on incident shock wave intensity: reflecting of shock wave with lagging behind combustion zone, formation of detonation wave in reflection and focusing, and intermediate transient regimes.

Electron-impact ionization and electron attachment cross sections of radicals important in transient gaseous discharges

NASA Technical Reports Server (NTRS)

Lee, Long C.; Srivastava, Santosh K.

1990-01-01

Electron-impact ionization and electron attachment cross sections of radicals and excited molecules were measured using an apparatus that consists of an electron beam, a molecular beam and a laser beam. The information obtained is needed for the pulse power applications in the areas of high power gaseous discharge switches, high energy lasers, particle beam experiments, and electromagnetic pulse systems. The basic data needed for the development of optically-controlled discharge switches were also investigated. Transient current pulses induced by laser irradiation of discharge media were observed and applied for the study of electron-molecule reaction kinetics in gaseous discharges.

Effect of Alkali Metal Cations on Slow Inactivation of Cardiac Na+ Channels

PubMed Central

Townsend, Claire; Horn, Richard

1997-01-01

Human heart Na+ channels were expressed transiently in both mammalian cells and Xenopus oocytes, and Na+ currents measured using 150 mM intracellular Na+. The kinetics of decaying outward Na+ current in response to 1-s depolarizations in the F1485Q mutant depends on the predominant cation in the extracellular solution, suggesting an effect on slow inactivation. The decay rate is lower for the alkali metal cations Li+, Na+, K+, Rb+, and Cs+ than for the organic cations Tris, tetramethylammonium, N-methylglucamine, and choline. In whole cell recordings, raising [Na+]o from 10 to 150 mM increases the rate of recovery from slow inactivation at −140 mV, decreases the rate of slow inactivation at relatively depolarized voltages, and shifts steady-state slow inactivation in a depolarized direction. Single channel recordings of F1485Q show a decrease in the number of blank (i.e., null) records when [Na+]o is increased. Significant clustering of blank records when depolarizing at a frequency of 0.5 Hz suggests that periods of inactivity represent the sojourn of a channel in a slow-inactivated state. Examination of the single channel kinetics at +60 mV during 90-ms depolarizations shows that neither open time, closed time, nor first latency is significantly affected by [Na+]o. However raising [Na+]o decreases the duration of the last closed interval terminated by the end of the depolarization, leading to an increased number of openings at the depolarized voltage. Analysis of single channel data indicates that at a depolarized voltage a single rate constant for entry into a slow-inactivated state is reduced in high [Na+]o, suggesting that the binding of an alkali metal cation, perhaps in the ion-conducting pore, inhibits the closing of the slow inactivation gate. PMID:9234168

Probing the Non-Native H Helix Translocation in Apomyoglobin Folding Intermediates

PubMed Central

2015-01-01

Apomyoglobin folds via sequential helical intermediates that are formed by rapid collapse of the A, B, G, and H helix regions. An equilibrium molten globule with a similar structure is formed near pH 4. Previous studies suggested that the folding intermediates are kinetically trapped states in which folding is impeded by non-native packing of the G and H helices. Fluorescence spectra of mutant proteins in which cysteine residues were introduced at several positions in the G and H helices show differential quenching of W14 fluorescence, providing direct evidence of translocation of the H helix relative to helices A and G in both the kinetic and equilibrium intermediates. Förster resonance energy transfer measurements show that a 5-({2-[(acetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid acceptor coupled to K140C (helix H) is closer to Trp14 (helix A) in the equilibrium molten globule than in the native state, by a distance that is consistent with sliding of the H helix in an N-terminal direction by approximately one helical turn. Formation of an S108C–L135C disulfide prevents H helix translocation in the equilibrium molten globule by locking the G and H helices into their native register. By enforcing nativelike packing of the A, G, and H helices, the disulfide resolves local energetic frustration and facilitates transient docking of the E helix region onto the hydrophobic core but has only a small effect on the refolding rate. The apomyoglobin folding landscape is highly rugged, with several energetic bottlenecks that frustrate folding; relief of any one of the major identified bottlenecks is insufficient to speed progression to the transition state. PMID:24857522

Transgenic mouse α- and β-cardiac myosins containing the R403Q mutation show isoform-dependent transient kinetic differences.

PubMed

Lowey, Susan; Bretton, Vera; Gulick, James; Robbins, Jeffrey; Trybus, Kathleen M

2013-05-24

Familial hypertrophic cardiomyopathy (FHC) is a major cause of sudden cardiac death in young athletes. The discovery in 1990 that a point mutation at residue 403 (R403Q) in the β-myosin heavy chain (MHC) caused a severe form of FHC was the first of many demonstrations linking FHC to mutations in muscle proteins. A mouse model for FHC has been widely used to study the mechanochemical properties of mutated cardiac myosin, but mouse hearts express α-MHC, whereas the ventricles of larger mammals express predominantly β-MHC. To address the role of the isoform backbone on function, we generated a transgenic mouse in which the endogenous α-MHC was partially replaced with transgenically encoded β-MHC or α-MHC. A His6 tag was cloned at the N terminus, along with R403Q, to facilitate isolation of myosin subfragment 1 (S1). Stopped flow kinetics were used to measure the equilibrium constants and rates of nucleotide binding and release for the mouse S1 isoforms bound to actin. For the wild-type isoforms, we found that the affinity of MgADP for α-S1 (100 μM) is ~ 4-fold weaker than for β-S1 (25 μM). Correspondingly, the MgADP release rate for α-S1 (350 s(-1)) is ~3-fold greater than for β-S1 (120 s(-1)). Introducing the R403Q mutation caused only a minor reduction in kinetics for β-S1, but R403Q in α-S1 caused the ADP release rate to increase by 20% (430 s(-1)). These transient kinetic studies on mouse cardiac myosins provide strong evidence that the functional impact of an FHC mutation on myosin depends on the isoform backbone.

Coupled reactor kinetics and heat transfer model for heat pipe cooled reactors

NASA Astrophysics Data System (ADS)

Wright, Steven A.; Houts, Michael

2001-02-01

Heat pipes are often proposed as cooling system components for small fission reactors. SAFE-300 and STAR-C are two reactor concepts that use heat pipes as an integral part of the cooling system. Heat pipes have been used in reactors to cool components within radiation tests (Deverall, 1973); however, no reactor has been built or tested that uses heat pipes solely as the primary cooling system. Heat pipe cooled reactors will likely require the development of a test reactor to determine the main differences in operational behavior from forced cooled reactors. The purpose of this paper is to describe the results of a systems code capable of modeling the coupling between the reactor kinetics and heat pipe controlled heat transport. Heat transport in heat pipe reactors is complex and highly system dependent. Nevertheless, in general terms it relies on heat flowing from the fuel pins through the heat pipe, to the heat exchanger, and then ultimately into the power conversion system and heat sink. A system model is described that is capable of modeling coupled reactor kinetics phenomena, heat transfer dynamics within the fuel pins, and the transient behavior of heat pipes (including the melting of the working fluid). This paper focuses primarily on the coupling effects caused by reactor feedback and compares the observations with forced cooled reactors. A number of reactor startup transients have been modeled, and issues such as power peaking, and power-to-flow mismatches, and loading transients were examined, including the possibility of heat flow from the heat exchanger back into the reactor. This system model is envisioned as a tool to be used for screening various heat pipe cooled reactor concepts, for designing and developing test facility requirements, for use in safety evaluations, and for developing test criteria for in-pile and out-of-pile test facilities. .

Theoretical Basis for Estimated Test Times and Conditions for Drop Tower and Space-Based Droplet Burning Experiments With Methanol and N-Heptane

NASA Technical Reports Server (NTRS)

Marchese, Anthony J.; Dryer, Fredrick L.; Choi, Mun Y.

1994-01-01

In order to develop an extensive envelope of test conditions for NASA's space-based Droplet Combustion Experiment (DCE) as well those droplet experiments which can be performed using a drop tower, the transient vaporization and combustion of methanol and n-heptane droplets were simulated using a recently developed fully time-dependent, spherically symmetric droplet combustion model. The transient vaporization of methanol and n-heptane was modeled to characterize the instantaneous gas phase composition surrounding the droplet prior to the introduction of an ignition source. The results for methanol/air showed that the entire gas phase surrounding a 2 mm methanol droplet deployed in zero-g .quickly falls outside the lean flammability limit. The gas phase surrounding an identically-sized n-heptane droplet, on the other hand, remains flammable. The combustion of methanol was then modeled considering a detailed gas phase chemical kinetic mechanism (168 steps, 26 species) and the effect of the dissolution of flame-generated water into the liquid droplet. These results were used to determine the critical ignition diameter required to achieve quasi-steady droplet combustion in a given oxidizing environment. For droplet diameters greater than the critical ignition diameter, the model predicted a finite diameter at which the flame would extinguish. These extinction diameters were found to vary significantly with initial droplet diameter. This phenomenon appears to be unique to the transient heat transfer, mass transfer and chemical kinetics of the system and thus has not been reported elsewhere to date. The extinction diameter was also shown to vary significantly with the liquid phase Lewis number since the amount of water present in the droplet at extinction is largely governed by the rate at which water is transported into the droplet via mass diffusion. Finally, the numerical results for n-heptane combustion were obtained using both 2 step and 96 step semi-emperical chemical kinetic mechanisms. Neither mechanism exhibited the variation of extinction diameter with initial diameter.

Terminal Transient Phase of Chaotic Transients

NASA Astrophysics Data System (ADS)

Lilienkamp, Thomas; Parlitz, Ulrich

2018-03-01

Transient chaos in spatially extended systems can be characterized by the length of the transient phase, which typically grows quickly with the system size (supertransients). For a large class of these systems, the chaotic phase terminates abruptly, without any obvious precursors in commonly used observables. Here we investigate transient spatiotemporal chaos in two different models of this class. By probing the state space using perturbed trajectories we show the existence of a "terminal transient phase," which occurs prior to the abrupt collapse of chaotic dynamics. During this phase the impact of perturbations is significantly different from the earlier transient and particular patterns of (non)susceptible regions in state space occur close to the chaotic trajectories. We therefore hypothesize that even without perturbations proper precursors for the collapse of chaotic transients exist, which might be highly relevant for coping with spatiotemporal chaos in cardiac arrhythmias or brain functionality, for example.

Kinetic analysis of butyrylcholinesterase-catalyzed hydrolysis of acetanilides.

PubMed

Masson, Patrick; Froment, Marie-Thérèse; Gillon, Emilie; Nachon, Florian; Darvesh, Sultan; Schopfer, Lawrence M

2007-09-01

The aryl-acylamidase (AAA) activity of butyrylcholinesterase (BuChE) has been known for a long time. However, the kinetic mechanism of aryl-acylamide hydrolysis by BuChE has not been investigated. Therefore, the catalytic properties of human BuChE and its peripheral site mutant (D70G) toward neutral and charged aryl-acylamides were determined. Three neutral (o-nitroacetanilide, m-nitroacetanilide, o-nitrophenyltrifluoroacetamide) and one positively charged (3-(acetamido) N,N,N-trimethylanilinium, ATMA) acetanilides were studied. Hydrolysis of ATMA by wild-type and D70G enzymes showed a long transient phase preceding the steady state. The induction phase was characterized by a hysteretic "burst". This reflects the existence of two enzyme states in slow equilibrium with different catalytic properties. Steady-state parameters for hydrolysis of the three acetanilides were compared to catalytic parameters for hydrolysis of esters giving the same acetyl intermediate. Wild-type BuChE showed substrate activation while D70G displayed a Michaelian behavior with ATMA as with positively charged esters. Owing to the low affinity of BuChE for amide substrates, the hydrolysis kinetics of neutral amides was first order. Acylation was the rate-determining step for hydrolysis of aryl-acetylamide substrates. Slow acylation of the enzyme, relative to that by esters may, in part, be due suboptimal fit of the aryl-acylamides in the active center of BuChE. The hypothesis that AAA and esterase active sites of BuChE are non-identical was tested with mutant BuChE. It was found that mutations on the catalytic serine, S198C and S198D, led to complete loss of both activities. The silent variant (FS117) had neither esterase nor AAA activity. Mutation in the peripheral site (D70G) had the same effect on esterase and AAA activities. Echothiophate inhibited both activities identically. It was concluded that the active sites for esterase and AAA activities are identical, i.e. S198. This excludes any other residue present in the gorge for being the catalytic nucleophile pole.

Evaluation of the Intramolecular Charge-Transfer Properties in Solvatochromic and Electrochromic Zinc Octa(carbazolyl)phthalocyanines.

PubMed

Majeed, Shereen A; Ghazal, Basma; Nevonen, Dustin E; Goff, Philip C; Blank, David A; Nemykin, Victor N; Makhseed, Saad

2017-10-02

2,3,9,10,16,17,23·24-Octakis-(9H-carbazol-9-yl) phthalocyaninato zinc(II) (3) and 2,3,9,10,16,17,23·24-octakis-(3,6-di-tert-butyl-9H-carbazole) phthalocyaninato zinc(II) (4) complexes were prepared and characterized by NMR and UV-vis spectroscopies, magnetic circular dichroism (MCD), matrix-assisted laser desorption ionization mass spectrometry, and X-ray crystallography. UV-vis and MCD data are indicative of the interligand charge-transfer nature of the broad band observed in 450-500 nm range for 3 and 4. The redox properties of 3 and 4 were probed by electrochemical and spectro-electrochemical methods, which are suggestive of phthalocyanine-centered first oxidation and reduction processes. Photophysics of 3 and 4 were investigated by steady-state fluorescence and time-resolved transient absorption spectroscopy demonstrating the influence of the carbazole substituents on deactivation from the first excited state in 3 and 4. Protonation of the meso-nitrogen atoms in 3 results in much faster deactivation kinetics from the first excited state. Spectroscopic data were correlated with density functional theory (DFT) and time-dependent DFT calculations on 3 and 4.

Linking Microstructural Evolution and Tribology in Metallic Contacts

NASA Astrophysics Data System (ADS)

Chandross, Michael; Cheng, Shengfeng; Argibay, Nicolas

Tribologists rely on phenomenological models to describe the seemingly disjointed steady-state regimes of metal wear. Pure metals such as gold - frequently used in electrical contacts - exhibit high friction and wear. In contrast, nanocrystalline metals often show much lower friction and wear. The engineering community has generally used a phenomenological connection between hardness and friction/wear to explain this macroscale response and guide designs. We present results of recent simulations and experiments that demonstrate a general framework for connecting materials properties (i.e. microstructural evolution) to tribological response. We present evidence that competition between grain refinement (from cold working), grain coarsening (from stress-induced grain growth), and wear (delamination and plowing) can be used to describe transient and steady state tribological behavior of metals, alloys and composites. We explore the seemingly disjointed steady-state friction regimes of metals and alloys, with a goal of elucidating the structure-property relationships, allowing for the engineering of tribological materials and contacts based on the kinetics of grain boundary motion. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II.

PubMed

Isobe, Hiroshi; Shoji, Mitsuo; Shen, Jian-Ren; Yamaguchi, Kizashi

2016-01-19

We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S3 state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol(-1) that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn4CaO5 cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which Mn-O and O-O bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed.

Solution Phase Exciton Diffusion Dynamics of a Charge-Transfer Copolymer PTB7 and a Homopolymer P3HT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Sung; Rolczynski, Brian S.; Xu, Tao

2015-06-18

Using ultrafast polarization-controlled transient absorption (TA) measurements, dynamics of the initial exciton states were investigated on the time scale of tens of femtoseconds to about 80 ps in two different types of conjugated polymers extensively used in active layers of organic photovoltaic devices. These polymers are poly(3-fluorothienothiophenebenzodithiophene) (PTB7) and poly-3-hexylthiophene (P3HT), which are charge-transfer polymers and homopolymers, respectively. In PTB7, the initial excitons with excess vibrational energy display two observable ultrafast time constants, corresponding to coherent exciton diffusion before the vibrational relaxation, and followed by incoherent exciton diffusion processes to a neighboring local state after the vibrational relaxation. In contrast,more » P3HT shows only one exciton diffusion or conformational motion time constant of 34 ps, even though its exciton decay kinetics are multiexponential. Based on the experimental results, an exciton dynamics mechanism is conceived taking into account the excitation energy and structural dependence in coherent and incoherent exciton diffusion processes, as well as other possible deactivation processes including the formation of the pseudo-charge-transfer and charge separate states, as well as interchain exciton hopping or coherent diffusion.« less

Solution Phase Exciton Diffusion Dynamics of a Charge-Transfer Copolymer PTB7 and a Homopolymer P3HT.

PubMed

Cho, Sung; Rolczynski, Brian S; Xu, Tao; Yu, Luping; Chen, Lin X

2015-06-18

Using ultrafast polarization-controlled transient absorption (TA) measurements, dynamics of the initial exciton states were investigated on the time scale of tens of femtoseconds to about 80 ps in two different types of conjugated polymers extensively used in active layers of organic photovoltaic devices. These polymers are poly(3-fluorothienothiophenebenzodithiophene) (PTB7) and poly-3-hexylthiophene (P3HT), which are charge-transfer polymers and homopolymers, respectively. In PTB7, the initial excitons with excess vibrational energy display two observable ultrafast time constants, corresponding to coherent exciton diffusion before the vibrational relaxation, and followed by incoherent exciton diffusion processes to a neighboring local state after the vibrational relaxation. In contrast, P3HT shows only one exciton diffusion or conformational motion time constant of 34 ps, even though its exciton decay kinetics are multiexponential. Based on the experimental results, an exciton dynamics mechanism is conceived taking into account the excitation energy and structural dependence in coherent and incoherent exciton diffusion processes, as well as other possible deactivation processes including the formation of the pseudo-charge-transfer and charge separate states, as well as interchain exciton hopping or coherent diffusion.

Initial Neutronics Analyses for HEU to LEU Fuel Conversion of the Transient Reactor Test Facility (TREAT) at the Idaho National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kontogeorgakos, D.; Derstine, K.; Wright, A.

2013-06-01

The purpose of the TREAT reactor is to generate large transient neutron pulses in test samples without over-heating the core to simulate fuel assembly accident conditions. The power transients in the present HEU core are inherently self-limiting such that the core prevents itself from overheating even in the event of a reactivity insertion accident. The objective of this study was to support the assessment of the feasibility of the TREAT core conversion based on the present reactor performance metrics and the technical specifications of the HEU core. The LEU fuel assembly studied had the same overall design, materials (UO 2more » particles finely dispersed in graphite) and impurities content as the HEU fuel assembly. The Monte Carlo N–Particle code (MCNP) and the point kinetics code TREKIN were used in the analyses.« less

Heat Pipe Reactor Dynamic Response Tests: SAFE-100 Reactor Core Prototype

NASA Technical Reports Server (NTRS)

Bragg-Sitton, Shannon M.

2005-01-01

The SAFE-I00a test article at the NASA Marshall Space Flight Center was used to simulate a variety of potential reactor transients; the SAFEl00a is a resistively heated, stainless-steel heat-pipe (HP)-reactor core segment, coupled to a gas-flow heat exchanger (HX). For these transients the core power was controlled by a point kinetics model with reactivity feedback based on core average temperature; the neutron generation time and the temperature feedback coefficient are provided as model inputs. This type of non-nuclear test is expected to provide reasonable approximation of reactor transient behavior because reactivity feedback is very simple in a compact fast reactor (simple, negative, and relatively monotonic temperature feedback, caused mostly by thermal expansion) and calculations show there are no significant reactivity effects associated with fluid in the HP (the worth of the entire inventory of Na in the core is .

Transient removal of proflavine inhibition of bovine beta-trypsin by the bovine basic pancreatic trypsin inhibitor (Kunitz). A case for "chronosteric effects".

PubMed

Antonini, E; Ascenzi, P; Bolognesi, M; Menegatti, E; Guarneri, M

1983-04-25

The formation of the bovine beta-trypsin-bovine basic pancreatic trypsin inhibitor (Kunitz) (BPTI) complex was monitored, making use of three different signals: proflavine displacement, optical density changes in the ultraviolet region, and the loss of the catalytic activity. The rates of the reactions indicated by the three different signals were similar at neutral pH, but diverged at low pH. At pH 3.50, proflavine displacement precedes the optical density changes in the ultraviolet and the loss of enzyme activity by several orders of magnitude in time (Antonini, E., Ascenzi, P., Menegatti, E., and Guarneri, M. (1983) Biopolymers 22, 363-375). These data indicated that the bovine beta-trypsin-BPTI complex formation is a multistage process and led to the prediction that, at pH 3.50, BPTI addition to the bovine beta-trypsin-proflavine complex would remove proflavine inhibition and the enzyme would recover transiently its catalytic activity before being irreversibly inhibited by completion of BPTI binding. The kinetic evidences, by completion of BPTI binding. The kinetic evidences, here shown, verified this prediction, indicating that during the bovine beta-trypsin-BPTI complex formation one transient intermediate occurs, which is not able to bind proflavine but may bind and hydrolyze the substrate. Thus, the observed peculiar catalytic behavior is in line with the proposed reaction mechanism for the bovine beta-trypsin-BPTI complex formation, which postulates a sequence of distinct polar and apolar interactions at the contact area.

Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats

PubMed Central

Qi, Nathan R.

2018-01-01

High capacity and low capacity running rats, HCR and LCR respectively, have been bred to represent two extremes of running endurance and have recently demonstrated disparities in fuel usage during transient aerobic exercise. HCR rats can maintain fatty acid (FA) utilization throughout the course of transient aerobic exercise whereas LCR rats rely predominantly on glucose utilization. We hypothesized that the difference between HCR and LCR fuel utilization could be explained by a difference in mitochondrial density. To test this hypothesis and to investigate mechanisms of fuel selection, we used a constraint-based kinetic analysis of whole-body metabolism to analyze transient exercise data from these rats. Our model analysis used a thermodynamically constrained kinetic framework that accounts for glycolysis, the TCA cycle, and mitochondrial FA transport and oxidation. The model can effectively match the observed relative rates of oxidation of glucose versus FA, as a function of ATP demand. In searching for the minimal differences required to explain metabolic function in HCR versus LCR rats, it was determined that the whole-body metabolic phenotype of LCR, compared to the HCR, could be explained by a ~50% reduction in total mitochondrial activity with an additional 5-fold reduction in mitochondrial FA transport activity. Finally, we postulate that over sustained periods of exercise that LCR can partly overcome the initial deficit in FA catabolic activity by upregulating FA transport and/or oxidation processes. PMID:29474500

A User Guide to PARET/ANL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olson, A. P.; Dionne, B.; Marin-Lafleche, A.

2015-01-01

PARET was originally created in 1969 at what is now Idaho National Laboratory (INL), to analyze reactivity insertion events in research and test reactor cores cooled by light or heavy water, with fuel composed of either plates or pins. The use of PARET is also appropriate for fuel assemblies with curved fuel plates when their radii of curvatures are large with respect to the fuel plate thickness. The PARET/ANL version of the code has been developed at Argonne National Laboratory (ANL) under the sponsorship of the U.S. Department of Energy/NNSA, and has been used by the Reactor Conversion Program tomore » determine the expected transient behavior of a large number of reactors. PARET/ANL models the various fueled regions of a reactor core as channels. Each of these channels consists of a single flat fuel plate/pin (including cladding and, optionally, a gap) with water coolant on each side. In slab geometry the coolant channels for a given fuel plate are of identical dimensions (mirror symmetry), but they can be of different thickness in each channel. There can be many channels, but each channel is independent and coupled only through reactivity feedback effects to the whole core. The time-dependent differential equations that represent the system are replaced by an equivalent set of finite-difference equations in space and time, which are integrated numerically. PARET/ANL uses fundamentally the same numerical scheme as RELAP5 for the time-integration of the point-kinetics equations. The one-dimensional thermal-hydraulic model includes temperature-dependent thermal properties of the solid materials, such as heat capacity and thermal conductivity, as well as the transient heat production and heat transfer from the fuel meat to the coolant. Temperature- and pressure-dependent thermal properties of the coolant such as enthalpy, density, thermal conductivity, and viscosity are also used in determining parameters such as friction factors and heat transfer coefficients. The code first determines the steady-state solution for the initial state. Then the solution of the transient is obtained by integration in time and space. Multiple heat transfer, DNB and flow instability correlations are available. The code was originally developed to model reactors cooled by an open loop, which was adequate for rapid transients in pool-type cores. An external loop model appropriate for Miniature Neutron Source Reactors (MNSR’s) was also added to PARET/ANL to model natural circulation within the vessel, heat transfer from the vessel to pool and heat loss by evaporation from the pool. PARET/ANL also contains models for decay heat after shutdown, control rod reactivity versus time or position, time-dependent pump flow, and loss-of-flow event with flow reversal as well as logic for trips on period, power, and flow. Feedback reactivity effects from coolant density changes and temperature changes are represented by tables. Feedback reactivity from fuel heat-up (Doppler Effect) is represented by a four-term polynomial in powers of fuel temperature. Photo-neutrons produced in beryllium or in heavy water may be included in the point-kinetics equations by using additional delayed neutron groups.« less

Characteristics of Southern Hemisphere 200 mb flow as determined from satellite data

NASA Technical Reports Server (NTRS)

Adler, R. F.

1976-01-01

Characteristics of Southern Hemisphere 200 mb flow are examined using geopotential height fields constructed with the aid of satellite based thermal structure. Similar Northern Hemisphere, satellite based fields are developed in order to make interhemispheric comparisons. Results indicate that both the zonal and meridional components of the S.H. eddy kinetic energy are as large as their N.H. counterparts. In winter the principal interhemispheric difference with respect to eddy kinetic energy is that the S.H. standing eddies are much less important only to the meridional component. Zonal component standing energy is about equal in the two hemispheres. In summer the S.H. has larger zonal eddy kinetic energy than the N.H. and smaller standing eddy contributions in both components. The meridional spectra show a preference for intermediate size transient waves.

Characterization of Dye-decolorizing Peroxidase (DyP) from Thermomonospora curvata Reveals Unique Catalytic Properties of A-type DyPs*

PubMed Central

Chen, Chao; Shrestha, Ruben; Jia, Kaimin; Gao, Philip F.; Geisbrecht, Brian V.; Bossmann, Stefan H.; Shi, Jishu; Li, Ping

2015-01-01

Dye-decolorizing peroxidases (DyPs) comprise a new family of heme peroxidases, which has received much attention due to their potential applications in lignin degradation. A new DyP from Thermomonospora curvata (TcDyP) was identified and characterized. Unlike other A-type enzymes, TcDyP is highly active toward a wide range of substrates including model lignin compounds, in which the catalytic efficiency with ABTS (kcatapp/Kmapp = (1.7 × 107) m−1 s−1) is close to that of fungal DyPs. Stopped-flow spectroscopy was employed to elucidate the transient intermediates as well as the catalytic cycle involving wild-type (wt) and mutant TcDyPs. Although residues Asp220 and Arg327 are found necessary for compound I formation, His312 is proposed to play roles in compound II reduction. Transient kinetics of hydroquinone (HQ) oxidation by wt-TcDyP showed that conversion of the compound II to resting state is a rate-limiting step, which will explain the contradictory observation made with the aspartate mutants of A-type DyPs. Moreover, replacement of His312 and Arg327 has significant effects on the oligomerization and redox potential (E°′) of the enzyme. Both mutants were found to promote the formation of dimeric state and to shift E°′ to a more negative potential. Not only do these results reveal the unique catalytic property of the A-type DyPs, but they will also facilitate the development of these enzymes as lignin degraders. PMID:26205819

Transient transition from free carrier metallic state to exciton insulating state in GaAs by ultrafast photoexcitation

NASA Astrophysics Data System (ADS)

Nie, X. C.; Song, Hai-Ying; Zhang, Xiu; Gu, Peng; Liu, Shi-Bing; Li, Fan; Meng, Jian-Qiao; Duan, Yu-Xia; Liu, H. Y.

2018-03-01

We present systematic studies of the transient dynamics of GaAs by ultrafast time-resolved reflectivity. In photoexcited non-equilibrium states, we found a sign reverse in reflectivity change ΔR/R, from positive around room temperature to negative at cryogenic temperatures. The former corresponds to a free carrier metallic state, while the latter is attributed to an exciton insulating state, in which the transient electronic properties is mostly dominated by excitons, resulting in a transient metal–insulator transition (MIT). Two transition temperatures (T 1 and T 2) are well identified by analyzing the intensity change of the transient reflectivity. We found that photoexcited MIT starts emerging at T 1 as high as ∼ 230 K, in terms of a dip feature at 0.4 ps, and becomes stabilized below T 2 that is up to ∼ 180 K, associated with a negative constant after 40 ps. Our results address a phase diagram that provides a framework for the inducing of MIT through temperature and photoexcitation, and may shed light on the understanding of light-semiconductor interaction and exciton physics.

Quasi-steady-state voltammetry of rapid electron transfer reactions at the macroscopic substrate of the scanning electrochemical microscope.

PubMed

Nioradze, Nikoloz; Kim, Jiyeon; Amemiya, Shigeru

2011-02-01

We report on a novel theory and experiment for scanning electrochemical microscopy (SECM) to enable quasi-steady-state voltammetry of rapid electron transfer (ET) reactions at macroscopic substrates. With this powerful approach, the substrate potential is cycled widely across the formal potential of a redox couple while the reactant or product of a substrate reaction is amperometrically detected at the tip in the feedback or substrate generation/tip collection mode, respectively. The plot of tip current versus substrate potential features the retraceable sigmoidal shape of a quasi-steady-state voltammogram although a transient voltammogram is obtained at the macroscopic substrate. Finite element simulations reveal that a short tip-substrate distance and a reversible substrate reaction (except under the tip) are required for quasi-steady-state voltammetry. Advantageously, a pair of quasi-steady-state voltammograms is obtained by employing both operation modes to reliably determine all transport, thermodynamic, and kinetic parameters as confirmed experimentally for rapid ET reactions of ferrocenemethanol and 7,7,8,8-tetracyanoquinodimethane at a Pt substrate with ∼0.5 μm-radius Pt tips positioned at 90 nm-1 μm distances. Standard ET rate constants of ∼7 cm/s were obtained for the latter mediator as the largest determined for a substrate reaction by SECM. Various potential applications of quasi-steady-state voltammetry are also proposed.

Control of surface adatom kinetics for the growth of high-indium content InGaN throughout the miscibility gap

NASA Astrophysics Data System (ADS)

Moseley, Michael; Lowder, Jonathan; Billingsley, Daniel; Doolittle, W. Alan

2010-11-01

The surface kinetics of InGaN alloys grown via metal-modulated epitaxy (MME) are explored in combination with transient reflection high-energy electron diffraction intensities. A method for monitoring and controlling indium segregation in situ is demonstrated. It is found that indium segregation is more accurately associated with the quantity of excess adsorbed metal, rather than the metal-rich growth regime in general. A modified form of MME is developed in which the excess metal dose is managed via shuttered growth, and high-quality InGaN films throughout the miscibility gap are grown.

Ab initio simulation of particle momentum distributions in high-pressure water

NASA Astrophysics Data System (ADS)

Ceriotti, M.

2014-12-01

Applying pressure to water reduces the average oxygen-oxygen distance, and facilitates the delocalisation of protons along the hydrogen bond. This pressure-induced delocalisation is further enhanced by the quantum nature of hydrogen nuclei, which is very significant even well above room temperature. Here we will evaluate the quantum kinetic energy and the particle momentum distribution of hydrogen and oxygen nuclei in water at extreme pressure, using ab initio path integral molecular dynamics. We will show that (transient) dissociation of water molecules induce measurable changes in the kinetic energy hydrogen atoms, although current deep inelastic scattering experiments are probably unable to capture the heterogeneity of the sample.

A molecular signaling model of platelet phosphoinositide and calcium regulation during homeostasis and P2Y1 activation.

PubMed

Purvis, Jeremy E; Chatterjee, Manash S; Brass, Lawrence F; Diamond, Scott L

2008-11-15

To quantify how various molecular mechanisms are integrated to maintain platelet homeostasis and allow responsiveness to adenosine diphosphate (ADP), we developed a computational model of the human platelet. Existing kinetic information for 77 reactions, 132 fixed kinetic rate constants, and 70 species was combined with electrochemical calculations, measurements of platelet ultrastructure, novel experimental results, and published single-cell data. The model accurately predicted: (1) steady-state resting concentrations for intracellular calcium, inositol 1,4,5-trisphosphate, diacylglycerol, phosphatidic acid, phosphatidylinositol, phosphatidylinositol phosphate, and phosphatidylinositol 4,5-bisphosphate; (2) transient increases in intracellular calcium, inositol 1,4,5-trisphosphate, and G(q)-GTP in response to ADP; and (3) the volume of the platelet dense tubular system. A more stringent test of the model involved stochastic simulation of individual platelets, which display an asynchronous calcium spiking behavior in response to ADP. Simulations accurately reproduced the broad frequency distribution of measured spiking events and demonstrated that asynchronous spiking was a consequence of stochastic fluctuations resulting from the small volume of the platelet. The model also provided insights into possible mechanisms of negative-feedback signaling, the relative potency of platelet agonists, and cell-to-cell variation across platelet populations. This integrative approach to platelet biology offers a novel and complementary strategy to traditional reductionist methods.

On the origin of the slow M-T chlorophyll a fluorescence decline in cyanobacteria: interplay of short-term light-responses.

PubMed

Bernát, Gábor; Steinbach, Gábor; Kaňa, Radek; Govindjee; Misra, Amarendra N; Prašil, Ondřej

2018-05-01

The slow kinetic phases of the chlorophyll a fluorescence transient (induction) are valuable tools in studying dynamic regulation of light harvesting, light energy distribution between photosystems, and heat dissipation in photosynthetic organisms. However, the origin of these phases are not yet fully understood. This is especially true in the case of prokaryotic oxygenic photoautotrophs, the cyanobacteria. To understand the origin of the slowest (tens of minutes) kinetic phase, the M-T fluorescence decline, in the context of light acclimation of these globally important microorganisms, we have compared spectrally resolved fluorescence induction data from the wild type Synechocystis sp. PCC 6803 cells, using orange (λ = 593 nm) actinic light, with those of mutants, ΔapcD and ΔOCP, that are unable to perform either state transition or fluorescence quenching by orange carotenoid protein (OCP), respectively. Our results suggest a multiple origin of the M-T decline and reveal a complex interplay of various known regulatory processes in maintaining the redox homeostasis of a cyanobacterial cell. In addition, they lead us to suggest that a new type of regulatory process, operating on the timescale of minutes to hours, is involved in dissipating excess light energy in cyanobacteria.

Function suggests nano-structure: towards a unified theory for secretion rate, a statistical mechanics approach.

PubMed

Hammel, Ilan; Meilijson, Isaac

2013-11-06

The inventory of secretory granules along the plasma membrane can be viewed as maintained in two restricted compartments. The release-ready pool represents docked granules available for an initial stage of fast, immediate secretion, followed by a second stage of granule set-aside secretion pool, with significantly slower rate. Transmission electron microscopy ultra-structural investigations correlated with electrophysiological techniques and mathematical modelling have allowed the categorization of these secretory vesicle compartments, in which vesicles can be in various states of secretory competence. Using the above-mentioned approaches, the kinetics of single vesicle exocytosis can be worked out. The ultra-fast kinetics, explored in this study, represents the immediately available release-ready pool, in which granules bound to the plasma membrane are exocytosed upon Ca(2+) influx at the SNARE rosette at the base of porosomes. Formalizing Dodge and Rahamimoff findings on the effect of calcium concentration and incorporating the effect of SNARE transient rosette size, we postulate that secretion rate (rate), the number (X) of intracellular calcium ions available for fusion, calcium capacity (0 ≤ M ≤ 5) and the fusion nano-machine size (as measured by the SNARE rosette size K) satisfy the parsimonious M-K relation rate ≈ C × [Ca(2+)](min(X,M))e(-K/2).

Force generation and temperature-jump and length-jump tension transients in muscle fibers.

PubMed Central

Davis, J S; Rodgers, M E

1995-01-01

Muscle tension rises with increasing temperature. The kinetics that govern the tension rise of maximally Ca(2+)-activated, skinned rabbit psoas fibers over a temperature range of 0-30 degrees C was characterized in laser temperature-jump experiments. The kinetic response is simple and can be readily interpreted in terms of a basic three-step mechanism of contraction, which includes a temperature-sensitive rapid preequilibrium(a) linked to a temperature-insensitive rate-limiting step and followed by a temperature-sensitive tension-generating step. These data and mechanism are compared and contrasted with the more complex length-jump Huxley-Simmons phases in which all states that generate tension or bear tension are perturbed. The rate of the Huxley-Simmons phase 4 is temperature sensitive at low temperatures but plateaus at high temperatures, indicating a change in rate-limiting step from a temperature-sensitive (phase 4a) to a temperature-insensitive reaction (phase 4b); the latter appears to correlate with the slow, temperature-insensitive temperature-jump relaxation. Phase 3 is absent in the temperature-jump, which excludes it from tension generation. We confirm that de novo tension generation occurs as an order-disorder transition during phase 2slow and the equivalent, temperature-sensitive temperature-jump relaxation. PMID:7612845

The Effect of Spatial Heterogeneities on Nucleation Kinetics in Amorphous Aluminum Alloys

NASA Astrophysics Data System (ADS)

Shen, Ye

The mechanical property of the Al based metallic glass could be enhanced significantly by introducing the high number density of Al-fcc nanocrystals (1021 ˜1023 m-3) to the amorphous matrix through annealing treatments, which motivates the study of the nucleation kinetics for the microstructure control. With the presence of a high number density (1025 m-3) of aluminum-like medium range order (MRO), the Al-Y-Fe metallic glass is considered to be spatially heterogeneous. Combining the classical nucleation theory with the structural configuration, a MRO seeded nucleation model has been proposed and yields theoretical steady state nucleation rates consistent with the experimental results. In addition, this model satisfies all the thermodynamic and kinetic constraints to be reasonable. Compared with the Al-Y-Fe system, the primary crystallization onset temperature decreases significantly and the transient delay time (tau) is shorter in the Al-Y-Fe-Pb(In) systems because the insoluble Pb and In nanoparticles in the amorphous matrix served as extrinsic spatial heterogeneity to provide the nucleation sites for Al-fcc precipitation and the high-resolution transmission electron microscopy (HRTEM) images of the Pb-Al interface revealed a good wetting behavior between the Al and Pb nanoparticles. The study of the transient delay time (tau) could provide insight on the transport behavior during the nucleation and a more convenient approach to evaluate the delay time has been developed by measuring the Al-Y-Fe amorphous alloy glass transition temperature (Tg) shift with the increasing annealing time (tannealing) in FlashDSC. The break point in the Tg vs. log(tannealing) plot has been identified to correspond to the delay time by the TEM characterization. FlashDSC tests with different heating rates and different compositions (Al-Y-Fe-Pb and Zn-Mg-Ca-Yb amorphous alloys) further confirmed the break point and delay time relationship. The amorphous matrix composition and the enthalpy analysis indicates that there are different mechanisms leading to the Tg shift before and after the break point. Before the break point, Tg shifts solely due to the increased glass stability through a relaxation process. However, after the break point, Tg shifts to higher temperatures because of both the relaxation and the composition change effects.

Steady and transient sliding under rate-and-state friction

NASA Astrophysics Data System (ADS)

Putelat, Thibaut; Dawes, Jonathan H. P.

2015-05-01

The physics of dry friction is often modelled by assuming that static and kinetic frictional forces can be represented by a pair of coefficients usually referred to as μs and μk, respectively. In this paper we re-examine this discontinuous dichotomy and relate it quantitatively to the more general, and smooth, framework of rate-and-state friction. This is important because it enables us to link the ideas behind the widely used static and dynamic coefficients to the more complex concepts that lie behind the rate-and-state framework. Further, we introduce a generic framework for rate-and-state friction that unifies different approaches found in the literature. We consider specific dynamical models for the motion of a rigid block sliding on an inclined surface. In the Coulomb model with constant dynamic friction coefficient, sliding at constant velocity is not possible. In the rate-and-state formalism steady sliding states exist, and analysing their existence and stability enables us to show that the static friction coefficient μs should be interpreted as the local maximum at very small slip rates of the steady state rate-and-state friction law. Next, we revisit the often-cited experiments of Rabinowicz (J. Appl. Phys., 22:1373-1379, 1951). Rabinowicz further developed the idea of static and kinetic friction by proposing that the friction coefficient maintains its higher and static value μs over a persistence length before dropping to the value μk. We show that there is a natural identification of the persistence length with the distance that the block slips as measured along the stable manifold of the saddle point equilibrium in the phase space of the rate-and-state dynamics. This enables us explicitly to define μs in terms of the rate-and-state variables and hence link Rabinowicz's ideas to rate-and-state friction laws. This stable manifold naturally separates two basins of attraction in the phase space: initial conditions in the first one lead to the block eventually stopping, while in the second basin of attraction the sliding motion continues indefinitely. We show that a second definition of μs is possible, compatible with the first one, as the weighted average of the rate-and-state friction coefficient over the time the block is in motion.

Transient Droplet Behavior and Droplet Breakup during Bulk and Confined Shear Flow in Blends with One Viscoelastic Component: Experiments, Modelling and Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardinaels, Ruth; Verhulst, Kristof; Moldenaers, Paula

2008-07-07

The transient droplet deformation and droplet orientation after inception of shear, the shape relaxation after cessation of shear and droplet breakup during shear, are microscopically studied, both under bulk and confined conditions. The studied blends contain one viscoelastic Boger fluid phase. A counter rotating setup, based on a Paar Physica MCR300, is used for the droplet visualisation. For bulk shear flow, it is shown that the droplet deformation during startup of shear flow and the shape relaxation after cessation of shear flow are hardly influenced by droplet viscoelasticity, even at moderate to high capillary and Deborah numbers. The effects ofmore » droplet viscoelasticity only become visible close to the critical conditions and a novel break-up mechanism is observed. Matrix viscoelasticity has a more pronounced effect, causing overshoots in the deformation and significantly inhibiting relaxation. However, different applied capillary numbers prior to cessation of shear flow, with the Deborah number fixed, still result in a single master curve for shape retraction, as in fully Newtonian systems. The long tail in the droplet relaxation can be qualitatively described with a phenomenological model for droplet deformation, when using a 5-mode Giesekus model for the fluid rheology. It is found that the shear flow history significantly affects the droplet shape evolution and the breakup process in blends with one viscoelastic component. Confining a droplet between two plates accelerates the droplet deformation kinetics, similar to fully Newtonian systems. However, the increased droplet deformation, due to wall effects, causes the steady state to be reached at a later instant in time. Droplet relaxation is less sensitive to confinement, leading to slower relaxation kinetics only for highly confined droplets. For the blend with a viscoelastic droplet, a non-monotonous trend is found for the critical capillary number as a function of the confinement ratio. Finally, experimental data are compared with 3D simulations, performed with a volume-of-fluid algorithm.« less

Evidence for proton tunneling and a transient covalent flavin-substrate adduct in choline oxidase S101A.

PubMed

Uluisik, Rizvan; Romero, Elvira; Gadda, Giovanni

2017-11-01

The effect of temperature on the reaction of alcohol oxidation catalyzed by choline oxidase was investigated with the S101A variant of choline oxidase. Anaerobic enzyme reduction in a stopped-flow spectrophotometer was biphasic using either choline or 1,2-[ 2 H 4 ]-choline as a substrate. The limiting rate constants k lim1 and k lim2 at saturating substrate were well separated (k lim1 /k lim2 >9), and were >15-fold slower than for wild-type choline oxidase. Solvent deuterium kinetic isotope effects (KIEs) ~4 established that k lim1 probes the proton transfer from the substrate hydroxyl to a catalytic base. Primary substrate deuterium KIEs ≥7 demonstrated that k lim2 reports on hydride transfer from the choline alkoxide to the flavin. Between 15°C and 39°C the k lim1 and k lim2 values increased with increasing temperature, allowing for the analyses of H + and H - transfers using Eyring and Arrhenius formalisms. Temperature-independent KIE on the k lim1 value ( H2O k lim1 / D2O k lim1 ) suggests that proton transfer occurs within a highly reorganized tunneling-ready-state with a narrow distribution of donor-acceptor distances. Eyring analysis of the k lim2 value gave lines with the slope (choline) >slope (D-choline) , suggesting kinetic complexity. Spectral evidence for the transient occurrence of a covalent flavin-substrate adduct during the first phase of the anaerobic reaction of S101A CHO with choline is presented, supporting the notion that an important role of amino acid residues in the active site of flavin-dependent enzymes is to eliminate alternative reactions of the versatile enzyme-bound flavin for the reaction that needs to be catalyzed. Copyright © 2017 Elsevier B.V. All rights reserved.

Three-dimensional transient rip currents: Bathymetric excitation of low-frequency intrinsic variability

NASA Astrophysics Data System (ADS)

Uchiyama, Yusuke; McWilliams, James C.; Akan, Cigdem

2017-07-01

The ROMS-WEC model [Uchiyama et al., 2010] based on an Eulerian wave-averaged vortex-force asymptotic theory of McWilliams et al. (2004) is applied to analyze 3-D transient wave-driven rip currents and associated intrinsic very low-frequency (VLF) variability in the surf zone on a surveyed bathymetry under spatiotemporally uniform offshore incident waves. The 3-D rip currents are substantially depth-dependent due to the vertical recirculation, composed of pairs of counter-rotating longitudinal overturning roll cells that promote surface convergence. The vortex force plays an important role in vorticity budget, preconditioning overall vorticity reduction. These rip currents are intrinsically unstable and contribute about 70% to kinetic energy (KE) as eddy kinetic energy (EKE), consistent with observations. The dominant fluctuation period fits the VLF band, at about 18 min. The current effect on waves (CEW) alters not only the mean rip structure, but also the associated turbulence as the modified cross-shore EKE profile with considerable accentuation in the inner surf zone. Increased alongshore bathymetric variability proportionally intensifies KE and intrinsic EKE, whereas it reduces the VLF period. With a guide of a pseudo 2D model, we reveal that vortex tilting effect due to the horizontal vorticity inherent in the 3-D rip currents promotes collapse of the 3-D eddies through an enhanced forward kinetic energy cascade, leading to short-lived, laterally-stretched 3-D eddies resulting in elongated filaments that decay more quickly than coherent, long-lived, circular 2-D eddies.

APEX (Aqueous Photochemistry of Environmentally occurring Xenobiotics): a free software tool to predict the kinetics of photochemical processes in surface waters.

PubMed

Bodrato, Marco; Vione, Davide

2014-04-01

The APEX software predicts the photochemical transformation kinetics of xenobiotics in surface waters as a function of: photoreactivity parameters (direct photolysis quantum yield and second-order reaction rate constants with transient species, namely ˙OH, CO₃(-)˙, (1)O₂ and the triplet states of chromophoric dissolved organic matter, (3)CDOM*), water chemistry (nitrate, nitrite, bicarbonate, carbonate, bromide and dissolved organic carbon, DOC), and water depth (more specifically, the optical path length of sunlight in water). It applies to well-mixed surface water layers, including the epilimnion of stratified lakes, and the output data are average values over the considered water column. Based on intermediate formation yields from the parent compound via the different photochemical pathways, the software can also predict intermediate formation kinetics and overall yield. APEX is based on a photochemical model that has been validated against available field data of pollutant phototransformation, with good agreement between model predictions and field results. The APEX software makes allowance for different levels of knowledge of a photochemical system. For instance, the absorption spectrum of surface water can be used if known, or otherwise it can be modelled from the values of DOC. Also the direct photolysis quantum yield can be entered as a detailed wavelength trend, as a single value (constant or average), or it can be defined as a variable if unknown. APEX is based on the free software Octave. Additional applications are provided within APEX to assess the σ-level uncertainty of the results and the seasonal trend of photochemical processes.

Applying the Brakes to Multi-Site SR Protein Phosphorylation: Substrate-Induced Effects on the Splicing Kinase SRPK1†

PubMed Central

Aubol, Brandon E.; Adams, Joseph A.

2011-01-01

To investigate how a protein kinase interacts with its protein substrate during extended, multi-site phosphorylation, the kinetic mechanism of a protein kinase involved in mRNA splicing control was investigated using rapid quench flow techniques. The protein kinase SRPK1 phosphorylates approximately 10 serines in the arginine-serine-rich domain (RS domain) of the SR protein SRSF1 in a C-to-N-terminal direction, a modification that directs this essential splicing factor from the cytoplasm to the nucleus. Transient-state kinetic experiments illustrate that the first phosphate is added rapidly onto the RS domain of SRSF1 (t1/2 = 0.1 sec) followed by slower, multi-site phosphorylation at the remaining serines (t1/2 = 15 sec). Mutagenesis experiments suggest that efficient phosphorylation rates are maintained by an extensive hydrogen bonding and electrostatic network between the RS domain of the SR protein and the active site and docking groove of the kinase. Catalytic trapping and viscosometric experiments demonstrate that while the phosphoryl transfer step is fast, ADP release limits multi-site phosphorylation. By studying phosphate incorporation into selectively pre-phosphorylated forms of the enzyme-substrate complex, the kinetic mechanism for site-specific phosphorylation along the reaction coordinate was assessed. The binding affinity of the SR protein, the phosphoryl transfer rate and ADP exchange rate were found to decline significantly as a function of progressive phosphorylation in the RS domain. These findings indicate that the protein substrate actively modulates initiation, extension and termination events associated with prolonged, multi-site phosphorylation. PMID:21728354

Trace element zoning as a record of chemical disequilibrium during garnet growth

NASA Astrophysics Data System (ADS)

Chernoff, Carlotta B.; Carlson, William D.

1999-06-01

Trace element concentrations in pelitic garnets from the Picuris Range of New Mexico display precipitous changes coincident with abrupt variations in Ca concentration. These patterns probably arise from the transitory participation of different trace element enriched phases in the garnet forming reaction. Changes in the reactant and product assemblages occur at different times during the reaction history for crystals of different size, so they cannot be the result of any event affecting the entire rock, such as a change in pressure, temperature, or fluid composition. Instead, they reflect kinetic factors that cause Ca, Y, Yb, P, Ti, Sc, Zr, Hf, Sr, Na, and Li to fail to achieve chemical equilibrium during garnet growth. Caution is needed to avoid misinterpreting excursions in the concentration of these elements as event markers recording simultaneous rockwide changes in intensive parameters, when in fact they may record transient disequilibrium states that are local in scope, and not contemporaneous.

Patched bimetallic surfaces are active catalysts for ammonia decomposition.

PubMed

Guo, Wei; Vlachos, Dionisios G

2015-10-07

Ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material's structure. Core-shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core-shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-H bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.

Non-equilibrium dissipative supramolecular materials with a tunable lifetime

NASA Astrophysics Data System (ADS)

Tena-Solsona, Marta; Rieß, Benedikt; Grötsch, Raphael K.; Löhrer, Franziska C.; Wanzke, Caren; Käsdorf, Benjamin; Bausch, Andreas R.; Müller-Buschbaum, Peter; Lieleg, Oliver; Boekhoven, Job

2017-07-01

Many biological materials exist in non-equilibrium states driven by the irreversible consumption of high-energy molecules like ATP or GTP. These energy-dissipating structures are governed by kinetics and are thus endowed with unique properties including spatiotemporal control over their presence. Here we show man-made equivalents of materials driven by the consumption of high-energy molecules and explore their unique properties. A chemical reaction network converts dicarboxylates into metastable anhydrides driven by the irreversible consumption of carbodiimide fuels. The anhydrides hydrolyse rapidly to the original dicarboxylates and are designed to assemble into hydrophobic colloids, hydrogels or inks. The spatiotemporal control over the formation and degradation of materials allows for the development of colloids that release hydrophobic contents in a predictable fashion, temporary self-erasing inks and transient hydrogels. Moreover, we show that each material can be re-used for several cycles.

Ultrafast carrier dynamics in a p-type GaN wafer under different carrier distributions

NASA Astrophysics Data System (ADS)

Fang, Yu; Yang, Junyi; Yang, Yong; Wu, Xingzhi; Xiao, Zhengguo; Zhou, Feng; Song, Yinglin

2016-02-01

The dependence of the carrier distribution on photoexcited carrier dynamics in a p-type Mg-doped GaN (GaN:Mg) wafer were systematically measured by femtosecond transient absorption (TA) spectroscopy. The homogeneity of the carrier distribution was modified by tuning the wavelength of the UV pulse excitation around the band gap of GaN:Mg. The TA kinetics appeared to be biexponential for all carrier distributions, and only the slower component decayed faster as the inhomogeneity of the carrier distribution increased. It was concluded that the faster component (50-70 ps) corresponded to the trap process of holes by the Mg acceptors, and the slower component (150-600 ps) corresponded to the combination of non-radiative surface recombination and intrinsic carrier recombination via dislocations. Moreover, the slower component increased gradually with the incident fluence due to the saturation of surface states.

Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

NASA Astrophysics Data System (ADS)

Lépinoux, J.; Sigli, C.

2018-01-01

In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.

Improved turbine disk design to increase reliability of aircraft jet engines

NASA Technical Reports Server (NTRS)

Alver, A. S.; Wong, J. K.

1975-01-01

An analytical study was conducted on a bore entry cooled turbine disk for the first stage of the JT8D-17 high pressure turbine which had the potential to improve disk life over existing design. The disk analysis included the consideration of transient and steady state temperature, blade loading, creep, low cycle fatigue, fracture mechanics and manufacturing flaws. The improvement in life of the bore entry cooled turbine disk was determined by comparing it with the existing disk made of both conventional and advanced (Astroloy) disk materials. The improvement in crack initiation life of the Astroloy bore entry cooled disk is 87% and 67% over the existing disk made of Waspaloy and Astroloy, respectively. Improvement in crack propagation life is 124% over the Waspaloy and 465% over the Astroloy disks. The available kinetic energies of disk fragments calculated for the three disks indicate a lower fragment energy level for the bore entry cooled turbine disk.

The effects of bound state motion on macromolecular diffusion

NASA Astrophysics Data System (ADS)

Hough, Loren; Stefferson, Michael; Norris, Samantha; Maguire, Laura; Vernerey, Franck; Betterton, Meredith

The diffusion of macromolecules is modified in crowded environments by both inert obstacles and interaction sites. Molecules are generally slowed in their movement inducing transient anomalous subdiffusion. Obstacles also modify the kinetics and equilibrium behavior of interaction between mobile proteins. In some biophysical contexts, bound molecules can still experience mobility, for example transcription factors sliding along DNA, membrane proteins with some entry and diffusion within lipid domains, or proteins that can enter into non-membrane bound compartments such as the nucleolus. We used lattice and continuum models to study the diffusive behavior of tracer particles which bind to obstacles and can diffuse within them. We show that binding significantly alters the motion of tracers. The type and degree of motion while bound is a key determinant of the tracer mobility. Our work has implications for protein-protein movement and interactions within living cells, including those involving intrinsically disordered proteins.

Direct real-time detection of the structural and biochemical events in the myosin power stroke.

PubMed

Muretta, Joseph M; Rohde, John A; Johnsrud, Daniel O; Cornea, Sinziana; Thomas, David D

2015-11-17

A principal goal of molecular biophysics is to show how protein structural transitions explain physiology. We have developed a strategic tool, transient time-resolved FRET [(TR)(2)FRET], for this purpose and use it here to measure directly, with millisecond resolution, the structural and biochemical kinetics of muscle myosin and to determine directly how myosin's power stroke is coupled to the thermodynamic drive for force generation, actin-activated phosphate release, and the weak-to-strong actin-binding transition. We find that actin initiates the power stroke before phosphate dissociation and not after, as many models propose. This result supports a model for muscle contraction in which power output and efficiency are tuned by the distribution of myosin structural states. This technology should have wide application to other systems in which questions about the temporal coupling of allosteric structural and biochemical transitions remain unanswered.

Investigating anomalous transport of electrolytes in charged porous media

NASA Astrophysics Data System (ADS)

Skjøde Bolet, Asger Johannes; Mathiesen, Joachim

2017-04-01

Surface charge is know to play an important role in microfluidics devices when dealing with electrolytes and their transport properties. Similarly, surface charge could play a role for transport in porous rock with submicron pore sizes. Estimates of the streaming potentials and electro osmotic are mostly considered in simple geometries both using analytic and numerical tools, however it is unclear at present how realistic complex geometries will modify the dynamics. Our work have focused on doing numerical studies of the full three-dimensional Stokes-Poisson-Nernst-Planck problem for electrolyte transport in porous rock. As the numerical implementation, we have used a finite element solver made using the FEniCS project code base, which can both solve for a steady state configuration and the full transient. In the presentation, we will show our results on anomalous transport due to electro kinetic effects such as the streaming potential or the electro osmotic effect.

A Native to Amyloidogenic Transition Regulated by a Backbone Trigger

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eakin,C.; Berman, A.; Miranker, A.

2006-01-01

Many polypeptides can self-associate into linear, aggregated assemblies termed amyloid fibers. High-resolution structural insights into the mechanism of fibrillogenesis are elusive owing to the transient and mixed oligomeric nature of assembly intermediates. Here, we report the conformational changes that initiate fiber formation by beta-2-microglobulin (beta2m) in dialysis-related amyloidosis. Access of beta2m to amyloidogenic conformations is catalyzed by selective binding of divalent cations. The chemical basis of this process was determined to be backbone isomerization of a conserved proline. On the basis of this finding, we designed a beta2m variant that closely adopts this intermediate state. The variant has kinetic, thermodynamicmore » and catalytic properties consistent with its being a fibrillogenic intermediate of wild-type beta2m. Furthermore, it is stable and folded, enabling us to unambiguously determine the initiating conformational changes for amyloid assembly at atomic resolution.« less

Evidence for Interfacial Halogen Bonding.

PubMed

Swords, Wesley B; Simon, Sarah J C; Parlane, Fraser G L; Dean, Rebecca K; Kellett, Cameron W; Hu, Ke; Meyer, Gerald J; Berlinguette, Curtis P

2016-05-10

A homologous series of donor-π-acceptor dyes was synthesized, differing only in the identity of the halogen substituents about the triphenylamine (TPA; donor) portion of each molecule. Each Dye-X (X=F, Cl, Br, and I) was immobilized on a TiO2 surface to investigate how the halogen substituents affect the reaction between the light-induced charge-separated state, TiO2 (e(-) )/Dye-X(+) , with iodide in solution. Transient absorption spectroscopy showed progressively faster reactivity towards nucleophilic iodide with more polarizable halogen substituents: Dye-F < Dye-Cl < Dye-Br < Dye-I. Given that all other structural and electronic properties for the series are held at parity, with the exception of an increasingly larger electropositive σ-hole on the heavier halogens, the differences in dye regeneration kinetics for Dye-Cl, Dye-Br, and Dye-I are ascribed to the extent of halogen bonding with the nucleophilic solution species. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-equilibrium dissipative supramolecular materials with a tunable lifetime

PubMed Central

Tena-Solsona, Marta; Rieß, Benedikt; Grötsch, Raphael K.; Löhrer, Franziska C.; Wanzke, Caren; Käsdorf, Benjamin; Bausch, Andreas R.; Müller-Buschbaum, Peter; Lieleg, Oliver; Boekhoven, Job

2017-01-01

Many biological materials exist in non-equilibrium states driven by the irreversible consumption of high-energy molecules like ATP or GTP. These energy-dissipating structures are governed by kinetics and are thus endowed with unique properties including spatiotemporal control over their presence. Here we show man-made equivalents of materials driven by the consumption of high-energy molecules and explore their unique properties. A chemical reaction network converts dicarboxylates into metastable anhydrides driven by the irreversible consumption of carbodiimide fuels. The anhydrides hydrolyse rapidly to the original dicarboxylates and are designed to assemble into hydrophobic colloids, hydrogels or inks. The spatiotemporal control over the formation and degradation of materials allows for the development of colloids that release hydrophobic contents in a predictable fashion, temporary self-erasing inks and transient hydrogels. Moreover, we show that each material can be re-used for several cycles. PMID:28719591

Current challenges in organic photovoltaic solar energy conversion.

PubMed

Schlenker, Cody W; Thompson, Mark E

2012-01-01

Over the last 10 years, significant interest in utilizing conjugated organic molecules for solid-state solar to electric conversion has produced rapid improvement in device efficiencies. Organic photovoltaic (OPV) devices are attractive for their compatibility with low-cost processing techniques and thin-film applicability to flexible and conformal applications. However, many of the processes that lead to power losses in these systems still remain poorly understood, posing a significant challenge for the future efficiency improvements required to make these devices an attractive solar technology. While semiconductor band models have been employed to describe OPV operation, a more appropriate molecular picture of the pertinent processes is beginning to emerge. This chapter presents mechanisms of OPV device operation, based on the bound molecular nature of the involved transient species. With the intention to underscore the importance of considering both thermodynamic and kinetic factors, recent progress in elucidating molecular characteristics that dictate photovoltage losses in heterojunction organic photovoltaics is also discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Hao; Zhang, Yu; Guo, Sibei

The aggregation of amyloid beta (Aβ) peptides plays a crucial role in the pathology and etiology of Alzheimer's disease. Experimental evidence shows that copper ion is an aggregation-prone species with the ability to coordinately bind to Aβ and further induce the formation of neurotoxic Aβ oligomers. However, the detailed structures of Cu(II)–Aβ complexes have not been illustrated, and the kinetics and dynamics of the Cu(II) binding are not well understood. Two Cu(II)–Aβ complexes have been proposed to exist under physiological conditions, and another two might exist at higher pH values. By using ab initio simulations for the spontaneous resonance Ramanmore » and time domain stimulated resonance Raman spectroscopy signals, we obtained the characteristic Raman vibronic features of each complex. Finally, these signals contain rich structural information with high temporal resolution, enabling the characterization of transient states during the fast Cu–Aβ binding and interconversion processes.« less

Continuous microalgal cultivation in a laboratory-scale photobioreactor under seasonal day-night irradiation: experiments and simulation.

PubMed

Bertucco, Alberto; Beraldi, Mariaelena; Sforza, Eleonora

2014-08-01

In this work, the production of Scenedesmus obliquus in a continuous flat-plate laboratory-scale photobioreactor (PBR) under alternated day-night cycles was tested both experimentally and theoretically. Variation of light intensity according to the four seasons of the year were simulated experimentally by a tunable LED lamp, and effects on microalgal growth and productivity were measured to evaluate the conversion efficiency of light energy into biomass during the different seasons. These results were used to validate a mathematical model for algae growth that can be applied to simulate a large-scale production unit, carried out in a flat-plate PBR of similar geometry. The cellular concentration in the PBR was calculated in both steady-state and transient conditions, and the value of the maintenance kinetic term was correlated to experimental profiles. The relevance of this parameter was finally outlined.

Patched bimetallic surfaces are active catalysts for ammonia decomposition

NASA Astrophysics Data System (ADS)

Guo, Wei; Vlachos, Dionisios G.

2015-10-01

Ammonia decomposition is often used as an archetypical reaction for predicting new catalytic materials and understanding the very reason of why some reactions are sensitive on material's structure. Core-shell or surface-segregated bimetallic nanoparticles expose outstanding activity for many heterogeneously catalysed reactions but the reasons remain elusive owing to the difficulties in experimentally characterizing active sites. Here by performing multiscale simulations in ammonia decomposition on various nickel loadings on platinum (111), we show that the very high activity of core-shell structures requires patches of the guest metal to create and sustain dual active sites: nickel terraces catalyse N-H bond breaking and nickel edge sites drive atomic nitrogen association. The structure sensitivity on these active catalysts depends profoundly on reaction conditions due to kinetically competing relevant elementary reaction steps. We expose a remarkable difference in active sites between transient and steady-state studies and provide insights into optimal material design.

The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts

NASA Astrophysics Data System (ADS)

Rinaldi, Arlie J.; Lund, Paul E.; Blanco, Mario R.; Walter, Nils G.

2016-01-01

In response to intracellular signals in Gram-negative bacteria, translational riboswitches--commonly embedded in messenger RNAs (mRNAs)--regulate gene expression through inhibition of translation initiation. It is generally thought that this regulation originates from occlusion of the Shine-Dalgarno (SD) sequence upon ligand binding; however, little direct evidence exists. Here we develop Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to investigate the ligand-dependent accessibility of the SD sequence of an mRNA hosting the 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch. Spike train analysis reveals that individual mRNA molecules alternate between two conformational states, distinguished by `bursts' of probe binding associated with increased SD sequence accessibility. Addition of preQ1 decreases the lifetime of the SD's high-accessibility (bursting) state and prolongs the time between bursts. In addition, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules. Such complex ligand sensing by individual mRNA molecules rationalizes the nuanced ligand response observed during bulk mRNA translation.

Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics

PubMed Central

Liu, Jianqiao; Gao, Yinglin; Wu, Xu; Jin, Guohua; Zhai, Zhaoxia; Liu, Huan

2017-01-01

The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacancy was proposed based on the effects of cooling rate and re-annealing on semiconductive thin films. The model established the diffusion equations of oxygen vacancy according to the defect kinetics of diffusion and exclusion. We described that the steady-state and transient-state oxygen vacancy distributions, which were used to calculate the gas-sensing characteristics of the sensor resistance and response to reducing gases under two different conditions. The gradient-distributed oxygen vacancy model had the applications in simulating the sensor performances, such as the power law, the grain size effect and the effect of depletion layer width. PMID:28796167

Inhomogeneous Oxygen Vacancy Distribution in Semiconductor Gas Sensors: Formation, Migration and Determination on Gas Sensing Characteristics.

PubMed

Liu, Jianqiao; Gao, Yinglin; Wu, Xu; Jin, Guohua; Zhai, Zhaoxia; Liu, Huan

2017-08-10

The density of oxygen vacancies in semiconductor gas sensors was often assumed to be identical throughout the grain in the numerical discussion of the gas-sensing mechanism of the devices. In contrast, the actual devices had grains with inhomogeneous distribution of oxygen vacancy under non-ideal conditions. This conflict between reality and discussion drove us to study the formation and migration of the oxygen defects in semiconductor grains. A model of the gradient-distributed oxygen vacancy was proposed based on the effects of cooling rate and re-annealing on semiconductive thin films. The model established the diffusion equations of oxygen vacancy according to the defect kinetics of diffusion and exclusion. We described that the steady-state and transient-state oxygen vacancy distributions, which were used to calculate the gas-sensing characteristics of the sensor resistance and response to reducing gases under two different conditions. The gradient-distributed oxygen vacancy model had the applications in simulating the sensor performances, such as the power law, the grain size effect and the effect of depletion layer width.

Transient times in linear metabolic pathways under constant affinity constraints.

PubMed

Lloréns, M; Nuño, J C; Montero, F

1997-10-15

In the early seventies, Easterby began the analytical study of transition times for linear reaction schemes [Easterby (1973) Biochim. Biophys. Acta 293, 552-558]. In this pioneer work and in subsequent papers, a state function (the transient time) was used to measure the period before the stationary state, for systems constrained to work under both constant and variable input flux, was reached. Despite the undoubted usefulness of this quantity to describe the time-dependent features of these kinds of systems, its application to the study of chemical reactions under other constraints is questionable. In the present work, a generalization of these magnitudes to linear metabolic pathways functioning under a constant-affinity constraint is carried out. It is proved that classical definitions of transient times do not reflect the actual properties of the transition to the steady state in systems evolving under this restriction. Alternatively, a more adequate framework for interpretation of the transient times for systems with both constant and variable input flux is suggested. Within this context, new definitions that reflect more accurately the transient characteristics of constant affinity systems are stated. Finally, the meaning of these transient times is discussed.

Laser Flash Photolysis Generation of High-Valent Transition Metal-Oxo Species: Insights from Kinetic Studies in Real Time

PubMed Central

Zhang, Rui; Newcomb, Martin

2010-01-01

Conspectus High-valent transition metal-oxo species are active oxidizing species in many metal-catalyzed oxidation reactions in both Nature and the laboratory. In homogeneous catalytic oxidations, a transition metal catalyst is oxidized to a metal-oxo species by a sacrificial oxidant, and the activated transition metal-oxo intermediate oxidizes substrates. Mechanistic studies of these oxidizing species can provide insights for understanding commercially important catalytic oxidations and the oxidants in cytochrome P450 enzymes. In many cases, however, the transition metal oxidants are so reactive that they do not accumulate to detectable levels in mixing experiments, which have millisecond mixing times, and successful generation and direct spectroscopic characterization of these highly reactive transients remain a considerable challenge. Our strategy for understanding homogeneous catalysis intermediates employs photochemical generation of the transients with spectroscopic detection on time-scales as short as nanoseconds and direct kinetic studies of their reactions with substrates by laser flash photolysis (LFP) methods. This Account describes studies of high-valent manganese- and iron-oxo intermediates. Irradiation of porphyrin-manganese(III) nitrates and chlorates or corrole-manganese(IV) chlorates resulted in homolytic cleavage of the O-X bonds in the ligands, whereas irradiation of porphyrin-manganese(III) perchlorates resulted in heterolytic cleavage of O-Cl bonds to give porphyrin-manganese(V)-oxo cations. Similar reactions of corrole- and porphyrin-iron(IV) complexes gave highly reactive transients that were tentatively identified as macrocyclic ligand-iron(V)-oxo species. Kinetic studies demonstrated high reactivity of the manganese(V)-oxo species, and even higher reactivities of the putative iron(V)-oxo transients. For example, second-order rate constants for oxidations of cis-cyclooctene at room temperature were 6 × 103 M−1 s−1 for a corrole-iron(V)-oxo species and 1.6 × 106 M−1 s−1 for the putative tetramesitylporphyrin-iron(V)-oxo perchlorate species. The latter rate constant is 25,000 times larger than that for oxidation of cis-cyclooctene by iron(IV)-oxo perchlorate tetramesitylporphyrin radical cation, which is the thermodynamically favored electronic isomer of the putative iron(V)-oxo species. The LFP-determined rate constants can be used to implicate the transient oxidants in catalytic reactions under turnover conditions where high-valent species are not observable. Similarly, the observed reactivities of the putative porphyrin-iron(V)-oxo species might explain the unusually high reactivity of oxidants produced in the cytochrome P450 enzymes, heme-thiolate enzymes that are capable of oxidizing unactivated carbon-hydrogen bonds in substrates so rapidly that iron-oxo intermediates have not been detected under physiological conditions. PMID:18278877

Laser flash photolysis generation of high-valent transition metal-oxo species: insights from kinetic studies in real time.

PubMed

Zhang, Rui; Newcomb, Martin

2008-03-01

High-valenttransition metal-oxo species are active oxidizing species in many metal-catalyzed oxidation reactions in both Nature and the laboratory. In homogeneous catalytic oxidations, a transition metal catalyst is oxidized to a metal-oxo species by a sacrificial oxidant, and the activated transition metal-oxo intermediate oxidizes substrates. Mechanistic studies of these oxidizing species can provide insights for understanding commercially important catalytic oxidations and the oxidants in cytochrome P450 enzymes. In many cases, however, the transition metal oxidants are so reactive that they do not accumulate to detectable levels in mixing experiments, which have millisecond mixing times, and successful generation and direct spectroscopic characterization of these highly reactive transients remain a considerable challenge. Our strategy for understanding homogeneous catalysis intermediates employs photochemical generation of the transients with spectroscopic detection on time scales as short as nanoseconds and direct kinetic studies of their reactions with substrates by laser flash photolysis (LFP) methods. This Account describes studies of high-valent manganese- and iron-oxo intermediates. Irradiation of porphyrin-manganese(III) nitrates and chlorates or corrole-manganese(IV) chlorates resulted in homolytic cleavage of the O-X bonds in the ligands, whereas irradiation of porphyrin-manganese(III) perchlorates resulted in heterolytic cleavage of O-Cl bonds to give porphyrin-manganese(V)-oxo cations. Similar reactions of corrole- and porphyrin-iron(IV) complexes gave highly reactive transients that were tentatively identified as macrocyclic ligand-iron(V)-oxo species. Kinetic studies demonstrated high reactivity of the manganese(V)-oxo species, and even higher reactivities of the putative iron(V)-oxo transients. For example, second-order rate constants for oxidations of cis-cyclooctene at room temperature were 6 x 10(3) M(-1) s(-1) for a corrole-iron(V)-oxo species and 1.6 x 10(6) M(-1) s(-1) for the putative tetramesitylporphyrin-iron(V)-oxo perchlorate species. The latter rate constant is 25,000 times larger than that for oxidation of cis-cyclooctene by iron(IV)-oxo perchlorate tetramesitylporphyrin radical cation, which is the thermodynamically favored electronic isomer of the putative iron(V)-oxo species. The LFP-determined rate constants can be used to implicate the transient oxidants in catalytic reactions under turnover conditions where high-valent species are not observable. Similarly, the observed reactivities of the putative porphyrin-iron(V)-oxo species might explain the unusually high reactivity of oxidants produced in the cytochrome P450 enzymes, heme-thiolate enzymes that are capable of oxidizing unactivated carbon-hydrogen bonds in substrates so rapidly that iron-oxo intermediates have not been detected under physiological conditions.

Multilayer Insulation Ascent Venting Model

NASA Technical Reports Server (NTRS)

Tramel, R. W.; Sutherlin, S. G.; Johnson, W. L.

2017-01-01

The thermal and venting transient experienced by tank-applied multilayer insulation (MLI) in the Earth-to-orbit environment is very dynamic and not well characterized. This new predictive code is a first principles-based engineering model which tracks the time history of the mass and temperature (internal energy) of the gas in each MLI layer. A continuum-based model is used for early portions of the trajectory while a kinetic theory-based model is used for the later portions of the trajectory, and the models are blended based on a reference mean free path. This new capability should improve understanding of the Earth-to-orbit transient and enable better insulation system designs for in-space cryogenic propellant systems.

Characterization of thermoplastic polyimide NEW-TPI

NASA Technical Reports Server (NTRS)

Hou, T. H.; Reddy, R. M.

1991-01-01

Thermal and rheological properties of a commercial thermoplastic polyimide, NEW-TPI, were characterized. The as-received material possesses initially a transient crystallite form with a bimodal distribution in peak melting temperatures. After the meltings of the initial crystallite structures, the sample can be recrystallized by various thermal treatments. A bimodal or single-modal melting peak distribution is formed for annealing temperatures below or above 360 C, respectively. The recrystallized crystallinities are all transient in nature. The polymers are unable to be recrystallized after being subjected to elevated temperature annealing above 450 C. The recrystallization mechanism was postulated, and a simple kinetics model was found to describe the behavior satisfactorily under conditions of prolonged thermal annealing.

V02 'overshoot' during moderate-intensity exercise in endurance-trained athletes: the influence of exercise modality.

PubMed

Kilding, Andrew E; Jones, Andrew M

2008-02-01

The purpose of this study was to investigate the influence of exercise modality on the 'overshoot' in V(O2) that has been reported following the onset of moderate-intensity (below the gas exchange threshold, GET) exercise in endurance athletes. Seven trained endurance cyclists and seven trained endurance runners completed six square-wave transitions to a work-rate or running speed requiring 80% of mode-specific GET during both cycle and treadmill running exercise. The kinetics of V(O2) was assessed using non-linear regression and any overshoot in V(O2) was quantified as the integrated volume (IV) of O(2) consumed above the steady-state requirement. During cycling, an overshoot in V(O2) was evident in all seven cyclists (IV = 136 +/- 41 ml) and in four runners (IV = 81 +/- 94 ml). During running, an overshoot in V(O2) was evident in four runners (IV = 72 +/- 61 ml) but no cyclists. These data challenge the notion that V(O2) always rises towards a steady-state with near-exponential kinetics in this exercise intensity domain. The greater incidence of the V(O2) overshoot during cycling (11/14 subjects) compared to running (4/14 subjects) indicates that the overshoot phenomenon is related to an interaction between high levels of aerobic fitness and exercise modality. We speculate that a transient loss in muscle efficiency as a consequence of a non-constant ATP requirement following the onset of constant-work-rate exercise or an initially excessive recruitment of motor units (relative to the work-rate) might contribute to the overshoot phenomenon.

Toward Two-Color Sub-Doppler Saturation Recovery Kinetics in CN (x, v = 0, J)

NASA Astrophysics Data System (ADS)

Xu, Hong; Forthomme, Damien; Sears, Trevor; Hall, Gregory; Dagdigian, Paul

2015-06-01

Collision-induced rotational energy transfer among rotational levels of ground state CN (X 2σ+, v = 0) radicals has been probed by saturation recovery experiments, using high-resolution, polarized transient FM spectroscopy to probe the recovery of population and the decay of alignment following ns pulsed laser depletion of selected CN rotational levels. Despite the lack of Doppler selection in the pulsed depletion and the thermal distribution of collision velocities, the recovery kinetics are found to depend on the probed Doppler shift of the depleted signal. The observed Doppler-shift-dependent recovery rates are a measure of the velocity dependence of the inelastic cross sections, combined with the moderating effects of velocity-changing elastic collisions. New experiments are underway, in which the pulsed saturation is performed with sub-Doppler velocity selection. The time evolution of the spectral hole bleached in the initially thermal CN absorption spectrum can characterize speed-dependent inelastic collisions along with competing elastic velocity-changing collisions, all as a function of the initially bleached velocity group and rotational state. The initial time evolution of the depletion recovery spectrum can be compared to a stochastic model, using differential cross sections for elastic scattering as well as speed-dependent total inelastic cross sections, derived from ab initio scattering calculations. Progress to date will be reported. Acknowledgments: Work at Brookhaven National Laboratory was carried out under Contract No. DE-AC02-98CH10886 and DE-SC0012704 with the U.S. Department of Energy and supported by its Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences.

Complete Monitoring of Coherent and Incoherent Spin Flip Domains in the Recombination of Charge-Separated States of Donor-Iridium Complex-Acceptor Triads.

PubMed

Klein, Johannes H; Schmidt, David; Steiner, Ulrich E; Lambert, Christoph

2015-09-02

The spin chemistry of photoinduced charge-separated (CS) states of three triads comprising one or two triarylamine donors, a cyclometalated iridium complex sensitizer and a naphthalene diimide (NDI) acceptor, was investigated by transient absorption spectroscopy in the ns-μs time regime. Strong magnetic-field effects (MFE) were observed for two triads with a phenylene bridge between iridium complex sensitizer and NDI acceptor. For these triads, the lifetimes of the CS states increased from 0.6 μs at zero field to 40 μs at about 2 T. Substituting the phenylene by a biphenyl bridge causes the lifetime of the CS state at zero field to increase by more than 2 orders of magnitude (τ = 79 μs) and the MFE to disappear almost completely. The kinetic MFE was analyzed in the framework of a generalized Hayashi-Nagakura scheme describing coherent (S, T0 ↔ T±) as well as incoherent (S, T0 ⇌ T±) processes by a single rate constant k±. The magnetic-field dependence of k± of the triads with phenylene bridge spans 2 orders of magnitude and exhibits a biphasic behavior characterized by a superposition of two Lorentzians. This biphasic MFE is observed for the first time and is clearly attributable to the coherent (B < 10 mT) and incoherent (10 mT < B < 2 T) domains of spin motion induced by isotropic and anisotropic hyperfine coupling. The parameters of both domains are well understood in terms of the structural properties of the two triads, including the effect of electron hopping in the triad with two donor moieties. The kinetic model also accounts for the reduction of the MFE on reducing the rate constant of charge recombination in the triad with the biphenyl bridge.

Influence of Proton Acceptors on the Proton-Coupled Electron Transfer Reaction Kinetics of a Ruthenium-Tyrosine Complex.

PubMed

Lennox, J Christian; Dempsey, Jillian L

2017-11-22

A polypyridyl ruthenium complex with fluorinated bipyridine ligands and a covalently bound tyrosine moiety was synthesized, and its photo-induced proton-coupled electron transfer (PCET) reactivity in acetonitrile was investigated with transient absorption spectroscopy. Using flash-quench methodology with methyl viologen as an oxidative quencher, a Ru 3+ species is generated that is capable of initiating the intramolecular PCET oxidation of the tyrosine moiety. Using a series of substituted pyridine bases, the reaction kinetics were found to vary as a function of proton acceptor concentration and identity, with no significant H/D kinetic isotope effect. Through analysis of the kinetics traces and comparison to a control complex without the tyrosine moiety, PCET reactivity was found to proceed through an equilibrium electron transfer followed by proton transfer (ET-PT) pathway in which irreversible deprotonation of the tyrosine radical cation shifts the ET equilibrium, conferring a base dependence on the reaction. Comprehensive kinetics modeling allowed for deconvolution of complex kinetics and determination of rate constants for each elementary step. Across the five pyridine bases explored, spanning a range of 4.2 pK a units, a linear free-energy relationship was found for the proton transfer rate constant with a slope of 0.32. These findings highlight the influence that proton transfer driving force exerts on PCET reaction kinetics.

Steady-state pattern electroretinogram and short-duration transient visual evoked potentials in glaucomatous and healthy eyes.

PubMed

Amarasekera, Dilru C; Resende, Arthur F; Waisbourd, Michael; Puri, Sanjeev; Moster, Marlene R; Hark, Lisa A; Katz, L Jay; Fudemberg, Scott J; Mantravadi, Anand V

2018-01-01

This study evaluates two rapid electrophysiological glaucoma diagnostic tests that may add a functional perspective to glaucoma diagnosis. This study aimed to determine the ability of two office-based electrophysiological diagnostic tests, steady-state pattern electroretinogram and short-duration transient visual evoked potentials, to discern between glaucomatous and healthy eyes. This is a cross-sectional study in a hospital setting. Forty-one patients with glaucoma and 41 healthy volunteers participated in the study. Steady-state pattern electroretinogram and short-duration transient visual evoked potential testing was conducted in glaucomatous and healthy eyes. A 64-bar-size stimulus with both a low-contrast and high-contrast setting was used to compare steady-state pattern electroretinogram parameters in both groups. A low-contrast and high-contrast checkerboard stimulus was used to measure short-duration transient visual evoked potential parameters in both groups. Steady-state pattern electroretinogram parameters compared were MagnitudeD, MagnitudeD/Magnitude ratio, and the signal-to-noise ratio. Short-duration transient visual evoked potential parameters compared were amplitude and latency. MagnitudeD was significantly lower in glaucoma patients when using a low-contrast (P = 0.001) and high-contrast (P < 0.001) 64-bar-size steady-state pattern electroretinogram stimulus. MagnitudeD/Magnitude ratio and SNR were significantly lower in the glaucoma group when using a high-contrast 64-bar-size stimulus (P < 0.001 and P = 0.010, respectively). Short-duration transient visual evoked potential amplitude and latency were not significantly different between the two groups. Steady-state pattern electroretinogram was effectively able to discern between glaucomatous and healthy eyes. Steady-state pattern electroretinogram may thus have a role as a clinically useful electrophysiological diagnostic tool. © 2017 Royal Australian and New Zealand College of Ophthalmologists.

Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

NASA Astrophysics Data System (ADS)

Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

2018-04-01

A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

Kinetics of lipid-nanoparticle-mediated intracellular mRNA delivery and function

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.

2017-10-01

mRNA delivery into cells forms the basis for one of the new and promising ways to treat various diseases. Among suitable carriers, lipid nanoparticles (LNPs) with a size of about 100 nm are now often employed. Despite high current interest in this area, the understanding of the basic details of LNP-mediated mRNA delivery and function is limited. To clarify the kinetics of mRNA release from LNPs, the author uses three generic models implying (i) exponential, (ii) diffusion-controlled, and (iii) detachment-controlled kinetic regimes, respectively. Despite the distinct differences in these kinetics, the associated transient kinetics of mRNA translation to the corresponding protein and its degradation are shown to be not too sensitive to the details of the mRNA delivery by LNPs (or other nanocarriers). In addition, the author illustrates how this protein may temporarily influence the expression of one gene or a few equivalent genes. The analysis includes positive or negative regulation of the gene transcription via the attachment of the protein without or with positive or negative feedback in the gene expression. Stable, bistable, and oscillatory schemes have been scrutinized in this context.

Multistage adsorption of diffusing macromolecules and viruses

NASA Astrophysics Data System (ADS)

Chou, Tom; D'Orsogna, Maria R.

2007-09-01

We derive the equations that describe adsorption of diffusing particles onto a surface followed by additional surface kinetic steps before being transported across the interface. Multistage surface kinetics occurs during membrane protein insertion, cell signaling, and the infection of cells by virus particles. For example, viral entry into healthy cells is possible only after a series of receptor and coreceptor binding events occurs at the cellular surface. We couple the diffusion of particles in the bulk phase with the multistage surface kinetics and derive an effective, integrodifferential boundary condition that contains a memory kernel embodying the delay induced by the surface reactions. This boundary condition takes the form of a singular perturbation problem in the limit where particle-surface interactions are short ranged. Moreover, depending on the surface kinetics, the delay kernel induces a nonmonotonic, transient replenishment of the bulk particle concentration near the interface. The approach generalizes that of Ward and Tordai [J. Chem. Phys. 14, 453 (1946)] and Diamant and Andelman [Colloids Surf. A 183-185, 259 (2001)] to include surface kinetics, giving rise to qualitatively new behaviors. Our analysis also suggests a simple scheme by which stochastic surface reactions may be coupled to deterministic bulk diffusion.

Investigation of natural circulation instability and transients in passively safe novel modular reactor

NASA Astrophysics Data System (ADS)

Shi, Shanbin

The Purdue Novel Modular Reactor (NMR) is a new type small modular reactor (SMR) that belongs to the design of boiling water reactor (BWR). Specifically, the NMR is one third the height and area of a conventional BWR reactor pressure vessel (RPV) with an electric output of 50 MWe. The fuel cycle length of the NMR-50 is extended up to 10 years due to optimized neutronics design. The NMR-50 is designed with double passive engineering safety system. However, natural circulation BWRs (NCBWR) could experience certain operational difficulties due to flow instabilities that occur at low pressure and low power conditions. Static instabilities (i.e. flow excursion (Ledinegg) instability and flow pattern transition instability) and dynamic instabilities (i.e. density wave instability and flashing/condensation instability) pose a significant challenge in two-phase natural circulation systems. In order to experimentally study the natural circulation flow instability, a proper scaling methodology is needed to build a reduced-size test facility. The scaling analysis of the NMR uses a three-level scaling method, which was developed and applied for the design of the Purdue Multi-dimensional Integral Test Assembly (PUMA). Scaling criteria is derived from dimensionless field equations and constitutive equations. The scaling process is validated by the RELAP5 analysis for both steady state and startup transients. A new well-scaled natural circulation test facility is designed and constructed based on the scaling analysis of the NMR-50. The experimental facility is installed with different equipment to measure various thermal-hydraulic parameters such as pressure, temperature, mass flow rate and void fraction. Characterization tests are performed before the startup transient tests and quasi-steady tests to determine the loop flow resistance. The controlling system and data acquisition system are programmed with LabVIEW to realize the real-time control and data storage. The thermal-hydraulic and nuclear coupled startup transients are performed to investigate the flow instabilities at low pressure and low power conditions. Two different power ramps are chosen to study the effect of power density on the flow instability. The experimental startup transient tests show the existence of three different flow instability mechanisms during the low pressure startup transients, i.e., flashing instability, condensation induced instability, and density wave oscillations. Flashing instability in the chimney section of the test loop and density wave oscillation are the main flow instabilities observed when the system pressure is below 0.5 MPa. They show completely different type of oscillations, i.e., intermittent oscillation and sinusoidal oscillation, in void fraction profile during the startup transients. In order to perform nuclear-coupled startup transients with void reactivity feedback, the Point Kinetics model is utilized to calculate the transient power during the startup transients. In addition, the differences between the electric resistance heaters and typical fuel element are taken into account. The reactor power calculated shows some oscillations due to flashing instability during the transients. However, the void reactivity feedback does not have significant influence on the flow instability during the startup procedure for the NMR-50. Further investigation of very small power ramp on the startup transients is carried out for the thermal-hydraulic startup transients. It is found that very small power density can eliminate the flashing oscillation in the single phase natural circulation and stabilize the flow oscillations in the phase of net vapor generation. Furthermore, initially pressurized startup procedure is investigated to eliminate the main flow instabilities. The results show that the pressurized startup procedure can suppress the flashing instability at low pressure and low power conditions. In order to have a deep understanding of natural circulation flow instability, the quasi-steady tests are performed using the test facility installed with preheater and subcooler. The effects of system pressure, core inlet subcooling, core power density, inlet flow resistance coefficient, and void reactivity feedback are investigated in the quasi-steady state tests. The stability boundaries are determined between unstable and stable flow conditions in the dimensionless stability plane of inlet subcooling number and Zuber number. In order to predict the stability boundary theoretically, linear stability analysis in the frequency domain is performed at four sections of the loop. The flashing in the chimney is considered as an axially uniform heat source. The dimensionless characteristic equation of the pressure drop perturbation is obtained by considering the void fraction effect and outlet flow resistance in the chimney section. The flashing boundary shows some discrepancies with previous experimental data from the quasi-steady state tests. In the future, thermal non-equilibrium is recommended to improve the accuracy of flashing instability boundary.

Formation and dissolution of bacterial colonies.

PubMed

Weber, Christoph A; Lin, Yen Ting; Biais, Nicolas; Zaburdaev, Vasily

2015-09-01

Many organisms form colonies for a transient period of time to withstand environmental pressure. Bacterial biofilms are a prototypical example of such behavior. Despite significant interest across disciplines, physical mechanisms governing the formation and dissolution of bacterial colonies are still poorly understood. Starting from a kinetic description of motile and interacting cells we derive a hydrodynamic equation for their density on a surface, where most of the kinetic coefficients are estimated from experimental data for N. gonorrhoeae bacteria. We use it to describe the formation of multiple colonies with sizes consistent with experimental observations. Finally, we show how the changes in the cell-to-cell interactions lead to the dissolution of the bacterial colonies. The successful application of kinetic theory to a complex far from equilibrium system such as formation and dissolution of living bacterial colonies potentially paves the way for the physical quantification of the initial stages of biofilm formation.

Nonequilibrium phase coexistence and criticality near the second explosion limit of hydrogen combustion

NASA Astrophysics Data System (ADS)

Newcomb, Lucas B.; Alaghemandi, Mohammad; Green, Jason R.

2017-07-01

While hydrogen is a promising source of clean energy, the safety and optimization of hydrogen technologies rely on controlling ignition through explosion limits: pressure-temperature boundaries separating explosive behavior from comparatively slow burning. Here, we show that the emergent nonequilibrium chemistry of combustible mixtures can exhibit the quantitative features of a phase transition. With stochastic simulations of the chemical kinetics for a model mechanism of hydrogen combustion, we show that the boundaries marking explosive domains of kinetic behavior are nonequilibrium critical points. Near the pressure of the second explosion limit, these critical points terminate the transient coexistence of dynamical phases—one that autoignites and another that progresses slowly. Below the critical point temperature, the chemistry of these phases is indistinguishable. In the large system limit, the pseudo-critical temperature converges to the temperature of the second explosion limit derived from mass-action kinetics.

Crystal nucleation in amorphous (Au/100-y/Cu/y/)77Si9Ge14 alloys

NASA Technical Reports Server (NTRS)

Thompson, C. V.; Greer, A. L.; Spaepen, F.

1983-01-01

Because, unlike most metallic glasses, melt-spun alloys of the series (Au/100-y/Cu/y/)77Si9Ge14 exhibit well separated glass transition and kinetic crystallization temperatures, crystallization can be studied in the fully relaxed amorphous phase. An isothermal calorimetric analysis of the devitrification kinetics of the amorphous alloy indicates sporadic nucleation and a constant growth rate. It is found for the cases of alloys with y values lower than 25 that the classical theory of homogeneous nucleation is consistent with observations, including transient effects. An analysis of the crystallization kinetics shows that slow crystal growth rates play an important role in glass formation in these alloys. Although the reduced glass transition temperature increases with Cu content, glass formation is more difficult at high Cu contents, perhaps because of a difference in nucleus composition.

Pressure dependence of the photocycle kinetics of bacteriorhodopsin.

PubMed Central

Klink, B U; Winter, R; Engelhard, M; Chizhov, I

2002-01-01

The pressure dependence of the photocycle kinetics of bacteriorhodopsin from Halobacterium salinarium was investigated at pressures up to 4 kbar at 25 degrees C and 40 degrees C. The kinetics can be adequately modeled by nine apparent rate constants, which are assigned to irreversible transitions of a single relaxation chain of nine kinetically distinguishable states P(1) to P(9). All states except P(1) and P(9) consist of two or more spectral components. The kinetic states P(2) to P(6) comprise only the two fast equilibrating spectral states L and M. From the pressure dependence, the volume differences DeltaV(o)(LM) between these two spectral states could be determined that range from DeltaV(o)(LM) = -11.4 +/- 0.7 ml/mol (P(2)) to DeltaV(o)(LM) = 14.6 +/- 2.8 mL/mol (P(6)). A model is developed that explains the dependence of DeltaV(o)(LM) on the kinetic state by the electrostriction effect of charges, which are formed and neutralized during the L/M transition. PMID:12496115

Do fluorescence and transient absorption probe the same intramolecular charge transfer state of 4-(dimethylamino)benzonitrile?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gustavsson, Thomas; Coto, Pedro B.; Serrano-Andres, Luis

2009-07-21

We present here the results of time-resolved absorption and emission experiments for 4-(dimethylamino)benzonitrile in solution, which suggest that the fluorescent intramolecular charge transfer (ICT) state may differ from the twisted ICT (TICT) state observed in transient absorption.

Transient Electromagnetic Wave Propagation in a Plasma Waveguide

DTIC Science & Technology

2011-10-24

dielectric. The calculation of the propagation characteristics is based upon tangential continuity of the electric and magnetic field components...filament as a time-dependent resistance , we have determined the electron density, the kinetic parameters for electron attachment and recombination, and...wall conductivity simplifies the imposition of the boundary conditions. The tangential component of the electric field and the normal component of the

Transient spatiotemporal chaos in the Morris-Lecar neuronal ring network.

PubMed

Keplinger, Keegan; Wackerbauer, Renate

2014-03-01

Transient behavior is thought to play an integral role in brain functionality. Numerical simulations of the firing activity of diffusively coupled, excitable Morris-Lecar neurons reveal transient spatiotemporal chaos in the parameter regime below the saddle-node on invariant circle bifurcation point. The neighborhood of the chaotic saddle is reached through perturbations of the rest state, in which few initially active neurons at an effective spatial distance can initiate spatiotemporal chaos. The system escapes from the neighborhood of the chaotic saddle to either the rest state or to a state of pulse propagation. The lifetime of the chaotic transients is manipulated in a statistical sense through a singular application of a synchronous perturbation to a group of neurons.

Transient Mass-loss Analysis of Solar Observations Using Stellar Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crosley, M. K.; Norman, C.; Osten, R. A.

Low-frequency dynamic spectra of radio bursts from nearby stars offer the best chance to directly detect the stellar signature of transient mass loss on low-mass stars. Crosley et al. (2016) proposes a multi-wavelength methodology to determine coronal mass ejection (CME) parameters, such as speed, mass, and kinetic energy. We test the validity and accuracy of the results derived from the methodology by using Geostationary Operational Environmental Satellite X-ray observations and Bruny Island Radio Spectrometer radio observations. These are analogous observations to those that would be found in the stellar studies. Derived results from these observations are compared to direct whitemore » light measurements of the Large Angle and Spectrometric Coronagraph. We find that, when a pre-event temperature can be determined, the accuracy of CME speeds are within a few hundred km s{sup −1}, and are reliable when specific criteria has been met. CME mass and kinetic energies are only useful in determining the approximate order of magnitude measurements when considering the large errors associated to them. These results will be directly applicable to the interpretation of any detected stellar events and the derivation of stellar CME properties.« less

Three H₂O₂ molecules are involved in the "Fenton-like" reaction between Co(H₂O)₆²⁺ and H₂O₂.

PubMed

Burg, Ariela; Shusterman, Inna; Kornweitz, Haya; Meyerstein, Dan

2014-06-28

Co(II) complexes and Co(H2O)6(2+) are used as catalysts in advanced oxidation processes. Therefore it was decided to study the kinetics of reaction of Co(H2O)6(2+) with H2O2. Surprisingly, the kinetic results point out that the process involves three consecutive reactions, each of them requiring an H2O2 molecule, i.e. three H2O2 molecules ligate to the central cobalt cation prior to the formation of radicals. DFT analysis suggests that the transient (H2O)3Co(II)(OOH)2(H2O2) decomposes via: (H2O)3Co(II)(OOH)2(H2O2) → (H2O)3Co(II)(OOH)(˙OOH)(OH) + ˙OH ΔG(0) = -5.975 kcal mol(-1), with no evidence for the formation of a Co(III) transient. It is proposed that analogous mechanisms are involved whenever the redox potential of the central cation is too high to enable the reaction: M(H2O)6(n+) + H2O2 → M((n+1)+)aq + ˙OH + OH(-).

The variability, structure and energy conversion of the northern hemisphere traveling waves simulated in a Mars general circulation model

NASA Astrophysics Data System (ADS)

Wang, Huiqun; Toigo, Anthony D.

2016-06-01

Investigations of the variability, structure and energetics of the m = 1-3 traveling waves in the northern hemisphere of Mars are conducted with the MarsWRF general circulation model. Using a simple, annually repeatable dust scenario, the model reproduces many general characteristics of the observed traveling waves. The simulated m = 1 and m = 3 traveling waves show large differences in terms of their structures and energetics. For each representative wave mode, the geopotential signature maximizes at a higher altitude than the temperature signature, and the wave energetics suggests a mixed baroclinic-barotropic nature. There is a large contrast in wave energetics between the near-surface and higher altitudes, as well as between the lower latitudes and higher latitudes at high altitudes. Both barotropic and baroclinic conversions can act as either sources or sinks of eddy kinetic energy. Band-pass filtered transient eddies exhibit strong zonal variations in eddy kinetic energy and various energy transfer terms. Transient eddies are mainly interacting with the time mean flow. However, there appear to be non-negligible wave-wave interactions associated with wave mode transitions. These interactions include those between traveling waves and thermal tides and those among traveling waves.

Transient swelling behavior and drug delivery from a dissolving film deploying anti-HIV microbicide

NASA Astrophysics Data System (ADS)

Tasoglu, Savas; Katz, David F.; Szeri, Andrew J.

2010-11-01

Despite more than two decades of HIV vaccine research, there is still no efficacious HIV vaccine. Very recently, a research group has shown that a microbicide gel formulation of antiretroviral drug Tenofovir, significantly inhibits HIV transmission to women [1]. However, there is a widespread agreement that more effective and diverse drug delivery vehicles must be developed. In this setting, there is now great interest in developing different delivery vehicles such as vaginal rings, gels, and films. Here, we develop a model for transient fluid uptake and swelling behavior, and subsequent dissolution and drug deployment from a film containing anti-HIV microbicide. In the model, the polymer structural relaxation via water uptake is assumed to follow first order kinetics. In the case of a film loaded with an osmotically active solute, the kinetic equation is modified to account for the osmotic effect. The transport rate of solvent and solute within the matrix is characterized by a diffusion equation. After the matrix is relaxed to a specified concentration of solvent, lubrication theory and convective-diffusive transport are employed for flow of the liquefied matrix and drug dispersion respectively. [1] Karim, et al., Science, 2010.

A simplified model for tritium permeation transient predictions when trapping is active*1

NASA Astrophysics Data System (ADS)

Longhurst, G. R.

1994-09-01

This report describes a simplified one-dimensional tritium permeation and retention model. The model makes use of the same physical mechanisms as more sophisticated, time-transient codes such as implantation, recombination, diffusion, trapping and thermal gradient effects. It takes advantage of a number of simplifications and approximations to solve the steady-state problem and then provides interpolating functions to make estimates of intermediate states based on the steady-state solution. Comparison calculations with the verified and validated TMAP4 transient code show good agreement.

Intramolecular charge transfer of 4-(dimethylamino)benzonitrile probed by time-resolved fluorescence and transient absorption: No evidence for two ICT states and a {pi}{sigma}{sup *} reaction intermediate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zachariasse, Klaas A.; Druzhinin, Sergey I.; Senyushkina, Tamara

2009-12-14

For the double exponential fluorescence decays of the locally excited (LE) and intramolecular charge transfer (ICT) states of 4-(dimethylamino)benzonitrile (DMABN) in acetonitrile (MeCN) the same times {tau}{sub 1} and {tau}{sub 2} are observed. This means that the reversible LE<-->ICT reaction, starting from the initially excited LE state, can be adequately described by a two state mechanism. The most important factor responsible for the sometimes experimentally observed differences in the nanosecond decay time, with {tau}{sub 1}(LE)<{tau}{sub 1}(ICT), is photoproduct formation. By employing a global analysis of the LE and ICT fluorescence response functions with a time resolution of 0.5 ps/channel inmore » 1200 channels reliable kinetic and thermodynamic data can be obtained. The arguments presented in the literature in favor of a {pi}{sigma}* state with a bent CN group as an intermediate in the ICT reaction of DMABN are discussed. From the appearance of an excited state absorption (ESA) band in the spectral region between 700 and 800 nm in MeCN for N,N-dimethylanilines with CN, Br, F, CF{sub 3}, and C(=O)OC{sub 2}H{sub 2} p-substituents, it is concluded that this ESA band cannot be attributed to a {pi}{sigma}{sup *} state, as only the C-C{identical_to}N group can undergo the required 120 deg. bending.« less

LMFBR system-wide transient analysis: the state of the art and US validation needs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khatib-Rahbar, M.; Guppy, J.G.; Cerbone, R.J.

1982-01-01

This paper summarizes the computational capabilities in the area of liquid metal fast breeder reactor (LMFBR) system-wide transient analysis in the United States, identifies various numerical and physical approximations, the degree of empiricism, range of applicability, model verification and experimental needs for a wide class of protected transients, in particular, natural circulation shutdown heat removal for both loop- and pool-type plants.

Excitation of photosystem I by 760 nm femtosecond laser pulses: transient absorption spectra and intermediates

NASA Astrophysics Data System (ADS)

Cherepanov, Dmitry A.; Shelaev, Ivan V.; Gostev, Fedor E.; Mamedov, Mahir D.; Petrova, Anastasia A.; Aybush, Arseniy V.; Shuvalov, Vladimir A.; Semenov, Alexey Yu; Nadtochenko, Victor A.

2017-09-01

Excitation of photosystem I (PS I) by a femtosecond 760 nm pump leads to one- and two-photon absorption. The one-photon excitation produces intermediates with transient absorption spectra similar to the spectra of the primary [{{{P}}700}+{{{A}}0}-{{A}}1] and secondary [{{{P}}700}+{{A}}0{{{A}}1}-] ion-radical pairs in the PS I reaction center. The two-photon absorption generates the upper level excited states of chlorophyll (Chl) and carotenoid molecules in the antenna. These excited states are converted into the long-lived intermediates and can be tentatively attributed to the excited and charge-transfer ion-radical states of Chl molecules and to the excited states of carotenoids in the antenna. The transient spectra of intermediates generated by two-photon excitation differ from the transient one-photon spectra of the primary and secondary ion-radical pairs.

Analysis of transient fission gas behaviour in oxide fuel using BISON and TRANSURANUS

DOE PAGES

Barani, T.; Bruschi, E.; Pizzocri, D.; ...

2017-01-03

The modelling of fission gas behaviour is a crucial aspect of nuclear fuel analysis in view of the related effects on the thermo-mechanical performance of the fuel rod, which can be particularly significant during transients. Experimental observations indicate that substantial fission gas release (FGR) can occur on a small time scale during transients (burst release). To accurately reproduce the rapid kinetics of burst release in fuel performance calculations, a model that accounts for non-diffusional mechanisms such as fuel micro-cracking is needed. In this work, we present and assess a model for transient fission gas behaviour in oxide fuel, which ismore » applied as an extension of diffusion-based models to allow for the burst release effect. The concept and governing equations of the model are presented, and the effect of the newly introduced parameters is evaluated through an analytic sensitivity analysis. Then, the model is assessed for application to integral fuel rod analysis. The approach that we take for model assessment involves implementation in two structurally different fuel performance codes, namely, BISON (multi-dimensional finite element code) and TRANSURANUS (1.5D semi-analytic code). The model is validated against 19 Light Water Reactor fuel rod irradiation experiments from the OECD/NEA IFPE (International Fuel Performance Experiments) database, all of which are simulated with both codes. The results point out an improvement in both the qualitative representation of the FGR kinetics and the quantitative predictions of integral fuel rod FGR, relative to the canonical, purely diffusion-based models, with both codes. The overall quantitative improvement of the FGR predictions in the two codes is comparable. Furthermore, calculated radial profiles of xenon concentration are investigated and compared to experimental data, demonstrating the representation of the underlying mechanisms of burst release by the new model.« less

Persistent order due to transiently enhanced nesting in an electronically excited charge density wave

DOE PAGES

Rettig, L.; Cortés, R.; Chu, J. -H.; ...

2016-01-25

Non-equilibrium conditions may lead to novel properties of materials with broken symmetry ground states not accessible in equilibrium as vividly demonstrated by non-linearly driven mid-infrared active phonon excitation. Potential energy surfaces of electronically excited states also allow to direct nuclear motion, but relaxation of the excess energy typically excites fluctuations leading to a reduced or even vanishing order parameter as characterized by an electronic energy gap. Here, using femtosecond time-and angle-resolved photoemission spectroscopy, we demonstrate a tendency towards transient stabilization of a charge density wave after near-infrared excitation, counteracting the suppression of order in the non-equilibrium state. Analysis of themore » dynamic electronic structure reveals a remaining energy gap in a highly excited transient state. In conclusion, our observation can be explained by a competition between fluctuations in the electronically excited state, which tend to reduce order, and transiently enhanced Fermi surface nesting stabilizing the order.« less

Using steady-state equations for transient flow calculation in natural gas pipelines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maddox, R.N.; Zhou, P.

1984-04-02

Maddox and Zhou have extended their technique for calculating the unsteady-state behavior of straight gas pipelines to complex pipeline systems and networks. After developing the steady-state flow rate and pressure profile for each pipe in the network, analysts can perform the transient-state analysis in the real-time step-wise manner described for this technique.

Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design.

PubMed

Kekilli, Demet; Petersen, Christine A; Pixton, David A; Ghafoor, Dlzar D; Abdullah, Gaylany H; Dworkowski, Florian S N; Wilson, Michael T; Heyes, Derren J; Hardman, Samantha J O; Murphy, Loretta M; Strange, Richard W; Scrutton, Nigel S; Andrew, Colin R; Hough, Michael A

2017-03-01

Proximal vs. distal heme-NO coordination is a novel strategy for selective gas response in heme-based NO-sensors. In the case of Alcaligenes xylosoxidans cytochrome c' (AXCP), formation of a transient distal 6cNO complex is followed by scission of the trans Fe-His bond and conversion to a proximal 5cNO product via a putative dinitrosyl species. Here we show that replacement of the AXCP distal Leu16 residue with smaller or similar sized residues (Ala, Val or Ile) traps the distal 6cNO complex, whereas Leu or Phe residues lead to a proximal 5cNO product with a transient or non-detectable distal 6cNO precursor. Crystallographic, spectroscopic, and kinetic measurements of 6cNO AXCP complexes show that increased distal steric hindrance leads to distortion of the Fe-N-O angle and flipping of the heme 7-propionate. However, it is the kinetic parameters of the distal NO ligand that determine whether 6cNO or proximal 5cNO end products are formed. Our data support a 'balance of affinities' mechanism in which proximal 5cNO coordination depends on relatively rapid release of the distal NO from the dinitrosyl precursor. This mechanism, which is applicable to other proteins that form transient dinitrosyls, represents a novel strategy for 5cNO formation that does not rely on an inherently weak Fe-His bond. Our data suggest a general means of engineering selective gas response into biologically-derived gas sensors in synthetic biology.

Nucleation and growth kinetics of electrodeposited sulfate-doped polypyrrole: determination of the diffusion coefficient of SO(4)(2-) in the polymeric membrane.

PubMed

Licona-Sánchez, T de J; Alvarez-Romero, G A; Mendoza-Huizar, L H; Galán-Vidal, C A; Palomar-Pardavé, M; Romero-Romo, M; Herrera-Hernández, H; Uruchurtu, J; Juárez-García, J M

2010-08-05

A kinetic study for the electrosynthesis of polypyrrole (Ppy) doped with SO(4)(2-) ions is presented. Ppy films were electrochemically polymerized onto a graphite-epoxy resin electrode. Experimental current density transients (j-t) were obtained for three different potentiometric behaviors: anionic, cationic, and a combination. Theoretical models were used to fit the experimental j-t data to determine the nucleation and growth processes controlling the polymer synthesis. It was encountered that, in all cases, pyrrole electropolimerization involves two concomitant processes, namely, a Ppy diffusion limited multiple 3D nucleation and growth and pyrrole electro-oxidation on the growing surface of the Ppy nuclei. SEM analysis of the electrodes surfaces reveals that Ppy deposition occurred over most of the electrode surface by multiple nucleation of hemispheres, as the theoretical model used for the analysis of the current transients required. Hemispherical particles formed the polymeric film displaying different sizes. The order for the particle size was as follows: anionic > anionic-cationic > cationic. These results are congruent with those obtained by theoretical analysis of the corresponding current transients. Analysis of the impedance measurements recorded on the anionic Ppy film, immersed in an aqueous solution with different sulfate ion concentrations evidenced that SO(4)(2-) ions diffuse through the Ppy film provoking a decrease of its electrical resistance and an increase of its dielectric constant. From the Warburg impedance coefficient, the sulfate coefficient of diffusion in the Ppy film was 1.38 x 10(-9) cm(2) s(-1).

The Kinetic Mechanism for DNA Unwinding by Multiple Molecules of Dda Helicase Aligned on DNA†

PubMed Central

Eoff, Robert L.; Raney, Kevin D.

2010-01-01

Helicases catalyze the separation of double-stranded nucleic acids to form single-stranded intermediates. Using transient state kinetic methods we have determined the kinetic properties of DNA unwinding under conditions that favor a monomeric form of the Dda helicase as well as conditions that allow multiple molecules to function on the same substrate. Multiple helicase molecules can align like a train on the DNA track. The number of base pairs unwound in a single binding event for Dda is increased from ~19 bp for the monomeric form to ~64 bp when as many as four Dda molecules are aligned on the same substrate, while the kinetic step-size (3.2 ± 0.7 bp) and unwinding rate (242 ± 25 bp s−1) appear to be independent of the number of Dda molecules present on a given substrate. The data support a model in which the helicase molecules bound to the same substrate move along the DNA track independently during DNA unwinding. The observed increase in processivity arises from the increased probability that at least one of the helicases will completely unwind the DNA prior to dissociation. These results are in contrast to previous reports in which multiple Dda molecules on the same track greatly enhanced the rate and amplitude for displacement of protein blocks on the track. Therefore, only when the progress of the lead molecule in the train is impeded by some type of block, such as a protein bound to DNA, do the trailing molecules interact with the lead molecule in order to overcome the block. The fact that trailing helicase molecules have little impact on the lead molecule in the train during routine DNA unwinding suggests that the trailing molecules are moving at similar rates as the lead molecule. This result implicates a step in the translocation mechanism as contributing greatly to the overall rate-limiting step for unwinding of duplex DNA. PMID:20408588

New core-reflector boundary conditions for transient nodal reactor calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, E.K.; Kim, C.H.; Joo, H.K.

1995-09-01

New core-reflector boundary conditions designed for the exclusion of the reflector region in transient nodal reactor calculations are formulated. Spatially flat frequency approximations for the temporal neutron behavior and two types of transverse leakage approximations in the reflector region are introduced to solve the transverse-integrated time-dependent one-dimensional diffusion equation and then to obtain relationships between net current and flux at the core-reflector interfaces. To examine the effectiveness of new core-reflector boundary conditions in transient nodal reactor computations, nodal expansion method (NEM) computations with and without explicit representation of the reflector are performed for Laboratorium fuer Reaktorregelung und Anlagen (LRA) boilingmore » water reactor (BWR) and Nuclear Energy Agency Committee on Reactor Physics (NEACRP) pressurized water reactor (PWR) rod ejection kinetics benchmark problems. Good agreement between two NEM computations is demonstrated in all the important transient parameters of two benchmark problems. A significant amount of CPU time saving is also demonstrated with the boundary condition model with transverse leakage (BCMTL) approximations in the reflector region. In the three-dimensional LRA BWR, the BCMTL and the explicit reflector model computations differ by {approximately}4% in transient peak power density while the BCMTL results in >40% of CPU time saving by excluding both the axial and the radial reflector regions from explicit computational nodes. In the NEACRP PWR problem, which includes six different transient cases, the largest difference is 24.4% in the transient maximum power in the one-node-per-assembly B1 transient results. This difference in the transient maximum power of the B1 case is shown to reduce to 11.7% in the four-node-per-assembly computations. As for the computing time, BCMTL is shown to reduce the CPU time >20% in all six transient cases of the NEACRP PWR.« less

Usefulness of cardiotoxicity assessment using calcium transient in human induced pluripotent stem cell-derived cardiomyocytes.

PubMed

Watanabe, Hitoshi; Honda, Yayoi; Deguchi, Jiro; Yamada, Toru; Bando, Kiyoko

2017-01-01

Monitoring dramatic changes in intracellular calcium ion levels during cardiac contraction and relaxation, known as calcium transient, in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) would be an attractive strategy for assessing compounds on cardiac contractility. In addition, as arrhythmogenic compounds are known to induce characteristic waveform changes in hiPSC-CMs, it is expected that calcium transient would allow evaluation of not only compound-induced effects on cardiac contractility, but also compound arrhythmogenic potential. Using a combination of calcium transient in hiPSC-CMs and a fast kinetic fluorescence imaging detection system, we examined in this study changes in calcium transient waveforms induced by a series of 17 compounds that include positive/negative inotropic agents as well as cardiac ion channel activators/inhibitors. We found that all positive inotropic compounds induced an increase in peak frequency and/or peak amplitude. The effects of a negative inotropic compound could clearly be detected in the presence of a β-adrenergic receptor agonist. Furthermore, most arrhythmogenic compounds raised the ratio of peak decay time to peak rise time (D/R ratio) in calcium transient waveforms. Compound concentrations at which these parameters exceeded cutoff values correlated well with systemic exposure levels at which arrhythmias were reported to be evoked. In conclusion, we believe that peak analysis of calcium transient and determination of D/R ratio are reliable methods for assessing compounds' cardiac contractility and arrhythmogenic potential, respectively. Using these approaches would allow selection of compounds with low cardiotoxic potential at the early stage of drug discovery.

Blood-testis barrier dynamics are regulated by testosterone and cytokines via their differential effects on the kinetics of protein endocytosis and recycling in Sertoli cells

PubMed Central

Yan, Helen H. N.; Mruk, Dolores D.; Lee, Will M.; Cheng, C. Yan

2009-01-01

During spermatogenesis in the mammalian testis, preleptotene/leptotene spermatocytes differentiate from type B spermatogonia and traverse the blood-testis barrier (BTB) at stage VIII of the seminiferous epithelial cycle for further development. This timely movement of germ cells involves extensive junction restructuring at the BTB. Previous studies have shown that these events are regulated by testosterone (T) and cytokines [e.g., the transforming growth factor (TGF) -βs], which promote and disrupt the BTB assembly, respectively. However, the mechanisms underlying the “opening” of the BTB above a migrating preleptotene/leptotene spermatocyte and the “resealing” of the barrier underneath this cell remain obscure. We now report findings on a novel mechanism utilized by the testes to regulate these events. Using cell surface protein biotinylation coupled with immunoblotting and immunofluorescent microscopy, we assessed the kinetics of endocytosis and recycling of BTB-associated integral membrane proteins: occludin, JAM-A, and N-cadherin. It was shown that these proteins were continuously endocytosed and recycled back to the Sertoli cell surface via the clathrin-mediated but not the caveolin-mediated pathway. When T or TGF-β2 was added to Sertoli cell cultures with established functional BTB, both factors accelerated the kinetics of internalization of BTB proteins from the cell surface, perhaps above the migrating preleptotene spermatocyte, thereby opening the BTB. Likewise, T also enhanced the kinetics of recycling of internalized biotinylated proteins back to the cell surface, plausibly relocating these proteins beneath the migrating spermatocyte to reassemble the BTB. In contrast, TGF-β2 targeted internalized biotinylated proteins to late endosomes for degradation, destabilizing the BTB. In summary, the transient opening of the BTB that facilitates germ cell movement is mediated via the differential effects of T and cytokines on the kinetics of endocytosis and recycling of integral membrane proteins at the BTB. The net result of these interactions, in turn, determines the steady-state protein levels at the Sertoli-Sertoli cell interface at the BTB. PMID:18192323

Perfluorinated Surfactant Chain-Length Effects on Sonochemical Kinetics

NASA Astrophysics Data System (ADS)

Campbell, Tammy Y.; Vecitis, Chad D.; Mader, Brian T.; Hoffmann, Michael R.

2009-08-01

The sonochemical degradation kinetics of the aqueous perfluorochemicals (PFCs) perfluorobutanoate (PFBA), perfluorobutanesulfonate (PFBS), perfluorohexanoate (PFHA), and perfluorohexanesulfonate (PFHS) have been investigated. Surface tension measurements were used to evaluate chain-length effects on equilibrium air-water interface partitioning. The PFC air-water interface partitioning coefficients, KeqPF, and maximum surface concentrations, ΓmaxPF, were determined from the surface pressure equation of state for PFBA, PFBS, PFHA, and PFHS. Relative KeqPF values were dependent upon chain length KeqPFHS ≅ 2.1KeqPFHA ≅ 3.9KeqPFBS ≅ 5.0KeqPFBA, whereas relative ΓmaxPF values had minimal chain length dependence ΓmaxPFHS ≅ ΓmaxPFHA ≅ ΓmaxPFBS ≅ 2.2ΓmaxPFBA. The rates of sonolytic degradation were determined over a range of frequencies from 202 to 1060 kHz at dilute (<1 μM) initial PFC concentrations and are compared to previously reported results for their C8 analogs: perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA). Under all conditions, the time-dependent PFC sonolytic degradation was observed to follow pseudo-first-order kinetics, i.e., below kinetic saturation, suggesting bubble-water interface populations were significantly below the adsorption maximum. The PFHX (where X = A or S) sonolysis rate constant was observed to peak at an ultrasonic frequency of 358 kHz, similar to that for PFOX. In contrast, the PFBX degradation rate constants had an apparent maximum at 610 kHz. Degradation rates observed for PFHX are similar to previously determined PFOX rates, kapp,358PFOX ≅ kapp,358PFHX. PFOX is sonolytically pyrolyzed at the transiently cavitating bubble-water interface, suggesting that rates should be proportional to equilibrium interfacial partitioning. However, relative equilibrium air-water interfacial partitioning predicts that KeqPFOX ≅ 5KeqPFHX. This suggests that at dilute PFC concentrations, adsorption to the bubble-water interface is ultrasonically enhanced due to high-velocity radial bubble oscillations. PFC sonochemical kinetics are slower for PFBS and further diminished for PFBA as compared to longer analogs, suggesting that PFBX surface films are of lower stability due to their greater water solubility.

Nascent RNA kinetics: Transient and steady state behavior of models of transcription

NASA Astrophysics Data System (ADS)

Choubey, Sandeep

2018-02-01

Regulation of transcription is a vital process in cells, but mechanistic details of this regulation still remain elusive. The dominant approach to unravel the dynamics of transcriptional regulation is to first develop mathematical models of transcription and then experimentally test the predictions these models make for the distribution of mRNA and protein molecules at the individual cell level. However, these measurements are affected by a multitude of downstream processes which make it difficult to interpret the measurements. Recent experimental advancements allow for counting the nascent mRNA number of a gene as a function of time at the single-inglr cell level. These measurements closely reflect the dynamics of transcription. In this paper, we consider a general mechanism of transcription with stochastic initiation and deterministic elongation and probe its impact on the temporal behavior of nascent RNA levels. Using techniques from queueing theory, we derive exact analytical expressions for the mean and variance of the nascent RNA distribution as functions of time. We apply these analytical results to obtain the mean and variance of nascent RNA distribution for specific models of transcription. These models of initiation exhibit qualitatively distinct transient behaviors for both the mean and variance which further allows us to discriminate between them. Stochastic simulations confirm these results. Overall the analytical results presented here provide the necessary tools to connect mechanisms of transcription initiation to single-cell measurements of nascent RNA.

Sulfidation of 310 stainless steel at sulfur potentials encountered in coal conversion systems

NASA Technical Reports Server (NTRS)

Rao, D. B.; Nelson, H. G.

1976-01-01

The sulfidation of SAE 310 stainless steel was carried out in gas mixtures of hydrogen and hydrogen sulfide over a range of sulfur potentials anticipated in advanced coal gasification processes. The kinetics, composition, and morphology of sulfide scale formation were studied at a fixed temperature of 1,065 K over a range of sulfur potentials from .00015 Nm to the -2nd power to 900 Nm to the -2nd power. At all sulfur potentials investigated, the sulfide scales were found to be multilayered. The relative thickness of the individual layers as well as the composition was found to depend on the sulfur potential. The reaction was found to obey the parabolic rate law after an initial transient period. Considerably longer transient periods were found to be due to unsteady state conditions resulting from compositional variations in the spinel layer. The sulfur pressure dependence on the parabolic rate constant was found to best fit the equation K sub p equals const. (P sub S2) to the 1/nth power, where n equals 3.7. The growth of the outer layers was found to be primarily due to the diffusion of metal ions, iron being the predominant species. The inner layer growth was due to the dissociation of the primary product at the alloy scale interface and depended on the activity of chromium.

Multiple stable isotope fronts during non-isothermal fluid flow

NASA Astrophysics Data System (ADS)

Fekete, Szandra; Weis, Philipp; Scott, Samuel; Driesner, Thomas

2018-02-01

Stable isotope signatures of oxygen, hydrogen and other elements in minerals from hydrothermal veins and metasomatized host rocks are widely used to investigate fluid sources and paths. Previous theoretical studies mostly focused on analyzing stable isotope fronts developing during single-phase, isothermal fluid flow. In this study, numerical simulations were performed to assess how temperature changes, transport phenomena, kinetic vs. equilibrium isotope exchange, and isotopic source signals determine mineral oxygen isotopic compositions during fluid-rock interaction. The simulations focus on one-dimensional scenarios, with non-isothermal single- and two-phase fluid flow, and include the effects of quartz precipitation and dissolution. If isotope exchange between fluid and mineral is fast, a previously unrecognized, significant enrichment in heavy oxygen isotopes of fluids and minerals occurs at the thermal front. The maximum enrichment depends on the initial isotopic composition of fluid and mineral, the fluid-rock ratio and the maximum change in temperature, but is independent of the isotopic composition of the incoming fluid. This thermally induced isotope front propagates faster than the signal related to the initial isotopic composition of the incoming fluid, which forms a trailing front behind the zone of transient heavy oxygen isotope enrichment. Temperature-dependent kinetic rates of isotope exchange between fluid and rock strongly influence the degree of enrichment at the thermal front. In systems where initial isotope values of fluids and rocks are far from equilibrium and isotope fractionation is controlled by kinetics, the temperature increase accelerates the approach of the fluid to equilibrium conditions with the host rock. Consequently, the increase at the thermal front can be less dominant and can even generate fluid values below the initial isotopic composition of the input fluid. As kinetics limit the degree of isotope exchange, a third front may develop in kinetically limited systems, which propagates with the advection speed of the incoming fluid and is, therefore, traveling fastest. The results show that oxygen isotope signatures at thermal fronts recorded in rocks and veins that experienced isotope exchange with fluids can easily be misinterpreted, namely if bulk analytical techniques are applied. However, stable isotope microanalysis on precipitated minerals may - if later isotope exchange is kinetically limited - provide a valuable archive of the transient thermal and hydrological evolution of a system.

Exercise intensity and oxygen uptake kinetics in African-American and Caucasian women.

PubMed

Lai, Nicola; Tolentino-Silva, Fatima; Nasca, Melita M; Silva, Marco A; Gladden, L Bruce; Cabrera, Marco E

2012-03-01

The effect of exercise intensity on the on- and off-transient kinetics of oxygen uptake (VO(2)) was investigated in African American (AA) and Caucasian (C) women. African American (n = 7) and Caucasian (n = 6) women of similar age, body mass index and weight, performed an incremental test and bouts of square-wave exercise at moderate, heavy and very heavy intensities on a cycle ergometer. Gas exchange threshold (LT(GE)) was lower in AA (13.6 ± 2.3 mL kg(-1) min(-1)) than C (18.6 ± 5.6 mL kg(-1) min(-1)). The dynamic exercise and recovery VO(2) responses were characterized by mathematical models. There were no significant differences in (1) peak oxygen uptake (VO(2peak)) between AA (28.5 ± 5 mL kg(-1) min(-1)) and C (31.1 ± 6.6 mL kg(-1) min(-1)) and (2) VO(2) kinetics at any exercise intensity. At moderate exercise, the on- and off- VO(2) kinetics was described by a monoexponential function with similar time constants τ (1,on) (39.4 ± 12.5; 38.8 ± 15 s) and τ (1,off) (52.7 ± 10.1; 40.7 ± 4.4 s) for AA and C, respectively. At heavy and very heavy exercise, the VO(2) kinetics was described by a double-exponential function. The parameter values for heavy and very heavy exercise in the AA group were, respectively: τ (1,on) (47.0 ± 10.8; 44.3 ± 10 s), τ (2,on) (289 ± 63; 219 ± 90 s), τ (1,off) (45.9 ± 6.2; 50.7 ± 10 s), τ (2,off) (259 ± 120; 243 ± 93 s) while in the C group were, respectively: τ (1,on) (41 ± 12; 43.2 ± 15 s); τ (2, on) (277 ± 81; 215 ± 36 s), τ (1,off) (40.2 ± 3.4; 42.3 ± 7.2 s), τ (2,off) (215 ± 133; 228 ± 64 s). The on- and off-transients were symmetrical with respect to model order and dependent on exercise intensity regardless of race. Despite similar VO(2) kinetics, LT(GE) and gain of the VO(2) on-kinetics at moderate intensity were lower in AA than C. However, generalization to the African American and Caucasian populations is constrained by the small subject numbers.

Chemical Control of Charge Trapping and Charge Transfer Processes at the Organic-Inorganic Interface within Quantum Dot-Organic Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weiss, Emily A.

Within the research program funded through the Early Career Research Award we designed complexes of colloidal semiconductor quantum dots (QDs) and organic molecules in which the interfacial chemistry controls the electronic structure and dynamics of the excitonic state of the QD. The program included two main projects; (1) investigation of the mechanisms by which organic surfactants control the quantum confinement of excitonic charge carriers; and (2) development of models for electron transfer between QDs and adsorbed molecules as a function of interfacial chemistry. This project was extremely successful in that our achievements in those two areas addressed the great majoritymore » of questions we outlined in the original proposal and answered questions I did not think to ask in that original proposal. Our work led to the discovery of “exciton delocalizing ligands”, which change the electronic structure of colloidal semiconductor nanocrystals by altering, with small synthetic modifications to their surfaces, their most defining characteristic – the quantum confinement of their excited states. It also led to detailed, quantitative descriptions of how the surface chemistry of a QD dictates, thermodynamically and kinetically, the probability of exchange of electrons between the QD and a small molecule. We used two of the three major techniques in the proposal (transient photoluminescence and transient absorption). Electrogenerated chemiluminescence was also proposed, but was too technically difficult with these systems to be useful. Instead, NMR spectroscopy emerged as a major analytical tool in our studies. With the fundamental advancements we made with this project, we believe that we can design QDs to be the next great class of visible-light photocatalysts.« less

Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH.

PubMed

Ding, Yun; Fleming, Aaron M; He, Lidong; Burrows, Cynthia J

2015-07-22

Cytosine (C)-rich DNA can adopt i-motif folds under acidic conditions, with the human telomere i-motif providing a well-studied example. The dimensions of this i-motif are appropriate for capture in the nanocavity of the α-hemolysin (α-HL) protein pore under an electrophoretic force. Interrogation of the current vs time (i-t) traces when the i-motif interacts with α-HL identified characteristic signals that were pH dependent. These features were evaluated from pH 5.0 to 7.2, a region surrounding the transition pH of the i-motif (6.1). When the i-motif without polynucleotide tails was studied at pH 5.0, the folded structure entered the nanocavity of α-HL from either the top or bottom face to yield characteristic current patterns. Addition of a 5' 25-mer poly-2'-deoxyadensosine tail allowed capture of the i-motif from the unfolded terminus, and this was used to analyze the pH dependency of unfolding. At pH values below the transition point, only folded strands were observed, and when the pH was increased above the transition pH, the number of folded events decreased, while the unfolded events increased. At pH 6.8 and 7.2 4% and 2% of the strands were still folded, respectively. The lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms, respectively, at 160 mV electrophoretic force. These lifetimes are sufficiently long to affect enzymes operating on DNA. Furthermore, these transient lifetimes are readily obtained using the α-HL nanopore, a feature that is not easily achievable by other methods.

Low light adaptation: energy transfer processes in different types of light harvesting complexes from Rhodopseudomonas palustris.

PubMed

Moulisová, Vladimíra; Luer, Larry; Hoseinkhani, Sajjad; Brotosudarmo, Tatas H P; Collins, Aaron M; Lanzani, Guglielmo; Blankenship, Robert E; Cogdell, Richard J

2009-12-02

Energy transfer processes in photosynthetic light harvesting 2 (LH2) complexes isolated from purple bacterium Rhodopseudomonas palustris grown at different light intensities were studied by ground state and transient absorption spectroscopy. The decomposition of ground state absorption spectra shows contributions from B800 and B850 bacteriochlorophyll (BChl) a rings, the latter component splitting into a low energy and a high energy band in samples grown under low light (LL) conditions. A spectral analysis reveals strong inhomogeneity of the B850 excitons in the LL samples that is well reproduced by an exponential-type distribution. Transient spectra show a bleach of both the low energy and high energy bands, together with the respective blue-shifted exciton-to-biexciton transitions. The different spectral evolutions were analyzed by a global fitting procedure. Energy transfer from B800 to B850 occurs in a mono-exponential process and the rate of this process is only slightly reduced in LL compared to high light samples. In LL samples, spectral relaxation of the B850 exciton follows strongly nonexponential kinetics that can be described by a reduction of the bleach of the high energy excitonic component and a red-shift of the low energetic one. We explain these spectral changes by picosecond exciton relaxation caused by a small coupling parameter of the excitonic splitting of the BChl a molecules to the surrounding bath. The splitting of exciton energy into two excitonic bands in LL complex is most probably caused by heterogenous composition of LH2 apoproteins that gives some of the BChls in the B850 ring B820-like site energies, and causes a disorder in LH2 structure.

Femtosecond fluorescence dynamics of porphyrin in solution and solid films: the effects of aggregation and interfacial electron transfer between porphyrin and TiO2.

PubMed

Luo, Liyang; Lo, Chen-Fu; Lin, Ching-Yao; Chang, I-Jy; Diau, Eric Wei-Guang

2006-01-12

The excited-state relaxation dynamics of a synthetic porphyrin, ZnCAPEBPP, in solution, coated on a glass substrate as solid films, mixed with PMMA and coated on a glass substrate as solid films, and sensitized on nanocrystalline TiO2 films were investigated by using femtosecond fluorescence up-conversion spectroscopy with excitation in the Soret band, S2. We found that the S2--> S1 electronic relaxation of ZnCAPEBPP in solution and on PMMA films occurs in 910 and 690 fs, respectively, but it becomes extremely rapid, <100 fs, in solid films and TiO2 films due to formation of porphyrin aggregates. When probed in the S1 state of porphyrin, the fluorescence transients of the solid films show a biphasic kinetic feature with the rapid and slow components decaying in 1.9-2.4 and 19-26 ps, respectively. The transients in ZnCAPEBPP/TiO2 films also feature two relaxation processes but they occur on different time scales, 100-300 fs and 0.8-4.1 ps, and contain a small offset. According to the variation of relaxation period as a function of molecular density on a TiO2 surface, we assigned the femtosecond component of the TiO2 films as due to indirect interfacial electron transfer through a phenylethynyl bridge attached to one of four meso positions of the porphyrin ring, and the picosecond component arising from intermolecular energy transfer among porphyrins. The observed variation of aggregate-induced relaxation periods between solid and TiO2 films is due mainly to aggregation of two types: J-type aggregation is dominant in the former case whereas H-type aggregation prevails in the latter case.

Transient Kinetic Analysis of Hydrogen Sulfide Oxidation Catalyzed by Human Sulfide Quinone Oxidoreductase*

PubMed Central

Mishanina, Tatiana V.; Yadav, Pramod K.; Ballou, David P.; Banerjee, Ruma

2015-01-01

The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be −123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation. PMID:26318450

Transient Kinetic Analysis of Hydrogen Sulfide Oxidation Catalyzed by Human Sulfide Quinone Oxidoreductase.

PubMed

Mishanina, Tatiana V; Yadav, Pramod K; Ballou, David P; Banerjee, Ruma

2015-10-09

The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be -123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Transient kinetic studies of pH-dependent hydrolyses by exo-type carboxypeptidase P on a 27-MHz quartz crystal microbalance.

PubMed

Furusawa, Hiroyuki; Takano, Hiroki; Okahata, Yoshio

2008-02-15

pH-Dependent kinetic parameters (k(on), k(off), and k(cat)) of protein (myoglobin) hydrolyses catalyzed by exo-enzyme (carboxypeptidase P, CPP) were obtained by using a protein-immobilized quartz crystal microbalance (QCM) in acidic aqueous solutions. The formation of the enzyme-substrate (ES) complex (k(on)), the decay of the ES complex (k(off)), and the formation of the product (k(cat)) could be analyzed by transient kinetics as mass changes on the QCM plate. The Kd (k(off)/k(on)) value was different from the Michaelis constant Km calculated from (k(off) + k(cat))/k(on) due to k(cat) > k(off). The rate-determining step was the binding step (k(on), and the catalytic rate k(cat) was faster than other k(on) and k(off) values. In the range of pH 2.5-5.0, values of k(on) gradually increased with decreasing pH showing a maximum at pH 3.7, values of k(off) were independent of pH, and k(cat) increased gradually with decreasing pH. As a result, the apparent rate constant (k(cat)/Km) showed a maximum at pH 3.7 and gradually increased with decreasing pH. The optimum pH at 3.7 of k(on) is explained by the optimum binding ability of CPP to the COOH terminus of the substrate with hydrogen bonds. The increase of k(cat) at the lower pH correlated with the decrease of alpha-helix contents of the myoglobin substrate on the QCM.

Simplified Modeling of Steady-State and Transient Brillouin Gain in Magnetoactive Non-Centrosymmetric Semiconductors

NASA Astrophysics Data System (ADS)

Singh, M.; Aghamkar, P.; Sen, P. K.

With the aid of a hydrodynamic model of semiconductor-plasmas, a detailed analytical investigation is made to study both the steady-state and the transient Brillouin gain in magnetized non-centrosymmetric III-V semiconductors arising from the nonlinear interaction of an intense pump beam with the internally-generated acoustic wave, due to piezoelectric and electrostrictive properties of the crystal. Using the fact that the origin of coherent Brillouin scattering (CBS) lies in the third-order (Brillouin) susceptibility of the medium, we obtained an expression of the gain coefficient of backward Stokes mode in steady-state and transient regimes and studied the dependence of piezoelectricity, magnetic field and pump pulse duration on its growth rate. The threshold-pump intensity and optimum pulse duration for the onset of transient CBS are estimated. The piezoelectricity and externally-applied magnetic field substantially enhances the transient CBS gain coefficient in III-V semiconductors which can be of great use in the compression of scattered pulses.

Observations on autoregulation in skeletal muscle - The effects of arterial hypoxia

NASA Technical Reports Server (NTRS)

Pohost, G. M.; Newell, J. B.; Hamlin, N. P.; Powell, W. J., Jr.

1976-01-01

An experimental study was carried out on 25 mongrel dogs of both sexes to re-evaluate autoregulation of blood flow in skeletal muscle, with particular reference to the steady-state resistance and transient response in muscle blood flow following a square wave increase in arterial perfusion pressure and to the examination of the effect of arterial hypoxia on this transient response. The data emphasize the importance of considering the transient changes in blood flow in evaluating the autoregulatory response in skeletal muscle. For quantification purposes, a parameter termed alpha is introduced which represents the ratio between the increase in blood flow from baseline to peak and the return of blood flow from the peak to the new steady-state. Such a quantification of the transient response in flow with step increases in perfusion pressure demonstrates substantial transient responses under conditions of normal oxygenation and progressive attenuation of flow transients with increasing hypoxia.

The kinetics and mechanism of nanoconfined molten salt reactions: trimerization of potassium and rubidium dicyanamide.

PubMed

Yancey, Benjamin; Vyazovkin, Sergey

2015-04-21

This study highlights the effect of the aggregate state of a reactant on the reaction kinetics under the conditions of nanoconfinement. Our previous work (Phys. Chem. Chem. Phys., 2014, 16, 11409) has demonstrated considerable deceleration of the solid state trimerization of sodium dicyanamide in organically modified silica nanopores. In the present study we use FTIR, NMR, pXRD, TGA and DSC to analyze the kinetics and mechanism of the liquid state trimerization of potassium and rubidium dicyanamide under similar conditions of nanoconfinement. It is found that nanoconfinement accelerates dramatically the kinetics of the liquid state trimerization, whereas it does not appear to affect the reaction mechanism. Kinetic analysis indicates that the acceleration is associated with an increase in the preexponential factor. Although nanoconfinement has the opposite effects on the respective kinetics of solid and liquid state trimerization, both effects are linked to a change in the preexponential factor. The results obtained are consistent with our hypothesis that the effects differ because nanoconfinement may promote disordering of the solid and ordering of the liquid reaction media.

Instrumented Taylor anvil-on-rod impact tests for validating applicability of standard strength models to transient deformation states

NASA Astrophysics Data System (ADS)

Eakins, D. E.; Thadhani, N. N.

2006-10-01

Instrumented Taylor anvil-on-rod impact tests have been conducted on oxygen-free electronic copper to validate the accuracy of current strength models for predicting transient states during dynamic deformation events. The experiments coupled the use of high-speed digital photography to record the transient deformation states and laser interferometry to monitor the sample back (free surface) velocity as a measure of the elastic/plastic wave propagation through the sample length. Numerical continuum dynamics simulations of the impact and plastic wave propagation employing the Johnson-Cook [Proceedings of the Seventh International Symposium on Ballistics, 1983, The Netherlands (Am. Def. Prep. Assoc. (ADPA)), pp. 541-547], Zerilli-Armstrong [J. Appl. Phys. C1, 1816 (1987)], and Steinberg-Guinan [J. Appl. Phys. 51, 1498 (1980)] constitutive equations were used to generate transient deformation profiles and the free surface velocity traces. While these simulations showed good correlation with the measured free surface velocity traces and the final deformed sample shape, varying degrees of deviations were observed between the photographed and calculated specimen profiles at intermediate deformation states. The results illustrate the usefulness of the instrumented Taylor anvil-on-rod impact technique for validating constitutive equations that can describe the path-dependent deformation response and can therefore predict the transient and final deformation states.

Dynamic near-infrared imaging reveals transient phototropic change in retinal rod photoreceptors.

PubMed

Lu, Rongwen; Levy, Alexander M; Zhang, Qiuxiang; Pittler, Steven J; Yao, Xincheng

2013-10-01

Stiles-Crawford effect (SCE) is exclusively observed in cone photoreceptors, but why the SCE is absent in rod photoreceptors is still a mystery. In this study, we employed dynamic near infrared light imaging to monitor photoreceptor kinetics in freshly isolated frog and mouse retinas stimulated by oblique visible light flashes. It was observed that retinal rods could rapidly (onset: ∼10 ms for frog and 5 ms for mouse; time-to-peak: ∼200 ms for frog and 30 ms for mouse) shift toward the direction of the visible light, which might quickly compensate for the loss of luminous efficiency due to oblique illumination. In contrast, such directional movement was negligible in retinal cones. Moreover, transient rod phototropism could contribute to characteristic intrinsic optical signal (IOS). We anticipate that further study of the transient rod phototropism may not only provide insight into better understanding of the nature of vision but also promise an IOS biomarker for functional mapping of rod physiology at high resolution.

Transient phenomena in the pulse radiolysis of retinyl polyenes. 5. Association of radical cations with parent molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bobrowski, K.; Das, P.K.

1986-02-27

At relatively high concentrations (1-10 mM) in O/sub 2/-saturated acetone, pulse radiolysis of all-trans-retinal, -retinoic acid, and -methyl retinoate gives rise to fast transient absorption processes that are best explained in terms of association of radical cations with parent polyenes to form dimers. From the concentration dependence of initial decay/formation kinetics, equilibrium constants (K) for monomer/dimer interconversion are measured to be 220-440 M/sup -1/ (in acetone). On going from acetone to 1,2-dichloroethane, K values for retinal and retinoic acid increase almost by an order of magnitude. For all trans-retinol and retinyl acetate, radical cation dimer formation appears to be negligiblemore » in the concentration range 1-10 mM of the polyene substrates (based on the lack of transient absorption changes seen with retinal and retinoic acid/ester). 24 references, 6 figures, 1 table.« less

Output Beam Polarisation of X-ray Lasers with Transient Inversion

NASA Astrophysics Data System (ADS)

Janulewicz, K. A.; Kim, C. M.; Matouš, B.; Stiel, H.; Nishikino, M.; Hasegawa, N.; Kawachi, T.

It is commonly accepted that X-ray lasers, as the devices based on amplified spontaneous emission (ASE), did not show any specific polarization in the output beam. The theoretical analysis within the uniform (single-mode) approximation suggested that the output radiation should show some defined polarization feature, but randomly changing from shot-to-shot. This hypothesis has been verified by experiment using traditional double-pulse scheme of transient inversion. Membrane beam-splitter was used as a polarization selector. It was found that the output radiation has a significant component of p-polarisation in each shot. To explain the effect and place it in the line with available, but scarce data, propagation and kinetic effects in the non-uniform plasma have been analysed.

Time-resolved spectroscopy of dye-labeled photoactive yellow protein suggests a pathway of light-induced structural changes in the N-terminal cap.

PubMed

Hoersch, Daniel; Otto, Harald; Cusanovich, Michael A; Heyn, Maarten P

2009-07-14

The photoreceptor PYP responds to light activation with global conformational changes. These changes are mainly located in the N-terminal cap of the protein, which is approximately 20 A away from the chromophore binding pocket and separated from it by the central beta-sheet. The question of the propagation of the structural change across the central beta-sheet is of general interest for the superfamily of PAS domain proteins, for which PYP is the structural prototype. Here we measured the kinetics of the structural changes in the N-terminal cap by transient absorption spectroscopy on the ns to second timescale. For this purpose the cysteine mutants A5C and N13C were prepared and labeled with thiol reactive 5-iodoacetamidofluorescein (IAF). A5 is located close to the N-terminus, while N13 is part of helix alpha1 near the functionally important salt bridge E12-K110 between the N-terminal cap and the central anti-parallel beta-sheet. The absorption spectrum of the dye is sensitive to its environment, and serves as a sensor for conformational changes near the labeling site. In both labeled mutants light activation results in a transient red-shift of the fluorescein absorption spectrum. To correlate the conformational changes with the photocycle intermediates of the protein, we compared the kinetics of the transient absorption signal of the dye with that of the p-hydroxycinnamoyl chromophore. While the structural change near A5 is synchronized with the rise of the I(2) intermediate, which is formed in approximately 200 mus, the change near N13 is delayed and rises with the next intermediate I(2)', which forms in approximately 2 ms. This indicates that different parts of the N-terminal cap respond to light activation with different kinetics. For the signaling pathway of photoactive yellow protein we propose a model in which the structural signal propagates from the chromophore binding pocket across the central beta-sheet via the N-terminal region to helix alpha1, resulting in a large change in the protein conformation.

Kinetic, pharmacological and activity-dependent separation of two Ca2+ signalling pathways mediated by type 1 metabotropic glutamate receptors in rat Purkinje neurones

PubMed Central

Canepari, Marco; Ogden, David

2006-01-01

Type 1 metabotropic glutamate receptors (mGluR1) in Purkinje neurones (PNs) are important for motor learning and coordination. Here, two divergent mGluR1 Ca2+-signalling pathways and the associated membrane conductances were distinguished kinetically and pharmacologically after activation by 1-ms photorelease of l-glutamate or by bursts of parallel fibre (PF) stimulation. A new, mGluR1-mediated transient K+ conductance was seen prior to the slow EPSC (sEPSC). It was seen only in PNs previously allowed to fire spontaneously or held at depolarized potentials for several seconds and was slowly inhibited by agatoxin IVA, which blocks P/Q-type Ca2+ channels. It peaked in 148 ms, had well-defined kinetics and, unlike the sEPSC, was abolished by the phospholipase C (PLC) inhibitor U73122. It was blocked by the BK Ca2+-activated K+ channel blocker iberiotoxin and unaffected by apamin, indicating selective activation of BK channels by PLC-dependent store-released Ca2+. The K+ conductance and underlying transient Ca2+ release showed a highly reproducible delay of 99.5 ms following PF burst stimulation, with a precision of 1–2 ms in repeated responses of the same PN, and a subsequent fast rise and fall of Ca2+ concentration. Analysis of Ca2+ signals showed that activation of the K+ conductance by Ca2+ release occured in small dendrites and subresolution structures, most probably spines. The results show that PF burst stimulation activates two pathways of mGluR1 signalling in PNs. First, transient, PLC-dependent Ca2+ release from stores with precisely reproducible timing and second, slower Ca2+ influx in the cation-permeable sEPSC channel. The priming by prior Ca2+ influx in P/Q-type Ca2+ channels may determine the path of mGluR1 signalling. The precise timing of PLC-mediated store release may be important for interactions of PF mGluR1 signalling with other inputs to the PN. PMID:16497716

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kohler, Lars; Hadt, Ryan G.; Hayes, Dugan

In this paper we describe the synthesis of a new phenanthroline ligand, 2,9-di(2,4,6-tri-isopropyl-phenyl)-1,10-phenanthroline (bL2) and its use as the blocking ligand in the preparation of two new heteroleptic Cu(I)diimine complexes. Analysis of the CuHETPHEN single crystal structures shows a distinct distortion from an ideal tetrahedral geometry around the Cu(I) center, forced by the secondary phenanthroline ligand rotating to accommodate the isopropyl groups of bL2. The increased steric bulk of bL2 as compared to the more commonly used 2,9-dimesityl-1,10-phenanthroline blocking ligand prohibits intramolecular ligand–ligand interaction, which is unique among CuHETPHEN complexes. The ground state optical and redox properties of CuHETPHEN complexesmore » are responsive to the substitution on the blocking ligand even though the differences in structure are far removed from the Cu(I) center. Transient optical spectroscopy was used to understand the excited state kinetics in both coordinating and non-coordinating solvents following visible excitation. Substitution of the blocking phenanthroline ligand has a significant impact on the 3MLCT decay and can be used to increase the excited state lifetime by 50%. Electronic structure calculations established relationships between ground and excited state properties, and general entatic state concepts are discussed for copper photosensitizers. This work contributes to the growing library of CuHETPHEN complexes and broadens the fundamental understanding of their ground and excited state properties.« less

Self-resonance after inflation: Oscillons, transients, and radiation domination

NASA Astrophysics Data System (ADS)

Lozanov, Kaloian D.; Amin, Mustafa A.

2018-01-01

Homogeneous oscillations of the inflaton after inflation can be unstable to small spatial perturbations even without coupling to other fields. We show that for inflaton potentials ∝|ϕ |2n near |ϕ |=0 and flatter beyond some |ϕ |=M , the inflaton condensate oscillations can lead to self-resonance, followed by its complete fragmentation. We find that for nonquadratic minima (n >1 ), shortly after backreaction, the equation of state parameter, w →1 /3 . If M ≪mPl, radiation domination is established within less than an e -fold of expansion after the end of inflation. In this case self-resonance is efficient and the condensate fragments into transient, localised spherical objects which are unstable and decay, leaving behind them a virialized field with mean kinetic and gradient energies much greater than the potential energy. This end-state yields w =1 /3 . When M ˜mPl we observe slow and steady, self-resonance that can last many e -folds before backreaction eventually shuts it off, followed by fragmentation and w →1 /3 . We provide analytical estimates for the duration to w →1 /3 after inflation, which can be used as an upper bound (under certain assumptions) on the duration of the transition between the inflationary and the radiation dominated states of expansion. This upper bound can reduce uncertainties in CMB observables such as the spectral tilt ns, and the tensor-to-scalar ratio r . For quadratic minima (n =1 ), w →0 regardless of the value of M . This is because when M ≪mPl, long-lived oscillons form within an e -fold after inflation, and collectively behave as pressureless dust thereafter. For M ˜mPl, the self-resonance is inefficient and the condensate remains intact (ignoring long-term gravitational clustering) and keeps oscillating about the quadratic minimum, again implying w =0 .

A Role for DPPX Modulating External TEA Sensitivity of Kv4 Channels

PubMed Central

Colinas, Olaia; Pérez-Carretero, Francisco D.; López-López, José R.; Pérez-García, M. Teresa

2008-01-01

Shal-type (Kv4) channels are expressed in a large variety of tissues, where they contribute to transient voltage-dependent K+ currents. Kv4 are the molecular correlate of the A-type current of neurons (ISA), the fast component of ITO current in the heart, and also of the oxygen-sensitive K+ current (KO2) in rabbit carotid body (CB) chemoreceptor cells. The enormous degree of variability in the physiological properties of Kv4-mediated currents can be attributable to the complexity of their regulation together with the large number of ancillary subunits and scaffolding proteins that associate with Kv4 proteins to modify their trafficking and their kinetic properties. Among those, KChIPs and DPPX proteins have been demonstrated to be integral components of ISA and ITO currents, as their coexpression with Kv4 subunits recapitulates the kinetics of native currents. Here, we explore the presence and functional contribution of DPPX to KO2 currents in rabbit CB chemoreceptor cells by using DPPX functional knockdown with siRNA. Additionally, we investigate if the presence of DPPX endows Kv4 channels with new pharmacological properties, as we have observed anomalous tetraethylammonium (TEA) sensitivity in the native KO2 currents. DPPX association with Kv4 channels induced an increased TEA sensitivity both in heterologous expression systems and in CB chemoreceptor cells. Moreover, TEA application to Kv4-DPPX heteromultimers leads to marked kinetic effects that could be explained by an augmented closed-state inactivation. Our data suggest that DPPX proteins are integral components of KO2 currents, and that their association with Kv4 subunits modulate the pharmacological profile of the heteromultimers. PMID:18411327

Effects of altered nitric oxide availability on rat muscle microvascular oxygenation during contractions.

PubMed

Ferreira, L F; Padilla, D J; Williams, J; Hageman, K S; Musch, T I; Poole, D C

2006-03-01

To explore the role of nitric oxide (NO) in controlling microvascular O2 pressure (P(O2)mv) at rest and during contractions (1 Hz). We hypothesized that at the onset of contractions sodium nitroprusside (SNP) would raise P(O2)mv and slow the kinetics of P(O2)mv change whereas l-nitro arginine methyl ester (L-NAME) would decrease P(O2)mv and speed its kinetics. We superfused the spinotrapezius muscle of female Sprague-Dawley rats (n = 7, body mass = 298 +/- 10 g) with SNP (300 microM) and L-NAME (1.5 mm) and measured P(O2)mv (phosphorescence quenching) during contractions. SNP decreased mean arterial pressure (92 +/- 5 mmHg) below that of control (CON, 124 +/- 4 mmHg) and L-NAME (120 +/- 4 mmHg) conditions. SNP did not raise P(O2)mv at rest but it did elevate the P(O2)mv-to-MAP ratio (50% increase, P < 0.05) and slow the kinetics by lengthening the time-delay (TD, 14.0 +/- 5.0 s) and time constant (tau, 24.0 +/- 10.0 s) of the response compared with CON (TD, 8.4 +/- 3.3 s; tau, 16.0 +/- 4.5 s, P < 0.05 vs. SNP). L-NAME decreased P(O2)mv at rest and tended to speed tau (10.1 +/- 3.8 s, P = 0.1), while TD (8.1 +/- 1.0 s) was not significantly different. L-NAME also caused P(O2)mv to fall transiently below steady-state contracting values. These results indicate that NO availability can significantly affect P(O2)mv at rest and during contractions and suggests that P(O2)mv derangements in ageing and chronic disease conditions may potentially result from impairments in NO availability.

Ultrafast Electron Transfer Kinetics in the LM Dimer of Bacterial Photosynthetic Reaction Center from Rhodobacter sphaeroides.

PubMed

Sun, Chang; Carey, Anne-Marie; Gao, Bing-Rong; Wraight, Colin A; Woodbury, Neal W; Lin, Su

2016-06-23

It has become increasingly clear that dynamics plays a major role in the function of many protein systems. One system that has proven particularly facile for studying the effects of dynamics on protein-mediated chemistry is the bacterial photosynthetic reaction center from Rhodobacter sphaeroides. Previous experimental and computational analysis have suggested that the dynamics of the protein matrix surrounding the primary quinone acceptor, QA, may be particularly important in electron transfer involving this cofactor. One can substantially increase the flexibility of this region by removing one of the reaction center subunits, the H-subunit. Even with this large change in structure, photoinduced electron transfer to the quinone still takes place. To evaluate the effect of H-subunit removal on electron transfer to QA, we have compared the kinetics of electron transfer and associated spectral evolution for the LM dimer with that of the intact reaction center complex on picosecond to millisecond time scales. The transient absorption spectra associated with all measured electron transfer reactions are similar, with the exception of a broadening in the QX transition and a blue-shift in the QY transition bands of the special pair of bacteriochlorophylls (P) in the LM dimer. The kinetics of the electron transfer reactions not involving quinones are unaffected. There is, however, a 4-fold decrease in the electron transfer rate from the reduced bacteriopheophytin to QA in the LM dimer compared to the intact reaction center and a similar decrease in the recombination rate of the resulting charge-separated state (P(+)QA(-)). These results are consistent with the concept that the removal of the H-subunit results in increased flexibility in the region around the quinone and an associated shift in the reorganization energy associated with charge separation and recombination.

Band-Like Behavior of Localized States of Metal Silicide Precipitate in Silicon

NASA Astrophysics Data System (ADS)

Bondarenko, Anton; Vyvenko, Oleg

2018-03-01

Deep-level transient spectroscopy (DLTS) investigations of energy levels of charge-carrier traps associated with precipitates of metal silicide often show that they behave not like localized monoenergetic traps but as a continuous density of allowed states in the bandgap with fast carrier exchange between these states, so-called band-like behavior. This kind of behavior was ascribed to the dislocation loop bounding the platelet, which in addition exhibits an attractive potential caused by long-range elastic strain. In previous works, the presence of the dislocation-related deformation potential in combination with the external electric field of the Schottky diode was included to obtain a reasonable fit of the proposed model to experimental data. Another well-known particular property of extended defects—the presence of their own strong electric field in their vicinity that is manifested in the logarithmic kinetics of electron capture—was not taken into account. We derive herein a theoretical model that takes into account both the external electric field and the intrinsic electric field of dislocation self-charge as well as its deformation potential, which leads to strong temporal variation of the activation energy during charge-carrier emission. We performed numerical simulations of the DLTS spectra based on such a model for a monoenergetic trap, finding excellent agreement with available experimental data.