Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS

PubMed Central

Huang, William Y. C.; Yan, Qingrong; Lin, Wan-Chen; Chung, Jean K.; Hansen, Scott D.; Christensen, Sune M.; Tu, Hsiung-Lin; Kuriyan, John; Groves, Jay T.

2016-01-01

The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kinetics and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. The generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes. PMID:27370798

Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS.

PubMed

Huang, William Y C; Yan, Qingrong; Lin, Wan-Chen; Chung, Jean K; Hansen, Scott D; Christensen, Sune M; Tu, Hsiung-Lin; Kuriyan, John; Groves, Jay T

2016-07-19

The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kinetics and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. The generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes.

Picosecond absorption anisotropy of polymethine and squarylium dyes in liquid and polymeric media

NASA Astrophysics Data System (ADS)

Przhonska, Olga V.; Hagan, David J.; Novikov, Evgueni; Lepkowicz, Richard; Van Stryland, Eric W.; Bondar, Mikhail V.; Slominsky, Yuriy L.; Kachkovski, Alexei D.

2001-11-01

Time-resolved excitation-probe polarization measurements are performed for polymethine and squarylium dyes in ethanol and an elastopolymer of polyurethane acrylate (PUA). These molecules exhibit strong excited-state absorption in the visible, which results in reverse saturable absorption (RSA). In pump-probe experiments, we observe a strong angular dependence of the RSA decay kinetics upon variation of the angle between pump and probe polarizations. The difference in absorption anisotropy kinetics in ethanol and PUA is detected and analyzed. Anisotropy decay curves in ethanol follow a single exponential decay leading to complete depolarization of the excited state. We also observe complete depolarization in PUA, in which case the anisotropy decay follows a double exponential behavior. Possible rotations in the PUA polymeric matrix are connected with the existence of local microcavities of free volume. We believe that the fast decay component is connected with the rotation of molecular fragments and the slower decay component is connected with the rotation of entire molecules in local microcavities, which is possible because of the elasticity of the polymeric material.

Cell responses to single pheromone molecules may reflect the activation kinetics of olfactory receptor molecules.

PubMed

Minor, A V; Kaissling, K-E

2003-03-01

Olfactory receptor cells of the silkmoth Bombyx mori respond to single pheromone molecules with "elementary" electrical events that appear as discrete "bumps" a few milliseconds in duration, or bursts of bumps. As revealed by simulation, one bump may result from a series of random openings of one or several ion channels, producing an average inward membrane current of 1.5 pA. The distributions of durations of bumps and of gaps between bumps in a burst can be fitted by single exponentials with time constants of 10.2 ms and 40.5 ms, respectively. The distribution of burst durations is a sum of two exponentials; the number of bumps per burst obeyed a geometric distribution (mean 3.2 bumps per burst). Accordingly the elementary events could reflect transitions among three states of the pheromone receptor molecule: the vacant receptor (state 1), the pheromone-receptor complex (state 2), and the activated complex (state 3). The calculated rate constants of the transitions between states are k(21)=7.7 s(-1), k(23)=16.8 s(-1), and k(32)=98 s(-1).

Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS

DOE PAGES

Huang, William Y. C.; Yan, Qingrong; Lin, Wan-Chen; ...

2016-07-01

The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kineticsmore » and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. In conclusion, the generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes.« less

Stopped-flow kinetic studies of sphere-to-rod transitions of sodium alkyl sulfate micelles induced by hydrotropic salt.

PubMed

Zhang, Jingyan; Ge, Zhishen; Jiang, Xiaoze; Hassan, P A; Liu, Shiyong

2007-12-15

The kinetics and mechanism of sphere-to-rod transitions of sodium alkyl sulfate micelles induced by hydrotropic salt, p-toluidine hydrochloride (PTHC), were investigated by stopped-flow with light scattering detection. Spherical sodium dodecyl sulfate (SDS) micelles transform into short ellipsoidal shapes at low salt concentrations ([PTHC]/[SDS], chi(PTHC)=0.3 and 0.4). Upon stopped-flow mixing aqueous solutions of spherical SDS micelles with PTHC, the scattered light intensity gradually increases with time. Single exponential fitting of the dynamic traces leads to characteristic relaxation time, tau(g), for the growth process from spherical to ellipsoidal micelles, and it increases with increasing SDS concentrations. This suggests that ellipsoidal micelles might be produced by successive insertion of unimers into spherical micelles, similar to the case of formation of spherical micelles as suggested by Aniansson-Wall (A-W) theory. At chi(PTHC) > or = 0.5, rod-like micelles with much higher axial ratio form. The scattered light intensity exhibits an initially abrupt increase and then levels off. The dynamic curves can be well fitted with single exponential functions, and the obtained tau(g) decreases with increasing SDS concentration. Thus, the growth from spherical to rod-like micelles might proceed via fusion of spherical micelles, in agreement with mechanism proposed by Ikeda et al. At chi(PTHC)=0.3 and 0.6, the apparent activation energies obtained from temperature dependent kinetic studies for the micellar growth are 40.4 and 3.6 kJ/mol, respectively. The large differences between activation energies for the growth from spherical to ellipsoidal micelles at low chi(PTHC) and the sphere-to-rod transition at high chi(PTHC) further indicate that they should follow different mechanisms. Moreover, the sphere-to-rod transition kinetics of sodium alkyl sulfate with varying hydrophobic chain lengths (n=10, 12, 14, and 16) are also studied. The longer the carbon chain lengths, the slower the sphere-to-rod transition.

Kinetics of oxygen consumption after a single flash of light in photoreceptors of the drone (Apis mellifera)

PubMed Central

1982-01-01

The time course of the rate of oxygen consumption (QO2) after a single flash of light has been measured in 300-micrometers slices of drone retina at 22 degrees C. To measure delta QO2(t), the change in QO2 from its level in darkness, the transients of the partial pressure of O2 (PO2) were recorded with O2 microelectrodes simultaneously in two sites in the slice and delta QO2 was calculated by a computer using Fourier transforms. After a 40-ms flash of intense light, delta QO2, reached a peak of 40 microliters O2/g.min and then declined exponentially to the baseline with a time constant tau 1 = 4.96 +/- 0.49 s (SD, n = 10). The rising phase was characterized by a time constant tau 2 = 1.90 +/- 0.35 s (SD, n = 10). The peak amplitude of delta QO2 increased linearly with the log of the light intensity. Replacement of Na+ by choline, known to decrease greatly the light-induced transmembrane current, caused a 63% decrease of delta QO2. With these changes, however, the kinetics of delta QO2 (t) were unchanged. This suggest that the recovery phase is rate-limited by a single reaction with apparent first-order kinetics. Evidence is provided that suggests that this reaction may be the working of the sodium pump. Exposure of the retina to high concentrations of ouabain or strophanthidin (inhibitors of the sodium pump) reduced the peak amplitude of delta QO2 by approximately 80% and increased tau 1. The increase of tau 1 was an exponential function of the time of exposure to the cardioactive steroids. Hence, it seems likely that the greatest part of delta QO2 is used for the working of the pump, whose activity is the mechanism underlying the rate constant of the descending limb of delta QO2 (t). PMID:6288837

Erroneous Arrhenius: Modified Arrhenius model best explains the temperature dependence of ectotherm fitness

PubMed Central

Knies, Jennifer L.; Kingsolver, Joel G.

2013-01-01

The initial rise of fitness that occurs with increasing temperature is attributed to Arrhenius kinetics, in which rates of reaction increase exponentially with increasing temperature. Models based on Arrhenius typically assume single rate-limiting reaction(s) over some physiological temperature range for which all the rate-limiting enzymes are in 100% active conformation. We test this assumption using datasets for microbes that have measurements of fitness (intrinsic rate of population growth) at many temperatures and over a broad temperature range, and for diverse ectotherms that have measurements at fewer temperatures. When measurements are available at many temperatures, strictly Arrhenius kinetics is rejected over the physiological temperature range. However, over a narrower temperature range, we cannot reject strictly Arrhenius kinetics. The temperature range also affects estimates of the temperature dependence of fitness. These results indicate that Arrhenius kinetics only apply over a narrow range of temperatures for ectotherms, complicating attempts to identify general patterns of temperature dependence. PMID:20528477

Erroneous Arrhenius: modified arrhenius model best explains the temperature dependence of ectotherm fitness.

PubMed

Knies, Jennifer L; Kingsolver, Joel G

2010-08-01

The initial rise of fitness that occurs with increasing temperature is attributed to Arrhenius kinetics, in which rates of reaction increase exponentially with increasing temperature. Models based on Arrhenius typically assume single rate-limiting reactions over some physiological temperature range for which all the rate-limiting enzymes are in 100% active conformation. We test this assumption using data sets for microbes that have measurements of fitness (intrinsic rate of population growth) at many temperatures and over a broad temperature range and for diverse ectotherms that have measurements at fewer temperatures. When measurements are available at many temperatures, strictly Arrhenius kinetics are rejected over the physiological temperature range. However, over a narrower temperature range, we cannot reject strictly Arrhenius kinetics. The temperature range also affects estimates of the temperature dependence of fitness. These results indicate that Arrhenius kinetics only apply over a narrow range of temperatures for ectotherms, complicating attempts to identify general patterns of temperature dependence.

Submillisecond Dynamics of Mastoparan X Insertion into Lipid Membranes.

PubMed

Schuler, Erin E; Nagarajan, Sureshbabu; Dyer, R Brian

2016-09-01

The mechanism of protein insertion into a lipid bilayer is poorly understood because the kinetics of this process is difficult to measure. We developed a new approach to study insertion of the antimicrobial peptide Mastoparan X into zwitterionic lipid vesicles, using a laser-induced temperature-jump to initiate insertion on the microsecond time scale and infrared and fluorescence spectroscopies to follow the kinetics. Infrared probes the desolvation of the peptide backbone and yields biphasic kinetics with relaxation lifetimes of 12 and 117 μs, whereas fluorescence probes the intrinsic tryptophan residue located near the N-terminus and yields a single exponential phase with a lifetime of 440 μs. Arrhenius analysis of the temperature-dependent rates yields an activation energy for insertion of 96 kJ/mol. These results demonstrate the complexity of the insertion process and provide mechanistic insight into the interplay between peptides and the lipid bilayer required for peptide transport across cellular membranes.

Light-Curing Volumetric Shrinkage in Dimethacrylate-Based Dental Composites by Nanoindentation and PAL Study.

PubMed

Shpotyuk, Olha; Adamiak, Stanislaw; Bezvushko, Elvira; Cebulski, Jozef; Iskiv, Maryana; Shpotyuk, Oleh; Balitska, Valentina

2017-12-01

Light-curing volumetric shrinkage in dimethacrylate-based dental resin composites Dipol® is examined through comprehensive kinetics research employing nanoindentation measurements and nanoscale atomic-deficient study with lifetime spectroscopy of annihilating positrons. Photopolymerization kinetics determined through nanoindentation testing is shown to be described via single-exponential relaxation function with character time constants reaching respectively 15.0 and 18.7 s for nanohardness and elastic modulus. Atomic-deficient characteristics of composites are extracted from positron lifetime spectra parameterized employing unconstrained x3-term fitting. The tested photopolymerization kinetics can be adequately reflected in time-dependent changes observed in average positron lifetime (with 17.9 s time constant) and fractional free volume of positronium traps (with 18.6 s time constant). This correlation proves that fragmentation of free-volume positronium-trapping sites accompanied by partial positronium-to-positron traps conversion determines the light-curing volumetric shrinkage in the studied composites.

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.

Theory and procedures for finding a correct kinetic model for the bacteriorhodopsin photocycle.

PubMed

Hendler, R W; Shrager, R; Bose, S

2001-04-26

In this paper, we present the implementation and results of new methodology based on linear algebra. The theory behind these methods is covered in detail in the Supporting Information, available electronically (Shragerand Hendler). In brief, the methods presented search through all possible forward sequential submodels in order to find candidates that can be used to construct a complete model for the BR-photocycle. The methodology is limited only to forward sequential models. If no such models are compatible with the experimental data,none will be found. The procedures apply objective tests and filters to eliminate possibilities that cannot be correct, thus cutting the total number of candidate sequences to be considered. In the current application,which uses six exponentials, the total sequences were cut from 1950 to 49. The remaining sequences were further screened using known experimental criteria. The approach led to a solution which consists of a pair of sequences, one with 5 exponentials showing BR* f L(f) M(f) N O BR and the other with three exponentials showing BR* L(s) M(s) BR. The deduced complete kinetic model for the BR photocycle is thus either a single photocycle branched at the L intermediate or a pair of two parallel photocycles. Reasons for preferring the parallel photocycles are presented. Synthetic data constructed on the basis of the parallel photocycles were indistinguishable from the experimental data in a number of analytical tests that were applied.

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

PubMed Central

Fleming, R.M.T.; Thiele, I.; Provan, G.; Nasheuer, H.P.

2010-01-01

The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in E. coli and compare favourably with in silico prediction by flux balance analysis. PMID:20230840

Exponential-fitted methods for integrating stiff systems of ordinary differential equations: Applications to homogeneous gas-phase chemical kinetics

NASA Technical Reports Server (NTRS)

Pratt, D. T.

1984-01-01

Conventional algorithms for the numerical integration of ordinary differential equations (ODEs) are based on the use of polynomial functions as interpolants. However, the exact solutions of stiff ODEs behave like decaying exponential functions, which are poorly approximated by polynomials. An obvious choice of interpolant are the exponential functions themselves, or their low-order diagonal Pade (rational function) approximants. A number of explicit, A-stable, integration algorithms were derived from the use of a three-parameter exponential function as interpolant, and their relationship to low-order, polynomial-based and rational-function-based implicit and explicit methods were shown by examining their low-order diagonal Pade approximants. A robust implicit formula was derived by exponential fitting the trapezoidal rule. Application of these algorithms to integration of the ODEs governing homogenous, gas-phase chemical kinetics was demonstrated in a developmental code CREK1D, which compares favorably with the Gear-Hindmarsh code LSODE in spite of the use of a primitive stepsize control strategy.

Modeling the degradation kinetics of ascorbic acid.

PubMed

Peleg, Micha; Normand, Mark D; Dixon, William R; Goulette, Timothy R

2018-06-13

Most published reports on ascorbic acid (AA) degradation during food storage and heat preservation suggest that it follows first-order kinetics. Deviations from this pattern include Weibullian decay, and exponential drop approaching finite nonzero retention. Almost invariably, the degradation rate constant's temperature-dependence followed the Arrhenius equation, and hence the simpler exponential model too. A formula and freely downloadable interactive Wolfram Demonstration to convert the Arrhenius model's energy of activation, E a , to the exponential model's c parameter, or vice versa, are provided. The AA's isothermal and non-isothermal degradation can be simulated with freely downloadable interactive Wolfram Demonstrations in which the model's parameters can be entered and modified by moving sliders on the screen. Where the degradation is known a priori to follow first or other fixed order kinetics, one can use the endpoints method, and in principle the successive points method too, to estimate the reaction's kinetic parameters from considerably fewer AA concentration determinations than in the traditional manner. Freeware to do the calculations by either method has been recently made available on the Internet. Once obtained in this way, the kinetic parameters can be used to reconstruct the entire degradation curves and predict those at different temperature profiles, isothermal or dynamic. Comparison of the predicted concentration ratios with experimental ones offers a way to validate or refute the kinetic model and the assumptions on which it is based.

Theoretical and experimental study on the effects of particle size and temperature on the reaction kinetics of cubic nano-Cu2O

NASA Astrophysics Data System (ADS)

Tang, Huanfeng; Huang, Zaiyin; Xiao, Ming; Liang, Min; Chen, Liying; Tan, XueCai

2017-09-01

The activities, selectivities, and stabilities of nanoparticles in heterogeneous reactions are size-dependent. In order to investigate the influencing laws of particle size and temperature on kinetic parameters in heterogeneous reactions, cubic nano-Cu2O particles of four different sizes in the range of 40-120 nm have been controllably synthesized. In situ microcalorimetry has been used to attain thermodynamic data on the reaction of Cu2O with aqueous HNO3 and, combined with thermodynamic principles and kinetic transition-state theory, the relevant reaction kinetic parameters have been evaluated. The size dependences of the kinetic parameters are discussed in terms of the established kinetic model and the experimental results. It was found that the reaction rate constants increased with decreasing particle size. Accordingly, the apparent activation energy, pre-exponential factor, activation enthalpy, activation entropy, and activation Gibbs energy decreased with decreasing particle size. The reaction rate constants and activation Gibbs energies increased with increasing temperature. Moreover, the logarithms of the apparent activation energies, pre-exponential factors, and rate constants were found to be linearly related to the reciprocal of particle size, consistent with the kinetic models. The influence of particle size on these reaction kinetic parameters may be explained as follows: the apparent activation energy is affected by the partial molar enthalpy, the pre-exponential factor is affected by the partial molar entropy, and the reaction rate constant is affected by the partial molar Gibbs energy. [Figure not available: see fulltext.

Equilibrium concentration profiles and sedimentation kinetics of colloidal gels under gravitational stress

NASA Astrophysics Data System (ADS)

Buzzaccaro, S.; Secchi, E.; Brambilla, G.; Piazza, R.; Cipelletti, L.

2012-07-01

We study the sedimentation of colloidal gels by using a combination of light scattering, polarimetry and video imaging. The asymptotic concentration profiles φ(z,t → ∞) exhibit remarkable scaling properties: profiles for gels prepared at different initial volume fractions and particle interactions can be superimposed onto a single master curve by using suitable reduced variables. We show theoretically that this behavior stems from a power law dependence of the compressive elastic modulus versus φ, which we directly test experimentally. The sedimentation kinetics comprises an initial latency stage, followed by a rapid collapse where the gel height h decreases at constant velocity and a final compaction stage characterized by a stretched exponential relaxation of h toward a plateau. Analogies and differences with previous works are briefly discussed.

Proline 54 trans-cis isomerization is responsible for the kinetic partitioning at the last-step photocycle of photoactive yellow protein

PubMed Central

Lee, Byoung-Chul; Hoff, Wouter D.

2008-01-01

Photoactive yellow protein (PYP), a blue-light photoreceptor for Ectothiorhodospira halophila, has provided a unique system for studying protein folding that is coupled with a photocycle. Upon receptor activation by blue light, PYP proceeds through a photocycle that includes a partially folded signaling state. The last-step photocycle is a thermal recovery reaction from the signaling state to the native state. Bi-exponential kinetics had been observed for the last-step photocycle; however, the slow phase of the bi-exponential kinetics has not been extensively studied. Here we analyzed both fast and slow phases of the last-step photocycle in PYP. From the analysis of the denaturant dependence of the fast and slow phases, we found that the last-step photocycle proceeds through parallel channels of the folding pathway. The burial of the solvent-accessible area was responsible for the transition state of the fast phase, while structural rearrangement from the compact state to the native state was responsible for the transition state of the slow phase. The photocycle of PYP was linked to the thermodynamic cycle that includes both unfolding and refolding of the fast- and slow-phase intermediates. In order to test the hypothesis of proline-limited folding for the slow phase, we constructed two proline mutants: P54A and P68A. We found that only a single phase of the last-step photocycle was observed in P54A. This suggests that there is a low energy barrier between trans to cis conformation in P54 in the light-induced state of PYP, and the resulting cis conformation of P54 generates a slow-phase kinetic trap during the photocycle-coupled folding pathway of PYP. PMID:18794212

Kinetics of rapid covalent bond formation of aniline with humic acid: ESR investigations with nitroxide spin labels

NASA Astrophysics Data System (ADS)

Glinka, Kevin; Matthies, Michael; Theiling, Marius; Hideg, Kalman; Steinhoff, Heinz-Jürgen

2016-04-01

Sulfonamide antibiotics used in livestock farming are distributed to farmland by application of slurry as fertilizer. Previous work suggests rapid covalent binding of the aniline moiety to humic acids found in soil. In the current work, kinetics of this binding were measured in X-band EPR spectroscopy by incubating Leonardite humic acid (LHA) with a paramagnetic aniline spin label (anilino-NO (2,5,5-Trimethyl-2-(3-aminophenyl)pyrrolidin-1-oxyl)). Binding was detected by a pronounced broadening of the spectral lines after incubation of LHA with anilino-NO. The time evolution of the amplitude of this feature was used for determining the reaction kinetics. Single- and double-exponential models were fitted to the data obtained for modelling one or two first-order reactions. Reaction rates of 0.16 min-1 and 0.012 min-1, were found respectively. Addition of laccase peroxidase did not change the kinetics but significantly enhanced the reacting fraction of anilino-NO. This EPR-based method provides a technically simple and effective method for following rapid binding processes of a xenobiotic substance to humic acids.

Obstructive sleep apnea alters sleep stage transition dynamics.

PubMed

Bianchi, Matt T; Cash, Sydney S; Mietus, Joseph; Peng, Chung-Kang; Thomas, Robert

2010-06-28

Enhanced characterization of sleep architecture, compared with routine polysomnographic metrics such as stage percentages and sleep efficiency, may improve the predictive phenotyping of fragmented sleep. One approach involves using stage transition analysis to characterize sleep continuity. We analyzed hypnograms from Sleep Heart Health Study (SHHS) participants using the following stage designations: wake after sleep onset (WASO), non-rapid eye movement (NREM) sleep, and REM sleep. We show that individual patient hypnograms contain insufficient number of bouts to adequately describe the transition kinetics, necessitating pooling of data. We compared a control group of individuals free of medications, obstructive sleep apnea (OSA), medical co-morbidities, or sleepiness (n = 374) with mild (n = 496) or severe OSA (n = 338). WASO, REM sleep, and NREM sleep bout durations exhibited multi-exponential temporal dynamics. The presence of OSA accelerated the "decay" rate of NREM and REM sleep bouts, resulting in instability manifesting as shorter bouts and increased number of stage transitions. For WASO bouts, previously attributed to a power law process, a multi-exponential decay described the data well. Simulations demonstrated that a multi-exponential process can mimic a power law distribution. OSA alters sleep architecture dynamics by decreasing the temporal stability of NREM and REM sleep bouts. Multi-exponential fitting is superior to routine mono-exponential fitting, and may thus provide improved predictive metrics of sleep continuity. However, because a single night of sleep contains insufficient transitions to characterize these dynamics, extended monitoring of sleep, probably at home, would be necessary for individualized clinical application.

Kinetic study of the plastoquinone pool availability correlated with H2O2 release in seawater and antioxidant responses in the red alga Kappaphycus alvarezii exposed to single or combined high light, chilling and chemical stresses.

PubMed

Barros, Marcelo P; Necchi, Orlando; Colepicolo, Pio; Pedersén, Marianne

2006-11-01

Under biotic/abiotic stresses, the red alga Kappaphycus alvarezii reportedly releases massive amounts of H(2)O(2) into the surrounding seawater. As an essential redox signal, the role of chloroplast-originated H(2)O(2) in the orchestration of overall antioxidant responses in algal species has thus been questioned. This work purported to study the kinetic decay profiles of the redox-sensitive plastoquinone pool correlated to H(2)O(2) release in seawater, parameters of oxidative lesions and antioxidant enzyme activities in the red alga Kappaphycus alvarezii under the single or combined effects of high light, low temperature, and sub-lethal doses of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), which are inhibitors of the thylakoid electron transport system. Within 24 h, high light and chilling stresses distinctly affected the availability of the PQ pool for photosynthesis, following Gaussian and exponential kinetic profiles, respectively, whereas combined stimuli were mostly reflected in exponential decays. No significant correlation was found in a comparison of the PQ pool levels after 24 h with either catalase (CAT) or ascorbate peroxidase (APX) activities, although the H(2)O(2) concentration in seawater (R=0.673), total superoxide dismutase activity (R=0.689), and particularly indexes of protein (R=0.869) and lipid oxidation (R=0.864), were moderately correlated. These data suggest that the release of H(2)O(2) from plastids into seawater possibly impaired efficient and immediate responses of pivotal H(2)O(2)-scavenging activities of CAT and APX in the red alga K. alvarezii, culminating in short-term exacerbated levels of protein and lipid oxidation. These facts provided a molecular basis for the recognized limited resistance of the red alga K. alvarezii under unfavorable conditions, especially under chilling stress.

Ammonium Removal from Aqueous Solutions by Clinoptilolite: Determination of Isotherm and Thermodynamic Parameters and Comparison of Kinetics by the Double Exponential Model and Conventional Kinetic Models

PubMed Central

Tosun, İsmail

2012-01-01

The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R2) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients. PMID:22690177

Ammonium removal from aqueous solutions by clinoptilolite: determination of isotherm and thermodynamic parameters and comparison of kinetics by the double exponential model and conventional kinetic models.

PubMed

Tosun, Ismail

2012-03-01

The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R(2)) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients.

Compactness and robustness: Applications in the solution of integral equations for chemical kinetics and electromagnetic scattering

NASA Astrophysics Data System (ADS)

Zhou, Yajun

This thesis employs the topological concept of compactness to deduce robust solutions to two integral equations arising from chemistry and physics: the inverse Laplace problem in chemical kinetics and the vector wave scattering problem in dielectric optics. The inverse Laplace problem occurs in the quantitative understanding of biological processes that exhibit complex kinetic behavior: different subpopulations of transition events from the "reactant" state to the "product" state follow distinct reaction rate constants, which results in a weighted superposition of exponential decay modes. Reconstruction of the rate constant distribution from kinetic data is often critical for mechanistic understandings of chemical reactions related to biological macromolecules. We devise a "phase function approach" to recover the probability distribution of rate constants from decay data in the time domain. The robustness (numerical stability) of this reconstruction algorithm builds upon the continuity of the transformations connecting the relevant function spaces that are compact metric spaces. The robust "phase function approach" not only is useful for the analysis of heterogeneous subpopulations of exponential decays within a single transition step, but also is generalizable to the kinetic analysis of complex chemical reactions that involve multiple intermediate steps. A quantitative characterization of the light scattering is central to many meteoro-logical, optical, and medical applications. We give a rigorous treatment to electromagnetic scattering on arbitrarily shaped dielectric media via the Born equation: an integral equation with a strongly singular convolution kernel that corresponds to a non-compact Green operator. By constructing a quadratic polynomial of the Green operator that cancels out the kernel singularity and satisfies the compactness criterion, we reveal the universality of a real resonance mode in dielectric optics. Meanwhile, exploiting the properties of compact operators, we outline the geometric and physical conditions that guarantee a robust solution to the light scattering problem, and devise an asymptotic solution to the Born equation of electromagnetic scattering for arbitrarily shaped dielectric in a non-perturbative manner.

Evaluation of leaf litter leaching kinetics through commonly-used mathematical models

NASA Astrophysics Data System (ADS)

Montoya, J. V.; Bastianoni, A.; Mendez, C.; Paolini, J.

2012-04-01

Leaching is defined as the abiotic process by which soluble compounds of the litter are released into the water. Most studies dealing with leaf litter breakdown and leaching kinetics apply the single exponential decay model since it corresponds well with the understanding of the biology of decomposition. However, during leaching important mass losses occur and mathematical models often fail in describing this process adequately. During the initial hours of leaching leaf litter experience high decay rates which are not properly modelled. Adjusting leaching losses to mathematical models has not been investigated thoroughly and the use of models assuming constant decay rates leads to inappropriate assessments of leaching kinetics. We aim to describe, assess, and compare different leaching kinetics models fitted to leaf litter mass losses from six Neotropical riparian forest species. Leaf litter from each species was collected in the lower reaches of San Miguel stream in Northern Venezuela. Air-dried leaves from each species were incubated in 250 ml of water in the dark at room temperature. At 1h, 6h, 1d, 2d, 4d, 8d and 15d, three jars were removed from the assay in a no-replacement experimental design. At each time leaves from each jar were removed and oven-dried. Afterwards, dried up leaves were weighed and remaining dry mass was determined and expressed as ash-free dry mass. Mass losses of leaf litter showed steep declines for the first two days followed by a steady decrease in mass loss. Data was fitted to three different models: single-exponential, power and rational. Our results showed that the mass loss predicted with the single-exponential model did not reflect the real data at any stage of the leaching process. The power model showed a better adjustment, but fails predicting successfully the behavior during leaching's early stages. To evaluate the performance of our models we used three criteria: Adj-R2, Akaike's Information Criteria (AIC), and residual distribution. Higher Adj-R2 were obtained for the power and the rational-type models. However, when AIC and residuals distribution were used, the only model that could satisfactory predict the behavior of our dataset was the rational-type. Even if the Adj-R2 was higher for some species when using the power model compared to the rational-type; our results showed that this criterion alone cannot demonstrate the predicting performance of any model. Usually Adj-R2 is used when assessing the goodness of fit for any mathematical model disregarding the fact that a good Adj-R2 could be obtained even when statistical assumptions required for the validity of the model are not satisfied. Our results showed that sampling at the initial stages of leaching is necessary to adequately describe this process. We also provided evidence that using traditional mathematical models is not the best option to evaluate leaching kinetics because of its mathematical inability to properly describe the abrupt changes that occur during the early stages of leaching. We also found useful applying different criteria to evaluate the goodness-of-fit and performance of any model considered taking into account both statistical and biological meaning of the results.

Analytical Description of Degradation-Relaxation Transformations in Nanoinhomogeneous Spinel Ceramics.

PubMed

Shpotyuk, O; Brunner, M; Hadzaman, I; Balitska, V; Klym, H

2016-12-01

Mathematical models of degradation-relaxation kinetics are considered for jammed thick-film systems composed of screen-printed spinel Cu 0.1 Ni 0.1 Co 1.6 Mn 1.2 O 4 and conductive Ag or Ag-Pd alloys. Structurally intrinsic nanoinhomogeneous ceramics due to Ag and Ag-Pd diffusing agents embedded in a spinel phase environment are shown to define governing kinetics of thermally induced degradation under 170 °C obeying an obvious non-exponential behavior in a negative relative resistance drift. The characteristic stretched-to-compressed exponential crossover is detected for degradation-relaxation kinetics in thick-film systems with conductive contacts made of Ag-Pd and Ag alloys. Under essential migration of a conductive phase, Ag penetrates thick-film spinel ceramics via a considerable two-step diffusing process.

Coupling DAEM and CFD for simulating biomass fast pyrolysis in fluidized beds

DOE PAGES

Xiong, Qingang; Zhang, Jingchao; Wiggins, Gavin; ...

2015-12-03

We report results from computational simulations of an experimental, lab-scale bubbling bed biomass pyrolysis reactor that include a distributed activation energy model (DAEM) for the kinetics. In this study, we utilized multiphase computational fluid dynamics (CFD) to account for the turbulent hydrodynamics, and this was combined with the DAEM kinetics in a multi-component, multi-step reaction network. Our results indicate that it is possible to numerically integrate the coupled CFD–DAEM system without significantly increasing computational overhead. It is also clear, however, that reactor operating conditions, reaction kinetics, and multiphase flow dynamics all have major impacts on the pyrolysis products exiting themore » reactor. We find that, with the same pre-exponential factors and mean activation energies, inclusion of distributed activation energies in the kinetics can shift the predicted average value of the exit vapor-phase tar flux and its statistical distribution, compared to single-valued activation-energy kinetics. Perhaps the most interesting observed trend is that increasing the diversity of the DAEM activation energies appears to increase the mean tar yield, all else being equal. As a result, these findings imply that accurate resolution of the reaction activation energy distributions will be important for optimizing biomass pyrolysis processes.« less

Quasiperiodic energy dependence of exciton relaxation kinetics in the sexithiophene crystal.

PubMed

Petelenz, Piotr; Zak, Emil

2014-10-16

Femtosecond kinetics of fluorescence rise in the sexithiophene crystal is studied on a microscopic model of intraband relaxation, where exciton energy is assumed to be dissipated by phonon-accompanied scattering, with the rates calculated earlier. The temporal evolution of the exciton population is described by a set of kinetic equations, solved numerically to yield the population buildup at the band bottom. Not only the time scale but also the shape of the rise curves is found to be unusually sensitive to excitation energy, exhibiting unique quasiperiodic dependence thereon, which is rationalized in terms of the underlying model. Further simulations demonstrate that the main conclusions are robust with respect to experimental factors such as finite temperature and inherent spectral broadening of the exciting pulse, while the calculated fluorescence rise times are found to be in excellent agreement with experimental data available to date. As the rise profiles are composed of a number of exponential contributions, which varies with excitation energy, the common practice of characterizing the population buildup in the emitting state by a single value of relaxation time turns out to be an oversimplification. New experiments giving further insight into the kinetics and mechanism of intraband exciton relaxation are suggested.

General mechanism of two-state protein folding kinetics.

PubMed

Rollins, Geoffrey C; Dill, Ken A

2014-08-13

We describe here a general model of the kinetic mechanism of protein folding. In the Foldon Funnel Model, proteins fold in units of secondary structures, which form sequentially along the folding pathway, stabilized by tertiary interactions. The model predicts that the free energy landscape has a volcano shape, rather than a simple funnel, that folding is two-state (single-exponential) when secondary structures are intrinsically unstable, and that each structure along the folding path is a transition state for the previous structure. It shows how sequential pathways are consistent with multiple stochastic routes on funnel landscapes, and it gives good agreement with the 9 order of magnitude dependence of folding rates on protein size for a set of 93 proteins, at the same time it is consistent with the near independence of folding equilibrium constant on size. This model gives estimates of folding rates of proteomes, leading to a median folding time in Escherichia coli of about 5 s.

Comparison of the open-close kinetics of the cloned inward rectifier K+ channel IRK1 and its point mutant (Q140E) in the pore region.

PubMed

Guo, L; Kubo, Y

1998-01-01

To test whether a single amino-acid residue at the center of pore region can dictate the difference of open-close kinetics in a steady-state at hyperpolarized potentials among members of the inward K+ channel family, the Q140E mutant of the inward rectifier K+ channel (IRK1) was made and its gating properties were compared with those of IRK1 wild type (Wt) in Xenopus oocytes. The distinct differences were observed only at the single channel level. The open time constant of mutant tau(o)(Q140E) at -80 mV was over ten-fold shorter than that of Wt tau(o)(Wt); in Wt, the closed time distribution was fitted with a sum of two exponentials (c-slow and c-fast), whereas it could be fitted with three exponentials (c-slow, c-fast, and additional c-extrafast) in Q140E. However, the time constant of burst duration of mutant tau(b)(Q140E) was close to tau(o)(Wt) and both showed a similarly strong voltage dependence, and a high sensitivity to pH0 in the absence of Mg02+, indicating that tau(b)(Q140E) is closely related to tau(o)(Wt). These results demonstrated that Q140E shortened the channel openings by acquiring an extra-fast closing state. From the analysis of the effects of cations on both Wt and Q140E, it was suggested that the transition from the open state to this extra-fast closing state was not due to the block by H+ or Mg2+ but possibly by extracellular K+.

Sulfur poisoning of hydrocarbon oxidation by palladium. M.S. Thesis

NASA Technical Reports Server (NTRS)

Baumgartner, A. J.

1975-01-01

Using a differential bed recycle reactor the oxidation of ethane and diethyl ketone by a Pd catalyst was studied at the 0-30 ppm level in air. In both cases first order kinetics were observed. The ethane oxidation rate was characterized n the Arrhenius form by a pre-exponential of 1.0 x 10 to the 8th power cm/sec and an E sub a of 27 kcal/mole. The diethyl ketone oxidation rate was characterized by a pre-exponential of 5.7 x -1000 cm/sec and E sub a of 14 kcal/mole. Poisoning of ethan oxidation was also investigated by hydrogen sulfide and to a smaller extent by the refrigerants Freon 22 and Gentron 142-B. Poisoning by Gentron 142-B was much more severe than by hydrogen sulfide. Kinetic experiments indicated that only the pre-exponential was changing.

The diffusion of a Ga atom on GaAs(001)β2(2 × 4): Local superbasin kinetic Monte Carlo

NASA Astrophysics Data System (ADS)

Lin, Yangzheng; Fichthorn, Kristen A.

2017-10-01

We use first-principles density-functional theory to characterize the binding sites and diffusion mechanisms for a Ga adatom on the GaAs(001)β 2(2 × 4) surface. Diffusion in this system is a complex process involving eleven unique binding sites and sixteen different hops between neighboring binding sites. Among the binding sites, we can identify four different superbasins such that the motion between binding sites within a superbasin is much faster than hops exiting the superbasin. To describe diffusion, we use a recently developed local superbasin kinetic Monte Carlo (LSKMC) method, which accelerates a conventional kinetic Monte Carlo (KMC) simulation by describing the superbasins as absorbing Markov chains. We find that LSKMC is up to 4300 times faster than KMC for the conditions probed in this study. We characterize the distribution of exit times from the superbasins and find that these are sometimes, but not always, exponential and we characterize the conditions under which the superbasin exit-time distribution should be exponential. We demonstrate that LSKMC simulations assuming an exponential superbasin exit-time distribution yield the same diffusion coefficients as conventional KMC.

Real-time imaging and kinetics measurements of focused ultrasound-induced extravasation in skeletal muscle using SPECT/CT.

PubMed

Sanches, Pedro Gomes; Rossin, Raffaella; Böhmer, Marcel; Tiemann, Klaus; Grüll, Holger

2013-06-28

Drugs need to overcome several biological barriers such as the endothelium and cellular membranes in order to reach their target. Promising new therapeutics, many of which are charged and macromolecular, are not able to passively extravasate, let alone cross cell membranes, and stay mainly in the blood pool upon intravenous injection until clearance. Using focused ultrasound (fUS) in combination with circulating microbubbles (MBs) leads to temporary localized tissue permeabilization allowing extravasation of (macro) molecules from the vascular system. Thus, fUS is a promising approach for localized drug delivery. However, little is known about the permeabilization kinetics in skeletal muscle. In this study, we used single photon emission computed tomography (SPECT) to characterize the kinetics of extravasation of ¹¹¹In-labeled bovine serum albumin (BSA), a model macromolecular drug, in muscle treated with fUS and MBs. The same fUS protocol was applied to 6 groups of mice with different times, ∆t, between fUS application and BSA injection (∆t=-10, 2.5, 10, 30, 60, 90 min) followed by SPECT imaging. For ∆t ≤30min we observed an exponential accumulation of activity in an area of the treated muscle which extended to a volume larger than the fUS pattern with highest accumulation for short waiting times ∆t. The extent of extravasation decreased exponentially with increasing ∆t, with a calculated half-life of ca. 21 min, defining the time window of extravasation. The same treatment without MBs did not induce extravasation of BSA thus supporting MBs and drug co-injection strategies. These results provide essential information for the development of fUS based strategies for localized drug delivery. Copyright © 2013 Elsevier B.V. All rights reserved.

Graphical analysis for gel morphology II. New mathematical approach for stretched exponential function with β>1

NASA Astrophysics Data System (ADS)

Hashimoto, Chihiro; Panizza, Pascal; Rouch, Jacques; Ushiki, Hideharu

2005-10-01

A new analytical concept is applied to the kinetics of the shrinking process of poly(N-isopropylacrylamide) (PNIPA) gels. When PNIPA gels are put into hot water above the critical temperature, two-step shrinking is observed and the secondary shrinking of gels is fitted well by a stretched exponential function. The exponent β characterizing the stretched exponential is always higher than one, although there are few analytical concepts for the stretched exponential function with β>1. As a new interpretation for this function, we propose a superposition of step (Heaviside) function and a new distribution function of characteristic time is deduced.

Simplified Two-Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydorgen/Oxygen

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2005-01-01

A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two-time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (> 1 x 10(exp -20) moles/cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T4). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/air fuel and for the H2/O2. A similar correlation is also developed using data from NASA s Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T4) as a function of overall fuel/air ratio, pressure and initial temperature (T3). High values of the regression coefficient R2 are obtained.

Summary of Simplified Two Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydrogen/Oxygen

NASA Technical Reports Server (NTRS)

Marek, C. John; Molnar, Melissa

2005-01-01

A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (greater than l x 10(exp -20)) moles per cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T(sub 4)). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/Air fuel and for H2/O2. A similar correlation is also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T(sub 4)) as a function of overall fuel/air ratio, pressure and initial temperature (T(sub 3)). High values of the regression coefficient R squared are obtained.

The ATP hydrolysis and phosphate release steps control the time course of force development in rabbit skeletal muscle.

PubMed

Sleep, John; Irving, Malcolm; Burton, Kevin

2005-03-15

The time course of isometric force development following photolytic release of ATP in the presence of Ca(2+) was characterized in single skinned fibres from rabbit psoas muscle. Pre-photolysis force was minimized using apyrase to remove contaminating ATP and ADP. After the initial force rise induced by ATP release, a rapid shortening ramp terminated by a step stretch to the original length was imposed, and the time course of the subsequent force redevelopment was again characterized. Force development after ATP release was accurately described by a lag phase followed by one or two exponential components. At 20 degrees C, the lag was 5.6 +/- 0.4 ms (s.e.m., n = 11), and the force rise was well fitted by a single exponential with rate constant 71 +/- 4 s(-1). Force redevelopment after shortening-restretch began from about half the plateau force level, and its single-exponential rate constant was 68 +/- 3 s(-1), very similar to that following ATP release. When fibres were activated by the addition of Ca(2+) in ATP-containing solution, force developed more slowly, and the rate constant for force redevelopment following shortening-restretch reached a maximum value of 38 +/- 4 s(-1) (n = 6) after about 6 s of activation. This lower value may be associated with progressive sarcomere disorder at elevated temperature. Force development following ATP release was much slower at 5 degrees C than at 20 degrees C. The rate constant of a single-exponential fit to the force rise was 4.3 +/- 0.4 s(-1) (n = 22), and this was again similar to that after shortening-restretch in the same activation at this temperature, 3.8 +/- 0.2 s(-1). We conclude that force development after ATP release and shortening-restretch are controlled by the same steps in the actin-myosin ATPase cycle. The present results and much previous work on mechanical-chemical coupling in muscle can be explained by a kinetic scheme in which force is generated by a rapid conformational change bracketed by two biochemical steps with similar rate constants -- ATP hydrolysis and the release of inorganic phosphate -- both of which combine to control the rate of force development.

Effects of proliferation on the decay of thermotolerance in Chinese hamster cells.

PubMed

Armour, E P; Li, G C; Hahn, G M

1985-09-01

Development and decay of thermotolerance were observed in Chinese hamster HA-1 cells. The thermotolerance kinetics of exponentially growing and fed plateau-phase cells were compared. Following a 10-min heat exposure at 45 degrees C, cells in both growth states had similar rates of development of tolerance to a subsequent 45-min exposure at 45 degrees C. This thermotolerant state started to decay between 12 and 24 hr after the initial heat exposure. The decay appeared to initiate slightly sooner in the exponentially growing cells when compared to the fed plateau-phase cells. During the decay phase, the rate of thermotolerance decay was similar in the two growth conditions. In other experiments, cells were induced to divide at a slower rate by chronic growth (3 months) in a low concentration of fetal calf serum. Under these low serum conditions cells became more sensitive to heat and the rate of decay of thermotolerance remained the same for exponentially growing cells. Plateau-phase cells were also more sensitive, but thermotolerance decayed more rapidly in these cells. Although dramatic cell cycle perturbations were seen in the exponentially growing cells, these changes appeared not to be related to thermotolerance kinetics.

X-ray detection capability of a BaCl{sub 2} single crystal scintillator

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

Koshimizu, Masanori; CREST, Japan Science and Technology Agency, Sanbancho, Chiyoda-ku, Tokyo 102-0075; Onodera, Kazuya

2012-01-15

The x-ray detection capability of a scintillation detector equipped with a BaCl{sub 2} single crystal was evaluated. The scintillation decay kinetics can be expressed by a sum of two exponential decay components. The fast and slow components have lifetimes of 1.5 and 85 ns, respectively. The total light output is 5% that of YAP:Ce. A subnanosecond timing resolution was obtained. The detection efficiency of a 67.41 keV x-ray is 87% for a detector equipped with a BaCl{sub 2} crystal 6-mm thick. Thus, excellent timing resolution and high detection efficiency can be simultaneously achieved. Additionally, luminescence decay characteristics under vacuum ultravioletmore » excitation have been investigated. Radiative decay of self-trapped excitons is thought to be responsible for the fast scintillation component.« less

Spectroscopic study of shock-induced decomposition in ammonium perchlorate single crystals.

PubMed

Gruzdkov, Y A; Winey, J M; Gupta, Y M

2008-05-01

Time-resolved Raman scattering measurements were performed on ammonium perchlorate (AP) single crystals under stepwise shock loading. For particular temperature and pressure conditions, the intensity of the Raman spectra in shocked AP decayed exponentially with time. This decay is attributed to shock-induced chemical decomposition in AP. A series of shock experiments, reaching peak stresses from 10-18 GPa, demonstrated that higher stresses inhibit decomposition while higher temperatures promote it. No orientation dependence was found when AP crystals were shocked normal to the (210) and (001) crystallographic planes. VISAR (velocity interferometer system for any reflector) particle velocity measurements and time-resolved optical extinction measurements carried out to verify these observations are consistent with the Raman data. The combined kinetic and spectroscopic results are consistent with a proton-transfer reaction as the first decomposition step in shocked AP.

On the modeling of breath-by-breath oxygen uptake kinetics at the onset of high-intensity exercises: simulated annealing vs. GRG2 method.

PubMed

Bernard, Olivier; Alata, Olivier; Francaux, Marc

2006-03-01

Modeling in the time domain, the non-steady-state O2 uptake on-kinetics of high-intensity exercises with empirical models is commonly performed with gradient-descent-based methods. However, these procedures may impair the confidence of the parameter estimation when the modeling functions are not continuously differentiable and when the estimation corresponds to an ill-posed problem. To cope with these problems, an implementation of simulated annealing (SA) methods was compared with the GRG2 algorithm (a gradient-descent method known for its robustness). Forty simulated Vo2 on-responses were generated to mimic the real time course for transitions from light- to high-intensity exercises, with a signal-to-noise ratio equal to 20 dB. They were modeled twice with a discontinuous double-exponential function using both estimation methods. GRG2 significantly biased two estimated kinetic parameters of the first exponential (the time delay td1 and the time constant tau1) and impaired the precision (i.e., standard deviation) of the baseline A0, td1, and tau1 compared with SA. SA significantly improved the precision of the three parameters of the second exponential (the asymptotic increment A2, the time delay td2, and the time constant tau2). Nevertheless, td2 was significantly biased by both procedures, and the large confidence intervals of the whole second component parameters limit their interpretation. To compare both algorithms on experimental data, 26 subjects each performed two transitions from 80 W to 80% maximal O2 uptake on a cycle ergometer and O2 uptake was measured breath by breath. More than 88% of the kinetic parameter estimations done with the SA algorithm produced the lowest residual sum of squares between the experimental data points and the model. Repeatability coefficients were better with GRG2 for A1 although better with SA for A2 and tau2. Our results demonstrate that the implementation of SA improves significantly the estimation of most of these kinetic parameters, but a large inaccuracy remains in estimating the parameter values of the second exponential.

Habitual exercise training in older adults offsets the age-related prolongation in leg vasodilator kinetics during single limb lower body exercise.

PubMed

Hughes, William E; Kruse, Nicholas T; Ueda, Kenichi; Casey, Darren P

2018-06-01

We tested the hypothesis that aging is associated with prolonged leg vasodilator kinetics and habitual exercise training in older adults improves these responses relative to untrained older adults. Additionally, we examined the relationship between contraction-induced rapid onset vasodilation (ROV) and vasodilator kinetics. Young (n=10), older untrained (n=13) and older trained (n=14) adults performed single and rhythmic knee-extension contractions at 20% and 40% work-rate maximum (WR max ). Femoral artery diameter and mean blood velocity were measured by Doppler ultrasound. Vascular conductance (VC; ml·min -1 ·mmHg-1) was calculated using blood flow (ml·min -1 ) and mean arterial pressure (mmHg). The primary outcome was the kinetic response (mean response time; MRT), modeled using an exponential model, expressed as the number of duty cycles to change 63% of the steady-state amplitude. There was no age or training related differences in VC MRT between the groups at 20% WR max . Older untrained adults exhibited prolonged VC MRT at 40% WR max relative to young (37{plus minus}16 vs. 24{plus minus}10 duty-cycles; P<0.05) and older trained adults (37{plus minus}16 vs. 23{plus minus}14 duty-cycles; P<0.05). There were no differences in VC MRT between young and older trained adults at 40% WR max (P=0.96). There were no associations between peak ROV and VC MRT at 20% or 40% WR max (r=-0.08 and 0.22; P=0.67 and 0.20, respectively) in the group as a whole. Our data suggest 1) advancing age prolongs leg vasodilator kinetics; 2) habitual exercise training in older adults offsets this age-related prolongation; and 3) contraction-induced ROV is not related to vasodilator kinetics within a group of young and older adults.

Kinetic model-based feed-forward controlled fed-batch fermentation of Lactobacillus rhamnosus for the production of lactic acid from Arabic date juice.

PubMed

Choi, Minsung; Al-Zahrani, Saeed M; Lee, Sang Yup

2014-06-01

Arabic date is overproduced in Arabic countries such as Saudi Arabia and Iraq and is mostly composed of sugars (70-80 wt%). Here we developed a fed-batch fermentation process by using a kinetic model for the efficient production of lactic acid to a high concentration from Arabic date juice. First, a kinetic model of Lactobacillus rhamnosus grown on date juice in batch fermentation was constructed in EXCEL so that the estimation of parameters and simulation of the model can be easily performed. Then, several fed-batch fermentations were conducted by employing different feeding strategies including pulsed feeding, exponential feeding, and modified exponential feeding. Based on the results of fed-batch fermentations, the kinetic model for fed-batch fermentation was also developed. This new model was used to perform feed-forward controlled fed-batch fermentation, which resulted in the production of 171.79 g l(-1) of lactic acid with the productivity and yield of 1.58 and 0.87 g l(-1) h(-1), respectively.

Evaluation of the recrystallization kinetics of hot-melt extruded polymeric solid dispersions using an improved Avrami equation

PubMed Central

Feng, Xin; Ye, Xingyou; Park, Jun-Bom; Lu, Wenli; Morott, Joe; Beissner, Brad; Lian, Zhuoyang John; Pinto, Elanor; Bi, Vivian; Porter, Stu; Durig, Tom; Majumdar, Soumyajit; Repka, Michael A.

2017-01-01

The recrystallization of an amorphous drug in a solid dispersion system could lead to a loss in the drug solubility and bioavailability. The primary objective of the current research was to use an improved kinetic model to evaluate the recrystallization kinetics of amorphous structures and to further understand the factors influencing the physical stability of amorphous solid dispersions. Amorphous solid dispersions of fenofibrate with different molecular weights of hydroxypropylcellulose, HPC (Klucel™ LF, EF, ELF) were prepared utilizing hot-melt extrusion technology. Differential scanning calorimetry was utilized to quantitatively analyze the extent of recrystallization in the samples stored at different temperatures and relative humidity (RH) conditions. The experimental data were fitted into the improved kinetics model of a modified Avrami equation to calculate the recrystallization rate constants. Klucel LF, the largest molecular weight among the HPCs used, demonstrated the greatest inhibition of fenofibrate recrystallization. Additionally, the recrystallization rate (k) decreased with increasing polymer content, however exponentially increased with higher temperature. Also k increased linearly rather than exponentially over the range of RH studied. PMID:25224341

Evaluation of the recrystallization kinetics of hot-melt extruded polymeric solid dispersions using an improved Avrami equation.

PubMed

Feng, Xin; Ye, Xingyou; Park, Jun-Bom; Lu, Wenli; Morott, Joe; Beissner, Brad; Lian, Zhuoyang John; Pinto, Elanor; Bi, Vivian; Porter, Stu; Durig, Tom; Majumdar, Soumyajit; Repka, Michael A

2015-01-01

The recrystallization of an amorphous drug in a solid dispersion system could lead to a loss in the drug solubility and bioavailability. The primary objective of the current research was to use an improved kinetic model to evaluate the recrystallization kinetics of amorphous structures and to further understand the factors influencing the physical stability of amorphous solid dispersions. Amorphous solid dispersions of fenofibrate with different molecular weights of hydroxypropylcellulose, HPC (Klucel™ LF, EF, ELF) were prepared utilizing hot-melt extrusion technology. Differential scanning calorimetry was utilized to quantitatively analyze the extent of recrystallization in the samples stored at different temperatures and relative humidity (RH) conditions. The experimental data were fitted into the improved kinetics model of a modified Avrami equation to calculate the recrystallization rate constants. Klucel LF, the largest molecular weight among the HPCs used, demonstrated the greatest inhibition of fenofibrate recrystallization. Additionally, the recrystallization rate (k) decreased with increasing polymer content, however exponentially increased with higher temperature. Also k increased linearly rather than exponentially over the range of RH studied.

Shear-induced conformational ordering, relaxation, and crystallization of isotactic polypropylene.

PubMed

An, Haining; Li, Xiangyang; Geng, Yong; Wang, Yunlong; Wang, Xiao; Li, Liangbin; Li, Zhongming; Yang, Chuanlu

2008-10-02

The shear-induced coil-helix transition of isotactic polypropylene (iPP) has been studied with time-resolved Fourier transform infrared spectroscopy at various temperatures. The effects of temperature, shear rate, and strain on the coil-helix transition were studied systematically. The induced conformational order increases with the shear rate and strain. A threshold of shear strain is required to induce conformational ordering. High temperature reduces the effect of shear on the conformational order, though a simple correlation was not found. Following the shear-induced conformational ordering, relaxation of helices occurs, which follows the first-order exponential decay at temperatures well above the normal melting point of iPP. The relaxation time versus temperature is fitted with an Arrhenius law, which generates an activation energy of 135 kJ/mol for the helix-coil transition of iPP. At temperatures around the normal melting point, two exponential decays are needed to fit well on the relaxation kinetic of helices. This suggests that two different states of helices are induced by shear: (i) isolated single helices far away from each other without interactions, which have a fast relaxation kinetic; (ii) aggregations of helices or helical bundles with strong interactions among each other, which have a much slower relaxation process. The helical bundles are assumed to be the precursors of nuclei for crystallization. The different helix concentrations and distributions are the origin of the three different processes of crystallization after shear. The correlation between the shear-induced conformational order and crystallization is discussed.

Cross-catalytic hairpin assembly-based exponential signal amplification for CRET assay with low background noise.

PubMed

Yue, Shuzhen; Zhao, Tingting; Qi, Hongjie; Yan, Yongcun; Bi, Sai

2017-08-15

A toehold-mediated strand displacement (TMSD)-based cross-catalytic hairpin assembly (C-CHA) is demonstrated in this study, achieving exponential amplification of nucleic acids. Functionally, this system consists of four hairpins (H1, H2, H3 and H4) and one single-stranded initiator (I). Upon the introduction of I, the first CHA reaction (CHA1) is triggered, leading to the self-assembly of hybrid H1·H2 that then initiates the second CHA reaction (CHA2) to obtain the hybrid H3·H4. Since the single-stranded region in H3·H4 is identical to I, a new CHA1 is initiated, which thus achieves cross operation of CHA1 and CHA2 and exponential growth kinetics. Interestingly, because the C-CHA performs in a cascade manner, this system can be considered as multi-level molecular logic circuits with feedback mechanism. Moreover, through incorporating G-quadruplex subunits and fluorescein isothiocyanate (FITC) in the product of H1·H2, this C-CHA is readily utilized to fabricate a chemiluminescence resonance energy transfer (CRET) biosensing platform, achieving sensitive and selective detection of DNA and microRNA in real samples. Since the high background signal induced by FITC in the absence of initiator is greatly reduced through labeling quencher in H1, the signal-to-noise ratio and detection sensitivity are improved significantly. Therefore, our proposed C-CHA protocol holds a great potential for further applications in not only building complex autonomous systems but also the development of biosensing platforms and DNA nanotechnology. Copyright © 2017 Elsevier B.V. All rights reserved.

General Mechanism of Two-State Protein Folding Kinetics

PubMed Central

Rollins, Geoffrey C.; Dill, Ken A.

2016-01-01

We describe here a general model of the kinetic mechanism of protein folding. In the Foldon Funnel Model, proteins fold in units of secondary structures, which form sequentially along the folding pathway, stabilized by tertiary interactions. The model predicts that the free energy landscape has a volcano shape, rather than a simple funnel, that folding is two-state (single-exponential) when secondary structures are intrinsically unstable, and that each structure along the folding path is a transition state for the previous structure. It shows how sequential pathways are consistent with multiple stochastic routes on funnel landscapes, and it gives good agreement with the 9 order of magnitude dependence of folding rates on protein size for a set of 93 proteins, at the same time it is consistent with the near independence of folding equilibrium constant on size. This model gives estimates of folding rates of proteomes, leading to a median folding time in Escherichia coli of about 5 s. PMID:25056406

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

Noe, F; Diadone, Isabella; Lollmann, Marc

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is dynamical fingerprints which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observedmore » relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation.« less

Kinetic and Stochastic Models of 1D yeast ``prions"

NASA Astrophysics Data System (ADS)

Kunes, Kay

2005-03-01

Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeasts have proteins, which can undergo similar reconformation and aggregation processes to PrP; yeast ``prions" are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein (1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics along with our own stochastic approach (2). Both models assume reconformation only upon aggregation, and include aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates.

Effects of Nickel and Cobalt on Kinetics of Methanol Conversion by Methanogenic Sludge as Assessed by On-Line CH4 Monitoring

PubMed Central

Gonzalez-Gil, Graciela; Kleerebezem, Robbert; Lettinga, Gatze

1999-01-01

When metals were added in a pulse mode to methylotrophic-methanogenic biomass, three methane production rate phases were recognized. Increased concentrations of Ni and Co accelerated the initial exponential and final arithmetic increases in the methane production rate and reduced the temporary decrease in the rate. When Ni and Co were added continuously, the temporary decrease phase was eliminated and the exponential production rate increased. We hypothesize that the temporary decrease in the methane production rate and the final arithmetic increase in the methane production rate were due to micronutrient limitations and that the precipitation-dissolution kinetics of metal sulfides may play a key role in the biovailability of these compounds. PMID:10103284

Effects of nickel and cobalt on kinetics of methanol conversion by methanogenic sludge as assessed by on-line CH4 monitoring.

PubMed

Gonzalez-Gil, G; Kleerebezem, R; Lettinga, G

1999-04-01

When metals were added in a pulse mode to methylotrophic-methanogenic biomass, three methane production rate phases were recognized. Increased concentrations of Ni and Co accelerated the initial exponential and final arithmetic increases in the methane production rate and reduced the temporary decrease in the rate. When Ni and Co were added continuously, the temporary decrease phase was eliminated and the exponential production rate increased. We hypothesize that the temporary decrease in the methane production rate and the final arithmetic increase in the methane production rate were due to micronutrient limitations and that the precipitation-dissolution kinetics of metal sulfides may play a key role in the biovailability of these compounds.

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.

Calculation of Rate Spectra from Noisy Time Series Data

PubMed Central

Voelz, Vincent A.; Pande, Vijay S.

2011-01-01

As the resolution of experiments to measure folding kinetics continues to improve, it has become imperative to avoid bias that may come with fitting data to a predetermined mechanistic model. Towards this end, we present a rate spectrum approach to analyze timescales present in kinetic data. Computing rate spectra of noisy time series data via numerical discrete inverse Laplace transform is an ill-conditioned inverse problem, so a regularization procedure must be used to perform the calculation. Here, we show the results of different regularization procedures applied to noisy multi-exponential and stretched exponential time series, as well as data from time-resolved folding kinetics experiments. In each case, the rate spectrum method recapitulates the relevant distribution of timescales present in the data, with different priors on the rate amplitudes naturally corresponding to common biases toward simple phenomenological models. These results suggest an attractive alternative to the “Occam’s razor” philosophy of simply choosing models with the fewest number of relaxation rates. PMID:22095854

Bridgman growth and scintillation properties of calcium tungstate single crystal

NASA Astrophysics Data System (ADS)

Wang, Zhenhai; Jiang, Linwen; Chen, Yaping; Chen, Peng; Chen, Hongbing; Mao, Rihua

2017-12-01

CaWO4 single crystal with large size was grown by Bridgman method. The results of transmission spectra show that the transmittance of CaWO4 crystal reaches 79-85% in 320-800 nm wavelength range. The refraction index is near 1.80 in visible and infrared region. CaWO4 crystal shows a broad emission band centered at 424 nm under X-ray excitation and centered at 416 nm under ultraviolet (λex = 280 nm) excitation. The decay kinetics of CaWO4 single crystal shows double-exponential decay with fast decay constant τ1 = 5.4 μs and slow decay constant τ2 = 177.1 μs. The energy resolution of CaWO4 crystal was found to be 31.6% in the net peak of 545.9 channel. Meanwhile, the absolute output is at the lever of 19,000 ± 1000 photons/MeV. The results indicate the scintillator of CaWO4 single crystal has great potential in the applications of high-energy physics and nuclear physics due to its high light output and great energy resolution.

Evidence for a kinetic heterogeneity in ligand binding to R-state haemoglobin Kempsey [Asp-G1(99) beta----Asn].

PubMed Central

Coletta, M; Brittain, T; Brunori, M

1986-01-01

Thermodynamic and kinetic properties of O2 and CO binding to haemoglobin (Hb) Kempsey [Asp-G1(99) beta----Asn] were investigated and the activation parameters for the two ligands were determined. At every temperature the O2-binding isotherms display a weak co-operativity, n ranging between 1.1 and 1.2, and dissociation kinetics show a single-exponential behaviour. O2-binding kinetics were studied at 25 degrees C by temperature jump and are characterized at each saturation (from Y = 0.31 to Y = 1.0) by two processes, a fast bimolecular one and a slow monomolecular one (tau -1 = 20 s-1), which contributes to approx. 30% of the whole relaxation amplitude at every Y. CO-binding kinetics to Hb Kempsey were followed at several temperatures by flash photolysis and stopped flow. The process is biphasic, as reported elsewhere [Bunn, Wohl, Bradley, Cooley & Gibson (1974) J. Biol. Chem. 249, 7402-7409], and the relative contributions of the two bimolecular rates to the whole process are only slightly affected by temperature. On taking account for the fraction of dimers at every protein concentration, the slow phase corresponds to approx. 50% of the ligand binding to tetramers. Correlation of these results with previous spectroscopic data leads to the hypothesis that the biphasic time course of CO binding may be attributed to alpha/beta heterogeneity of the R-state of tetrameric Hb Kempsey. PMID:3800943

The role of multivalency in the association kinetics of patchy particle complexes.

PubMed

Newton, Arthur C; Groenewold, Jan; Kegel, Willem K; Bolhuis, Peter G

2017-06-21

Association and dissociation of particles are elementary steps in many natural and technological relevant processes. For many such processes, the presence of multiple binding sites is essential. For instance, protein complexes and regular structures such as virus shells are formed from elementary building blocks with multiple binding sites. Here we address a fundamental question concerning the role of multivalency of binding sites in the association kinetics of such complexes. Using single replica transition interface sampling simulations, we investigate the influence of the multivalency on the binding kinetics and the association mechanism of patchy particles that form polyhedral clusters. When the individual bond strength is fixed, the kinetics naturally is very dependent on the multivalency, with dissociation rate constants exponentially decreasing with the number of bonds. In contrast, we find that when the total bond energy per particle is kept constant, association and dissociation rate constants turn out rather independent of multivalency, although of course still very dependent on the total energy. The association and dissociation mechanisms, however, depend on the presence and nature of the intermediate states. For instance, pathways that visit intermediate states are less prevalent for particles with five binding sites compared to the case of particles with only three bonds. The presence of intermediate states can lead to kinetic trapping and malformed aggregates. We discuss implications for natural forming complexes such as virus shells and for the design of artificial colloidal patchy particles.

The role of multivalency in the association kinetics of patchy particle complexes

NASA Astrophysics Data System (ADS)

Newton, Arthur C.; Groenewold, Jan; Kegel, Willem K.; Bolhuis, Peter G.

2017-06-01

Association and dissociation of particles are elementary steps in many natural and technological relevant processes. For many such processes, the presence of multiple binding sites is essential. For instance, protein complexes and regular structures such as virus shells are formed from elementary building blocks with multiple binding sites. Here we address a fundamental question concerning the role of multivalency of binding sites in the association kinetics of such complexes. Using single replica transition interface sampling simulations, we investigate the influence of the multivalency on the binding kinetics and the association mechanism of patchy particles that form polyhedral clusters. When the individual bond strength is fixed, the kinetics naturally is very dependent on the multivalency, with dissociation rate constants exponentially decreasing with the number of bonds. In contrast, we find that when the total bond energy per particle is kept constant, association and dissociation rate constants turn out rather independent of multivalency, although of course still very dependent on the total energy. The association and dissociation mechanisms, however, depend on the presence and nature of the intermediate states. For instance, pathways that visit intermediate states are less prevalent for particles with five binding sites compared to the case of particles with only three bonds. The presence of intermediate states can lead to kinetic trapping and malformed aggregates. We discuss implications for natural forming complexes such as virus shells and for the design of artificial colloidal patchy particles.

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

PubMed Central

Zhou, Rui; Maisuradze, Gia G.; Suñol, David; Todorovski, Toni; Macias, Maria J.; Xiao, Yi; Scheraga, Harold A.; Czaplewski, Cezary; Liwo, Adam

2014-01-01

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding. PMID:25489078

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

PubMed

Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam

2014-12-23

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

Kinetics of chromatid break repair in G2-human fibroblasts exposed to low- and high-LET radiations

NASA Technical Reports Server (NTRS)

Kawata, T.; Durante, M.; George, K.; Furusawa, Y.; Gotoh, E.; Takai, N.; Wu, H.; Cucinotta, F. A.

2001-01-01

The purpose of this study is to determine the kinetics of chromatid break rejoining following exposure to radiations of different quality. Exponentially growing human fibroblast cells AG1522 were irradiated with gamma-rays, energetic carbon (290 MeV/u), silicon (490 MeV/u) and iron (200 MeV/u, 600 MeV/u). Chromosomes were prematurely condensed using calyculin A. Prematurely condensed chromosomes were collected after several post-irradiation incubation times, ranging from 5 to 600 minutes, and the number of chromatid breaks and exchanges in G2 cells were scored. The relative biological effectiveness (RBE) for initial chromatid breaks per unit dose showed LET dependency having a peak at 55 keV/micrometers silicon (2.4) or 80 keV/micrometers carbon particles (2.4) and then decreased with increasing LET. The kinetics of chromatid break rejoining following low- or high-LET irradiation consisted of two exponential components. Chromatid breaks decreased rapidly after exposure, and then continued to decrease at a slower rate. The rejoining kinetics was similar for exposure to each type of radiation, although the rate of unrejoined breaks was higher for high-LET radiation. Chromatid exchanges were also formed quickly.

A Method for Decomposition of the Basic Reaction of Biological Macromolecules into Exponential Components

NASA Astrophysics Data System (ADS)

Barabash, Yu. M.; Lyamets, A. K.

2016-12-01

The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al. (J Mol Cell Biol 12:88-118, 1965). The representation of multiexponential kinetics of the basic reaction in the form of a sum of exponential functions (A(t)={sum}_{i=1}^n{a}_i{e}^{-{k}_it}) is a multidimensional optimization problem. To solve this problem, a gradient method of optimization with software determination of the amount of exponents and reasonable calculation time is developed. This method is used to analyze the kinetics of photoinduced electron transport in the reaction centers (RC) of purple bacteria and the fluorescence induction in the granum thylakoid membranes which share a common function of converting light energy.

Regimes of stability and scaling relations for the removal time in the asteroid belt: a simple kinetic model and numerical tests

NASA Astrophysics Data System (ADS)

Cubrovic, Mihailo

2005-02-01

We report on our theoretical and numerical results concerning the transport mechanisms in the asteroid belt. We first derive a simple kinetic model of chaotic diffusion and show how it gives rise to some simple correlations (but not laws) between the removal time (the time for an asteroid to experience a qualitative change of dynamical behavior and enter a wide chaotic zone) and the Lyapunov time. The correlations are shown to arise in two different regimes, characterized by exponential and power-law scalings. We also show how is the so-called “stable chaos” (exponential regime) related to anomalous diffusion. Finally, we check our results numerically and discuss their possible applications in analyzing the motion of particular asteroids.

Preparation of an exponentially rising optical pulse for efficient excitation of single atoms in free space.

PubMed

Dao, Hoang Lan; Aljunid, Syed Abdullah; Maslennikov, Gleb; Kurtsiefer, Christian

2012-08-01

We report on a simple method to prepare optical pulses with exponentially rising envelope on the time scale of a few ns. The scheme is based on the exponential transfer function of a fast transistor, which generates an exponentially rising envelope that is transferred first on a radio frequency carrier, and then on a coherent cw laser beam with an electro-optical phase modulator. The temporally shaped sideband is then extracted with an optical resonator and can be used to efficiently excite a single (87)Rb atom.

Velocity distributions of granular gases with drag and with long-range interactions.

PubMed

Kohlstedt, K; Snezhko, A; Sapozhnikov, M V; Aranson, I S; Olafsen, J S; Ben-Naim, E

2005-08-05

We study velocity statistics of electrostatically driven granular gases. For two different experiments, (i) nonmagnetic particles in a viscous fluid and (ii) magnetic particles in air, the velocity distribution is non-Maxwellian, and its high-energy tail is exponential, P(upsilon) approximately exp(-/upsilon/). This behavior is consistent with the kinetic theory of driven dissipative particles. For particles immersed in a fluid, viscous damping is responsible for the exponential tail, while for magnetic particles, long-range interactions cause the exponential tail. We conclude that velocity statistics of dissipative gases are sensitive to the fluid environment and to the form of the particle interaction.

Deriving sulfamethoxazole dissipation endpoints in pasture soils using first order and biphasic kinetic models.

PubMed

Srinivasan, Prakash; Sarmah, Ajit K; Rohan, Maheswaran

2014-08-01

Single first-order (SFO) kinetic model is often used to derive the dissipation endpoints of an organic chemical in soil. This model is used due to its simplicity and requirement by regulatory agencies. However, using the SFO model for all types of decay pattern could lead to under- or overestimation of dissipation endpoints when the deviation from first-order is significant. In this study the performance of three biphasic kinetic models - bi-exponential decay (BEXP), first-order double exponential decay (FODED), and first-order two-compartment (FOTC) models was evaluated using dissipation datasets of sulfamethoxazole (SMO) antibiotic in three different soils under varying concentration, depth, temperature, and sterile conditions. Corresponding 50% (DT50) and 90% (DT90) dissipation times for the antibiotics were numerically obtained and compared against those obtained using the SFO model. The fit of each model to the measured values was evaluated based on an array of statistical measures such as coefficient of determination (R(2)adj), root mean square error (RMSE), chi-square (χ(2)) test at 1% significance, Bayesian Information Criteria (BIC) and % model error. Box-whisker residual plots were also used to compare the performance of each model to the measured datasets. The antibiotic dissipation was successfully predicted by all four models. However, the nonlinear biphasic models improved the goodness-of-fit parameters for all datasets. Deviations from datasets were also often less evident with the biphasic models. The fits of FOTC and FODED models for SMO dissipation datasets were identical in most cases, and were found to be superior to the BEXP model. Among the biphasic models, the FOTC model was found to be the most suitable for obtaining the endpoints and could provide a mechanistic explanation for SMO dissipation in the soils. Copyright © 2014 Elsevier B.V. All rights reserved.

PH-dependence of detergent-induced hemolysis and vesiculation of erythrocytes.

PubMed

Chernitsky, E A; Rozin, V V; Senkovich, O A

2001-01-01

The influence of pH of the medium on the parameters of detergent-induced fast hemolysis and vesiculation of human erythrocytes was studied. In the range of pH 6.3-7.2 neither the extent nor the rate of the vesiculation induced by 25 microM sodium dodecyl sulfate (SDS) changed. However, a decrease of pH from 8.0 to 5.8 strongly modified both the extent and the rate of the hemolysis induced by SDS. Within the range of pH 8.0-6.4, the effect can be ascribed to the increase of the positive charge of the membrane. This could lead to the accumulation of the membrane-bound anion detergent and, hence, to the change of the hemolysis parameters. Non-charged detergent Triton X-100 did not display any pH-dependence. At pH between 6.4 and 5.8 the extent and rate of hemolysis changed in a complicated manner. The kinetic curves of hemolysis could be approximated by a single exponential within the pH range between 8.0 and 7.2. Upon further reduction of pH, a second exponential component, with a larger time constant, appeared in the kinetic curves. At 5.8 < pH < 7.2, the contribution of the "fast" hemolysis dropped virtually to zero, with pK about 6.0. This points to a structural transition of the membrane, possibly involving histidine. We suggest that the parameters of the detergent-induced hemolysis are sensitive to the changes of the charge and structural state of erythrocyte membrane.

Dynamics of HIV-1 Assembly and Release

PubMed Central

Ivanchenko, Sergey; Godinez, William J.; Lampe, Marko; Kräusslich, Hans-Georg; Eils, Roland; Rohr, Karl; Bräuchle, Christoph; Müller, Barbara; Lamb, Don C.

2009-01-01

Assembly and release of human immunodeficiency virus (HIV) occur at the plasma membrane of infected cells and are driven by the Gag polyprotein. Previous studies analyzed viral morphogenesis using biochemical methods and static images, while dynamic and kinetic information has been lacking until very recently. Using a combination of wide-field and total internal reflection fluorescence microscopy, we have investigated the assembly and release of fluorescently labeled HIV-1 at the plasma membrane of living cells with high time resolution. Gag assembled into discrete clusters corresponding to single virions. Formation of multiple particles from the same site was rarely observed. Using a photoconvertible fluorescent protein fused to Gag, we determined that assembly was nucleated preferentially by Gag molecules that had recently attached to the plasma membrane or arrived directly from the cytosol. Both membrane-bound and cytosol derived Gag polyproteins contributed to the growing bud. After their initial appearance, assembly sites accumulated at the plasma membrane of individual cells over 1–2 hours. Assembly kinetics were rapid: the number of Gag molecules at a budding site increased, following a saturating exponential with a rate constant of ∼5×10−3 s−1, corresponding to 8–9 min for 90% completion of assembly for a single virion. Release of extracellular particles was observed at ∼1,500±700 s after the onset of assembly. The ability of the virus to recruit components of the cellular ESCRT machinery or to undergo proteolytic maturation, or the absence of Vpu did not significantly alter the assembly kinetics. PMID:19893629

Direct recovery of regional tracer kinetics from temporally inconsistent dynamic ECT projections using dimension-reduced time-activity basis

NASA Astrophysics Data System (ADS)

Maltz, Jonathan S.

2000-11-01

We present an algorithm of reduced computational cost which is able to estimate kinetic model parameters directly from dynamic ECT sinograms made up of temporally inconsistent projections. The algorithm exploits the extreme degree of parameter redundancy inherent in linear combinations of the exponential functions which represent the modes of first-order compartmental systems. The singular value decomposition is employed to find a small set of orthogonal functions, the linear combinations of which are able to accurately represent all modes within the physiologically anticipated range in a given study. The reduced-dimension basis is formed as the convolution of this orthogonal set with a measured input function. The Moore-Penrose pseudoinverse is used to find coefficients of this basis. Algorithm performance is evaluated at realistic count rates using MCAT phantom and clinical 99mTc-teboroxime myocardial study data. Phantom data are modelled as originating from a Poisson process. For estimates recovered from a single slice projection set containing 2.5×105 total counts, recovered tissue responses compare favourably with those obtained using more computationally intensive methods. The corresponding kinetic parameter estimates (coefficients of the new basis) exhibit negligible bias, while parameter variances are low, falling within 30% of the Cramér-Rao lower bound.

Characterization of the kinetic arrest of martensitic transformation in Ni45Co5Mn36.8In13.2 melt-spun ribbons

NASA Astrophysics Data System (ADS)

Lino-Zapata, F. M.; Yan, H. L.; Ríos-Jara, D.; Sánchez Llamazares, J. L.; Zhang, Y. D.; Zhao, X.; Zuo, L.

2018-01-01

The kinetic arrest (KA) of martensitic transformation (MT) observed in Ni45Co5Mn36.8In13.2 melt-spun ribbons has been studied. These alloy ribbons show an ordered columnar-like grain microstructure with the longer grain axis growing perpendicular to ribbon plane and transform martensitically from a single austenitic (AST) parent phase with the L21-type crystal structure to a monoclinic incommensurate 6 M modulated martensite (MST). Results show that the volume fraction of austenite frozen into the martensitic matrix is proportional to the applied magnetic field. A fully arrest of the structural transition is found for a magnetic field of 7 T. The metastable character of the non-equilibrium field-cooled glassy state was characterized by introducing thermal and magnetic field fluctuations or measuring the relaxation of magnetization. The relaxation of magnetization from a field-cooled kinetically arrested state at 5 and 7 T follows the Kohlrausch-Williams-Watts (KWW) stretched exponential function with a β exponent around 0.95 indicating the weak metastable nature of the system under the strong magnetic fields. The relationship between the occurrence of exchange bias and the frozen fraction of AST into the MST matrix was studied.

Dynamical analysis for a scalar-tensor model with kinetic and nonminimal couplings

NASA Astrophysics Data System (ADS)

Granda, L. N.; Jimenez, D. F.

We study the autonomous system for a scalar-tensor model of dark energy with nonminimal coupling to curvature and nonminimal kinetic coupling to the Einstein tensor. The critical points describe important stable asymptotic scenarios including quintessence, phantom and de Sitter attractor solutions. Two functional forms for the coupling functions and the scalar potential were considered: power-law and exponential functions of the scalar field. For power-law couplings, the restrictions on stable quintessence and phantom solutions lead to asymptotic freedom regime for the gravitational interaction. For the exponential functions, the stable quintessence, phantom or de Sitter solutions allow asymptotic behaviors where the effective Newtonian coupling can reach either the asymptotic freedom regime or constant value. The phantom solutions could be realized without appealing to ghost degrees of freedom. Transient inflationary and radiation dominated phases can also be described.

Paradoxical Long-Timespan Opening of the Hole in Self-Supported Water Films of Nanometer Thickness.

PubMed

Barkay, Z; Bormashenko, E

2017-05-16

The opening of holes in self-supported thin (nanoscaled) water films has been investigated in situ with the environmental scanning electron microscope. The opening of a hole occurs within a two-stage process. In the first stage, the rim surrounding a hole is formed, resembling the process that is observed under the puncturing of soap bubbles. In the second stage, the exponential growth of the hole is observed, with a characteristic time of a dozen seconds. We explain the exponential kinetics of hole growth by the balance between inertia (gravity) and viscous dissipation. The kinetics of opening a microscaled hole is governed by the processes taking place in the nanothick bulk of the self-supported liquid film. Nanoparticles provide markers for the visualization of the processes occurring in self-supported thin nanoscale liquid films.

Kinetic Model for 1D aggregation of yeast ``prions''

NASA Astrophysics Data System (ADS)

Kunes, Kay; Cox, Daniel; Singh, Rajiv

2004-03-01

Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeast have proteins which can undergo similar reconformation and aggregation processes to PrP; yeast forms are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein(1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics(2). The model assumes reconformation only upon aggregation, and includes aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates. We will compare to a more realistic stochastic kinetics model and present prelimary attempts to describe recent experiments on SUP35 strains. *-Supported by U.S. Army Congressionally Mandated Research Fund. 1) P. Chien and J.S. Weissman, Nature 410, 223 (2001); http://online.kitp.ucsb.edu/online/bionet03/collins/. 2) J. Masel, V.A.> Jansen, M.A. Nowak, Biophys. Chem. 77, 139 (1999).

Modeling the germination kinetics of clostridium botulinum 56A spores as affected by temperature, pH, and sodium chloride.

PubMed

Chea, F P; Chen, Y; Montville, T J; Schaffner, D W

2000-08-01

The germination kinetics of proteolytic Clostridium botulinum 56A spores were modeled as a function of temperature (15, 22, 30 degrees C), pH (5.5, 6.0, 6.5), and sodium chloride (0.5, 2.0, 4.0%). Germination in brain heart infusion (BHI) broth was followed with phase-contrast microscopy. Data collected were used to develop the mathematical models. The germination kinetics expressed as cumulated fraction of germinated spores over time at each environmental condition were best described by an exponential distribution. Quadratic polynomial models were developed by regression analysis to describe the exponential parameter (time to 63% germination) (r2 = 0.982) and the germination extent (r2 = 0.867) as a function of temperature, pH, and sodium chloride. Validation experiments in BHI broth (pH: 5.75, 6.25; NaCl: 1.0, 3.0%; temperature: 18, 26 degrees C) confirmed that the model's predictions were within an acceptable range compared to the experimental results and were fail-safe in most cases.

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

PubMed

Cobbs, Gary

2012-08-16

Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of initial target concentration. Model 1 was found to be slightly more robust than model 2 giving better estimates of initial target concentration when estimation of parameters was done for qPCR curves with very different initial target concentration. Both models may be used to estimate the initial absolute concentration of target sequence when a standard curve is not available. It is argued that the kinetic approach to modeling and interpreting quantitative PCR data has the potential to give more precise estimates of the true initial target concentrations than other methods currently used for analysis of qPCR data. The two models presented here give a unified model of the qPCR process in that they explain the shape of the qPCR curve for a wide variety of initial target concentrations.

Braid Entropy of Two-Dimensional Turbulence

NASA Astrophysics Data System (ADS)

Francois, Nicolas; Xia, Hua; Punzmann, Horst; Faber, Benjamin; Shats, Michael

2015-12-01

The evolving shape of material fluid lines in a flow underlies the quantitative prediction of the dissipation and material transport in many industrial and natural processes. However, collecting quantitative data on this dynamics remains an experimental challenge in particular in turbulent flows. Indeed the deformation of a fluid line, induced by its successive stretching and folding, can be difficult to determine because such description ultimately relies on often inaccessible multi-particle information. Here we report laboratory measurements in two-dimensional turbulence that offer an alternative topological viewpoint on this issue. This approach characterizes the dynamics of a braid of Lagrangian trajectories through a global measure of their entanglement. The topological length of material fluid lines can be derived from these braids. This length is found to grow exponentially with time, giving access to the braid topological entropy . The entropy increases as the square root of the turbulent kinetic energy and is directly related to the single-particle dispersion coefficient. At long times, the probability distribution of is positively skewed and shows strong exponential tails. Our results suggest that may serve as a measure of the irreversibility of turbulence based on minimal principles and sparse Lagrangian data.

Braid Entropy of Two-Dimensional Turbulence

PubMed Central

Francois, Nicolas; Xia, Hua; Punzmann, Horst; Faber, Benjamin; Shats, Michael

2015-01-01

The evolving shape of material fluid lines in a flow underlies the quantitative prediction of the dissipation and material transport in many industrial and natural processes. However, collecting quantitative data on this dynamics remains an experimental challenge in particular in turbulent flows. Indeed the deformation of a fluid line, induced by its successive stretching and folding, can be difficult to determine because such description ultimately relies on often inaccessible multi-particle information. Here we report laboratory measurements in two-dimensional turbulence that offer an alternative topological viewpoint on this issue. This approach characterizes the dynamics of a braid of Lagrangian trajectories through a global measure of their entanglement. The topological length of material fluid lines can be derived from these braids. This length is found to grow exponentially with time, giving access to the braid topological entropy . The entropy increases as the square root of the turbulent kinetic energy and is directly related to the single-particle dispersion coefficient. At long times, the probability distribution of is positively skewed and shows strong exponential tails. Our results suggest that may serve as a measure of the irreversibility of turbulence based on minimal principles and sparse Lagrangian data. PMID:26689261

Subcritical carbon dioxide-water hydrolysis of sugarcane bagasse pith for reducing sugars production.

PubMed

Liang, Jiezhen; Chen, Xiaopeng; Wang, Linlin; Wei, Xiaojie; Wang, Huasheng; Lu, Songzhou; Li, Yunhua

2017-03-01

The aim of present study was to obtain total reducing sugars (TRS) by hydrolysis in subcritical CO 2 -water from sugarcane bagasse pith (SCBP), the fibrous residue remaining after papermaking from sugarcane bagasse. The optimum hydrolysis conditions were evaluated by L 16 (4 5 ) orthogonal experiments. The TRS yield achieved 45.8% at the optimal conditions: 200°C, 40min, 500rmin -1 , CO 2 initial pressure of 1MPa and liquid-to-solid ratio of 50:1. Fourier transform infrared spectrometry and two-dimensional heteronuclear single quantum coherence nuclear magnetic resonance were used to characterize hydrolysis liquor, treated and untreated SCBP, resulting in the removal of hemicelluloses to mainly produce xylose, glucose and arabinose during hydrolysis. The severity factors had no correlation to TRS yield, indicating that the simple kinetic processes of biomass solubilisation cannot perfectly describe the SCBP hydrolysis. The first-order kinetic model based on consecutive reaction was used to obtain rate constants, activation energies and pre-exponential factors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetics of the pyrolysis of arundo, sawdust, corn stover and switch grass biomass by thermogravimetric analysis using a multi-stage model.

PubMed

Biney, Paul O; Gyamerah, Michael; Shen, Jiacheng; Menezes, Bruna

2015-03-01

A new multi-stage kinetic model has been developed for TGA pyrolysis of arundo, corn stover, sawdust and switch grass that accounts for the initial biomass weight (W0). The biomass were decomposed in a nitrogen atmosphere from 23°C to 900°C in a TGA at a single 20°C/min ramp rate in contrast with the isoconversion technique. The decomposition was divided into multiple stages based on the absolute local minimum values of conversion derivative, (dx/dT), obtained from DTG curves. This resulted in three decomposition stages for arundo, corn stover and sawdust and four stages for switch grass. A linearized multi-stage model was applied to the TGA data for each stage to determine the pre-exponential factor, activation energy, and reaction order. The activation energies ranged from 54.7 to 60.9 kJ/mol, 62.9 to 108.7 kJ/mol, and 18.4 to 257.9 kJ/mol for the first, second and the third decomposition stages respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative Studies of the Pyrolytic and Kinetic Characteristics of Maize Straw and the Seaweed Ulva pertusa

PubMed Central

Ye, Naihao; Li, Demao; Chen, Limei; Zhang, Xiaowen; Xu, Dong

2010-01-01

Seaweed has attracted considerable attention as a potential biofuel feedstock. The pyrolytic and kinetic characteristics of maize straw and the seaweed Ulva pertusa were studied and compared using heating rates of 10, 30 and 50°C min−1 under an inert atmosphere. The activation energy, and pre-exponential factors were calculated by the Flynn-Wall-Ozawa (FWO), Kissinger-Akahira-Sunose (KAS) and Popescu methods. The kinetic mechanism was deduced by the Popescu method. The results indicate that there are three stages to the pyrolysis; dehydration, primary devolatilization and residual decomposition. There were significant differences in average activation energy, thermal stability, final residuals and reaction rates between the two materials. The primary devolatilization stage of U. pertusa can be described by the Avramic-Erofeev equation (n = 3), whereas that of maize straw can be described by the Mampel Power Law (n = 2). The average activation energy of maize straw and U. pertusa were 153.0 and 148.7 KJ mol−1, respectively. The pyrolysis process of U.pertusa would be easier than maize straw. And co-firing of the two biomass may be require less external heat input and improve process stability. There were minor kinetic compensation effects between the pre-exponential factors and the activation energy. PMID:20844751

Driven fragmentation of granular gases.

PubMed

Cruz Hidalgo, Raúl; Pagonabarraga, Ignacio

2008-06-01

The dynamics of homogeneously heated granular gases which fragment due to particle collisions is analyzed. We introduce a kinetic model which accounts for correlations induced at the grain collisions and analyze both the kinetics and relevant distribution functions these systems develop. The work combines analytical and numerical studies based on direct simulation Monte Carlo calculations. A broad family of fragmentation probabilities is considered, and its implications for the system kinetics are discussed. We show that generically these driven materials evolve asymptotically into a dynamical scaling regime. If the fragmentation probability tends to a constant, the grain number diverges at a finite time, leading to a shattering singularity. If the fragmentation probability vanishes, then the number of grains grows monotonously as a power law. We consider different homogeneous thermostats and show that the kinetics of these systems depends weakly on both the grain inelasticity and driving. We observe that fragmentation plays a relevant role in the shape of the velocity distribution of the particles. When the fragmentation is driven by local stochastic events, the long velocity tail is essentially exponential independently of the heating frequency and the breaking rule. However, for a Lowe-Andersen thermostat, numerical evidence strongly supports the conjecture that the scaled velocity distribution follows a generalized exponential behavior f(c) approximately exp(-cn) , with n approximately 1.2 , regarding less the fragmentation mechanisms.

A density functional theory model of mechanically activated silyl ester hydrolysis

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

Pill, Michael F.; Schmidt, Sebastian W.; Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098 Kiel

2014-01-28

To elucidate the mechanism of the mechanically activated dissociation of chemical bonds between carboxymethylated amylose (CMA) and silane functionalized silicon dioxide, we have investigated the dissociation kinetics of the bonds connecting CMA to silicon oxide surfaces with density functional calculations including the effects of force, solvent polarizability, and pH. We have determined the activation energies, the pre-exponential factors, and the reaction rate constants of candidate reactions. The weakest bond was found to be the silyl ester bond between the silicon and the alkoxy oxygen atom. Under acidic conditions, spontaneous proton addition occurs close to the silyl ester such that neutralmore » reactions become insignificant. Upon proton addition at the most favored position, the activation energy for bond hydrolysis becomes 31 kJ mol{sup −1}, which agrees very well with experimental observation. Heterolytic bond scission in the protonated molecule has a much higher activation energy. The experimentally observed bi-exponential rupture kinetics can be explained by different side groups attached to the silicon atom of the silyl ester. The fact that different side groups lead to different dissociation kinetics provides an opportunity to deliberately modify and tune the kinetic parameters of mechanically activated bond dissociation of silyl esters.« less

Rate laws of the self-induced aggregation kinetics of Brownian particles

NASA Astrophysics Data System (ADS)

Mondal, Shrabani; Sen, Monoj Kumar; Baura, Alendu; Bag, Bidhan Chandra

2016-03-01

In this paper we have studied the self induced aggregation kinetics of Brownian particles in the presence of both multiplicative and additive noises. In addition to the drift due to the self aggregation process, the environment may induce a drift term in the presence of a multiplicative noise. Then there would be an interplay between the two drift terms. It may account qualitatively the appearance of the different laws of aggregation process. At low strength of white multiplicative noise, the cluster number decreases as a Gaussian function of time. If the noise strength becomes appreciably large then the variation of cluster number with time is fitted well by the mono exponentially decaying function of time. For additive noise driven case, the decrease of cluster number can be described by the power law. But in case of multiplicative colored driven process, cluster number decays multi exponentially. However, we have explored how the rate constant (in the mono exponentially cluster number decaying case) depends on strength of interference of the noises and their intensity. We have also explored how the structure factor at long time depends on the strength of the cross correlation (CC) between the additive and the multiplicative noises.

Use of Continuous Exponential Families to Link Forms via Anchor Tests. Research Report. ETS RR-11-11

ERIC Educational Resources Information Center

Haberman, Shelby J.; Yan, Duanli

2011-01-01

Continuous exponential families are applied to linking test forms via an internal anchor. This application combines work on continuous exponential families for single-group designs and work on continuous exponential families for equivalent-group designs. Results are compared to those for kernel and equipercentile equating in the case of chained…

Exponential propagators for the Schrödinger equation with a time-dependent potential.

PubMed

Bader, Philipp; Blanes, Sergio; Kopylov, Nikita

2018-06-28

We consider the numerical integration of the Schrödinger equation with a time-dependent Hamiltonian given as the sum of the kinetic energy and a time-dependent potential. Commutator-free (CF) propagators are exponential propagators that have shown to be highly efficient for general time-dependent Hamiltonians. We propose new CF propagators that are tailored for Hamiltonians of the said structure, showing a considerably improved performance. We obtain new fourth- and sixth-order CF propagators as well as a novel sixth-order propagator that incorporates a double commutator that only depends on coordinates, so this term can be considered as cost-free. The algorithms require the computation of the action of exponentials on a vector similar to the well-known exponential midpoint propagator, and this is carried out using the Lanczos method. We illustrate the performance of the new methods on several numerical examples.

A Library of Selenourea Precursors to PbSe Nanocrystals with Size Distributions near the Homogeneous Limit

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

Campos, Michael P.; Hendricks, Mark P.; Beecher, Alexander N.

Here, we report a tunable library of N,N,N'-trisubstituted selenourea precursors and their reaction with lead oleate at 60–150 °C to form carboxylate-terminated PbSe nanocrystals in quantitative yields. Single exponential conversion kinetics can be tailored over 4 orders of magnitude by adjusting the selenourea structure. The wide range of conversion reactivity allows the extent of nucleation ([nanocrystal] = 4.6–56.7 μM) and the size following complete precursor conversion (d = 1.7–6.6 nm) to be controlled. Narrow size distributions (σ = 0.5–2%) are obtained whose spectral line widths are dominated (73–83%) by the intrinsic single particle spectral broadening, as observed using spectral holemore » burning measurements. Here, the intrinsic broadening decreases with increasing size (fwhm = 320–65 meV, d = 1.6–4.4 nm) that derives from exciton fine structure and exciton–phonon coupling rather than broadening caused by the size distribution.« less

A Library of Selenourea Precursors to PbSe Nanocrystals with Size Distributions near the Homogeneous Limit

DOE PAGES

Campos, Michael P.; Hendricks, Mark P.; Beecher, Alexander N.; ...

2017-01-19

Here, we report a tunable library of N,N,N'-trisubstituted selenourea precursors and their reaction with lead oleate at 60–150 °C to form carboxylate-terminated PbSe nanocrystals in quantitative yields. Single exponential conversion kinetics can be tailored over 4 orders of magnitude by adjusting the selenourea structure. The wide range of conversion reactivity allows the extent of nucleation ([nanocrystal] = 4.6–56.7 μM) and the size following complete precursor conversion (d = 1.7–6.6 nm) to be controlled. Narrow size distributions (σ = 0.5–2%) are obtained whose spectral line widths are dominated (73–83%) by the intrinsic single particle spectral broadening, as observed using spectral holemore » burning measurements. Here, the intrinsic broadening decreases with increasing size (fwhm = 320–65 meV, d = 1.6–4.4 nm) that derives from exciton fine structure and exciton–phonon coupling rather than broadening caused by the size distribution.« less

Kinetic market models with single commodity having price fluctuations

NASA Astrophysics Data System (ADS)

Chatterjee, A.; Chakrabarti, B. K.

2006-12-01

We study here numerically the behavior of an ideal gas like model of markets having only one non-consumable commodity. We investigate the behavior of the steady-state distributions of money, commodity and total wealth, as the dynamics of trading or exchange of money and commodity proceeds, with local (in time) fluctuations in the price of the commodity. These distributions are studied in markets with agents having uniform and random saving factors. The self-organizing features in money distribution are similar to the cases without any commodity (or with consumable commodities), while the commodity distribution shows an exponential decay. The wealth distribution shows interesting behavior: gamma like distribution for uniform saving propensity and has the same power-law tail, as that of the money distribution, for a market with agents having random saving propensity.

Fluorescence kinetics of Trp-Trp dipeptide and its derivatives in water via ultrafast fluorescence spectroscopy.

PubMed

Jia, Menghui; Yi, Hua; Chang, Mengfang; Cao, Xiaodan; Li, Lei; Zhou, Zhongneng; Pan, Haifeng; Chen, Yan; Zhang, Sanjun; Xu, Jianhua

2015-08-01

Ultrafast fluorescence dynamics of Tryptophan-Tryptophan (Trp-Trp/Trp2) dipeptide and its derivatives in water have been investigated using a picosecond resolved time correlated single photon counting (TCSPC) apparatus together with a femtosecond resolved upconversion spectrophotofluorometer. The fluorescence decay profiles at multiple wavelengths were fitted by a global analysis technique. Nanosecond fluorescence kinetics of Trp2, N-tert-butyl carbonyl oxygen-N'-aldehyde group-l-tryptophan-l-tryptophan (NBTrp2), l-tryptophan-l-tryptophan methyl ester (Trp2Me), and N-acetyl-l-tryptophan-l-tryptophan methyl ester (NATrp2Me) exhibit multi-exponential decays with the average lifetimes of 1.99, 3.04, 0.72 and 1.22ns, respectively. Due to the intramolecular interaction between two Trp residues, the "water relaxation" lifetime was observed around 4ps, and it is noticed that Trp2 and its derivatives also exhibit a new decay with a lifetime of ∼100ps, while single-Trp fluorescence decay in dipeptides/proteins shows 20-30ps. The intramolecular interaction lifetime constants of Trp2, NBTrp2, Trp2Me and NATrp2Me were then calculated to be 3.64, 0.93, 11.52 and 2.40ns, respectively. Candidate mechanisms (including heterogeneity, solvent relaxation, quasi static self-quenching or ET/PT quenching) have been discussed. Copyright © 2015. Published by Elsevier B.V.

Non-exponential kinetics of unfolding under a constant force.

PubMed

Bell, Samuel; Terentjev, Eugene M

2016-11-14

We examine the population dynamics of naturally folded globular polymers, with a super-hydrophobic "core" inserted at a prescribed point in the polymer chain, unfolding under an application of external force, as in AFM force-clamp spectroscopy. This acts as a crude model for a large class of folded biomolecules with hydrophobic or hydrogen-bonded cores. We find that the introduction of super-hydrophobic units leads to a stochastic variation in the unfolding rate, even when the positions of the added monomers are fixed. This leads to the average non-exponential population dynamics, which is consistent with a variety of experimental data and does not require any intrinsic quenched disorder that was traditionally thought to be at the origin of non-exponential relaxation laws.

Non-exponential kinetics of unfolding under a constant force

NASA Astrophysics Data System (ADS)

Bell, Samuel; Terentjev, Eugene M.

2016-11-01

We examine the population dynamics of naturally folded globular polymers, with a super-hydrophobic "core" inserted at a prescribed point in the polymer chain, unfolding under an application of external force, as in AFM force-clamp spectroscopy. This acts as a crude model for a large class of folded biomolecules with hydrophobic or hydrogen-bonded cores. We find that the introduction of super-hydrophobic units leads to a stochastic variation in the unfolding rate, even when the positions of the added monomers are fixed. This leads to the average non-exponential population dynamics, which is consistent with a variety of experimental data and does not require any intrinsic quenched disorder that was traditionally thought to be at the origin of non-exponential relaxation laws.

Kinetics of the mechanochemical synthesis of alkaline-earth metal amides

NASA Astrophysics Data System (ADS)

Garroni, Sebastiano; Takacs, Laszlo; Leng, Haiyan; Delogu, Francesco

2014-07-01

A phenomenological framework is developed to model the kinetics of the formation of alkaline-earth metal amides by the ball milling induced reaction of their hydrides with gaseous ammonia. It is shown that the exponential character of the kinetic curves is modulated by the increase of the total volume of the powder inside the reactor due to the substantially larger molar volume of the products compared to the reactants. It is claimed that the volume of powder effectively processed during each collision connects the transformation rate to the physical and chemical processes underlying the mechanochemical transformations.

Interaction between permeation and gating in a putative pore domain mutant in the cystic fibrosis transmembrane conductance regulator.

PubMed Central

Zhang, Z R; McDonough, S I; McCarty, N A

2000-01-01

The cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel with distinctive kinetics. At the whole-cell level, CFTR currents in response to voltage steps are time independent for wild type and for the many mutants reported so far. Single channels open for periods lasting up to tens of seconds; the openings are interrupted by brief closures at hyperpolarized, but not depolarized, potentials. Here we report a serine-to-phenylalanine mutation (S1118F) in the 11th transmembrane domain that confers voltage-dependent, single-exponential current relaxations and moderate inward rectification of the macroscopic currents upon expression in Xenopus oocytes. At steady state, the S1118F-CFTR single-channel conductance rectifies, corresponding to the whole-cell rectification. In addition, the open-channel burst duration is decreased 10-fold compared with wild-type channels. S1118F-CFTR currents are blocked in a voltage-dependent manner by diphenylamine-2-carboxylate (DPC); the affinity of S1118F-CFTR for DPC is similar to that of the wild-type channel, but blockade exhibits moderately reduced voltage dependence. Selectivity of the channel to a range of anions is also affected by this mutation. Furthermore, the permeation properties change during the relaxations, which suggests that there is an interaction between gating and permeation in this mutant. The existence of a mutation that confers voltage dependence upon CFTR currents and that changes kinetics and permeation properties of the channel suggests a functional role for the 11th transmembrane domain in the pore in the wild-type channel. PMID:10866956

Pre-steady-state DNA unwinding by bacteriophage T4 Dda helicase reveals a monomeric molecular motor.

PubMed

Nanduri, Bindu; Byrd, Alicia K; Eoff, Robert L; Tackett, Alan J; Raney, Kevin D

2002-11-12

Helicases are molecular motor enzymes that unwind and translocate nucleic acids. One of the central questions regarding helicase activity is whether the process of coupling ATP hydrolysis to DNA unwinding requires an oligomeric form of the enzyme. We have applied a pre-steady-state kinetics approach to address this question with the bacteriophage T4 Dda helicase. If a helicase can function as a monomer, then the burst amplitude in the pre-steady state might be similar to the concentration of enzyme, whereas if the helicase required oligomerization, then the amplitude would be significantly less than the enzyme concentration. DNA unwinding of an oligonucleotide substrate was conducted by using a Kintek rapid quench-flow instrument. The substrate consisted of 12 bp adjacent to 12 nucleotides of single-stranded DNA. Dda (4 nM) was incubated with substrate (16 nM) in buffer, and the unwinding reaction was initiated by the addition of ATP (5 mM) and Mg(2+) (10 mM). The reaction was stopped by the addition of 400 mM EDTA. Product formation exhibited biphasic kinetics, and the data were fit to the equation for a single exponential followed by a steady state. The amplitude of the first phase was 3.5 +/- 0.2 nM, consistent with a monomeric helicase. The burst amplitude of product formation was measured over a range of enzyme and substrate concentrations and remained consistent with a functional monomer. Thus, Dda can rapidly unwind oligonucleotide substrates as a monomer, indicating that the functional molecular motor component of a helicase can reside within a single polypeptide.

Defining Nitrogen Kinetics for Air Break in Prebreath

NASA Technical Reports Server (NTRS)

Conkin, Johnny

2010-01-01

Actual tissue nitrogen (N2) kinetics are complex; the uptake and elimination is often approximated with a single half-time compartment in statistical descriptions of denitrogenation [prebreathe(PB)] protocols. Air breaks during PB complicate N2 kinetics. A comparison of symmetrical versus asymmetrical N2 kinetics was performed using the time to onset of hypobaric decompression sickness (DCS) as a surrogate for actual venous N2 tension. METHODS: Published results of 12 tests involving 179 hypobaric exposures in altitude chambers after PB, with and without airbreaks, provide the complex protocols from which to model N2 kinetics. DCS survival time for combined control and airbreaks were described with an accelerated log logistic model where N2 uptake and elimination before, during, and after the airbreak was computed with a simple exponential function or a function that changed half-time depending on ambient N2 partial pressure. P1N2-P2 = (Delta)P defined decompression dose for each altitude exposure, where P2 was the test altitude and P1N2 was computed N2 pressure at the beginning of the altitude exposure. RESULTS: The log likelihood (LL) without decompression dose (null model) was -155.6, and improved (best-fit) to -97.2 when dose was defined with a 240 min half-time for both N2 elimination and uptake during the PB. The description of DCS survival time was less precise with asymmetrical N2 kinetics, for example, LL was -98.9 with 240 min half-time elimination and 120 min half-time uptake. CONCLUSION: The statistical regression described survival time mechanistically linked to symmetrical N2 kinetics during PBs that also included airbreaks. The results are data-specific, and additional data may change the conclusion. The regression is useful to compute additional PB time to compensate for an airbreak in PB within the narrow range of tested conditions.

Defining Nitrogen Kinetics for Air Break in Prebreathe

NASA Technical Reports Server (NTRS)

Conkin, Johnny

2009-01-01

Actual tissue nitrogen (N2) kinetics are complex; the uptake and elimination is often approximated with a single half-time compartment in statistical descriptions of denitrogenation [prebreathe (PB)] protocols. Air breaks during PB complicate N2 kinetics. A comparison of symmetrical versus asymmetrical N2 kinetics was performed using the time to onset of hypobaric decompression sickness (DCS) as a surrogate for actual venous N2 tension. Published results of 12 tests involving 179 hypobaric exposures in altitude chambers after PB, with and without air breaks, provide the complex protocols from which to model N2 kinetics. DCS survival time for combined control and air breaks were described with an accelerated log logistic model where N2 uptake and elimination before, during, and after the air break was computed with a simple exponential function or a function that changed half-time depending on ambient N2 partial pressure. P1N2-P2 = delta P defined DCS dose for each altitude exposure, where P2 was the test altitude and P1N2 was computed N2 pressure at the beginning of the altitude exposure. The log likelihood (LL) without DCS dose (null model) was -155.6, and improved (best-fit) to -97.2 when dose was defined with a 240 min half-time for both N2 elimination and uptake during the PB. The description of DCS survival time was less precise with asymmetrical N2 kinetics, for example, LL was -98.9 with 240 min half-time elimination and 120 min half-time uptake. The statistical regression described survival time mechanistically linked to symmetrical N2 kinetics during PBs that also included air breaks. The results are data-specific, and additional data may change the conclusion. The regression is useful to compute additional PB time to compensate for an air break in PB within the narrow range of tested conditions.

Sorption kinetics of Hg and HgCl[sub 2] on Kirkwood-Cohansey aquifer sediments from the New Jersey Coastal Plain

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

MacLeod, C.; Peterson, J.

1992-01-01

Anomalously high Hg concentrations have been detected from domestic wells in the Kirkwood-Cohansey Aquifer System, New Jersey Coastal Plain. Mercury concentrations ranging from 0.2--83.0 [mu]g/l in relatively shallow wells ([lt] 100 feet) have been detected. Concentrations in excess of 2.0 [mu]g/l, (the USEPA Drinking Water Standard) have been detected in wells where the Cohansey Sand is overlain by the Bridgeton Formation; a fluvial iron-rich sand with some gravelly channel deposits containing goethite and gibbsite nodules. In this study, Bridgeton Fm. sediments were used to determine the sorption kinetics for solutions containing HgCl[sub 2] and for solutions containing dissolved elemental Hgmore » in order to assess the potential for the Bridgeton sediments to act as a conduit for Hg mobilized from the surface. Results of batch equilibrium experiments suggest that dissolved elemental Hg sorbs to Bridgeton sediments by a risk-order kinetic process. Sorption of the Hg proceeded exponentially and equilibrium was reached within 14 hours. The sorption kinetics for the HgCl[sub 2] solutions, however, appear to be of a second or higher order. For this compound sorption to the sediments begins exponentially, but after 6 hours desorption into the water begins to predominate followed by a slower exponential sorption step that requires nearly 36 hours to reach equilibrium. These experiments illustrate the necessity of determining the distribution coefficients of possible source compounds when attempting to evaluate mobilization potential of a contaminant in the unsaturated zone. Moreover, these data also suggest that HgCl[sub 2], a seed dressing for corn, medial bacteriacide, and embalming fluid ingredient, is more mobile in the environment than dissolved elemental Hg. Consequently, the ground water contamination potential appears to be greater for HgCl[sub 2] than for elemental Hg.« less

The study of the effect of aluminum powders dispersion on the oxidation and kinetic characteristics

NASA Astrophysics Data System (ADS)

Gorbenko, T. I.; Gorbenko, M. V.; Orlova, M. P.; Volkov, S. A.

2017-11-01

Differential-scanning calorimetry (DSC) and thermogravimetric analysis (TG) were used to study micro-sized aluminum powder ASD-4 and nano-sized powder Alex. The dependence of the oxidation process on the dispersion of the sample particles is shown. The influence of thermogravimetric conditions on the thermal regime of the process was considered, and its kinetic parameters were determined. Calculations of the activation energy and the pre-exponential factor were carried out.

Growth rate for blackhole instabilities

NASA Astrophysics Data System (ADS)

Prabhu, Kartik; Wald, Robert

2015-04-01

Hollands and Wald showed that dynamic stability of stationary axisymmetric black holes is equivalent to positivity of canonical energy on a space of linearised axisymmetric perturbations satisfying certain boundary and gauge conditions. Using a reflection isometry of the background, we split the energy into kinetic and potential parts. We show that the kinetic energy is positive. In the case that potential energy is negative, we show existence of exponentially growing perturbations and further obtain a variational formula for the growth rate.

Stability of infinite derivative Abelian Higgs models

NASA Astrophysics Data System (ADS)

Ghoshal, Anish; Mazumdar, Anupam; Okada, Nobuchika; Villalba, Desmond

2018-04-01

Motivated by the stringy effects by modifying the local kinetic term of an Abelian Higgs field by the Gaussian kinetic term, we show that the Higgs field does not possess any instability; the Yukawa coupling between the scalar and the fermion, the gauge coupling, and the self interaction of the Higgs yields exponentially suppressed running at high energies, showing that such class of theory never suffers from vacuum instability. We briefly discuss its implications for the early Universe cosmology.

A kinetic approach to some quasi-linear laws of macroeconomics

NASA Astrophysics Data System (ADS)

Gligor, M.; Ignat, M.

2002-11-01

Some previous works have presented the data on wealth and income distributions in developed countries and have found that the great majority of population is described by an exponential distribution, which results in idea that the kinetic approach could be adequate to describe this empirical evidence. The aim of our paper is to extend this framework by developing a systematic kinetic approach of the socio-economic systems and to explain how linear laws, modelling correlations between macroeconomic variables, may arise in this context. Firstly we construct the Boltzmann kinetic equation for an idealised system composed by many individuals (workers, officers, business men, etc.), each of them getting a certain income and spending money for their needs. To each individual a certain time variable amount of money is associated this meaning him/her phase space coordinate. In this way the exponential distribution of money in a closed economy is explicitly found. The extension of this result, including states near the equilibrium, give us the possibility to take into account the regular increase of the total amount of money, according to the modern economic theories. The Kubo-Green-Onsager linear response theory leads us to a set of linear equations between some macroeconomic variables. Finally, the validity of such laws is discussed in relation with the time reversal symmetry and is tested empirically using some macroeconomic time series.

Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

NASA Astrophysics Data System (ADS)

Zhang, Hong; Zuo, Ran; Zhang, Guoyi

2017-11-01

In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.

Effect of DNA Binding on Geminate CO Recombination Kinetics in CO-sensing Transcription Factor CooA*

PubMed Central

Benabbas, Abdelkrim; Karunakaran, Venugopal; Youn, Hwan; Poulos, Thomas L.; Champion, Paul M.

2012-01-01

Carbon monoxide oxidation activator (CooA) proteins are heme-based CO-sensing transcription factors. Here we study the ultrafast dynamics of geminate CO rebinding in two CooA homologues, Rhodospirillum rubrum (RrCooA) and Carboxydothermus hydrogenoformans (ChCooA). The effects of DNA binding and the truncation of the DNA-binding domain on the CO geminate recombination kinetics were specifically investigated. The CO rebinding kinetics in these CooA complexes take place on ultrafast time scales but remain non-exponential over many decades in time. We show that this non-exponential kinetic response is due to a quenched enthalpic barrier distribution resulting from a distribution of heme geometries that is frozen or slowly evolving on the time scale of CO rebinding. We also show that, upon CO binding, the distal pocket of the heme in the CooA proteins relaxes to form a very efficient hydrophobic trap for CO. DNA binding further tightens the narrow distal pocket and slightly weakens the iron-proximal histidine bond. Comparison of the CO rebinding kinetics of RrCooA, truncated RrCooA, and DNA-bound RrCooA proteins reveals that the uncomplexed and inherently flexible DNA-binding domain adds additional structural heterogeneity to the heme doming coordinate. When CooA forms a complex with DNA, the flexibility of the DNA-binding domain decreases, and the distribution of the conformations available in the heme domain becomes restricted. The kinetic studies also offer insights into how the architecture of the heme environment can tune entropic barriers in order to control the geminate recombination of CO in heme proteins, whereas spin selection rules play a minor or non-existent role. PMID:22544803

Effect of DNA binding on geminate CO recombination kinetics in CO-sensing transcription factor CooA.

PubMed

Benabbas, Abdelkrim; Karunakaran, Venugopal; Youn, Hwan; Poulos, Thomas L; Champion, Paul M

2012-06-22

Carbon monoxide oxidation activator (CooA) proteins are heme-based CO-sensing transcription factors. Here we study the ultrafast dynamics of geminate CO rebinding in two CooA homologues, Rhodospirillum rubrum (RrCooA) and Carboxydothermus hydrogenoformans (ChCooA). The effects of DNA binding and the truncation of the DNA-binding domain on the CO geminate recombination kinetics were specifically investigated. The CO rebinding kinetics in these CooA complexes take place on ultrafast time scales but remain non-exponential over many decades in time. We show that this non-exponential kinetic response is due to a quenched enthalpic barrier distribution resulting from a distribution of heme geometries that is frozen or slowly evolving on the time scale of CO rebinding. We also show that, upon CO binding, the distal pocket of the heme in the CooA proteins relaxes to form a very efficient hydrophobic trap for CO. DNA binding further tightens the narrow distal pocket and slightly weakens the iron-proximal histidine bond. Comparison of the CO rebinding kinetics of RrCooA, truncated RrCooA, and DNA-bound RrCooA proteins reveals that the uncomplexed and inherently flexible DNA-binding domain adds additional structural heterogeneity to the heme doming coordinate. When CooA forms a complex with DNA, the flexibility of the DNA-binding domain decreases, and the distribution of the conformations available in the heme domain becomes restricted. The kinetic studies also offer insights into how the architecture of the heme environment can tune entropic barriers in order to control the geminate recombination of CO in heme proteins, whereas spin selection rules play a minor or non-existent role.

Modeling of single event transients with dual double-exponential current sources: Implications for logic cell characterization

DOE PAGES

Black, Dolores Archuleta; Robinson, William H.; Wilcox, Ian Zachary; ...

2015-08-07

Single event effects (SEE) are a reliability concern for modern microelectronics. Bit corruptions can be caused by single event upsets (SEUs) in the storage cells or by sampling single event transients (SETs) from a logic path. Likewise, an accurate prediction of soft error susceptibility from SETs requires good models to convert collected charge into compact descriptions of the current injection process. This paper describes a simple, yet effective, method to model the current waveform resulting from a charge collection event for SET circuit simulations. The model uses two double-exponential current sources in parallel, and the results illustrate why a conventionalmore » model based on one double-exponential source can be incomplete. Furthermore, a small set of logic cells with varying input conditions, drive strength, and output loading are simulated to extract the parameters for the dual double-exponential current sources. As a result, the parameters are based upon both the node capacitance and the restoring current (i.e., drive strength) of the logic cell.« less

Preparation, crystal structure and thermal decomposition kinetics of 1-(2,4-dinitrophenyl)azo-1-nitrocyclohexane

NASA Astrophysics Data System (ADS)

Yang, Desuo; Ma, Haixia; Hu, Rongzu; Song, Jirong; Zhao, Fengqi

2005-11-01

A new three-nitro-group compound of 1-(2,4-dinitrophenyl)azo-1-nitrocyclohexane was prepared by the reaction of cyclohexanone-2,4-dinitrophenylhydrazine with nitric oxide at ambient temperature. The single crystal structure has been determined by a four-circle X-ray diffractometer. The compound is monoclinic with space group P2(1)/ c and unit-cell parameters a=11.300(2) Å, b=12.993(2) Å, c=10.155(1) Å, β=98.33(1) o, F(000)=672, the unit-cell volume V=1475.2(5) Å 3, the molecule number in one unit-cell Z=4, the absorption coefficient μ=1.19 cm -1, the calculated density Dc=1.456 g cm -3. The exothermic decomposition reaction kinetics of the compound has been studied by DSC. The kinetic model function in differential form, apparent activation energy and pre-exponential constant of this reaction are (3/4)(1-α)[-ln(1-α)] 1/4, 123.88 kJ mol -1 and 10 11.49 s -1, respectively. The critical temperature of thermal explosion of the title compound is 161.15 oC and the entropy of activation (ΔS), enthalpy of activation (ΔH), and free energy of activation (ΔG) are -34.16 J mol -1 K -1, 115.7, and 130.48 kJ mol -1, respectively.

Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex

PubMed Central

Almaqwashi, Ali A.; Paramanathan, Thayaparan; Lincoln, Per; Rouzina, Ioulia; Westerlund, Fredrik; Williams, Mark C.

2014-01-01

DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes. PMID:25245944

Methanol Kinetics in Chronic Kidney Disease After Fomepizole: A Case Report.

PubMed

Maskell, Kevin F; Beckett, Sara; Cumpston, Kirk L

Methanol is a common toxicant in the United States, especially from automotive products. Its kinetics have been described previously and typically involve little urinary excretion. We present a case of prolonged methanol half-life in a patient with chronic kidney disease. An 80-year-old male with a baseline glomerular filtration rate of 24 mL·min·1.73 m was transferred to our facility after unintentional methanol ingestion. The original facility had treated him with an oral ethanol load; upon arrival to our facility, he was immediately loaded with fomepizole. His initial serum methanol concentration was 66.1 mg/dL. After a risk/benefit discussion, we decided not to perform hemodialysis on the patient and he was treated with fomepizole and supportive care. After 6 days as an inpatient, the patient's methanol level had declined to 22 mg/dL, fomepizole was discontinued, and the patient was able to be discharged without apparent complications. Based on the exponential best fit line for the patient's methanol concentrations, his methanol half-life during fomepizole treatment was approximately 70 hours, significantly longer than the 30-50 hours typically reported. The reasons for this difference are unclear. This report is limited by being a single case. Further study on the kinetics of methanol in the setting of chronic kidney disease is needed.

Multiserver Queueing Model subject to Single Exponential Vacation

NASA Astrophysics Data System (ADS)

Vijayashree, K. V.; Janani, B.

2018-04-01

A multi-server queueing model subject to single exponential vacation is considered. The arrivals are allowed to join the queue according to a Poisson distribution and services takes place according to an exponential distribution. Whenever the system becomes empty, all the servers goes for a vacation and returns back after a fixed interval of time. The servers then starts providing service if there are waiting customers otherwise they will wait to complete the busy period. The vacation times are also assumed to be exponentially distributed. In this paper, the stationary and transient probabilities for the number of customers during ideal and functional state of the server are obtained explicitly. Also, numerical illustrations are added to visualize the effect of various parameters.

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

Practical Approaches to Protein Folding and Assembly

PubMed Central

Walters, Jad; Milam, Sara L.; Clark, A. Clay

2009-01-01

We describe here the use of several spectroscopies, such as fluorescence emission, circular dichroism, and differential quenching by acrylamide, in examining the equilibrium and kinetic folding of proteins. The first section regarding equilibrium techniques provides practical information for determining the conformational stability of a protein. In addition, several equilibrium-folding models are discussed, from two-state monomer to four-state homodimer, providing a comprehensive protocol for interpretation of folding curves. The second section focuses on the experimental design and interpretation of kinetic data, such as burst-phase analysis and exponential fits, used in elucidating kinetic folding pathways. In addition, simulation programs are used routinely to support folding models generated by kinetic experiments, and the fundamentals of simulations are covered. PMID:19289201

Energy-Transfer Kinetics for Xe (6p[1/2]0) Atoms in Kr, Ar, Ne, and He.

PubMed

He, Shan; Liu, Dong; Li, Xueyang; Chu, Junzhi; Guo, Jingwei; Liu, Jinbo; Hu, Shu; Sang, Fengting; Jin, Yuqi

2018-06-11

The kinetic processes for the Xe (6p[1/2] 0 ) atoms in Kr, Ar, Ne, and He buffer gases were studied. We found that Kr, Ar, and Ne atoms can be used to switch the amplified spontaneous emission (ASE) channel from 3408 nm (6p[1/2] 0 -6s'[1/2] 1 ) to 3680 nm (5d[1/2] 1 -6p[1/2] 1 ), while Xe and He atoms do not show such a phenomenon. This ASE channel switch is mainly ascribed to the fast transfer of 6p[1/2] 0 → 5d[1/2] 1 . On the basis of the rate equations for two-state coupling (energy-transfer processes between the two states are very rapid), the reason why the ASE channel switch effect normally coincides with a double exponential decay of the spontaneous emission at 828 nm (6p[1/2] 0 -6s[3/2] 1 ) is explained. The actual situations in Xe, Ar, Ne, and He follow this rule. However, the strictly single exponential decay of the spontaneous emission at 828 nm and strong ASE channel switch effect simultaneously emerge in Kr. This indicates that the transfer of 6p[1/2] 0 → 5d[1/2] 1 in Kr does not occur via two-state coupling, but via two steps of near-resonance collision through the 5s[3/2] 2 (Kr) state as the intermediate state (6p[1/2] 0 → 5s[3/2] 2 (Kr) → 5d[1/2] 1 ). In addition, we found Xe (6p[1/2] 0 ) atoms strongly tend to reach the 6p[3/2] 2 , 6p[3/2] 1 , and 6p[5/2] 2 states through the 5s[3/2] 2 (Kr) state as the intermediate state in Kr. The 5s[3/2] 2 (Kr) state plays a very important role in the energy-transfer kinetics for the Xe (6p[1/2] 0 ) atoms. Kr is probably an excellent buffer gas for laser systems based on Xe.

The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition

PubMed Central

Zheng, Xiliang; Wang, Jin

2015-01-01

We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

PubMed

Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

2018-02-06

A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

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.

Evaluating an alternative method for rapid urinary creatinine determination

EPA Science Inventory

Creatinine (CR) is an endogenously-produced chemical routinely assayed in urine specimens to assess kidney function, sample dilution. The industry-standard method for CR determination, known as the kinetic Jaffe (KJ) method, relies on an exponential rate of a colorimetric change,...

Fluorescence kinetics of emission from a small finite volume of a biological system

NASA Astrophysics Data System (ADS)

Dagen, A. J.; Alfano, R. R.; Zilinskas, B. A.; Swenberg, C. E.

1985-07-01

The fluorescence decay, apparent quantum yield and transmission from chromophores constrained to a microscopic volume using a single picosecond laser excitation were measured as a function of incident intensity. The β subunit of phycoeryhthrin aggregate isolated from the photosynthetic antenna system of Nostoc sp. was selected since it contains only four chromophores in a volume of less than 5.6×10 4 Å 3. The non-exponential fluorescence decay profiles were intensity independent for the intensity range studied (5 × 10 13 - 2 × 10 15 photon cm -2 per pulse). The apparent decrease in the relative fluorescence quantum yield and increase of the relative transmission with increasing excitation intensity is attributed to the combined effects of ground state depletion and upper excited state absorption. Evidence suggests that exciton annihilation is absent within isolated β subunits.

Kinetics of particle deposition at heterogeneous surfaces

NASA Astrophysics Data System (ADS)

Stojiljković, D. Lj.; Vrhovac, S. B.

2017-12-01

The random sequential adsorption (RSA) approach is used to analyze adsorption of spherical particles of fixed diameter d0 on nonuniform surfaces covered by square cells arranged in a square lattice pattern. To characterize such pattern two dimensionless parameters are used: the cell size α and the cell-cell separation β, measured in terms of the particle diameter d0. Adsorption is assumed to occur if the particle (projected) center lies within a cell area. We focus on the kinetics of deposition process in the case when no more than a single disk can be placed onto any square cell (α < 1 /√{ 2 } ≈ 0 . 707). We find that the asymptotic approach of the coverage fraction θ(t) to the jamming limit θJ is algebraic if the parameters α and β satisfy the simple condition, β + α / 2 < 1. If this condition is not satisfied, the late time kinetics of deposition process is not consistent with the power law behavior. However, if the geometry of the pattern approaches towards ;noninteracting conditions; (β > 1), when adsorption on each cell can be decoupled, approach of the coverage fraction θ(t) to θJ becomes closer to the exponential law. Consequently, changing the pattern parameters in the present model allows to interpolate the deposition kinetics between the continuum limit and the lattice-like behavior. Structural properties of the jammed-state coverings are studied in terms of the radial distribution function g(r) and spatial distribution of particles inside the cell. Various, non-trivial spatial distributions are observed depending on the geometry of the pattern.

A comparison of G2 phase radiation-induced chromatid break kinetics using calyculin-PCC with those obtained using colcemid block.

PubMed

Bryant, Peter E; Mozdarani, Hossein

2007-09-01

To study the possible influence of cell-cycle delay on cells reaching mitosis during conventional radiation-induced chromatid break experiments using colcemid as a blocking agent, we have compared the chromatid break kinetics following a single dose of gamma rays (0.75 Gy) in metaphase CHO cells using calyculin-induced premature chromosome condensation (PCC), with those using colcemid block. Calyculin-induced PCC causes very rapid condensation of G2 cell chromosomes without the need for a cell to progress to mitosis, hence eliminating any effect of cell-cycle checkpoint on chromatid break frequency. We found that the kinetics of the exponential first-order decrease in chromatid breaks with time after irradiation was similar (not significantly different) between the two methods of chromosome condensation. However, use of the calyculin-PCC technique resulted in a slightly increased rate of disappearance of chromatid breaks and thus higher frequencies of breaks at 1.5 and 2.5 h following irradiation. We also report on the effect of the nucleoside analogue ara A on chromatid break kinetics using the two chromosome condensation techniques. Ara A treatment of cells abrogated the decrease in chromatid breaks with time, both using the calyculin-PCC and colcemid methods. We conclude that cell-cycle delay may be a factor determining the absolute frequency of chromatid breaks at various times following irradiation of cells in G2 phase but that the first-order disappearance of chromatid breaks with time and its abrogation by ara A are not significantly influenced by the G2 checkpoint.

Exponential growth kinetics for Polyporus versicolor and Pleurotus ostreatus in submerged culture

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

Carroad, P.A.; Wilke, C.R.

1977-04-01

Simple mathematical models for a batch culture of pellet-forming fungi in submerged culture were tested on growth data for Polyporus versicolor (ATCC 12679) and Pleurotus ostreatus (ATCC 9415). A kinetic model based on a growth rate proportional to the two-thirds power of the cell mass was shown to be satisfactory. A model based on a growth rate directly proportional to the cell mass fitted the data equally well, however, and may be preferable because of mathematical simplicity.

Universality in stochastic exponential growth.

PubMed

Iyer-Biswas, Srividya; Crooks, Gavin E; Scherer, Norbert F; Dinner, Aaron R

2014-07-11

Recent imaging data for single bacterial cells reveal that their mean sizes grow exponentially in time and that their size distributions collapse to a single curve when rescaled by their means. An analogous result holds for the division-time distributions. A model is needed to delineate the minimal requirements for these scaling behaviors. We formulate a microscopic theory of stochastic exponential growth as a Master Equation that accounts for these observations, in contrast to existing quantitative models of stochastic exponential growth (e.g., the Black-Scholes equation or geometric Brownian motion). Our model, the stochastic Hinshelwood cycle (SHC), is an autocatalytic reaction cycle in which each molecular species catalyzes the production of the next. By finding exact analytical solutions to the SHC and the corresponding first passage time problem, we uncover universal signatures of fluctuations in exponential growth and division. The model makes minimal assumptions, and we describe how more complex reaction networks can reduce to such a cycle. We thus expect similar scalings to be discovered in stochastic processes resulting in exponential growth that appear in diverse contexts such as cosmology, finance, technology, and population growth.

Universality in Stochastic Exponential Growth

NASA Astrophysics Data System (ADS)

Iyer-Biswas, Srividya; Crooks, Gavin E.; Scherer, Norbert F.; Dinner, Aaron R.

2014-07-01

Recent imaging data for single bacterial cells reveal that their mean sizes grow exponentially in time and that their size distributions collapse to a single curve when rescaled by their means. An analogous result holds for the division-time distributions. A model is needed to delineate the minimal requirements for these scaling behaviors. We formulate a microscopic theory of stochastic exponential growth as a Master Equation that accounts for these observations, in contrast to existing quantitative models of stochastic exponential growth (e.g., the Black-Scholes equation or geometric Brownian motion). Our model, the stochastic Hinshelwood cycle (SHC), is an autocatalytic reaction cycle in which each molecular species catalyzes the production of the next. By finding exact analytical solutions to the SHC and the corresponding first passage time problem, we uncover universal signatures of fluctuations in exponential growth and division. The model makes minimal assumptions, and we describe how more complex reaction networks can reduce to such a cycle. We thus expect similar scalings to be discovered in stochastic processes resulting in exponential growth that appear in diverse contexts such as cosmology, finance, technology, and population growth.

KINETICS OF ION MOVEMENT IN THE SQUID GIANT AXON

PubMed Central

Shanes, Abraham M.; Berman, Morris D.

1955-01-01

The loss of Na22, K42, and Cl36 from single giant axons of the squid, Loligo pealii, following exposure to an artificial sea water containing these radioisotopes, occurs in two stages, an initial rapid one followed by an exponential decline. The time constants of the latter stage for the 3 ion species are, respectively, 290, 200, and 175 minutes. The outflux of sodium is depressed while that of potassium is accelerated in the absence of oxygen; the emergence of potassium is slowed by cocaine, while that of sodium is unaffected. One cm. ends of the axons take up about twice as much radiosodium as the central segment; this difference in activity is largely preserved during exposure to inactive solution. Such marked differences are not observed with radiopotassium. From the experimental data estimates are given of the influxes and outfluxes of the individual ions. The kinetics of outflux suggests a cortical layer of measureable thickness which contains the ions in different proportions from those in the medium and which governs the rate of emergence of these ions from the axon as though it contained very few but large (relative to ion dimensions) pores. PMID:13271727

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.

The Pre-exponential Factor in Electrochemistry.

PubMed

He, Zheng-Da; Chen, Yan-Xia; Santos, Elizabeth; Schmickler, Wolfgang

2018-07-02

Like many branches of science, not to mention culture in general, electrochemistry has a number of recurring topics: Areas of research that are popular for a certain time, then fade away as their possibilities seem to have been exhausted, only to return decades later as progress in experimental or theoretical techniques offer new possibilities for their investigation. A prime example are fuel cells, which have undergone five such cycles, but here we discuss a general concept of kinetics-the pre-exponential factor of a rate constant-which has undergone two such cycles. The first cycle was in the 1950-1980s, when the methods of electrochemical kinetics were developed, and the interpretation was based on transition-state theory. The second was triggered by the re-discovery of Kramers theory for reactions in condensed phases. This Minireview will show that the time has come for a third cycle based on recent progress in electrocatalysis. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Studies on color-center formation in glass utilizing measurements made during 1 to 3 MeV electron irradiation

NASA Technical Reports Server (NTRS)

Swyler, K. J.; Levy, P. W.

1976-01-01

The coloring of NBS 710 glass was studied using a facility for making optical absorption measurements during and after electron irradiation. The induced absorption contains three Gaussian shaped bands. The color center growth curves contain two saturating exponential and one linear components. After irradiation the coloring decays can be described by three decreasing exponentials. At room temperature both the coloring curve plateau and coloring rate increases with increasing dose rate. Coloring measurements made at fixed dose rate but at increasing temperature indicate: (1) The coloring curve plateau decreases with increasing temperature and coloring is barely measurable near 400 C. (2) The plateau is reached more rapidly as the temperature increases. (3) The decay occurring after irradiation cannot be described by Arrhenius kinetics. At each temperature the coloring can be explained by simple kinetics. The temperature dependence of the decay can be explained if it is assumed that the thermal untrapping is controlled by a distribution of activation energies.

A model stomach system to investigate disintegration kinetics of solid foods during gastric digestion.

PubMed

Kong, F; Singh, R P

2008-06-01

Knowledge of the disintegration kinetics of food particulates in the human stomach is essential for assessing the bioaccessibility of nutrients in solid foods and understanding stomach emptying. The objective of this study was to develop a model stomach system and to investigate the kinetics of food disintegration. Our system consisted mainly of a turntable and a jacketed glass chamber containing simulated gastric juice in which plastic beads were added to simulate food particulates as well as provide a suitable mechanical destructive force on food samples. The mechanical force on the samples was simultaneously measured using the load cell of a TA-XT2 texture analyzer. Cylindrical carrots and ham samples were used as representative foods. The system is capable of simulating the in vivo stomach in terms of providing a wide range of continuous and periodic forces comparable to those measured in vivo. The modified power exponential function of the form y(t)= 1 - (1 -e(-kt))(beta), where y(t) is the mass retention ratio at time t, provided a reasonable description for the disintegration performance of tested foods. The mass retention curve can be either a sigmoidal decay with an initial delay or an exponential decay, which are decided largely by the hardness of the foods during digestion and the extent of physical force acting on the foods. A good match was observed between the kinetics of food disintegration and in vivo stomach emptying.

On the origin of stretched exponential (Kohlrausch) relaxation kinetics in the room temperature luminescence decay of colloidal quantum dots.

PubMed

Bodunov, E N; Antonov, Yu A; Simões Gamboa, A L

2017-03-21

The non-exponential room temperature luminescence decay of colloidal quantum dots is often well described by a stretched exponential function. However, the physical meaning of the parameters of the function is not clear in the majority of cases reported in the literature. In this work, the room temperature stretched exponential luminescence decay of colloidal quantum dots is investigated theoretically in an attempt to identify the underlying physical mechanisms associated with the parameters of the function. Three classes of non-radiative transition processes between the excited and ground states of colloidal quantum dots are discussed: long-range resonance energy transfer, multiphonon relaxation, and contact quenching without diffusion. It is shown that multiphonon relaxation cannot explain a stretched exponential functional form of the luminescence decay while such dynamics of relaxation can be understood in terms of long-range resonance energy transfer to acceptors (molecules, quantum dots, or anharmonic molecular vibrations) in the environment of the quantum dots acting as energy-donors or by contact quenching by acceptors (surface traps or molecules) distributed statistically on the surface of the quantum dots. These non-radiative transition processes are assigned to different ranges of the stretching parameter β.

Correlating the stretched-exponential and super-Arrhenius behaviors in the structural relaxation of glass-forming liquids.

PubMed

Wang, Lianwen; Li, Jiangong; Fecht, Hans-Jörg

2011-04-20

Following the report of a single-exponential activation behavior behind the super-Arrhenius structural relaxation of glass-forming liquids in our preceding paper, we find that the non-exponentiality in the structural relaxation of glass-forming liquids is straightforwardly determined by the relaxation time, and could be calculated from the measured relaxation data. Comparisons between the calculated and measured non-exponentialities for typical glass-forming liquids, from fragile to intermediate, convincingly support the present analysis. Hence the origin of the non-exponentiality and its correlation with liquid fragility become clearer.

High-LET radiation-induced aberrations in prematurely condensed G2 chromosomes of human fibroblasts

NASA Technical Reports Server (NTRS)

Kawata, T.; Gotoh, E.; Durante, M.; Wu, H.; George, K.; Furusawa, Y.; Cucinotta, F. A.; Dicello, J. F. (Principal Investigator)

2000-01-01

PURPOSE: To determine the number of initial chromatid breaks induced by low- or high-LET irradiations, and to compare the kinetics of chromatid break rejoining for radiations of different quality. MATERIAL AND METHODS: Exponentially growing human fibroblast cells AG1522 were irradiated with gamma-rays, energetic carbon (290MeV/u), silicon (490MeV/u) and iron (200 and 600 MeV/u). Chromosomes were prematurely condensed using calyculin A. Chromatid breaks and exchanges in G2 cells were scored. PCC were collected after several post-irradiation incubation times, ranging from 5 to 600 min. RESULTS: The kinetics of chromatid break rejoining following low- or high-LET irradiation consisted of two exponential components representing a rapid and a slow time constant. Chromatid breaks decreased rapidly during the first 10min after exposure, then continued to decrease at a slower rate. The rejoining kinetics were similar for exposure to each type of radiation. Chromatid exchanges were also formed quickly. Compared to low-LET radiation, isochromatid breaks were produced more frequently and the proportion of unrejoined breaks was higher for high-LET radiation. CONCLUSIONS: Compared with gamma-rays, isochromatid breaks were observed more frequently in high-LET irradiated samples, suggesting that an increase in isochromatid breaks is a signature of high-LET radiation exposure.

Impact of jamming on collective cell migration

NASA Astrophysics Data System (ADS)

Nnetu, Kenechukwu David; Knorr, Melanie; Pawlizak, Steve; Fuhs, Thomas; Zink, Mareike; KäS, Josef A.

2012-02-01

Multi-cellular migration plays an important role in physiological processes such as embryogenesis, cancer metastasis and tissue repair. During migration, single cells undergo cycles of extension, adhesion and retraction resulting in morphological changes. In a confluent monolayer, there are inter-cellular interactions and crowding, however, the impact of these interactions on the dynamics and elasticity of the monolayer at the multi-cellular and single cell level is not well understood. Here we study the dynamics of a confluent epithelial monolayer by simultaneously measuring cell motion at the multi-cellular and single cell level for various cell densities and tensile elasticity. At the multi-cellular level, the system exhibited spatial kinetic transitions from isotropic to anisotropic migration on long times and the velocity of the monolayer decreased with increasing cell density. Moreover, the dynamics was spatially and temporally heterogeneous. Interestingly, the dynamics was also heterogeneous in wound-healing assays and the correlation length was fitted by compressed exponential. On the single cell scale, we observed transient caging effects with increasing cage rearrangement times as the system age due to an increase in density. Also, the density dependent elastic modulus of the monolayer scaled as a weak power law. Together, these findings suggest that caging effects at the single cell level initiates a slow and heterogeneous dynamics at the multi-cellular level which is similar to the glassy dynamics of deformable colloidal systems.

Measuring kinetics of complex single ion channel data using mean-variance histograms.

PubMed

Patlak, J B

1993-07-01

The measurement of single ion channel kinetics is difficult when those channels exhibit subconductance events. When the kinetics are fast, and when the current magnitudes are small, as is the case for Na+, Ca2+, and some K+ channels, these difficulties can lead to serious errors in the estimation of channel kinetics. I present here a method, based on the construction and analysis of mean-variance histograms, that can overcome these problems. A mean-variance histogram is constructed by calculating the mean current and the current variance within a brief "window" (a set of N consecutive data samples) superimposed on the digitized raw channel data. Systematic movement of this window over the data produces large numbers of mean-variance pairs which can be assembled into a two-dimensional histogram. Defined current levels (open, closed, or sublevel) appear in such plots as low variance regions. The total number of events in such low variance regions is estimated by curve fitting and plotted as a function of window width. This function decreases with the same time constants as the original dwell time probability distribution for each of the regions. The method can therefore be used: 1) to present a qualitative summary of the single channel data from which the signal-to-noise ratio, open channel noise, steadiness of the baseline, and number of conductance levels can be quickly determined; 2) to quantify the dwell time distribution in each of the levels exhibited. In this paper I present the analysis of a Na+ channel recording that had a number of complexities. The signal-to-noise ratio was only about 8 for the main open state, open channel noise, and fast flickers to other states were present, as were a substantial number of subconductance states. "Standard" half-amplitude threshold analysis of these data produce open and closed time histograms that were well fitted by the sum of two exponentials, but with apparently erroneous time constants, whereas the mean-variance histogram technique provided a more credible analysis of the open, closed, and subconductance times for the patch. I also show that the method produces accurate results on simulated data in a wide variety of conditions, whereas the half-amplitude method, when applied to complex simulated data shows the same errors as were apparent in the real data. The utility and the limitations of this new method are discussed.

Determining the Kinetic Parameters Characteristic of Microalgal Growth.

ERIC Educational Resources Information Center

Martinez Sancho, Maria Eugenie; And Others

1991-01-01

An activity in which students obtain a growth curve for algae, identify the exponential and linear growth phases, and calculate the parameters which characterize both phases is described. The procedure, a list of required materials, experimental conditions, analytical technique, and a discussion of the interpretations of individual results are…

Kinetics of force recovery following length changes in active skinned single fibres from rabbit psoas muscle

PubMed Central

Burton, Kevin; Simmons, Robert M; Sleep, John; Smith, David A

2006-01-01

Redevelopment of isometric force following shortening of skeletal muscle is thought to result from a redistribution of cross-bridge states. We varied the initial force and cross-bridge distribution by applying various length-change protocols to active skinned single fibres from rabbit psoas muscle, and observed the effect on the slowest phase of recovery (‘late recovery’) that follows transient changes. In response to step releases that reduced force to near zero (∼8 nm (half sarcomere)−1) or prolonged shortening at high velocity, late recovery was well described by two exponentials of approximately equal amplitude and rate constants of ∼2 s−1 and ∼9 s−1 at 5°C. When a large restretch was applied at the end of rapid shortening, recovery was accelerated by (1) the introduction of a slow falling component that truncated the rise in force, and (2) a relative increase in the contribution of the fast exponential component. The rate of the slow fall was similar to that observed after a small isometric step stretch, with a rate of 0.4–0.8 s−1, and its effects could be reversed by reducing force to near zero immediately after the stretch. Force at the start of late recovery was varied in a series of shortening steps or ramps in order to probe the effect of cross-bridge strain on force redevelopment. The rate constants of the two components fell by 40–50% as initial force was raised to 75–80% of steady isometric force. As initial force increased, the relative contribution of the fast component decreased, and this was associated with a length constant of about 2 nm. The results are consistent with a two-state strain-dependent cross-bridge model. In the model there is a continuous distribution of recovery rate constants, but two-exponential fits show that the fast component results from cross-bridges initially at moderate positive strain and the slow component from cross-bridges at high positive strain. PMID:16497718

Exponential Sum-Fitting of Dwell-Time Distributions without Specifying Starting Parameters

PubMed Central

Landowne, David; Yuan, Bin; Magleby, Karl L.

2013-01-01

Fitting dwell-time distributions with sums of exponentials is widely used to characterize histograms of open- and closed-interval durations recorded from single ion channels, as well as for other physical phenomena. However, it can be difficult to identify the contributing exponential components. Here we extend previous methods of exponential sum-fitting to present a maximum-likelihood approach that consistently detects all significant exponentials without the need for user-specified starting parameters. Instead of searching for exponentials, the fitting starts with a very large number of initial exponentials with logarithmically spaced time constants, so that none are missed. Maximum-likelihood fitting then determines the areas of all the initial exponentials keeping the time constants fixed. In an iterative manner, with refitting after each step, the analysis then removes exponentials with negligible area and combines closely spaced adjacent exponentials, until only those exponentials that make significant contributions to the dwell-time distribution remain. There is no limit on the number of significant exponentials and no starting parameters need be specified. We demonstrate fully automated detection for both experimental and simulated data, as well as for classical exponential-sum-fitting problems. PMID:23746510

Is it growing exponentially fast? -- Impact of assuming exponential growth for characterizing and forecasting epidemics with initial near-exponential growth dynamics.

PubMed

Chowell, Gerardo; Viboud, Cécile

2016-10-01

The increasing use of mathematical models for epidemic forecasting has highlighted the importance of designing models that capture the baseline transmission characteristics in order to generate reliable epidemic forecasts. Improved models for epidemic forecasting could be achieved by identifying signature features of epidemic growth, which could inform the design of models of disease spread and reveal important characteristics of the transmission process. In particular, it is often taken for granted that the early growth phase of different growth processes in nature follow early exponential growth dynamics. In the context of infectious disease spread, this assumption is often convenient to describe a transmission process with mass action kinetics using differential equations and generate analytic expressions and estimates of the reproduction number. In this article, we carry out a simulation study to illustrate the impact of incorrectly assuming an exponential-growth model to characterize the early phase (e.g., 3-5 disease generation intervals) of an infectious disease outbreak that follows near-exponential growth dynamics. Specifically, we assess the impact on: 1) goodness of fit, 2) bias on the growth parameter, and 3) the impact on short-term epidemic forecasts. Designing transmission models and statistical approaches that more flexibly capture the profile of epidemic growth could lead to enhanced model fit, improved estimates of key transmission parameters, and more realistic epidemic forecasts.

The significance of intergranular diffusion to the mechanisms and kinetics of porphyroblast crystallization

NASA Astrophysics Data System (ADS)

Carlson, William D.

1989-09-01

The spatial disposition, compositional zoning profiles, and size distributions of garnet crystals in 11 specimens of pelitic schist from the Picuris Range of New Mexico (USA) demonstrate that the kinetics of intergranular diffusion controlled the nucleation and growth mechanisms of porphyroblasts in these rocks. An ordered disposition of garnet centers and a significant correlation between crystal radius and near-neighbor distances manifest suppressed nucleation of new crystals in diffusionally depleted zones surrounding pre-existing crystals. Compositional zoning profiles require diffusionally controlled growth, the rate of which increases exponentially as temperature increases with time; an acceleration factor for growth rate can be estimated from a comparison of compositional profiles for crystals of different sizes in each specimen. Crystal size distributions are interpreted as the result of nucleation rates that accelerate exponentially with increasing temperature early in the crystallization process, but decline in the later stages because of suppression effects in the vicinity of earlier-formed nuclei. Simulations of porphyroblast crystallization, based upon thermally accelerated diffusionally influenced nucleation kinetics and diffusionally controlled growth kinetics, quantitatively replicate textural relations in the rocks. The simulations employ only two variable parameters, which are evaluated by fitting of crystal size distributions. Both have physical significance. The first is an acceleration factor for nucleation, with a magnitude reflecting the prograde increase during the nucleation interval of the chemical affinity for the reaction in undepleted regions of the rock. The second is a measure of the relative sizes of the porphyroblast and the diffusionally depleted zone surrounding it. Crystal size distributions for the Picuris Range garnets correspond very closely to those in the literature from a variety of other localities for garnet and other minerals. The same kinetic model accounts quantitatively for crystal size distributions of porphyroblastic garnet, phlogopite, sphene, and pyroxene in rocks from both regional and contact metamorphic occurrences. These commonalities indicate that intergranular diffusion may be the dominant kinetic factor in the crystallization of porphyroblasts in a wide variety of metamorphic environments.

Dynamic modeling of sludge compaction and consolidation processes in wastewater secondary settling tanks.

PubMed

Abusam, A; Keesman, K J

2009-01-01

The double exponential settling model is the widely accepted model for wastewater secondary settling tanks. However, this model does not estimate accurately solids concentrations in the settler underflow stream, mainly because sludge compression and consolidation processes are not considered. In activated sludge systems, accurate estimation of the solids in the underflow stream will facilitate the calibration process and can lead to correct estimates of particularly kinetic parameters related to biomass growth. Using principles of compaction and consolidation, as in soil mechanics, a dynamic model of the sludge consolidation processes taking place in the secondary settling tanks is developed and incorporated to the commonly used double exponential settling model. The modified double exponential model is calibrated and validated using data obtained from a full-scale wastewater treatment plant. Good agreement between predicted and measured data confirmed the validity of the modified model.

The Decompression Sickness and Venous Gas Emboli Consequences of Air Breaks During 100% Oxygen Prebreathe

NASA Technical Reports Server (NTRS)

Conkin, J.; Gernhardt, M. L.; Powell, M. R.

2004-01-01

Not enough is known about the increased risk of hypobaric decompression sickness (DCS) and production of venous (VGE) and arterial (AGE) gas emboli following an air break in an otherwise normal 100% resting oxygen (O2) prebreathe (PB), and certainly a break in PB when exercise is used to accelerate nitrogen (N2) elimination from the tissues. Current Aeromedical Flight Rules at the Johnson Space Center about additional PB payback times are untested, possibly too conservative, and therefore not optimized for operational use. A 10 min air break at 90 min into a 120 min PB that includes initial dual-cycle ergometry for 10 min will show a measurable increase in the risk of DCS and VGE after ascent to 4.3 psia compared to a 10 min break at 15 min into the PB, or when there is no break in PB. Data collection with humans begins in 2005, but here we first evaluate the hypothesis using three models of tissue N2 kinetics: Model I is a simple single half-time compartment exponential model, Model II is a three compartment half-time exponential model, and Model III is a variable half-time compartment model where the percentage of maximum O2 consumption for the subject during dual-cycle ergometry exercise defines the half-time compartment. Model I with large rate constants to simulate an exercise effect always showed a late break in PB had the greatest consequence. Model II showed an early break had the greatest consequence. Model III showed there was no difference between early or late break in exercise PB. Only one of these outcomes will be observed when humans are tested. Our results will favor one of these models, and so advance our understanding of tissue N2 kinetics, and of altitude DCS after an air break in PB.

Single-arm phase II trial design under parametric cure models.

PubMed

Wu, Jianrong

2015-01-01

The current practice of designing single-arm phase II survival trials is limited under the exponential model. Trial design under the exponential model may not be appropriate when a portion of patients are cured. There is no literature available for designing single-arm phase II trials under the parametric cure model. In this paper, a test statistic is proposed, and a sample size formula is derived for designing single-arm phase II trials under a class of parametric cure models. Extensive simulations showed that the proposed test and sample size formula perform very well under different scenarios. Copyright © 2015 John Wiley & Sons, Ltd.

Growth and development of Frankia spp. strain CcI3 at the single-hypha level in liquid culture.

PubMed

Huang, Ying; Benson, David R

2012-01-01

Filamentous actinobacteria from the genus Frankia grow by hyphal tip extension and branching. The growth kinetics and branching pattern of Frankia are not well studied, especially at the early stages of mycelial development. Here, we compare the growth of Frankia sp. strain CcI3 in liquid cultures with and without proteose peptone #3 (PP3) using time-lapse photomicrography and image analysis. Individual hyphae showed a pseudolinear increase in length at early stages of development, whereas at the mycelial level, the aggregate length of hyphae described an exponential rate before slowing. Growth based on optical density or microscopic observations was similar in medium with or without PP3. However, PP3 altered the pattern of mycelial development by increasing branching. Distances between the hyphal apex and first branches were on average shorter in PP3-containing media. The final interbranch distances were also shorter in PP3 medium indicating that hyphae tended to branch earlier and more often when supplemented with PP3 to give a more compact mycelium. Vesicle development in nitrogen-fixing cultures limited cell expansion as a result of vesicles truncating growth on new branches. The results provide some explanation for the growth kinetics of Frankia and some indication of how growth rates may be improved.

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

A luminescence-optical spectroscopy study of Rb2KTiOF5 single crystals

NASA Astrophysics Data System (ADS)

Pustovarov, V. A.; Ogorodnikov, I. N.; Kozlov, A. V.; Isaenko, L. I.

2018-06-01

Large single crystals of Rb2KTiOF5 (RKTF), grown by slow solidification method, were studied (7-400 K) for various types of optical and radiation effects. The optical absorption spectra, the parameters of the Urbach rule at 293 K (σ = 0.24 and EU = 105 meV), the low-temperature reflection spectra (T = 7 K, E = 3.7-22 eV) were determined. The luminescence spectra (1.2-6.2 eV) and luminescence decay kinetics are studied upon excitation by a nanosecond electron beam (PCL), ultraviolet and vacuum ultraviolet light (PL), or X-rays radiation (XRL). PL excitation spectra under selective photoexcitation by synchrotron radiation (E = 3.7-22 eV, T = 7 K), temperature dependences of the intensity of steady-state XRL in different emission bands, as well as thermoluminescence (7-400 K) are studied. In the visible spectral region, we detected three luminescence bands that were attributed to radiative annihilation of intrinsic excitons (2.25 eV), recombination-type luminescence (2.1 eV) and luminescence of higher TiOF5 complexes (1.9 eV). The exponential component with lifetime of about 19 μs was revealed in the PCL decay kinetics at 2.25 eV. The low-energy onset of the intrinsic host absorption Ec = 3.55 eV was determined on the basis of the experimental data obtained. Spectra of optical constants were calculated by the Kramers-Krönig method, the energy of the onset of the interband transitions Eg = 4.2 eV was determined, and the main peaks of the optical spectra were identified.

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.

Gasification Characteristics and Kinetics of Coke with Chlorine Addition

NASA Astrophysics Data System (ADS)

Wang, Cui; Zhang, Jianliang; Jiao, Kexin; Liu, Zhengjian; Chou, Kuochih

2017-10-01

The gasification process of metallurgical coke with 0, 1.122, 3.190, and 7.132 wt pct chlorine was investigated through thermogravimetric method from ambient temperature to 1593 K (1320 °C) in purified CO2 atmosphere. The variations in the temperature parameters that T i decreases gradually with increasing chlorine, T f and T max first decrease and then increase, but both in a downward trend indicated that the coke gasification process was catalyzed by the chlorine addition. Then the kinetic model of the chlorine-containing coke gasification was obtained through the advanced determination of the average apparent activation energy, the optimal reaction model, and the pre-exponential factor. The average apparent activation energies were 182.962, 118.525, 139.632, and 111.953 kJ/mol, respectively, which were in the same decreasing trend with the temperature parameters analyzed by the thermogravimetric method. It was also demonstrated that the coke gasification process was catalyzed by chlorine. The optimal kinetic model to describe the gasification process of chlorine-containing coke was the Šesták Berggren model using Málek's method, and the pre-exponential factors were 6.688 × 105, 2.786 × 103, 1.782 × 104, and 1.324 × 103 min-1, respectively. The predictions of chlorine-containing coke gasification from the Šesták Berggren model were well fitted with the experimental data.

Influence of curing mode with a LED unit on polymerization contraction kinetics and degree of conversion of dental resin-based materials.

PubMed

Mortier, Eric; Simon, Yorick; Dahoun, Abdelsellam; Gerdolle, David

2009-01-01

The purpose of this study was to evaluate the influence of photopolymerization mode with a light emitting diode (LED) lamp on the curing contraction kinetics and degree of conversion of 3 resin-based restorative materials. The curing contraction kinetics of Admira (ADM), Filtek P60 (P60), and Filtek Flow (FLO) were measured by the glass slide method. The materials were exposed to light from a 1,000 mW/cm-(2) power LED lamp (Elipar Freelight 2) in 3 modes: 2 continuous modes of 20 and 40 seconds (C20 and C40), and 1 exponential mode (E20; 5 seconds of exponential power increase followed by 15 seconds of maximum intensity). The degree of conversion (DC) was measured for each of the materials, and each of the modes by Fourier transformed infra-red spectrometry. P60 had the significantly lowest final contraction and FLO the highest among all light exposure modes. The C20 and C40 modes did not produce any difference in contraction or degree of conversion. The E20 mode led to a significant slowing of contraction speed combined with greater final contraction. Use of a LED lamp (1,000 mW/cm2) in continuous mode reduces the exposure time by half for identical curing shrinkage and degree of conversion.

Repopulation Kinetics and the Linear-Quadratic Model

NASA Astrophysics Data System (ADS)

O'Rourke, S. F. C.; McAneney, H.; Starrett, C.; O'Sullivan, J. M.

2009-08-01

The standard Linear-Quadratic (LQ) survival model for radiotherapy is used to investigate different schedules of radiation treatment planning for advanced head and neck cancer. We explore how these treament protocols may be affected by different tumour repopulation kinetics between treatments. The laws for tumour cell repopulation include the logistic and Gompertz models and this extends the work of Wheldon et al. [1], which was concerned with the case of exponential repopulation between treatments. Treatment schedules investigated include standarized and accelerated fractionation. Calculations based on the present work show, that even with growth laws scaled to ensure that the repopulation kinetics for advanced head and neck cancer are comparable, considerable variation in the survival fraction to orders of magnitude emerged. Calculations show that application of the Gompertz model results in a significantly poorer prognosis for tumour eradication. Gaps in treatment also highlight the differences in the LQ model with the effect of repopulation kinetics included.

Determination of oxygen diffusion kinetics during thin film ruthenium oxidation

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

Coloma Ribera, R., E-mail: r.colomaribera@utwente.nl; Kruijs, R. W. E. van de; Yakshin, A. E.

2015-08-07

In situ X-ray reflectivity was used to reveal oxygen diffusion kinetics for thermal oxidation of polycrystalline ruthenium thin films and accurate determination of activation energies for this process. Diffusion rates in nanometer thin RuO{sub 2} films were found to show Arrhenius behaviour. However, a gradual decrease in diffusion rates was observed with oxide growth, with the activation energy increasing from about 2.1 to 2.4 eV. Further exploration of the Arrhenius pre-exponential factor for diffusion process revealed that oxidation of polycrystalline ruthenium joins the class of materials that obey the Meyer-Neldel rule.

Accounting for disagreements on average cone loss rates in retinitis pigmentosa with a new kinetic model: Its relevance for clinical trials.

PubMed

Baumgartner, W A; Baumgartner, A M

2016-04-01

Since 1985, at least nine studies of the average rate of cone loss in retinitis pigmentosa (RP) populations have yielded conflicting average rate constant values (-k), differing by 90-160%. This is surprising, since, except for the first two investigations, the Harvard or Johns Hopkins' protocols used in these studies were identical with respect to: use of the same exponential decline model, calculation of average -k from individual patient k values, monitoring patients over similarly large time frames, and excluding data exhibiting floor and ceiling effects. A detailed analysis of Harvard's and Hopkins' protocols and data revealed two subtle differences: (i) Hopkins' use of half-life t0.5 (or t(1/e)) for expressing patient cone-loss rates rather than k as used by Harvard; (ii) Harvard obtaining substantially more +k from improving fields due to dormant-cone recovery effects and "small -k" values than Hopkins' ("small -k" is defined as less than -0.040 year(-1)), e.g., 16% +k, 31% small -k, vs. Hopkins' 3% and 6% respectively. Since t0.5=0.693/k, it follows that when k=0, or is very small, t0.5 (or t(1/e)) is respectively infinity or a very large number. This unfortunate mathematical property (which also prevents t0.5 (t(1/e)) histogram construction corresponding to -k to +k) caused Hopkins' to delete all "small -k" and all +k due to "strong leverage". Naturally this contributed to Hopkins' larger average -k. Difference (ii) led us to re-evaluate the Harvard/Hopkins' exponential unchanging -k model. In its place we propose a model of increasing biochemical stresses from dying rods on cones during RP progression: increasing oxidative stresses and trophic factor deficiencies (e.g., RdCVF), and RPE malfunction. Our kinetic analysis showed rod loss to follow exponential kinetics with unchanging -k due to constant genetic stresses, thereby providing a theoretical basis for Clarke et al.'s empirical observation of such kinetics with eleven animal models of RP. In contrast to this, we show that cone loss occurs in patients with increasing -k values during RP progression. And as the Hopkins' protocol selects more advanced RP cases than Harvard's to assure avoidance of ceiling effects (Harvard does this by kinetic monitoring), we show increasing -k kinetics to be the reason Harvard obtains more +k and small -k values. Thus the combined effects of (i) and (ii) produce Harvard's smaller average -k value. The relevance of the increasing biochemical stress model for optimizing clinical trials is discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Creep substructure formation in sodium chloride single crystals in the power law and exponential creep regimes

NASA Technical Reports Server (NTRS)

Raj, S. V.; Pharr, G. M.

1989-01-01

Creep tests conducted on NaCl single crystals in the temperature range from 373 to 1023 K show that true steady state creep is obtained only above 873 K when the ratio of the applied stress to the shear modulus is less than or equal to 0.0001. Under other stress and temperature conditions, corresponding to both power law and exponential creep, the creep rate decreases monotonically with increasing strain. The transition from power law to exponential creep is shown to be associated with increases in the dislocation density, the cell boundary width, and the aspect ratio of the subgrains along the primary slip planes. The relation between dislocation structure and creep behavior is also assessed.

Proceedings of the Third International Workshop on Multistrategy Learning, May 23-25 Harpers Ferry, WV.

DTIC Science & Technology

1996-09-16

approaches are: • Adaptive filtering • Single exponential smoothing (Brown, 1963) * The Box-Jenkins methodology ( ARIMA modeling ) - Linear exponential... ARIMA • Linear exponential smoothing: Holt’s two parameter modeling (Box and Jenkins, 1976). However, there are two approach (Holt et al., 1960) very...crucial disadvantages: The most important point in - Winters’ three parameter method (Winters, 1960) ARIMA modeling is model identification. As shown in

Detection of kinetic change points in piece-wise linear single molecule motion

NASA Astrophysics Data System (ADS)

Hill, Flynn R.; van Oijen, Antoine M.; Duderstadt, Karl E.

2018-03-01

Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here.

Background photobleaching in raman spectra of aqueous solutions of plant toxins

NASA Astrophysics Data System (ADS)

Brandt, Nikolai N.; Chikishev, Andrey Y.; Tonevitsky, Alexander G.

2002-05-01

Kinetics of background photobleaching in Raman spectra of aqueous solutions of ricin, ricin agglutinin and ricin binding subunit were measured. It was found that the spectrum of Raman background changes upon laser irradiation. Background intensity is lower for the samples with lower molecular weight. Photobleaching is characterized by oscillations in the multi exponentially decaying intensity.

A mechanical model of bacteriophage DNA ejection

NASA Astrophysics Data System (ADS)

Arun, Rahul; Ghosal, Sandip

2017-08-01

Single molecule experiments on bacteriophages show an exponential scaling for the dependence of mobility on the length of DNA within the capsid. It has been suggested that this could be due to the ;capstan mechanism; - the exponential amplification of friction forces that result when a rope is wound around a cylinder as in a ship's capstan. Here we describe a desktop experiment that illustrates the effect. Though our model phage is a million times larger, it exhibits the same scaling observed in single molecule experiments.

Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A

PubMed Central

Shea, Joan-Emma; Onuchic, José N.; Brooks, Charles L.

1999-01-01

Topological frustration in an energetically unfrustrated off-lattice model of the helical protein fragment B of protein A from Staphylococcus aureus was investigated. This Gō-type model exhibited thermodynamic and kinetic signatures of a well-designed two-state folder with concurrent collapse and folding transitions and single exponential kinetics at the transition temperature. Topological frustration is determined in the absence of energetic frustration by the distribution of Fersht φ values. Topologically unfrustrated systems present a unimodal distribution sharply peaked at intermediate φ, whereas highly frustrated systems display a bimodal distribution peaked at low and high φ values. The distribution of φ values in protein A was determined both thermodynamically and kinetically. Both methods yielded a unimodal distribution centered at φ = 0.3 with tails extending to low and high φ values, indicating the presence of a small amount of topological frustration. The contacts with high φ values were located in the turn regions between helices I and II and II and III, intimating that these hairpins are in large part required in the transition state. Our results are in good agreement with all-atom simulations of protein A, as well as lattice simulations of a three- letter code 27-mer (which can be compared with a 60-residue helical protein). The relatively broad unimodal distribution of φ values obtained from the all-atom simulations and that from the minimalist model for the same native fold suggest that the structure of the transition state ensemble is determined mostly by the protein topology and not energetic frustration. PMID:10535953

Neon diffusion kinetics and implications for cosmogenic neon paleothermometry in feldspars

NASA Astrophysics Data System (ADS)

Tremblay, Marissa M.; Shuster, David L.; Balco, Greg; Cassata, William S.

2017-05-01

Observations of cosmogenic neon concentrations in feldspars can potentially be used to constrain the surface exposure duration or surface temperature history of geologic samples. The applicability of cosmogenic neon to either application depends on the temperature-dependent diffusivity of neon isotopes. In this work, we investigate the kinetics of neon diffusion in feldspars of different compositions and geologic origins through stepwise degassing experiments on single, proton-irradiated crystals. To understand the potential causes of complex diffusion behavior that is sometimes manifest as nonlinearity in Arrhenius plots, we compare our results to argon stepwise degassing experiments previously conducted on the same feldspars. Many of the feldspars we studied exhibit linear Arrhenius behavior for neon whereas argon degassing from the same feldspars did not. This suggests that nonlinear behavior in argon experiments is an artifact of structural changes during laboratory heating. However, other feldspars that we examined exhibit nonlinear Arrhenius behavior for neon diffusion at temperatures far below any known structural changes, which suggests that some preexisting material property is responsible for the complex behavior. In general, neon diffusion kinetics vary widely across the different feldspars studied, with estimated activation energies (Ea) ranging from 83.3 to 110.7 kJ/mol and apparent pre-exponential factors (D0) spanning three orders of magnitude from 2.4 × 10-3 to 8.9 × 10-1 cm2 s-1. As a consequence of this variability, the ability to reconstruct temperatures or exposure durations from cosmogenic neon abundances will depend on both the specific feldspar and the surface temperature conditions at the geologic site of interest.

High-Performance Clock Synchronization Algorithms for Distributed Wireless Airborne Computer Networks with Applications to Localization and Tracking of Targets

DTIC Science & Technology

2010-06-01

GMKPF represents a better and more flexible alternative to the Gaussian Maximum Likelihood (GML), and Exponential Maximum Likelihood ( EML ...accurate results relative to GML and EML when the network delays are modeled in terms of a single non-Gaussian/non-exponential distribution or as a...to the Gaussian Maximum Likelihood (GML), and Exponential Maximum Likelihood ( EML ) estimators for clock offset estimation in non-Gaussian or non

Photoluminescence kinetics in CdS nanoclusters formed by the Langmuir-Blodgett technique

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

Zarubanov, A. A., E-mail: alexsundr@mail.ru; Zhuravlev, K. S.

2015-03-15

The photoluminescence kinetics in CdS nanocrystals produced by the Langmuir-Blodgett technique is studied at a temperature of 5 K. The photoluminescence kinetics is described by the sum of two exponential functions, with characteristic times of about 30 and 160 ns. It is found that the fast and slow decay times become longer, as the nanocrystal size increases. Analysis of the data shows that the fast decay time is controlled by trion recombination in nanocrystals with defects, whereas the slow decay time is controlled by the annihilation of optically inactive excitons in nanocrystals without defects. It is established that, as themore » nanocrystal size is decreased, the fraction of imperfect nanocrystals is reduced because of an increase in the energy of defect formation.« less

Kinetic Analysis of the Main Temperature Stage of Fast Pyrolysis

NASA Astrophysics Data System (ADS)

Yang, Xiaoxiao; Zhao, Yuying; Xu, Lanshu; Li, Rui

2017-10-01

Kinetics of the thermal decomposition of eucalyptus chips was evaluated using a high-rate thermogravimetric analyzer (BL-TGA) designed by our research group. The experiments were carried out under non-isothermal condition in order to determine the fast pyrolysis behavior of the main temperature stage (350-540ºC) at heating rates of 60, 120, 180, and 360ºC min-1. The Coats-Redfern integral method and four different reaction mechanism models were adopted to calculate the kinetic parameters including apparent activation energy and pre-exponential factor, and the Flynn-Wall-Ozawa method was employed to testify apparent activation energy. The results showed that estimation value was consistent with the values obtained by linear fitting equations, and the best-fit model for fast pyrolysis was found.

Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties

NASA Astrophysics Data System (ADS)

Schmid, Sonja; Hugel, Thorsten

2018-03-01

Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule Förster resonance energy transfer (smFRET) provides access to enzymatically important time scales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings—such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.

Mass transport in micellar surfactant solutions: 2. Theoretical modeling of adsorption at a quiescent interface.

PubMed

Danov, K D; Kralchevsky, P A; Denkov, N D; Ananthapadmanabhan, K P; Lips, A

2006-01-31

Here, we apply the detailed theoretical model of micellar kinetics from part 1 of this study to the case of surfactant adsorption at a quiescent interface, i.e., to the relaxation of surface tension and adsorption after a small initial perturbation. Our goal is to understand why for some surfactant solutions the surface tension relaxes as inverse-square-root of time, 1/t(1/2), but two different expressions for the characteristic relaxation time are applicable to different cases. In addition, our aim is to clarify why for other surfactant solutions the surface tension relaxes exponentially. For this goal, we carried out a computer modeling of the adsorption process, based on the general system of equations derived in part 1. This analysis reveals the existence of four different consecutive relaxation regimes (stages) for a given micellar solution: two exponential regimes and two inverse-square-root regimes, following one after another in alternating order. Experimentally, depending on the specific surfactant and method, one usually registers only one of these regimes. Therefore, to interpret properly the data, one has to identify which of these four kinetic regimes is observed in the given experiment. Our numerical results for the relaxation of the surface tension, micelle concentration and aggregation number are presented in the form of kinetic diagrams, which reveal the stages of the relaxation process. At low micelle concentrations, "rudimentary" kinetic diagrams could be observed, which are characterized by merging of some stages. Thus, the theoretical modeling reveals a general and physically rich picture of the adsorption process. To facilitate the interpretation of experimental data, we have derived convenient theoretical expressions for the time dependence of surface tension and adsorption in each of the four regimes.

Measuring kinetics of complex single ion channel data using mean-variance histograms.

PubMed Central

Patlak, J B

1993-01-01

The measurement of single ion channel kinetics is difficult when those channels exhibit subconductance events. When the kinetics are fast, and when the current magnitudes are small, as is the case for Na+, Ca2+, and some K+ channels, these difficulties can lead to serious errors in the estimation of channel kinetics. I present here a method, based on the construction and analysis of mean-variance histograms, that can overcome these problems. A mean-variance histogram is constructed by calculating the mean current and the current variance within a brief "window" (a set of N consecutive data samples) superimposed on the digitized raw channel data. Systematic movement of this window over the data produces large numbers of mean-variance pairs which can be assembled into a two-dimensional histogram. Defined current levels (open, closed, or sublevel) appear in such plots as low variance regions. The total number of events in such low variance regions is estimated by curve fitting and plotted as a function of window width. This function decreases with the same time constants as the original dwell time probability distribution for each of the regions. The method can therefore be used: 1) to present a qualitative summary of the single channel data from which the signal-to-noise ratio, open channel noise, steadiness of the baseline, and number of conductance levels can be quickly determined; 2) to quantify the dwell time distribution in each of the levels exhibited. In this paper I present the analysis of a Na+ channel recording that had a number of complexities. The signal-to-noise ratio was only about 8 for the main open state, open channel noise, and fast flickers to other states were present, as were a substantial number of subconductance states. "Standard" half-amplitude threshold analysis of these data produce open and closed time histograms that were well fitted by the sum of two exponentials, but with apparently erroneous time constants, whereas the mean-variance histogram technique provided a more credible analysis of the open, closed, and subconductance times for the patch. I also show that the method produces accurate results on simulated data in a wide variety of conditions, whereas the half-amplitude method, when applied to complex simulated data shows the same errors as were apparent in the real data. The utility and the limitations of this new method are discussed. Images FIGURE 2 FIGURE 4 FIGURE 8 FIGURE 9 PMID:7690261

Kinetic and Mechanistic Examination of Acid–Base Bifunctional Aminosilica Catalysts in Aldol and Nitroaldol Condensations

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

Collier, Virginia E.; Ellebracht, Nathan C.; Lindy, George I.

The kinetic and mechanistic understanding of cooperatively catalyzed aldol and nitroaldol condensations is probed using a series of mesoporous silicas functionalized with aminosilanes to provide bifunctional acid–base character. Mechanistically, a Hammett analysis is performed to determine the effects of electron-donating and electron-withdrawing groups of para-substituted benzaldehyde derivatives on the catalytic activity of each condensation reaction. This information is also used to discuss the validity of previously proposed catalytic mechanisms and to propose a revised mechanism with plausible reaction intermediates. For both reactions, electron-withdrawing groups increase the observed rates of reaction, though resonance effects play an important, yet subtle, role inmore » the nitroaldol condensation, in which a p-methoxy electron-donating group is also able to stabilize the proposed carbocation intermediate. Additionally, activation energies and pre-exponential factors are calculated via the Arrhenius analysis of two catalysts with similar amine loadings: one catalyst had silanols available for cooperative interactions (acid–base catalysis), while the other was treated with a silanol-capping reagent to prevent such cooperativity (base-only catalysis). The values obtained for activation energies and pre-exponential factors in each reaction are discussed in the context of the proposed mechanisms and the importance of cooperative interactions in each reaction. The catalytic activity decreases for all reactions when the silanols are capped with trimethylsilyl groups, and higher temperatures are required to make accurate rate measurements, emphasizing the vital role the weakly acidic silanols play in the catalytic cycles. The results indicate that loss of acid sites is more detrimental to the catalytic activity of the aldol condensation than the nitroaldol condensation, as evidenced by the significant decrease in the pre-exponential factor for the aldol condensation when silanols are unavailable for cooperative interactions. Cooperative catalysis is evidenced by significant changes in the pre-exponential factor, rather than the activation energy for the aldol condensation.« less

Kinetic and Mechanistic Examination of Acid–Base Bifunctional Aminosilica Catalysts in Aldol and Nitroaldol Condensations

DOE PAGES

Collier, Virginia E.; Ellebracht, Nathan C.; Lindy, George I.; ...

2015-12-09

The kinetic and mechanistic understanding of cooperatively catalyzed aldol and nitroaldol condensations is probed using a series of mesoporous silicas functionalized with aminosilanes to provide bifunctional acid–base character. Mechanistically, a Hammett analysis is performed to determine the effects of electron-donating and electron-withdrawing groups of para-substituted benzaldehyde derivatives on the catalytic activity of each condensation reaction. This information is also used to discuss the validity of previously proposed catalytic mechanisms and to propose a revised mechanism with plausible reaction intermediates. For both reactions, electron-withdrawing groups increase the observed rates of reaction, though resonance effects play an important, yet subtle, role inmore » the nitroaldol condensation, in which a p-methoxy electron-donating group is also able to stabilize the proposed carbocation intermediate. Additionally, activation energies and pre-exponential factors are calculated via the Arrhenius analysis of two catalysts with similar amine loadings: one catalyst had silanols available for cooperative interactions (acid–base catalysis), while the other was treated with a silanol-capping reagent to prevent such cooperativity (base-only catalysis). The values obtained for activation energies and pre-exponential factors in each reaction are discussed in the context of the proposed mechanisms and the importance of cooperative interactions in each reaction. The catalytic activity decreases for all reactions when the silanols are capped with trimethylsilyl groups, and higher temperatures are required to make accurate rate measurements, emphasizing the vital role the weakly acidic silanols play in the catalytic cycles. The results indicate that loss of acid sites is more detrimental to the catalytic activity of the aldol condensation than the nitroaldol condensation, as evidenced by the significant decrease in the pre-exponential factor for the aldol condensation when silanols are unavailable for cooperative interactions. Cooperative catalysis is evidenced by significant changes in the pre-exponential factor, rather than the activation energy for the aldol condensation.« less

Characterization of x-ray framing cameras for the National Ignition Facility using single photon pulse height analysis.

PubMed

Holder, J P; Benedetti, L R; Bradley, D K

2016-11-01

Single hit pulse height analysis is applied to National Ignition Facility x-ray framing cameras to quantify gain and gain variation in a single micro-channel plate-based instrument. This method allows the separation of gain from detectability in these photon-detecting devices. While pulse heights measured by standard-DC calibration methods follow the expected exponential distribution at the limit of a compound-Poisson process, gain-gated pulse heights follow a more complex distribution that may be approximated as a weighted sum of a few exponentials. We can reproduce this behavior with a simple statistical-sampling model.

Coarsening and persistence in a one-dimensional system of orienting arrowheads: Domain-wall kinetics with A +B →0

NASA Astrophysics Data System (ADS)

Khandkar, Mahendra D.; Stinchcombe, Robin; Barma, Mustansir

2017-01-01

We demonstrate the large-scale effects of the interplay between shape and hard-core interactions in a system with left- and right-pointing arrowheads <> on a line, with reorientation dynamics. This interplay leads to the formation of two types of domain walls, >< (A ) and <> (B ). The correlation length in the equilibrium state diverges exponentially with increasing arrowhead density, with an ordered state of like orientations arising in the limit. In this high-density limit, the A domain walls diffuse, while the B walls are static. In time, the approach to the ordered state is described by a coarsening process governed by the kinetics of domain-wall annihilation A +B →0 , quite different from the A +A →0 kinetics pertinent to the Glauber-Ising model. The survival probability of a finite set of walls is shown to decay exponentially with time, in contrast to the power-law decay known for A +A →0 . In the thermodynamic limit with a finite density of walls, coarsening as a function of time t is studied by simulation. While the number of walls falls as t-1/2, the fraction of persistent arrowheads decays as t-θ where θ is close to 1/4 , quite different from the Ising value. The global persistence too has θ =1/4 , as follows from a heuristic argument. In a generalization where the B walls diffuse slowly, θ varies continuously, increasing with increasing diffusion constant.

Coarsening and persistence in a one-dimensional system of orienting arrowheads: Domain-wall kinetics with A+B→0.

PubMed

Khandkar, Mahendra D; Stinchcombe, Robin; Barma, Mustansir

2017-01-01

We demonstrate the large-scale effects of the interplay between shape and hard-core interactions in a system with left- and right-pointing arrowheads <> on a line, with reorientation dynamics. This interplay leads to the formation of two types of domain walls, >< (A) and <> (B). The correlation length in the equilibrium state diverges exponentially with increasing arrowhead density, with an ordered state of like orientations arising in the limit. In this high-density limit, the A domain walls diffuse, while the B walls are static. In time, the approach to the ordered state is described by a coarsening process governed by the kinetics of domain-wall annihilation A+B→0, quite different from the A+A→0 kinetics pertinent to the Glauber-Ising model. The survival probability of a finite set of walls is shown to decay exponentially with time, in contrast to the power-law decay known for A+A→0. In the thermodynamic limit with a finite density of walls, coarsening as a function of time t is studied by simulation. While the number of walls falls as t^{-1/2}, the fraction of persistent arrowheads decays as t^{-θ} where θ is close to 1/4, quite different from the Ising value. The global persistence too has θ=1/4, as follows from a heuristic argument. In a generalization where the B walls diffuse slowly, θ varies continuously, increasing with increasing diffusion constant.

Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional tfdA Gene

PubMed Central

Bælum, Jacob; Prestat, Emmanuel; David, Maude M.; Strobel, Bjarne W.

2012-01-01

Mineralization potentials, rates, and kinetics of the three phenoxy acid (PA) herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 4-chloro-2-methylphenoxyacetic acid (MCPA), and 2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP), were investigated and compared in 15 soils collected from five continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event, tfdA genes were quantified using real-time PCR to estimate the genetic potential for degrading PA in the soils. In 25 of the 45 mineralization scenarios, ∼60% mineralization was observed within 118 days. Elevated concentrations of tfdA in the range 1 × 105 to 5 × 107 gene copies g−1 of soil were observed in soils where mineralization could be described by using growth-linked kinetic models. A clear trend was observed that the mineralization rates of the three PAs occurred in the order 2,4-D > MCPA > MCPP, and a correlation was observed between rapid mineralization and soils exposed to PA previously. Finally, for 2,4-D mineralization, all seven mineralization patterns which were best fitted by the exponential model yielded a higher tfdA gene potential after mineralization had occurred than the three mineralization patterns best fitted by the Lin model. PMID:22635998

Phase space analysis for a scalar-tensor model with kinetic and Gauss-Bonnet couplings

NASA Astrophysics Data System (ADS)

Granda, L. N.; Loaiza, E.

2016-09-01

We study the phase space for a scalar-tensor string inspired model of dark energy with nonminimal kinetic and Gauss-Bonnet couplings. The form of the scalar potential and of the coupling terms is of the exponential type, which gives rise to appealing cosmological solutions. The critical points describe a variety of cosmological scenarios that go from a matter or radiation dominated universe to a dark energy dominated universe. Trajectories were found in the phase space departing from unstable or saddle fixed points and arriving at the stable scalar field dominated point corresponding to late-time accelerated expansion.

Photo-thermal reactions of ethanol over Ag/TiO2 catalysts. The role of silver plasmon resonance in the reaction kinetics.

PubMed

Nadeem, M A; Idriss, H

2018-05-17

Photo-thermal catalytic reactions of ethanol over Ag/TiO2 were conducted in order to probe into the role of plasmonic resonance response in the reaction kinetics. In the 300-500 K temperature domain the increase in reaction rate is found to be mainly due to changes in the activation energy while above this temperature range the increase was due to the pre-exponential factor. These results might be linked to the role of plasmonic Ag particles in polarising the reaction intermediates and therefore increasing the reaction products at temperatures up to about 500 K.

Bounded energy states in homogeneous turbulent shear flow: An alternative view

NASA Technical Reports Server (NTRS)

Bernard, Peter S.; Speziale, Charles G.

1990-01-01

The equilibrium structure of homogeneous turbulent shear flow is investigated from a theoretical standpoint. Existing turbulence models, in apparent agreement with physical and numerical experiments, predict an unbounded exponential time growth of the turbulent kinetic energy and dissipation rate; only the anisotropy tensor and turbulent time scale reach a structural equilibrium. It is shown that if vortex stretching is accounted for in the dissipation rate transport equation, then there can exist equilibrium solutions, with bounded energy states, where the turbulence production is balanced by its dissipation. Illustrative calculations are present for a k-epsilon model modified to account for vortex stretching. The calculations indicate an initial exponential time growth of the turbulent kinetic energy and dissipation rate for elapsed times that are as large as those considered in any of the previously conducted physical or numerical experiments on homogeneous shear flow. However, vortex stretching eventually takes over and forces a production-equals-dissipation equilibrium with bounded energy states. The validity of this result is further supported by an independent theoretical argument. It is concluded that the generally accepted structural equilibrium for homogeneous shear flow with unbounded component energies is in need of re-examination.

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

Vasileiadis, Thomas; Department of Materials Science, University of Patras, GR-26504 Rio-Patras; Yannopoulos, Spyros N., E-mail: sny@iceht.forth.gr

Controlled photo-induced oxidation and amorphization of elemental trigonal tellurium are achieved by laser irradiation at optical wavelengths. These processes are monitored in situ by time-resolved Raman scattering and ex situ by electron microscopies. Ultrathin TeO₂ films form on Te surfaces, as a result of irradiation, with an interface layer of amorphous Te intervening between them. It is shown that irradiation, apart from enabling the controllable transformation of bulk Te to one-dimensional nanostructures, such as Te nanotubes and hybrid core-Te/sheath-TeO₂ nanowires, causes also a series of light-driven (athermal) phase transitions involving the crystallization of the amorphous TeO₂ layers and its transformationmore » to a multiplicity of crystalline phases including the γ-, β-, and α-TeO₂ crystalline phases. The kinetics of the above photo-induced processes is investigated by Raman scattering at various laser fluences revealing exponential and non-exponential kinetics at low and high fluence, respectively. In addition, the formation of ultrathin (less than 10 nm) layers of amorphous TeO₂ offers the possibility to explore structural transitions in 2D glasses by observing changes in the short- and medium-range structural order induced by spatial confinement.« less

Physical, chemical and kinetic factors affecting prion infectivity

PubMed Central

Properzi, Francesca; Badhan, Anjna; Klier, Steffi; Schmidt, Christian; Klöhn, Peter C.; Wadsworth, Jonathan D. F.; Clarke, Anthony R.; Jackson, Graham S.; Collinge, John

2016-01-01

ABSTRACT The mouse-adapted scrapie prion strain RML is one of the most widely used in prion research. The introduction of a cell culture-based assay of RML prions, the scrapie cell assay (SCA) allows more rapid and precise prion titration. A semi-automated version of this assay (ASCA) was applied to explore a range of conditions that might influence the infectivity and properties of RML prions. These include resistance to freeze-thaw procedures; stability to endogenous proteases in brain homogenate despite prolonged exposure to varying temperatures; distribution of infective material between pellet and supernatant after centrifugation, the effect of reducing agents and the influence of detergent additives on the efficiency of infection. Apparent infectivity is increased significantly by interaction with cationic detergents. Importantly, we have also elucidated the relationship between the duration of exposure of cells to RML prions and the transmission of infection. We established that the infection process following contact of cells with RML prions is rapid and followed an exponential time course, implying a single rate-limiting process. PMID:27282252

Physical, chemical and kinetic factors affecting prion infectivity.

PubMed

Properzi, Francesca; Badhan, Anjna; Klier, Steffi; Schmidt, Christian; Klöhn, Peter C; Wadsworth, Jonathan D F; Clarke, Anthony R; Jackson, Graham S; Collinge, John

2016-05-03

The mouse-adapted scrapie prion strain RML is one of the most widely used in prion research. The introduction of a cell culture-based assay of RML prions, the scrapie cell assay (SCA) allows more rapid and precise prion titration. A semi-automated version of this assay (ASCA) was applied to explore a range of conditions that might influence the infectivity and properties of RML prions. These include resistance to freeze-thaw procedures; stability to endogenous proteases in brain homogenate despite prolonged exposure to varying temperatures; distribution of infective material between pellet and supernatant after centrifugation, the effect of reducing agents and the influence of detergent additives on the efficiency of infection. Apparent infectivity is increased significantly by interaction with cationic detergents. Importantly, we have also elucidated the relationship between the duration of exposure of cells to RML prions and the transmission of infection. We established that the infection process following contact of cells with RML prions is rapid and followed an exponential time course, implying a single rate-limiting process.

Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

PubMed Central

Bian, Yunqiang; Zhang, Jian; Wang, Jun; Wang, Jihua; Wang, Wei

2015-01-01

How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA. PMID:26030098

Determination of co-metabolism for 1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane (DDT) degradation with enzymes from Trametes versicolor U97.

PubMed

Sari, Ajeng Arum; Tachibana, Sanro; Itoh, Kazutaka

2012-08-01

Trametes versicolor U97 isolated from nature degraded 73% of the 1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane (DDT) in a malt extract liquid medium after a 40-d incubation period. This paper presents a kinetic study of microbial growth using the Monod equation. T. versicolor U97 degraded DDT during an exponential growth phase, using glucose as a carbon source for growth. The growth of T. versicolor U97 was not affected by DDT. DDT was degraded by T. versicolor U97 only when the secondary metabolism coincided with the production of several enzymes. Furthermore, modeling of several inhibitors using the partial least squares function in Minitab 15, revealed lignin peroxidase (98.7 U/l) plays a role in the degradation of DDT. T. versicolor U97 produced several metabolites included a single-ring aromatic compound, 4-chlorobenzoic acid. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

The use of ESR spectroscopy for the identification and dose assessment of irradiated pink shrimp (Parapenaeus longirostris) from Turkey

NASA Astrophysics Data System (ADS)

Aydaş, Canan; Tepe Çam, Semra; Engin, Birol; Aydın, Talat; Polat, Mustafa

2013-03-01

Turkish pink shrimp (Parapenaeus longirostris) samples were studied by electron spin resonance (ESR) spectroscopy for identification and dose assessment purposes. In this work, the calcified shells of shrimps were used as a sample material. Before irradiation, all shrimp shell samples exhibit one weak ESR singlet with a g-factor of 2.0047. After irradiation, all samples exhibit two asymmetric ESR signal components centered at g-values of 2.0013 and 1.9959. The dose-response curves of the samples exposed to gamma radiations were found to be described well by a single saturation exponential function. Variation of ESR signal intensity of irradiated samples at room and-20 °C temperatures with time in a long-term showed that free radicals responsible from the ESR spectrum of shrimp shells were not stable but still detectable after 87 days. Also, the kinetic behavior of signal at g=2.0013 was studied and the additive dose method was used to evaluate the dose in the product.

Fluctuating bottleneck model studies on kinetics of DNA escape from α-hemolysin nanopores

NASA Astrophysics Data System (ADS)

Bian, Yukun; Wang, Zilin; Chen, Anpu; Zhao, Nanrong

2015-11-01

We have proposed a fluctuation bottleneck (FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels.

Limiting Energy Dissipation Induces Glassy Kinetics in Single-Cell High-Precision Responses

PubMed Central

Das, Jayajit

2016-01-01

Single cells often generate precise responses by involving dissipative out-of-thermodynamic-equilibrium processes in signaling networks. The available free energy to fuel these processes could become limited depending on the metabolic state of an individual cell. How does limiting dissipation affect the kinetics of high-precision responses in single cells? I address this question in the context of a kinetic proofreading scheme used in a simple model of early-time T cell signaling. Using exact analytical calculations and numerical simulations, I show that limiting dissipation qualitatively changes the kinetics in single cells marked by emergence of slow kinetics, large cell-to-cell variations of copy numbers, temporally correlated stochastic events (dynamic facilitation), and ergodicity breaking. Thus, constraints in energy dissipation, in addition to negatively affecting ligand discrimination in T cells, can create a fundamental difficulty in determining single-cell kinetics from cell-population results. PMID:26958894

Smoothing Forecasting Methods for Academic Library Circulations: An Evaluation and Recommendation.

ERIC Educational Resources Information Center

Brooks, Terrence A.; Forys, John W., Jr.

1986-01-01

Circulation time-series data from 50 midwest academic libraries were used to test 110 variants of 8 smoothing forecasting methods. Data and methodologies and illustrations of two recommended methods--the single exponential smoothing method and Brown's one-parameter linear exponential smoothing method--are given. Eight references are cited. (EJS)

Kinetics of Cell Fusion Induced by a Syncytia-Producing Mutant of Herpes Simplex Virus Type I

PubMed Central

Person, Stanley; Knowles, Robert W.; Read, G. Sullivan; Warner, Susan C.; Bond, Vincent C.

1976-01-01

We have isolated a number of plaque-morphology mutants from a strain of herpes simplex virus type I which, unlike the wild type, cause extensive cell fusion during a productive viral infection. After the onset of fusion, there is an exponential decrease in the number of single cells as a function of time after infection. At a multiplicity of infection (MOI) of 3.8 plaque-forming units per cell, fusion begins 5.3 h after infection with the number of single cells decreasing to 10% of the original number 10.2 h after infection. As the MOI is gradually increased from 0.4 to 8, the onset of fusion occurs earlier during infection. However, when the MOI is increased from 8 to 86, the onset of fusion does not occur any earlier. The rate of fusion is independent of the MOI for an MOI greater than 1. The rate of fusion varies linearly with initial cell density up to 3.5 × 104 cells/cm2 and is independent of initial cell density at higher cell concentrations. To assay cell fusion we have developed a simple quantitative assay using a Coulter counter to measure the number of single cells as a function of time after infection. Data obtained using a Coulter counter are similar to those obtained with a microscope assay. PMID:173881

Kinetics of human immunodeficiency virus budding and assembly

NASA Astrophysics Data System (ADS)

Zhang, Rui; Nguyen, Toan

2009-03-01

Human immunodeficiency virus (HIV) belongs to a large family of RNA viruses, retroviruses. Unlike budding of regular enveloped viruses, retroviruses bud concurrently with the assembly of retroviral capsids on the cell membrane. The kinetics of HIV (and other retroviruses) budding and assembly is therefore strongly affected by the elastic energy of the membrane and fundamentally different from regular viruses. The main result of this work shows that the kinetics is tunable from a fast budding process to a slow and effectively trapped partial budding process, by varying the attractive energy of retroviral proteins (call Gags), relative to the membrane elastic energy. When the Gag-Gag attraction is relatively high, the membrane elastic energy provides a kinetic barrier for the two pieces of the partial capsids to merge. This energy barrier determines the slowest step in the kinetics and the budding time. In the opposite limit, the membrane elastic energy provides not only a kinetic energy barrier, but a free energy barrier. The budding and assembly is effectively trapped at local free energy minimum, corresponding to a partially budded state. The time scale to escape from this metastable state is exponentially large. In both cases, our result fit with experimental measurements pretty well.

Ultrafast Carbon Dioxide Sorption Kinetics Using Lithium Silicate Nanowires.

PubMed

Nambo, Apolo; He, Juan; Nguyen, Tu Quang; Atla, Veerendra; Druffel, Thad; Sunkara, Mahendra

2017-06-14

In this paper, the Li 4 SiO 4 nanowires (NWs) were shown to be promising for CO 2 capture with ultrafast kinetics. Specifically, the nanowire powders exhibited an uptake of 0.35 g g -1 of CO 2 at an ultrafast adsorption rate of 0.22 g g -1 min -1 at 650-700 °C. Lithium silicate (Li 4 SiO 4 ) nanowires and nanopowders were synthesized using a "solvo-plasma" technique involving plasma oxidation of silicon precursors mixed with lithium hydroxide. The kinetic parameter values (k) extracted from sorption kinetics obtained using NW powders are 1 order of magnitude higher than those previously reported for the Li 4 SiO 4 -CO 2 reaction system. The time scales for CO 2 sorption using nanowires are approximately 3 min and two orders magnitude faster compared to those obtained using lithium silicate powders with spherical morphologies and aggregates. Furthermore, Li 4 SiO 4 nanowire powders showed reversibility through sorption-desorption cycles indicating their suitability for CO 2 capture applications. All of the morphologies of Li 4 SiO 4 powders exhibited a double exponential behavior in the adsorption kinetics indicating two distinct time constants for kinetic and the mass transfer limited regimes.

NMR spin-rotation relaxation and diffusion of methane

NASA Astrophysics Data System (ADS)

Singer, P. M.; Asthagiri, D.; Chapman, W. G.; Hirasaki, G. J.

2018-05-01

The translational diffusion-coefficient and the spin-rotation contribution to the 1H NMR relaxation rate for methane (CH4) are investigated using MD (molecular dynamics) simulations, over a wide range of densities and temperatures, spanning the liquid, supercritical, and gas phases. The simulated diffusion-coefficients agree well with measurements, without any adjustable parameters in the interpretation of the simulations. A minimization technique is developed to compute the angular velocity for non-rigid spherical molecules, which is used to simulate the autocorrelation function for spin-rotation interactions. With increasing diffusivity, the autocorrelation function shows increasing deviations from the single-exponential decay predicted by the Langevin theory for rigid spheres, and the deviations are quantified using inverse Laplace transforms. The 1H spin-rotation relaxation rate derived from the autocorrelation function using the "kinetic model" agrees well with measurements in the supercritical/gas phase, while the relaxation rate derived using the "diffusion model" agrees well with measurements in the liquid phase. 1H spin-rotation relaxation is shown to dominate over the MD-simulated 1H-1H dipole-dipole relaxation at high diffusivity, while the opposite is found at low diffusivity. At high diffusivity, the simulated spin-rotation correlation time agrees with the kinetic collision time for gases, which is used to derive a new expression for 1H spin-rotation relaxation, without any adjustable parameters.

Studies on the nature of the primary reactions of photosystem II in photosynthesis. I. The electrochromic 515 nm absorption change as an appropriate indicator for the functional state of the photochemical active centers of system II in DCMY poisoned chloroplasts.

PubMed

Renger, G; Wolff, C

1975-01-01

The field indicating electrochromic 515 nm absorption change has been measured under different excitation conditions in DCMU poisoned chloroplasts in the presence of benzylviologen as electron acceptor. It has been found: 1. The amplitude of the 515 nm absorption change is nearly completely suppressed under repetitive single turnover flash excitation conditions which kinetically block the back reaction around system II (P. Bennoun, Biochim. Biophys. Acta 216, 357 [1970]). 2. The amplitude of the 515 nm absorption change measured under repetitive single turnover flash excitation conditions which allow the completion of the back reaction during the dark time between the flashes (measuring light beam switched off) amounts in the presence of 2 mum DCMU nearly 50% of the electrochromic 515 nm amplitude obtained in the absence of DCMU. In DCMU poisoned chloroplasts this amplitude is significantly decreased by hydroxylaminhydrochloride, but nearly doubled in the presence of CDIP+ascorbate. 3. The dependence of the 515 nm amplitude on the time td between the flashes kinetically resembles the back reaction around system ?II. The time course of the back reaction can be fairly described either by a second order reaction or by a two phase exponential kinetics. 4. 1,3-dinitrobenzene (DNE) or alpha-bromo-alpha-benzylmalodinitril (BBMD) reduce the 515 nm amplitude in DCMU poisoned chloroplasts, but seem to influecne only slightly the kinetics of the back reaction. 5. The dependence of the 515 nm amplitude on the flash light intensity (the amplitude normalized to 1 at 100% flash light intensity) is not changed by DNB. Based on these experimental data it has been concluded that in DCMU poisoned chloroplasts the amplitude of the 515 nm absorption change reflects the functional state of photosystem II centers (designated as photoelectric dipole generators II) under suitable excitation conditions. Furthermore, it is inferred that in DCMU poisoned chlorplasts the photoelectric dipole generators II either cooperate (probably as twin-pairs) or exist in two functionally different forms. With respect to BBMD and DNB it is assumed that these agents transform the phtooelectric dipole generators II into powerful nonphotochemical quenchers, which significantly reduce the variable fluorescence in DCMU-poisoned chloroplasts.

Effect of temperature on water diffusion during rehydration of sun-dried red pepper ( Capsicum annuum L.)

NASA Astrophysics Data System (ADS)

Demiray, Engin; Tulek, Yahya

2017-05-01

Rehydration, which is a complex process aimed at the restoration of raw material properties when dried material comes in contact with water. In the present research, studies were conducted to probe the kinetics of rehydration of sun-dried red peppers. The kinetics associated with rehydrating sun-dried red peppers was studied at three different temperatures (25, 35 and 45 °C). To describe the rehydration kinetics, four different models, Peleg's, Weibull, first order and exponential association, were considered. Between these four models proposed Weibull model gave a better fit for all rehydration conditions applied. The effective moisture diffusivity values of red peppers increased as water rehydration temperature increased. The values of the effective moisture diffusivity of red peppers were in the range 1.37 × 10-9-1.48 × 10-9 m2 s-1. On the other hand, the activation energy for rehydration kinetic was also calculated using Arrhenius equation and found as 3.17 kJ mol-1.

Kinetic Inductance Photodetectors Based on Nonequilibrium Response in Superconducting Thin-Film Structures

NASA Technical Reports Server (NTRS)

Sergeev, A. V.; Karasik, B. S.; Gogidze, I. G.; Mitin, V. V.

2001-01-01

While experimental studies of kinetic-inductance sensors have been limited so far by the temperature range near the superconducting transition, these detectors can be very sensitivity at temperatures well below the transition, where the number of equilibrium quasiparticles is exponentially small. In this regime, a shift of the quasiparticle chemical potential under radiation results in the change of the kinetic inductance, which can be measured by a sensitive SQUID readout. We modeled the kinetic inductance response of detectors made from disordered superconducting Nb, NbC, and MoRe films. Low phonon transparency of the interface between the superconductor and the substrate causes substantial re-trapping of phonons providing high quantum efficiency and the operating time of approximately 1 ms at 1 K. Due to the small number of quasiparticles, the noise equivalent power of the detector determined by the quasiparticle generation-recombination noise can be as small as approximately 10(exp -19) W/Hz(exp 1/2) at He4 temperatures.

Evaluation of the Kinetic Property of Single-Molecule Junctions by Tunneling Current Measurements.

PubMed

Harashima, Takanori; Hasegawa, Yusuke; Kiguchi, Manabu; Nishino, Tomoaki

2018-01-01

We investigated the formation and breaking of single-molecule junctions of two kinds of dithiol molecules by time-resolved tunneling current measurements in a metal nanogap. The resulting current trajectory was statistically analyzed to determine the single-molecule conductance and, more importantly, to reveal the kinetic property of the single-molecular junction. These results suggested that combining a measurement of the single-molecule conductance and statistical analysis is a promising method to uncover the kinetic properties of the single-molecule junction.

Modal gating of muscle nicotinic acetylcholine receptors

NASA Astrophysics Data System (ADS)

Vij, Ridhima

Many ion channels exhibit multiple patterns of kinetic activity in single-channel currents. This behavior is rare in WT mouse muscle nicotinic acetylcholine receptors (AChRs), where A2C↔A2O gating events are well-described by single exponentials. Also, single-channel open probability (PO) is essentially homogeneous at a given agonist concentration in the WT receptors. Here I report that perturbations of almost all the residues in loop C (alpha188-alpha199, at the agonist binding site) generate heterogeneity in PO ('modes'). Such unsettled activity was apparent with an alanine substitution at all positions in loop C (except alphaY190 and alphaY198) and with different side chain substitutions at alphaP197 for both adult- and fetal-type AChRs. I used single channel electrophysiology along with site-directed mutagenesis to study modal gating in AChRs consequent to mutations/deletions in loop C. The multiple patterns of kinetic activity arose from the difference in agonist affinity rather than in intrinsic AChR gating. Out of the four different agonists used to study the modal behavior, acetylcholine (ACh) showed a higher degree of kinetic heterogeneity compared to others. The time constant for switching between modes was long (~mins), suggesting that they arise from alternative, stable protein conformations. By studying AChRs having only 1 functional binding site, I attempted to find the source of the affinity difference, which was traced mainly to the alphadelta agonist site. Affinity at the neurotransmitter binding site is mainly determined by a core of five aromatic residues (alphaY93, alphaW149, alphaY190, alphaY198 and deltaW57). Phenylalanine substitutions at all aromatic residues except alphaY93 resulted in elimination of modes. Modes were also eliminated by alanine mutation at deltaW57 on the complementary side but not at other aromatics. Also, by substituting four gamma subunit residues into the delta subunit on the complementary beta sheet, I found that modes were reduced. Based on our results, we propose that WT loop C has an important role in determining resting affinity, in part by making stable interactions with the complementary surface of the alphadelta binding pocket. We suggest a possible structural basis for the fluctuations caused by loop C perturbations and propose that at the alphadelta agonist binding site, both loop C and the complementary subunit surface can adopt alternative conformations and interact with each other with respect to the aromatic core, to cause the variations in affinity.

Kinetic study of the inactivation of ascorbate peroxidase by hydrogen peroxide.

PubMed Central

Hiner, A N; Rodríguez-López, J N; Arnao, M B; Lloyd Raven, E; García-Cánovas, F; Acosta, M

2000-01-01

The activity of ascorbate peroxidase (APX) has been studied with H(2)O(2) and various reducing substrates. The activity decreased in the order pyrogallol>ascorbate>guaiacol>2, 2'-azino-bis-(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS). The inactivation of APX with H(2)O(2) as the sole substrate was studied. The number of H(2)O(2) molecules required for maximal inactivation of the enzyme was determined as approx. 2.5. Enzymic activity of approx. 20% of the original remained at the end of the inactivation process (i.e. approx. 20% resistance) when ascorbate or ABTS was used as the substrate in activity assays. With pyrogallol or guaiacol no resistance was seen. Inactivation by H(2)O(2) followed over time with ascorbate or pyrogallol assays exhibited single-exponential decreases in enzymic activity. Hyperbolic saturation kinetics were observed in both assay systems; a similar dissociation constant (0.8 microM) for H(2)O(2) was obtained in each case. However, the maximum rate constant (lambda(max)) obtained from the plots differed depending on the assay substrate. The presence of reducing substrate in addition to H(2)O(2) partly or completely protected the enzyme from inactivation, depending on how many molar equivalents of reducing substrate were added. An oxygen electrode system has been used to confirm that APX does not exhibit a catalase-like oxygen-releasing reaction. A kinetic model was developed to interpret the experimental results; both the results and the model are compared and contrasted with previously obtained results for horseradish peroxidase C. The kinetic model has led us to the conclusion that the inactivation of APX by H(2)O(2) represents an unusual situation in which no enzyme turnover occurs but there is a partition of the enzyme between two forms, one inactive and the other with activity towards reducing substrates such as ascorbate and ABTS only. The partition ratio is less than 1. PMID:10816425

Correlation between the change in the kinetics of the ribosomal RNA rrnB P2 promoter and the transition from lag to exponential phase with Pseudomonas fluorescens.

PubMed

McKellar, Robin C

2008-01-15

Developing accurate mathematical models to describe the pre-exponential lag phase in food-borne pathogens presents a considerable challenge to food microbiologists. While the growth rate is influenced by current environmental conditions, the lag phase is affected in addition by the history of the inoculum. A deeper understanding of physiological changes taking place during the lag phase would improve accuracy of models, and in earlier studies a strain of Pseudomonas fluorescens containing the Tn7-luxCDABE gene cassette regulated by the rRNA promoter rrnB P2 was used to measure the influence of starvation, growth temperature and sub-lethal heating on promoter expression and subsequent growth. The present study expands the models developed earlier to include a model which describes the change from exponential to linear increase in promoter expression with time when the exponential phase of growth commences. A two-phase linear model with Poisson weighting was used to estimate the lag (LPDLin) and the rate (RLin) for this linear increase in bioluminescence. The Spearman rank correlation coefficient (r=0.830) between the LPDLin and the growth lag phase (LPDOD) was extremely significant (P

Kinetic Studies on Enzyme-Catalyzed Reactions: Oxidation of Glucose, Decomposition of Hydrogen Peroxide and Their Combination

PubMed Central

Tao, Zhimin; Raffel, Ryan A.; Souid, Abdul-Kader; Goodisman, Jerry

2009-01-01

The kinetics of the glucose oxidase-catalyzed reaction of glucose with O2, which produces gluconic acid and hydrogen peroxide, and the catalase-assisted breakdown of hydrogen peroxide to generate oxygen, have been measured via the rate of O2 depletion or production. The O2 concentrations in air-saturated phosphate-buffered salt solutions were monitored by measuring the decay of phosphorescence from a Pd phosphor in solution; the decay rate was obtained by fitting the tail of the phosphorescence intensity profile to an exponential. For glucose oxidation in the presence of glucose oxidase, the rate constant determined for the rate-limiting step was k = (3.0 ± 0.7) ×104 M−1s−1 at 37°C. For catalase-catalyzed H2O2 breakdown, the reaction order in [H2O2] was somewhat greater than unity at 37°C and well above unity at 25°C, suggesting different temperature dependences of the rate constants for various steps in the reaction. The two reactions were combined in a single experiment: addition of glucose oxidase to glucose-rich cell-free media caused a rapid drop in [O2], and subsequent addition of catalase caused [O2] to rise and then decrease to zero. The best fit of [O2] to a kinetic model is obtained with the rate constants for glucose oxidation and peroxide decomposition equal to 0.116 s−1 and 0.090 s−1 respectively. Cellular respiration in the presence of glucose was found to be three times as rapid as that in glucose-deprived cells. Added NaCN inhibited O2 consumption completely, confirming that oxidation occurred in the cellular mitochondrial respiratory chain. PMID:19348778

Neon diffusion kinetics and implications for cosmogenic neon paleothermometry in feldspars

DOE PAGES

Tremblay, Marissa M.; Shuster, David L.; Balco, Greg; ...

2017-02-20

Observations of cosmogenic neon concentrations in feldspars can potentially be used to constrain the surface exposure duration or surface temperature history of geologic samples. The applicability of cosmogenic neon to either application depends on the temperature-dependent diffusivity of neon isotopes. Here in this work, we investigate the kinetics of neon diffusion in feldspars of different compositions and geologic origins through stepwise degassing experiments on single, proton-irradiated crystals. To understand the potential causes of complex diffusion behavior that is sometimes manifest as nonlinearity in Arrhenius plots, we compare our results to argon stepwise degassing experiments previously conducted on the same feldspars.more » Many of the feldspars we studied exhibit linear Arrhenius behavior for neon whereas argon degassing from the same feldspars did not. This suggests that nonlinear behavior in argon experiments is an artifact of structural changes during laboratory heating. However, other feldspars that we examined exhibit nonlinear Arrhenius behavior for neon diffusion at temperatures far below any known structural changes, which suggests that some preexisting material property is responsible for the complex behavior. In general, neon diffusion kinetics vary widely across the different feldspars studied, with estimated activation energies (E a) ranging from 83.3 to 110.7 kJ/mol and apparent pre-exponential factors (D 0) spanning three orders of magnitude from 2.4 ×10 -3 to 8.9 × 10 -1 cm 2 s -1. Finally, as a consequence of this variability, the ability to reconstruct temperatures or exposure durations from cosmogenic neon abundances will depend on both the specific feldspar and the surface temperature conditions at the geologic site of interest.« less

Disruption of Human Plasma High Density Lipoproteins by Streptococcal Serum Opacity Factor Requires Labile Apolipoprotein A-I

PubMed Central

Han, Mikyung; Gillard, Baiba K.; Courtney, Harry S.; Ward, Kathryn; Rosales, Corina; Khant, Htet; Ludtke, Steven J.; Pownall, Henry J.

2010-01-01

Human plasma high density lipoproteins (HDL), the primary vehicle for reverse cholesterol transport, are the target of serum opacity factor (SOF), a virulence determinant of Streptococcus pyogenes that turns serum opaque. HDL comprise a core of neutral lipids–cholesteryl esters and some triglyceride–surrounded by a surface monolayer of cholesterol, phospholipids, and specialized proteins–apolipoproteins (apos) A-I and A-II. HDL is an unstable particle residing in a kinetic trap from which it can escape via chaotropic, detergent or thermal perturbation. Recombinant (r) SOF catalyzes the transfer of nearly all neutral lipids of ~100,000 HDL particles (D ~ 8.5 nm) into a single, large cholesteryl ester-rich microemulsion (CERM; D >100 nm) leaving a new HDL-like particle–neo HDL (D ~5.8 nm) while releasing lipid-free (LF) apo A-I. CERM formation and apo A-I release have similar kinetics suggesting parallel or rapid consecutive steps. By using complementary physico-chemical methods, we have refined the mechanistic model for HDL opacification. According to size exclusion chromatography, HDL containing non-labile apo A-I resists rSOF-mediated opacification. Based on kinetic cryo electron microscopy, rSOF (10 nM) catalyzes the conversion of HDL (4 μM) to neo HDL via a step-wise mechanism in which intermediate-size particles are seen. Kinetic turbidimetry revealed opacification as a rising exponential reaction with a rate constant k = (4.400 ± 0.004) × 10−2 min−1. Analysis of the kinetic data using transition state theory gave an enthalpy, entropy and free energy of activation of ΔH‡ = 73.9 kJ/mol, ΔS‡ = −66.87 J/°K, and ΔG‡ = 94.6 kJ/mol respectively. The free energy of activation for opacification is nearly identical to that for the displacement of apo A-I from HDL by guanidine hydrochloride. We conclude that apo A-I lability is required for HDL opacification, LF apo A-I desorption is the rate-limiting step, and nearly all HDL particles contain at least one labile copy of apo A-I. PMID:19191587

Steady-state kinetics of solitary batrachotoxin-treated sodium channels. Kinetics on a bounded continuum of polymer conformations.

PubMed Central

Rubinson, K A

1992-01-01

The underlying principles of the kinetics and equilibrium of a solitary sodium channel in the steady state are examined. Both the open and closed kinetics are postulated to result from round-trip excursions from a transition region that separates the openable and closed forms. Exponential behavior of the kinetics can have origins different from small-molecule systems. These differences suggest that the probability density functions (PDFs) that describe the time dependences of the open and closed forms arise from a distribution of rate constants. The distribution is likely to arise from a thermal modulation of the channel structure, and this provides a physical basis for the following three-variable equation: [formula; see text] Here, A0 is a scaling term, k is the mean rate constant, and sigma quantifies the Gaussian spread for the contributions of a range of effective rate constants. The maximum contribution is made by k, with rates faster and slower contributing less. (When sigma, the standard deviation of the spread, goes to zero, then p(f) = A0 e-kt.) The equation is applied to the single-channel steady-state probability density functions for batrachotoxin-treated sodium channels (1986. Keller et al. J. Gen. Physiol. 88: 1-23). The following characteristics are found: (a) The data for both open and closed forms of the channel are fit well with the above equation, which represents a Gaussian distribution of first-order rate processes. (b) The simple relationship [formula; see text] holds for the mean effective rat constants. Or, equivalently stated, the values of P open calculated from the k values closely agree with the P open values found directly from the PDF data. (c) In agreement with the known behavior of voltage-dependent rate constants, the voltage dependences of the mean effective rate constants for the opening and closing of the channel are equal and opposite over the voltage range studied. That is, [formula; see text] "Bursts" are related to the well-known cage effect of solution chemistry. PMID:1312365

Limiting Energy Dissipation Induces Glassy Kinetics in Single-Cell High-Precision Responses.

PubMed

Das, Jayajit

2016-03-08

Single cells often generate precise responses by involving dissipative out-of-thermodynamic-equilibrium processes in signaling networks. The available free energy to fuel these processes could become limited depending on the metabolic state of an individual cell. How does limiting dissipation affect the kinetics of high-precision responses in single cells? I address this question in the context of a kinetic proofreading scheme used in a simple model of early-time T cell signaling. Using exact analytical calculations and numerical simulations, I show that limiting dissipation qualitatively changes the kinetics in single cells marked by emergence of slow kinetics, large cell-to-cell variations of copy numbers, temporally correlated stochastic events (dynamic facilitation), and ergodicity breaking. Thus, constraints in energy dissipation, in addition to negatively affecting ligand discrimination in T cells, can create a fundamental difficulty in determining single-cell kinetics from cell-population results. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Kinetics of microstructure formation of high-pressure induced gel from a whey protein isolate

NASA Astrophysics Data System (ADS)

He, Jin-Song; Yang, Hongwei; Zhu, Wanpeng; Mu, Tai-Hua

2010-03-01

The kinetic process of pressure-induced gelation of whey protein isolate (WPI) solutions was studied using in situ light scattering. The relationship of the logarithm of scattered light intensity (I) versus time (t) was linear after the induced time and could be described by the Cahn-Hilliard linear theory. With increasing time, the scattered intensity deviated from the exponential relationship, and the time evolution of the scattered light intensity maximum Im and the corresponding wavenumber qm could be described in terms of the power-law relationship as Im~fβ and qm~f-α, respectively. These results indicated that phase separation occurred during the gelation of WPI solutions under high pressure.

Non-thermal plasma destruction of allyl alcohol in waste gas: kinetics and modelling

NASA Astrophysics Data System (ADS)

DeVisscher, A.; Dewulf, J.; Van Durme, J.; Leys, C.; Morent, R.; Van Langenhove, H.

2008-02-01

Non-thermal plasma treatment is a promising technique for the destruction of volatile organic compounds in waste gas. A relatively unexplored technique is the atmospheric negative dc multi-pin-to-plate glow discharge. This paper reports experimental results of allyl alcohol degradation and ozone production in this type of plasma. A new model was developed to describe these processes quantitatively. The model contains a detailed chemical degradation scheme, and describes the physics of the plasma by assuming that the fraction of electrons that takes part in chemical reactions is an exponential function of the reduced field. The model captured the experimental kinetic data to less than 2 ppm standard deviation.

Kinetic signature of fractal-like filament networks formed by orientational linear epitaxy.

PubMed

Hwang, Wonmuk; Eryilmaz, Esma

2014-07-11

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

Measurement of nucleotide exchange rate constants in single rabbit soleus myofibrils during shortening and lengthening using a fluorescent ATP analog.

PubMed Central

Shirakawa, I; Chaen, S; Bagshaw, C R; Sugi, H

2000-01-01

The kinetics of displacement of a fluorescent nucleotide, 2'(3')-O-[N[2-[[Cy3]amido]ethyl]carbamoyl]-adenosine 5'-triphosphate (Cy3-EDA-ATP), bound to rabbit soleus muscle myofibrils were studied using flash photolysis of caged ATP. Use of myofibrils from this slow twitch muscle allowed better resolution of the kinetics of nucleotide exchange than previous studies with psoas muscle myofibrils (, Biophys. J. 73:2033-2042). Soleus myofibrils in the presence of Cy3-EDA-nucleotides (Cy3-EDA-ATP or Cy3-EDA-ADP) showed selective fluorescence staining of the A-band. The K(m) for Cy3-EDA-ATP and the K(d) for Cy3-EDA-ADP binding to the myofibril A-band were 1.9 microM and 3.8 microM, respectively, indicating stronger binding of nucleotide to soleus cross-bridges compared to psoas cross-bridges (2.6 microM and 50 microM, respectively). After flash photolysis of caged ATP, the A-band fluorescence of the myofibril in the Cy3-EDA-ATP solution under isometric conditions decayed exponentially with a rate constant of 0.045 +/- 0.007 s(-1) (n = 32) at 10 degrees C, which was about seven times slower than that for psoas myofibrils. When a myofibril was allowed to shorten with a constant velocity, the nucleotide displacement rate constant increased from 0.066 s(-1) (isometric) to 0.14 s(-1) at 20 degrees C with increasing shortening velocity up to 0.1 myofibril length/s (V(max), the shortening velocity under no load was approximately 0. 2 myofibril lengths/s). The rate constant was not significantly affected by an isovelocity stretch of up to 0.1 myofibril lengths/s. These results suggest that the cross-bridge kinetics are not significantly affected at higher strain during lengthening but depend on the lower strain during shortening. These data also indicate that the interaction distance between a cross-bridge and the actin filament is at least 16 nm for a single cycle of the ATPase. PMID:10653804

Distributions of Autocorrelated First-Order Kinetic Outcomes: Illness Severity

PubMed Central

Englehardt, James D.

2015-01-01

Many complex systems produce outcomes having recurring, power law-like distributions over wide ranges. However, the form necessarily breaks down at extremes, whereas the Weibull distribution has been demonstrated over the full observed range. Here the Weibull distribution is derived as the asymptotic distribution of generalized first-order kinetic processes, with convergence driven by autocorrelation, and entropy maximization subject to finite positive mean, of the incremental compounding rates. Process increments represent multiplicative causes. In particular, illness severities are modeled as such, occurring in proportion to products of, e.g., chronic toxicant fractions passed by organs along a pathway, or rates of interacting oncogenic mutations. The Weibull form is also argued theoretically and by simulation to be robust to the onset of saturation kinetics. The Weibull exponential parameter is shown to indicate the number and widths of the first-order compounding increments, the extent of rate autocorrelation, and the degree to which process increments are distributed exponential. In contrast with the Gaussian result in linear independent systems, the form is driven not by independence and multiplicity of process increments, but by increment autocorrelation and entropy. In some physical systems the form may be attracting, due to multiplicative evolution of outcome magnitudes towards extreme values potentially much larger and smaller than control mechanisms can contain. The Weibull distribution is demonstrated in preference to the lognormal and Pareto I for illness severities versus (a) toxicokinetic models, (b) biologically-based network models, (c) scholastic and psychological test score data for children with prenatal mercury exposure, and (d) time-to-tumor data of the ED01 study. PMID:26061263

Influence of preadsorbed oxygen on activated chemisorption of methane on Pd(110)

NASA Astrophysics Data System (ADS)

Valden, M.; Pere, J.; Xiang, N.; Pessa, M.

1996-07-01

Dissociative chemisorption of methane on clean and oxygen modified Pd(110) has been studied by using molecular beam surface scattering. The absolute dissociation probability of CH 4 ( Stot) is found to increase exponentially with the incident normal energy ( En) of CH 4 and with surface temperature ( TS) on clean Pd(110). The kinetic isotope effect is also found; namely, Stot of CD 4 is 4 to 5 times smaller than Stot of CH 4 throughout the entire range of En studied. These results are consistent with a direct dissociation mechanism. Measurements on preadsorbed oxygen on Pd(110) show that Stot of CH 4 decreases linearly, as oxygen coverage is increased from 0 to 0.4 ML in good agreement with the first-order Langmuir kinetics when approximately two active sites are blocked by one oxygen atom. No influence of the oxygen induced surface reconstructions on the dissociative adsorption kinetics of CH 4 is observed.

`Un-Darkening' the Cosmos: New laws of physics for an expanding universe

NASA Astrophysics Data System (ADS)

George, William

2017-11-01

Dark matter is believed to exist because Newton's Laws are inconsistent with the visible matter in galaxies. Dark energy is necessary to explain the universe expansion. (also available from www.turbulence-online.com) suggested that the equations themselves might be in error because they implicitly assume that time is measured in linear increments. This presentation couples the possible non-linearity of time with an expanding universe. Maxwell's equations for an expanding universe with constant speed of light are shown to be invariant only if time itself is non-linear. Both linear and exponential expansion rates are considered. A linearly expanding universe corresponds to logarithmic time, while exponential expansion corresponds to exponentially varying time. Revised Newton's laws using either leads to different definitions of mass and kinetic energy, both of which appear time-dependent if expressed in linear time. And provide the possibility of explaining the astronomical observations without either dark matter or dark energy. We would have never noticed the differences on earth, since the leading term in both expansions is linear in δ /to where to is the current age.

Live cell imaging combined with high-energy single-ion microbeam

NASA Astrophysics Data System (ADS)

Guo, Na; Du, Guanghua; Liu, Wenjing; Guo, Jinlong; Wu, Ruqun; Chen, Hao; Wei, Junzhe

2016-03-01

DNA strand breaks can lead to cell carcinogenesis or cell death if not repaired rapidly and efficiently. An online live cell imaging system was established at the high energy microbeam facility at the Institute of Modern Physics to study early and fast cellular response to DNA damage after high linear energy transfer ion radiation. The HT1080 cells expressing XRCC1-RFP were irradiated with single high energy nickel ions, and time-lapse images of the irradiated cells were obtained online. The live cell imaging analysis shows that strand-break repair protein XRCC1 was recruited to the ion hit position within 20 s in the cells and formed bright foci in the cell nucleus. The fast recruitment of XRCC1 at the ion hits reached a maximum at about 200 s post-irradiation and then was followed by a slower release into the nucleoplasm. The measured dual-exponential kinetics of XRCC1 protein are consistent with the proposed consecutive reaction model, and the measurements obtained that the reaction rate constant of the XRCC1 recruitment to DNA strand break is 1.2 × 10-3 s-1 and the reaction rate constant of the XRCC1 release from the break-XRCC1 complex is 1.2 × 10-2 s-1.

Modeling the Role of Dislocation Substructure During Class M and Exponential Creep. Revised

NASA Technical Reports Server (NTRS)

Raj, S. V.; Iskovitz, Ilana Seiden; Freed, A. D.

1995-01-01

The different substructures that form in the power-law and exponential creep regimes for single phase crystalline materials under various conditions of stress, temperature and strain are reviewed. The microstructure is correlated both qualitatively and quantitatively with power-law and exponential creep as well as with steady state and non-steady state deformation behavior. These observations suggest that creep is influenced by a complex interaction between several elements of the microstructure, such as dislocations, cells and subgrains. The stability of the creep substructure is examined in both of these creep regimes during stress and temperature change experiments. These observations are rationalized on the basis of a phenomenological model, where normal primary creep is interpreted as a series of constant structure exponential creep rate-stress relationships. The implications of this viewpoint on the magnitude of the stress exponent and steady state behavior are discussed. A theory is developed to predict the macroscopic creep behavior of a single phase material using quantitative microstructural data. In this technique the thermally activated deformation mechanisms proposed by dislocation physics are interlinked with a previously developed multiphase, three-dimensional. dislocation substructure creep model. This procedure leads to several coupled differential equations interrelating macroscopic creep plasticity with microstructural evolution.

Kinetics of DNA Tile Dimerization

PubMed Central

2015-01-01

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile–tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency. PMID:24794259

Kinetics of DNA tile dimerization.

PubMed

Jiang, Shuoxing; Yan, Hao; Liu, Yan

2014-06-24

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

The effects of intensity on V̇O2 kinetics during incremental free swimming.

PubMed

de Jesus, Kelly; Sousa, Ana; de Jesus, Karla; Ribeiro, João; Machado, Leandro; Rodríguez, Ferran; Keskinen, Kari; Vilas-Boas, João Paulo; Fernandes, Ricardo J

2015-09-01

Swimming and training are carried out with wide variability in distances and intensities. However, oxygen uptake kinetics for the intensities seen in swimming has not been reported. The purpose of this study was to assess and compare the oxygen uptake kinetics throughout low-moderate to severe intensities during incremental swimming exercise. We hypothesized that the oxygen uptake kinetic parameters would be affected by swimming intensity. Twenty male trained swimmers completed an incremental protocol of seven 200-m crawl swims to exhaustion (0.05 m·s(-1) increments and 30-s intervals). Oxygen uptake was continuously measured by a portable gas analyzer connected to a respiratory snorkel and valve system. Oxygen uptake kinetics was assessed using a double exponential regression model that yielded both fast and slow components of the response of oxygen uptake to exercise. From low-moderate to severe swimming intensities changes occurred for the first and second oxygen uptake amplitudes (P ≤ 0.04), time constants (P = 0.01), and time delays (P ≤ 0.02). At the heavy and severe intensities, a notable oxygen uptake slow component (>255 mL·min(-1)) occurred in all swimmers. Oxygen uptake kinetics whilst swimming at different intensities offers relevant information regarding cardiorespiratory and metabolic stress that might be useful for appropriate performance diagnosis and training prescription.

Arrhenius curves of hydrogen transfers: tunnel effects, isotope effects and effects of pre-equilibria

PubMed Central

Limbach, Hans-Heinrich; Miguel Lopez, Juan; Kohen, Amnon

2006-01-01

In this paper, the Arrhenius curves of selected hydrogen-transfer reactions for which kinetic data are available in a large temperature range are reviewed. The curves are discussed in terms of the one-dimensional Bell–Limbach tunnelling model. The main parameters of this model are the barrier heights of the isotopic reactions, barrier width of the H-reaction, tunnelling masses, pre-exponential factor and minimum energy for tunnelling to occur. The model allows one to compare different reactions in a simple way and prepare the kinetic data for more-dimensional treatments. The first type of reactions is concerned with reactions where the geometries of the reacting molecules are well established and the kinetic data of the isotopic reactions are available in a large temperature range. Here, it is possible to study the relation between kinetic isotope effects (KIEs) and chemical structure. Examples are the tautomerism of porphyrin, the porphyrin anion and related compounds exhibiting intramolecular hydrogen bonds of medium strength. We observe pre-exponential factors of the order of kT/h≅1013 s−1 corresponding to vanishing activation entropies in terms of transition state theory. This result is important for the second type of reactions discussed in this paper, referring mostly to liquid solutions. Here, the reacting molecular configurations may be involved in equilibria with non- or less-reactive forms. Several cases are discussed, where the less-reactive forms dominate at low or at high temperature, leading to unusual Arrhenius curves. These cases include examples from small molecule solution chemistry like the base-catalysed intramolecular H-transfer in diaryltriazene, 2-(2′-hydroxyphenyl)-benzoxazole, 2-hydroxy-phenoxyl radicals, as well as in the case of an enzymatic system, thermophilic alcohol dehydrogenase. In the latter case, temperature-dependent KIEs are interpreted in terms of a transition between two regimes with different temperature-independent KIEs. PMID:16873127

Arrhenius curves of hydrogen transfers: tunnel effects, isotope effects and effects of pre-equilibria.

PubMed

Limbach, Hans-Heinrich; Miguel Lopez, Juan; Kohen, Amnon

2006-08-29

In this paper, the Arrhenius curves of selected hydrogen-transfer reactions for which kinetic data are available in a large temperature range are reviewed. The curves are discussed in terms of the one-dimensional Bell-Limbach tunnelling model. The main parameters of this model are the barrier heights of the isotopic reactions, barrier width of the H-reaction, tunnelling masses, pre-exponential factor and minimum energy for tunnelling to occur. The model allows one to compare different reactions in a simple way and prepare the kinetic data for more-dimensional treatments. The first type of reactions is concerned with reactions where the geometries of the reacting molecules are well established and the kinetic data of the isotopic reactions are available in a large temperature range. Here, it is possible to study the relation between kinetic isotope effects (KIEs) and chemical structure. Examples are the tautomerism of porphyrin, the porphyrin anion and related compounds exhibiting intramolecular hydrogen bonds of medium strength. We observe pre-exponential factors of the order of kT/h congruent with 10(13) s-1 corresponding to vanishing activation entropies in terms of transition state theory. This result is important for the second type of reactions discussed in this paper, referring mostly to liquid solutions. Here, the reacting molecular configurations may be involved in equilibria with non- or less-reactive forms. Several cases are discussed, where the less-reactive forms dominate at low or at high temperature, leading to unusual Arrhenius curves. These cases include examples from small molecule solution chemistry like the base-catalysed intramolecular H-transfer in diaryltriazene, 2-(2'-hydroxyphenyl)-benzoxazole, 2-hydroxy-phenoxyl radicals, as well as in the case of an enzymatic system, thermophilic alcohol dehydrogenase. In the latter case, temperature-dependent KIEs are interpreted in terms of a transition between two regimes with different temperature-independent KIEs.

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.

Nucleation and growth kinetics during metal-induced layer exchange crystallization of Ge thin films at low temperatures

NASA Astrophysics Data System (ADS)

Hu, Shu; McIntyre, Paul C.

2012-02-01

The kinetics of Al-catalyzed layer exchange crystallization of amorphous germanium (Ge) thin films at low temperatures is reported. Observation of Ge mass transport from an underlying amorphous Ge layer to the Al film surface through an interposed sub-nanometer GeOx interfacial layer allows independent measurement of the areal density and average area of crystalline Ge islands formed on the film surface. We show that bias-voltage stressing of the interfacial layer can be used to control the areal density of nucleated Ge islands. Based on experimental observations, the Johnson-Mehl-Avrami-Kolmogorov phase transformation theory is used to model nanoscale nucleation and growth of Ge islands in two dimensions. Ge island nucleation kinetics follows an exponentially decaying nucleation rate with time. Ge island growth kinetics switches from linear growth at a constant growth velocity to diffusion-limited growth as the growth front advances. The transition point between these two regimes depends on the Ge nucleation site density and the annealing temperature. Knowledge of the kinetics of low-temperature crystallization is important in achieving textured polycrystalline Ge thin films with large grains for applications in large-area electronics and solar energy conversion.

Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques

NASA Astrophysics Data System (ADS)

Fernandez, Julio M.

2008-03-01

The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule atomic force microscopy (AFM) techniques, as shown here, can probe dynamic rearrangements within an enzyme's active site which cannot be resolved with any other current structural biological technique. Furthermore, our work at the single bond level directly demonstrates that thiol/disulfide exchange in proteins is a force-dependent chemical reaction. Our findings suggest that mechanical force plays a role in disulfide reduction in vivo, a property which has never been explored by traditional biochemistry. 1.-Wiita, A.P., Ainavarapu, S.R.K., Huang, H.H. and Julio M. Fernandez (2006) Force-dependent chemical kinetics of disulfide bond reduction observed with single molecule techniques. Proc Natl Acad Sci U S A. 103(19):7222-7 2.-Wiita, A.P., Perez-Jimenez, R., Walther, K.A., Gräter, F. Berne, B.J., Holmgren, A., Sanchez-Ruiz, J.M., and Fernandez, J.M. (2007) Probing the chemistry of thioredoxin catalysis with force. Nature, 450:124-7.

Anomalous NMR Relaxation in Cartilage Matrix Components and Native Cartilage: Fractional-Order Models

PubMed Central

Magin, Richard L.; Li, Weiguo; Velasco, M. Pilar; Trujillo, Juan; Reiter, David A.; Morgenstern, Ashley; Spencer, Richard G.

2011-01-01

We present a fractional-order extension of the Bloch equations to describe anomalous NMR relaxation phenomena (T1 and T2). The model has solutions in the form of Mittag-Leffler and stretched exponential functions that generalize conventional exponential relaxation. Such functions have been shown by others to be useful for describing dielectric and viscoelastic relaxation in complex, heterogeneous materials. Here, we apply these fractional-order T1 and T2 relaxation models to experiments performed at 9.4 and 11.7 Tesla on type I collagen gels, chondroitin sulfate mixtures, and to bovine nasal cartilage (BNC), a largely isotropic and homogeneous form of cartilage. The results show that the fractional-order analysis captures important features of NMR relaxation that are typically described by multi-exponential decay models. We find that the T2 relaxation of BNC can be described in a unique way by a single fractional-order parameter (α), in contrast to the lack of uniqueness of multi-exponential fits in the realistic setting of a finite signal-to-noise ratio. No anomalous behavior of T1 was observed in BNC. In the single-component gels, for T2 measurements, increasing the concentration of the largest components of cartilage matrix, collagen and chondroitin sulfate, results in a decrease in α, reflecting a more restricted aqueous environment. The quality of the curve fits obtained using Mittag-Leffler and stretched exponential functions are in some cases superior to those obtained using mono- and bi-exponential models. In both gels and BNC, α appears to account for microstructural complexity in the setting of an altered distribution of relaxation times. This work suggests the utility of fractional-order models to describe T2 NMR relaxation processes in biological tissues. PMID:21498095

Anomalous NMR relaxation in cartilage matrix components and native cartilage: Fractional-order models

NASA Astrophysics Data System (ADS)

Magin, Richard L.; Li, Weiguo; Pilar Velasco, M.; Trujillo, Juan; Reiter, David A.; Morgenstern, Ashley; Spencer, Richard G.

2011-06-01

We present a fractional-order extension of the Bloch equations to describe anomalous NMR relaxation phenomena ( T1 and T2). The model has solutions in the form of Mittag-Leffler and stretched exponential functions that generalize conventional exponential relaxation. Such functions have been shown by others to be useful for describing dielectric and viscoelastic relaxation in complex, heterogeneous materials. Here, we apply these fractional-order T1 and T2 relaxation models to experiments performed at 9.4 and 11.7 Tesla on type I collagen gels, chondroitin sulfate mixtures, and to bovine nasal cartilage (BNC), a largely isotropic and homogeneous form of cartilage. The results show that the fractional-order analysis captures important features of NMR relaxation that are typically described by multi-exponential decay models. We find that the T2 relaxation of BNC can be described in a unique way by a single fractional-order parameter ( α), in contrast to the lack of uniqueness of multi-exponential fits in the realistic setting of a finite signal-to-noise ratio. No anomalous behavior of T1 was observed in BNC. In the single-component gels, for T2 measurements, increasing the concentration of the largest components of cartilage matrix, collagen and chondroitin sulfate, results in a decrease in α, reflecting a more restricted aqueous environment. The quality of the curve fits obtained using Mittag-Leffler and stretched exponential functions are in some cases superior to those obtained using mono- and bi-exponential models. In both gels and BNC, α appears to account for micro-structural complexity in the setting of an altered distribution of relaxation times. This work suggests the utility of fractional-order models to describe T2 NMR relaxation processes in biological tissues.

On the heterogeneity of fluorescence lifetime of room temperature ionic liquids: onset of a journey for exploring red emitting dyes.

PubMed

Ghosh, Anup; Chatterjee, Tanmay; Mandal, Prasun K

2012-06-25

An excitation and emission wavelength dependent non-exponential fluorescence decay behaviour of room temperature ionic liquids (RTILs) has been noted. Average fluorescence lifetimes have been found to vary by a factor of three or more. Red emitting dyes dissolved in RTILs are found to follow hitherto unobserved single exponential fluorescence decay behaviour.

Relaxation processes in a low-order three-dimensional magnetohydrodynamics model

NASA Technical Reports Server (NTRS)

Stribling, Troy; Matthaeus, William H.

1991-01-01

The time asymptotic behavior of a Galerkin model of 3D magnetohydrodynamics (MHD) has been interpreted using the selective decay and dynamic alignment relaxation theories. A large number of simulations has been performed that scan a parameter space defined by the rugged ideal invariants, including energy, cross helicity, and magnetic helicity. It is concluded that time asymptotic state can be interpreted as a relaxation to minimum energy. A simple decay model, based on absolute equilibrium theory, is found to predict a mapping of initial onto time asymptotic states, and to accurately describe the long time behavior of the runs when magnetic helicity is present. Attention is also given to two processes, operating on time scales shorter than selective decay and dynamic alignment, in which the ratio of kinetic to magnetic energy relaxes to values 0(1). The faster of the two processes takes states initially dominant in magnetic energy to a state of near-equipartition between kinetic and magnetic energy through power law growth of kinetic energy. The other process takes states initially dominant in kinetic energy to the near-equipartitioned state through exponential growth of magnetic energy.

VO2 kinetics in supra-anaerobic threshold constant tests allow the visualization and quantification of the O2 saving after cytochrome c oxidase inhibition by aerobic training or nitrate administration.

PubMed

Maione, D; Cicero, A Fg; Bacchelli, S; Cosentino, E; Degli Esposti, D; Senaldi, R; Strocchi, E; D'Addato, S; Borghi, C

2013-01-01

We tested whether the known cytochrome c oxidase (COX) inhibition by nitric oxide (NO) could be quantified by VO(2) kinetics during constant load supra-Anaerobic Threshold (AT) exercises in healthy trained or untrained subjects following aerobic training or nitrate administration. In cycle ergometer constant load exercises supra-AT, identified in previous incremental tests, VO(2) kinetics describe a double exponential curve, one rapid and one appreciably slower, allowing the area between them to be calculate in O(2) l. After training, with increased NO availability, this area decreases in inverse ratio to treatment efficacy. In fact, in 11 healthy subjects after aerobic training for 6-7 weeks, area was decreased on average by 51 %. In 11 untrained subjects, following the assumption of an NO donor, 20 mg isosorbide 5 mononitrate, area was decreased on average by 53 %. In conclusion, supra-AT VO(2) kinetics in constant load exercises permit the quantification of the inhibitory effect NO-dependent on COX after either physical training or nitrate assumption.

A new approach to the extraction of single exponential diode model parameters

NASA Astrophysics Data System (ADS)

Ortiz-Conde, Adelmo; García-Sánchez, Francisco J.

2018-06-01

A new integration method is presented for the extraction of the parameters of a single exponential diode model with series resistance from the measured forward I-V characteristics. The extraction is performed using auxiliary functions based on the integration of the data which allow to isolate the effects of each of the model parameters. A differentiation method is also presented for data with low level of experimental noise. Measured and simulated data are used to verify the applicability of both proposed method. Physical insight about the validity of the model is also obtained by using the proposed graphical determinations of the parameters.

Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis

NASA Astrophysics Data System (ADS)

Castellanos, Milagros; Carrillo, Pablo J. P.; Mateu, Mauricio G.

2015-03-01

Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07046a

Computerized glow curve deconvolution of thermoluminescent emission from polyminerals of Jamaica Mexican flower

NASA Astrophysics Data System (ADS)

Favalli, A.; Furetta, C.; Zaragoza, E. Cruz; Reyes, A.

The aim of this work is to study the main thermoluminescence (TL) characteristics of the inorganic polyminerals extracted from dehydrated Jamaica flower or roselle (Hibiscus sabdariffa L.) belonging to Malvaceae family of Mexican origin. TL emission properties of the polymineral fraction in powder were studied using the initial rise (IR) method. The complex structure and kinetic parameters of the glow curves have been analysed accurately using the computerized glow curve deconvolution (CGCD) assuming an exponential distribution of trapping levels. The extension of the IR method to the case of a continuous and exponential distribution of traps is reported, such as the derivation of the TL glow curve deconvolution functions for continuous trap distribution. CGCD is performed both in the case of frequency factor, s, temperature independent, and in the case with the s function of temperature.

Fractional calculus and morphogen gradient formation

NASA Astrophysics Data System (ADS)

Yuste, Santos Bravo; Abad, Enrique; Lindenberg, Katja

2012-12-01

Some microscopic models for reactive systems where the reaction kinetics is limited by subdiffusion are described by means of reaction-subdiffusion equations where fractional derivatives play a key role. In particular, we consider subdiffusive particles described by means of a Continuous Time Random Walk (CTRW) model subject to a linear (first-order) death process. The resulting fractional equation is employed to study the developmental biology key problem of morphogen gradient formation for the case in which the morphogens are subdiffusive. If the morphogen degradation rate (reactivity) is constant, we find exponentially decreasing stationary concentration profiles, which are similar to the profiles found when the morphogens diffuse normally. However, for the case in which the degradation rate decays exponentially with the distance to the morphogen source, we find that the morphogen profiles are qualitatively different from the profiles obtained when the morphogens diffuse normally.

Thermodynamics and kinetics of the sulfation of porous calcium silicate

NASA Technical Reports Server (NTRS)

Miller, R. A.; Kohl, F. J.

1981-01-01

The sulfation of plasma sprayed calcium silicate in flowing SO2/air mixtures at 900 and 1000 C was investigated thermogravimetrically. Reaction products were analyzed using electron microprobe and X-ray diffraction analysis techniques, and results were compared with thermodynamic predictions. The percentage, by volume, of SO2 in air was varied between 0.036 and 10 percent. At 10 percent SO2 the weight gain curve displays a concave downward shoulder early in the sulfation process. An analytical model was developed which treats the initial process as one which decays exponentially with increasing time and the subsequent process as one which decays exponentially with increasing weight gain. At lower SO2 levels the initial rate is controlled by the reactant flow rate. At 1100 C and 0.036 percent SO2 there is no reaction, in agreement with thermodynamic predictions.

Drug release from slabs and the effects of surface roughness.

PubMed

Kalosakas, George; Martini, Dimitra

2015-12-30

We discuss diffusion-controlled drug release from slabs or thin films. Analytical and numerical results are presented for slabs with flat surfaces, having a uniform thickness. Then, considering slabs with rough surfaces, the influence of a non-uniform slab thickness on release kinetics is numerically investigated. The numerical release profiles are obtained using Monte Carlo simulations. Release kinetics is quantified through the stretched exponential (or Weibull) function and the resulting dependence of the two parameters of this function on the thickness of the slab, for flat surfaces, and the amplitude of surface fluctuations (or the degree of thickness variability) in case of roughness. We find that a higher surface roughness leads to a faster drug release. Copyright © 2015 Elsevier B.V. All rights reserved.

Explicit equilibria in a kinetic model of gambling

NASA Astrophysics Data System (ADS)

Bassetti, F.; Toscani, G.

2010-06-01

We introduce and discuss a nonlinear kinetic equation of Boltzmann type which describes the evolution of wealth in a pure gambling process, where the entire sum of wealths of two agents is up for gambling, and randomly shared between the agents. For this equation the analytical form of the steady states is found for various realizations of the random fraction of the sum which is shared to the agents. Among others, the exponential distribution appears as steady state in case of a uniformly distributed random fraction, while Gamma distribution appears for a random fraction which is Beta distributed. The case in which the gambling game is only conservative-in-the-mean is shown to lead to an explicit heavy tailed distribution.

Generation kinetics of boron-oxygen complexes in p-type compensated c-Si

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

Wu, Yichao; Yu, Xuegong, E-mail: yuxuegong@zju.edu.cn; Chen, Peng

2014-03-10

Kinetics characteristics of boron-oxygen complexes responsible for light-induced degradation in p-type compensated c-Si have been investigated. The generation of B-O complexes is well fitted by a fast-forming process and a slow-forming one. Activation energies of complexes generation during the fast-forming process are determined to be 0.29 and 0.24 eV in compensated and non-compensated c-Si, respectively, and those during the slow-forming process are the same, about 0.44 eV. Moreover, it is found that the pre-exponential factors of complexes generation in compensated c-Si is proportional to the square of the net doping concentration, which suggests that the latent centers should exist.

Pressure-jump small-angle x-ray scattering detected kinetics of staphylococcal nuclease folding.

PubMed Central

Woenckhaus, J; Köhling, R; Thiyagarajan, P; Littrell, K C; Seifert, S; Royer, C A; Winter, R

2001-01-01

The kinetics of chain disruption and collapse of staphylococcal nuclease after positive or negative pressure jumps was monitored by real-time small-angle x-ray scattering under pressure. We used this method to probe the overall conformation of the protein by measuring its radius of gyration and pair-distance-distribution function p(r) which are sensitive to the spatial extent and shape of the particle. At all pressures and temperatures tested, the relaxation profiles were well described by a single exponential function. No fast collapse was observed, indicating that the rate limiting step for chain collapse is the same as that for secondary and tertiary structure formation. Whereas refolding at low pressures occurred in a few seconds, at high pressures the relaxation was quite slow, approximately 1 h, due to a large positive activation volume for the rate-limiting step for chain collapse. A large increase in the system volume upon folding implies significant dehydration of the transition state and a high degree of similarity in terms of the packing density between the native and transition states in this system. This study of the time-dependence of the tertiary structure in pressure-induced folding/unfolding reactions demonstrates that novel information about the nature of protein folding transitions and transition states can be obtained from a combination of small-angle x-ray scattering using high intensity synchrotron radiation with the high pressure perturbation technique. PMID:11222312

Turbulent particle transport in streams: can exponential settling be reconciled with fluid mechanics?

PubMed

McNair, James N; Newbold, J Denis

2012-05-07

Most ecological studies of particle transport in streams that focus on fine particulate organic matter or benthic invertebrates use the Exponential Settling Model (ESM) to characterize the longitudinal pattern of particle settling on the bed. The ESM predicts that if particles are released into a stream, the proportion that have not yet settled will decline exponentially with transport time or distance and will be independent of the release elevation above the bed. To date, no credible basis in fluid mechanics has been established for this model, nor has it been rigorously tested against more-mechanistic alternative models. One alternative is the Local Exchange Model (LEM), which is a stochastic advection-diffusion model that includes both longitudinal and vertical spatial dimensions and is based on classical fluid mechanics. The LEM predicts that particle settling will be non-exponential in the near field but will become exponential in the far field, providing a new theoretical justification for far-field exponential settling that is based on plausible fluid mechanics. We review properties of the ESM and LEM and compare these with available empirical evidence. Most evidence supports the prediction of both models that settling will be exponential in the far field but contradicts the ESM's prediction that a single exponential distribution will hold for all transport times and distances. Copyright © 2012 Elsevier Ltd. All rights reserved.

Permeabilization Activated Reduction in Fluorescence (PARF): a novel method to measure kinetics of protein interactions with intracellular structures

PubMed Central

Singh, Pali P.; Hawthorne, Jenci L.; Davis, Christie A.; Quintero, Omar A.

2016-01-01

Understanding kinetic information is fundamental in understanding biological function. Advanced imaging technologies have fostered the development of kinetic analyses in cells. We have developed Permeabilization Activated Reduction in Fluorescence (PARF) analysis for determination of apparent t1/2 and immobile fraction, describing the dissociation of a protein of interest from intracellular structures. To create conditions where dissociation events are observable, cells expressing a fluorescently-tagged protein are permeabilized with digitonin, diluting the unbound protein into the extracellular media. As the media volume is much larger than the cytosolic volume, the concentration of the unbound pool decreases drastically, shifting the system out of equilibrium--favoring dissociation events. Loss of bound protein is observed as loss of fluorescence from intracellular structures and can be fit to an exponential decay. We compared PARF dissociation kinetics with previously published equilibrium kinetics as determined by FRAP. PARF dissociation rates agreed with the equilibrium-based FRAP analysis predictions of the magnitude of those rates. When used to investigate binding kinetics of a panel of cytoskeletal proteins, PARF analysis revealed that filament stabilization resulted in slower fluorescence loss. Additionally, commonly used “general” F-actin labels display differences in kinetic properties, suggesting that not all fluorescently-tagged actin labels interact with the actin network in the same way. We also observed differential dissociation kinetics for GFP-VASP depending on which cellular structure was being labeled. These results demonstrate that PARF analysis of non-equilibrium systems reveals kinetic information without the infrastructure investment required for other quantitative approaches such as FRAP, photoactivation, or in vitro reconstitution assays. PMID:27126922

Enviromental influences on the {sup 137}Cs kinetics of the yellow-bellied turtle (Trachemys Scripta)

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

Peters, E.L.; Brisbin, L.I. Jr.

1996-02-01

Assessments of ecological risk require accurate predictions of contaminant dynamics in natural populations. However, simple deterministic models that assume constant uptake rates and elimination fractions may compromise both their ecological realism and their general application to animals with variable metabolism or diets. In particular, the temperature-dependent model of metabolic rates characteristic of ectotherms may lead to significant differences between observed and predicted contaminant kinetics. We examined the influence of a seasonally variable thermal environment on predicting the uptake and annual cycling of contaminants by ectotherms, using a temperature-dependent model of {sup 137}Cs kinetics in free-living yellow-bellied turtles, Trachemys scripta. Wemore » compared predictions from this model with those of deterministics negative exponential and flexibly shaped Richards sigmoidal models. Concentrations of {sup 137}Cs in a population if this species in Pond B, a radionuclide-contaminated nuclear reactor cooling reservoir, and {sup 137}Cs uptake by the uncontaminated turtles held captive in Pond B for 4 yr confirmed both the pattern of uptake and the equilibrium concentrations predicted by the temperature-dependent model. Almost 90% of the variance on the predicted time-integrated {sup 137}Cs concentration was explainable by linear relationships with model paramaters. The model was also relatively insensitive to uncertainties in the estimates of ambient temperature, suggesting that adequate estimates of temperature-dependent ingestion and elimination may require relatively few measurements of ambient conditions at sites of interest. Analyses of Richards sigmoidal models of {sup 137}Cs uptake indicated significant differences from a negative exponential trajectory in the 1st yr after the turtles` release into Pond B. 76 refs., 7 figs., 5 tabs.« less

Compressed exponential relaxation in liquid silicon: Universal feature of the crossover from ballistic to diffusive behavior in single-particle dynamics

NASA Astrophysics Data System (ADS)

Morishita, Tetsuya

2012-07-01

We report a first-principles molecular-dynamics study of the relaxation dynamics in liquid silicon (l-Si) over a wide temperature range (1000-2200 K). We find that the intermediate scattering function for l-Si exhibits a compressed exponential decay above 1200 K including the supercooled regime, which is in stark contrast to that for normal "dense" liquids which typically show stretched exponential decay in the supercooled regime. The coexistence of particles having ballistic-like motion and those having diffusive-like motion is demonstrated, which accounts for the compressed exponential decay in l-Si. An attempt to elucidate the crossover from the ballistic to the diffusive regime in the "time-dependent" diffusion coefficient is made and the temperature-independent universal feature of the crossover is disclosed.

Microtubule dissassembly in vivo: intercalary destabilization and breakdown of microtubules in the heliozoan Actinocoryne contractilis

PubMed Central

1992-01-01

In the marine heliozoan Actinocoryne contractilis, uninterrupted rods of microtubules stiffen the axopodia and the stalk. Stimulation in sea water elicits an extremely fast contraction (millisecond range) accompanied by almost complete Mt dissociation. Using high-speed cinematography and light transmittance measurements, we have studied the process of Mt disassembly in real time. In sea water, Mt disassembly follows an exponential decrease (mean half time of 4 ms) or proceeds by short steps. Cell contraction and Mt disassembly have been inhibited or slowed down through the use of artificial media. Although kinetics are slower (mean half time of 3 s), the curves of the length change against time look similar. The rapid as well as the slower process are accompanied by the formation of breakpoints on the stalk, from which disassembly proceeds. In specimens fixed during the slowed contraction, the presence across the Mt rods, of a single or multiple destabilization band that may consist of granular material and polymorphic forms of tubulin supports the hypothesis of "intercalary destabilization and breakdown" of axonemal Mts. PMID:1639845

Oxygen evolution from single- and multiple-turnover light pulses: temporal kinetics of electron transport through PSII in sunflower leaves.

PubMed

Oja, Vello; Eichelmann, Hillar; Laisk, Agu

2011-12-01

Oxygen evolution per single-turnover flash (STF) or multiple-turnover pulse (MTP) was measured with a zirconium O(2) analyzer from sunflower leaves at 22 °C. STF were generated by Xe arc lamp, MTP by red LED light of up to 18000 μmol quanta m(-2) s(-1). Ambient O(2) concentration was 10-30 ppm, STF and MTP were superimposed on far-red background light in order to oxidize plastoquinone (PQ) and randomize S-states. Electron (e(-)) flow was calculated as 4 times O(2) evolution. Q (A) → Q (B) electron transport was investigated firing double STF with a delay of 0 to 2 ms between the two. Total O(2) evolution per two flashes equaled to that from a single flash when the delay was zero and doubled when the delay exceeded 2 ms. This trend was fitted with two exponentials with time constants of 0.25 and 0.95 ms, equal amplitudes. Illumination with MTP of increasing length resulted in increasing O(2) evolution per pulse, which was differentiated with an aim to find the time course of O(2) evolution with sub-millisecond resolution. At the highest pulse intensity of 2.9 photons ms(-1) per PSII, 3 e(-) initially accumulated inside PSII and the catalytic rate of PQ reduction was determined from the throughput rate of the fourth and fifth e(-). A light response curve for the reduction of completely oxidized PQ was a rectangular hyperbola with the initial slope of 1.2 PSII quanta per e(-) and V (m) of 0.6 e(-) ms(-1) per PSII. When PQ was gradually reduced during longer MTP, V (m) decreased proportionally with the fraction of oxidized PQ. It is suggested that the linear kinetics with respect to PQ are apparent, caused by strong product inhibition due to about equal binding constants of PQ and PQH(2) to the Q (B) site. The strong product inhibition is an appropriate mechanism for down-regulation of PSII electron transport in accordance with rate of PQH(2) oxidation by cytochrome b(6)f. © Springer Science+Business Media B.V. 2011

The Arrhenius equation revisited.

PubMed

Peleg, Micha; Normand, Mark D; Corradini, Maria G

2012-01-01

The Arrhenius equation has been widely used as a model of the temperature effect on the rate of chemical reactions and biological processes in foods. Since the model requires that the rate increase monotonically with temperature, its applicability to enzymatic reactions and microbial growth, which have optimal temperature, is obviously limited. This is also true for microbial inactivation and chemical reactions that only start at an elevated temperature, and for complex processes and reactions that do not follow fixed order kinetics, that is, where the isothermal rate constant, however defined, is a function of both temperature and time. The linearity of the Arrhenius plot, that is, Ln[k(T)] vs. 1/T where T is in °K has been traditionally considered evidence of the model's validity. Consequently, the slope of the plot has been used to calculate the reaction or processes' "energy of activation," usually without independent verification. Many experimental and simulated rate constant vs. temperature relationships that yield linear Arrhenius plots can also be described by the simpler exponential model Ln[k(T)/k(T(reference))] = c(T-T(reference)). The use of the exponential model or similar empirical alternative would eliminate the confusing temperature axis inversion, the unnecessary compression of the temperature scale, and the need for kinetic assumptions that are hard to affirm in food systems. It would also eliminate the reference to the Universal gas constant in systems where a "mole" cannot be clearly identified. Unless proven otherwise by independent experiments, one cannot dismiss the notion that the apparent linearity of the Arrhenius plot in many food systems is due to a mathematical property of the model's equation rather than to the existence of a temperature independent "energy of activation." If T+273.16°C in the Arrhenius model's equation is replaced by T+b, where the numerical value of the arbitrary constant b is substantially larger than T and T(reference), the plot of Ln k(T) vs. 1/(T+b) will always appear almost perfectly linear. Both the modified Arrhenius model version having the arbitrary constant b, Ln[k(T)/k(T(reference)) = a[1/ (T(reference)+b)-1/ (T+b)], and the exponential model can faithfully describe temperature dependencies traditionally described by the Arrhenius equation without the assumption of a temperature independent "energy of activation." This is demonstrated mathematically and with computer simulations, and with reprocessed classical kinetic data and published food results.

Kinetic Studies of Calcium-Induced Calcium Release in Cardiac Sarcoplasmic Reticulum Vesicles

PubMed Central

Sánchez, Gina; Hidalgo, Cecilia; Donoso, Paulina

2003-01-01

Fast Ca2+ release kinetics were measured in cardiac sarcoplasmic reticulum vesicles actively loaded with Ca2+. Release was induced in solutions containing 1.2 mM free ATP and variable free [Ca2+] and [Mg2+]. Release rate constants (k) were 10-fold higher at pCa 6 than at pCa 5 whereas Ryanodine binding was highest at pCa ≤5. These results suggest that channels respond differently when exposed to sudden [Ca2+] changes than when exposed to Ca2+ for longer periods. Vesicles with severalfold different luminal calcium contents exhibited double exponential release kinetics at pCa 6, suggesting that channels undergo time-dependent activity changes. Addition of Mg2+ produced a marked inhibition of release kinetics at pCa 6 (K0.5 = 63 μM) but not at pCa 5. Coexistence of calcium activation and inhibition sites with equally fast binding kinetics is proposed to explain this behavior. Thimerosal activated release kinetics at pCa 5 at all [Mg2+] tested and increased at pCa 6 the K0.5 for Mg2+ inhibition, from 63 μM to 136 μM. We discuss the possible relevance of these results, which suggest release through RyR2 channels is subject to fast regulation by Ca2+ and Mg2+ followed by time-dependent regulation, to the physiological mechanisms of cardiac channel opening and closing. PMID:12668440

Thermogravimetric kinetic study of agricultural residue biomass pyrolysis based on combined kinetics.

PubMed

Wang, Xun; Hu, Mian; Hu, Wanyong; Chen, Zhihua; Liu, Shiming; Hu, Zhiquan; Xiao, Bo

2016-11-01

Pyrolytic kinetic of an agricultural residue (AR) feedstock, a mixture of plants (cotton, wheat, rich, corn) stems, was investigated based on combined kinetics. The most suitable mechanism for AR one-step pyrolysis was f(α)=(1-α)(1.1816)α(-1.8428) with kinetic parameters of: apparent activation energy 221.7kJ/mol, pre-exponential factor 4.17E16s(-1). Pyrolysis of AR feedstock could not be described by one-step reaction attributes to heterogeneous features of pyrolysis processes. Combined kinetics three-parallel-reaction (CK-TPR) model fitted the pyrolysis experimental data very well. Reaction mechanisms for pseudo hemicelluloses, cellulose, lignin in CK-TPR model was f(α)=(1-α)(1.6244)α(-0.3371)[-ln(1-α)](-0.0515), f(α)=(1-α)(1.0597)α(-0.6909)[-ln(1-α)](0.9026) and f(α)=(1-α)(2.9577)α(-4.7719), respectively. Apparent activation energy of three pseudo components followed the order of Elignin(197.3kJ/mol)>Ecellulose(176.3kJ/mol)>Ehemicelluloses (151.1kJ/mol). Mechanism of hemicelluloses pyrolysis could be further expressed as f(α)=(1-α)(1.4). The pyrolytic mechanism of cellulose met the Nucleation well. However, mechanism of lignin pyrolysis was complex, which possibly was the combined effects of Nucleation, Diffusion, Geometrical contraction, and Power law. Copyright © 2016 Elsevier Ltd. All rights reserved.

Single and multidose ocular kinetics and stability analysis of extemporaneous formulation of topical voriconazole in humans.

PubMed

Senthilkumari, Srinivasan; Lalitha, Prajna; Prajna, Namperumalsamy Venkatesh; Haripriya, Aravind; Nirmal, Jeyabalan; Gupta, Pankaj; Velpandian, Thirumurthy

2010-11-01

The purpose of the present study was to evaluate the kinetics of single and multiple doses of topical, non-preserved voriconazole (VZ) in human eyes. For single dose kinetics, 119 patients undergoing cataract surgery were divided into group I and group II and each group received a single drop (30 µl) of either 1% or 0.1% VZ formulation. Aqueous humor was collected at designated time intervals. For multidose kinetics, a single drop of 1% VZ was instilled 5 times either hourly or every 2 hr. The aqueous humor was tested for VZ at the 5th hr and 9th hr, respectively, after initial instillation. The stability and efficacy of the reconstituted VZ formulations were also evaluated after 30 days. Single dose ocular kinetics of 1% VZ resulted in a maximum mean aqueous concentration of 3.333 ± 1.61 µg/ml in 30 min whereas 0.1% showed a maximum mean aqueous concentration of 0.817 ±.36 µg/ml. In the multidose kinetic study, hourly and bi-hourly dosing resulted in mean aqueous concentrations of 7.47 ± 2.14 µg/ml and 4.69 ± 2.7 µg/ml, respectively. The reconstituted VZ formulations were stable at all studied temperatures, and their efficacy was maintained throughout the study period. The present study showed that the achieved mean concentration of VZ in both single dose and multi dose kinetic studies satisfactorily met the MIC(90) for almost all causative fungal organisms. The frequency of instillation may be designed for an "every 2 hr regimen" to maintain a therapeutic concentration for successful therapy.

Kinetic Equation for an Unstable Plasma

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

Balescu, R.

1963-01-01

A kinetic equation is derived for the description of the evolution in time of the distribution of velocities in a spatially homogeneous ionized gas that, at the initial time, is able to sustain exponentially growing oscillations. This equation is expressed in terms of a functional of the distribution finction that obeys the same integral equation as in the stable case. Although the method of solution used in the stable case breaks down, the equation can still be solved in closed form under unstable conditions, and hence an explicit form of the kinetic equation is obtained. The latter contains the normalmore » collision term and a new additional term describing the stabilization of the plasma. The latter acts through friction and diffusion and brings the plasma into a state of neutral stability. From there on the system evolves toward thermal equilibrium under the action of the normal collision term as well as of an additional Fokker-Planck- like term with timedependent coefficients, which however becomes less and less efficient as the plasma approaches equilibrium.« less

Kinetic analyses and pyrolytic behavior of Para grass (Urochloa mutica) for its bioenergy potential.

PubMed

Ahmad, Muhammad Sajjad; Mehmood, Muhammad Aamer; Al Ayed, Omar S; Ye, Guangbin; Luo, Huibo; Ibrahim, Muhammad; Rashid, Umer; Arbi Nehdi, Imededdine; Qadir, Ghulam

2017-01-01

The biomass of Urochloa mutica was subjected to thermal degradation analyses to understand its pyrolytic behavior for bioenergy production. Thermal degradation experiments were performed at three different heating rates, 10, 30 and 50°Cmin -1 using simultaneous thermogravimetric-differential scanning calorimetric analyzer, under an inert environment. The kinetic analyses were performed using isoconversional models of Kissenger-Akahira-Sunose (KAS) and Flynn-Wall-Ozawa (FWO). The high heating value was calculated as 15.04MJmol -1 . The activation energy (E) values were shown to be ranging from 103 through 233 kJmol -1 . Pre-exponential factors (A) indicated the reaction to follow first order kinetics. Gibbs free energy (ΔG) was measured to be ranging from 169 to 173kJmol -1 and 168 to 172kJmol -1 , calculated by KAS and FWO methods, respectively. We have shown that Para grass biomass has considerable bioenergy potential comparable to established bioenergy crops such as switchgrass and miscanthus. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pyrolysis and kinetic analyses of Camel grass (Cymbopogon schoenanthus) for bioenergy.

PubMed

Mehmood, Muhammad Aamer; Ye, Guangbin; Luo, Huibo; Liu, Chenguang; Malik, Sana; Afzal, Ifrah; Xu, Jianren; Ahmad, Muhammad Sajjad

2017-03-01

The aim of this work was to study the thermal degradation of grass (Cymbopogon schoenanthus) under an inert environment at three heating rates, including 10, 30, and 50°Cmin -1 in order to evaluate its bioenergy potential. Pyrolysis experiments were performed in a simultaneous Thermogravimetry-Differential Scanning Calorimetry analyzer. Thermal data were used to analyze kinetic parameters through isoconversional models of Flynn-Wall-Ozawa (FWO) and Kissenger-Akahira-Sunose (KSA) methods. The pre-exponential factors values have shown the reaction to follow first order kinetics. Activation energy values were shown to be 84-193 and 96-192kJmol -1 as calculated by KSA and FWO methods, respectively. Differences between activation energy and enthalpy of reaction values (∼5 to 6kJmol -1 ) showed product formation is favorable. The Gibb's free energy (173-177kJmol -1 ) and High Heating Value (15.00MJkg -1 ) have shown the considerable bioenergy potential of this low-cost biomass. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of pressure, temperature, and treatment time on oscillatory rheological properties and non-isothermal gelatinization kinetics of chickpea (Cicer arietinum L.) flour slurry

NASA Astrophysics Data System (ADS)

Canet, W.; Cuesta, F. J.; Fuentes, R.; Alvarez, M. D.

2017-10-01

The effect of high hydrostatic pressure (HHP), temperature at pressurization, and treatment time at three levels (200, 400, 600 MPa; 10, 25, 50 °C 5, 15, 25 min) on the gelatinization of chickpea flour (CF) slurry during non-isothermal heating from 25 to 95 °C and gel rheological properties after subsequent cooling to 25 °C was investigated. CF gelatinization kinetics from the cross-over of elastic modulus (G’) and viscous modulus (G″) to 95 °C were considered for rate estimation. Zero-order reaction kinetics adequately described the CF gelatinization process. Structure development rate (dG‧/dt) is described by two exponential functions with activation energies ranging from 51.2 to 576.6 and -128.9 to 538.9 kJ mol-1 for downward and upward gelatinization curves, respectively. Changes in dG‧/dt vs. temperature seem to be closely related to the degree of gelatinization induced by HHP pre-treatment.

G2 Chromatid Damage and Repair Kinetics in Normal Human Fibroblast Cells Exposed to Low-or High-LET Radiation

NASA Technical Reports Server (NTRS)

Kawata, T.; Ito, H.; Uno, T.; Saito, M.; Yamamoto, S.; Furusawa, Y.; Durante, M.; George, K.; Wu, H.; Cucinotta, F. A.

2004-01-01

Radiation-induced chromosome damage can be measured in interphase using the Premature Chromosome Condensation (PCC) technique. With the introduction of a new PCC technique using the potent phosphatase inhibitor calyculin-A, chromosomes can be condensed within five minutes, and it is now possible to examine the early damage induced by radiation. Using this method, it has been shown that high-LET radiation induces a higher frequency of chromatid breaks and a much higher frequency of isochromatid breaks than low-LET radiation. The kinetics of chromatid break rejoining consists of two exponential components representing a rapid and a slow time constant, which appears to be similar for low- and high- LET radiations. However, after high-LET radiation exposures, the rejoining process for isochromatid breaks influences the repair kinetics of chromatid-type breaks, and this plays an important role in the assessment of chromatid break rejoining in the G2 phase of the cell cycle.

Development of a modified independent parallel reactions kinetic model and comparison with the distributed activation energy model for the pyrolysis of a wide variety of biomass fuels.

PubMed

Sfakiotakis, Stelios; Vamvuka, Despina

2015-12-01

The pyrolysis of six waste biomass samples was studied and the fuels were kinetically evaluated. A modified independent parallel reactions scheme (IPR) and a distributed activation energy model (DAEM) were developed and their validity was assessed and compared by checking their accuracy of fitting the experimental results, as well as their prediction capability in different experimental conditions. The pyrolysis experiments were carried out in a thermogravimetric analyzer and a fitting procedure, based on least squares minimization, was performed simultaneously at different experimental conditions. A modification of the IPR model, considering dependence of the pre-exponential factor on heating rate, was proved to give better fit results for the same number of tuned kinetic parameters, comparing to the known IPR model and very good prediction results for stepwise experiments. Fit of calculated data to the experimental ones using the developed DAEM model was also proved to be very good. Copyright © 2015 Elsevier Ltd. All rights reserved.

Membrane crystallization of lysozyme: kinetic aspects

NASA Astrophysics Data System (ADS)

Profio, Gianluca Di; Curcio, Efrem; Cassetta, Alberto; Lamba, Doriano; Drioli, Enrico

2003-10-01

The relevant kinetic aspects related to an innovative method of biological macromolecules crystallization based on microporous hydrophobic membranes, used both as active surfaces to promote heterogeneous nucleation and as a mass-transfer apparatus to concentrate macromolecular solutions by solvent removal in vapour phase, have been evaluated. Polypropylene membranes, supplied in the form of hollow fibres, have been aligned in a versatile system, designed for an on-line spectrophotometric monitoring of hen egg white lysozyme crystallizing solutions (experimental conditions: 0.1 M NaAc/HAc Buffer pH 4.6, 0.5-5.8% wt/vol NaCl, 20°C). The turbidity measurements have been exploited in order to follow: (i) the induction time of crystallization, (ii) the early stage nucleation kinetics based on the Rayleigh scattering theory, and (iii) the crystal growth rate (coupled with data evaluated from image-analysis carried out by optical microscopy) under a model hypothesis of exponential growth of clusters. The crystals have been qualitatively assessed by an X-ray crystallographic analysis carried out at the synchrotron light laboratory ELETTRA.

Kinetics of antigen binding to arrays of antibodies in different sized spots

NASA Technical Reports Server (NTRS)

Sapsford, K. E.; Liron, Z.; Shubin, Y. S.; Ligler, F. S.

2001-01-01

A fluorescence-based array biosensor has been developed which can measure the binding kinetics of an antigen to an immobilized antibody in real time. A patterned array of antibodies immobilized on the surface of a planar waveguide was used to capture a Cy5-labeled antigen present in a solution that was continuously flowed over the surface. The CCD image of the waveguide was monitored continuously for 25 min. The resulting exponential rise in fluorescence signal was determined by image analysis software and fitted to a reaction-limited kinetics model, giving a kf of 3.6 x 10(5) M(-1) s(-1). Different spot sizes were then patterned on the surface of the waveguide using either a PDMS flow cell or laser exposure, producing width sizes ranging from 80 to 1145 microm. It was demonstrated that under flow conditions, the reduction of spot size did not alter the association rate of the antigen with immobilized antibody; however, as the spot width decreased to < 200 nm, the signal intensity also decreased.

Solvent and temperature effects on the decay dynamics of [p-N,N-(dialkylamino)benzylidene]malononitriles

NASA Astrophysics Data System (ADS)

Safarzadeh-Amiri, A.

1986-08-01

The effects of solvent and temperature on the decay kinetics of p-(dialkylamino)benzylidenemalononitrile (1) and julodinemalononitrile (3) has been studied in glycerol and triacetin. The fluorescence decay curves of these compounds were non-exponential and varied slightly with wavelength. This is attributed to the existence of two ground state conformers and to reorientation of the solvent cage around solute molecules. The results were explained in terms of trans → cisphotoisomerization.

Parameters of an avalanche of runaway electrons in air under atmospheric pressure

NASA Astrophysics Data System (ADS)

Oreshkin, E. V.

2018-01-01

The features of runaway-electron avalanches developing in air under atmospheric pressures are investigated in the framework of a three-dimensional numerical simulation. The simulation results indicate that an avalanche of this type can be characterized, besides the time and length of its exponential growth, by the propagation velocity and by the average kinetic energy of the runaway electrons. It is shown that these parameters obey the similarity laws applied to gas discharges.

Charge Transport Properties in Disordered Organic Semiconductor as a Function of Charge Density: Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Shukri, Seyfan Kelil

2017-01-01

We have done Kinetic Monte Carlo (KMC) simulations to investigate the effect of charge carrier density on the electrical conductivity and carrier mobility in disordered organic semiconductors using a lattice model. The density of state (DOS) of the system are considered to be Gaussian and exponential. Our simulations reveal that the mobility of the charge carrier increases with charge carrier density for both DOSs. In contrast, the mobility of charge carriers decreases as the disorder increases. In addition the shape of the DOS has a significance effect on the charge transport properties as a function of density which are clearly seen. On the other hand, for the same distribution width and at low carrier density, the change occurred on the conductivity and mobility for a Gaussian DOS is more pronounced than that for the exponential DOS.

Mathematical modeling of ethanol production in solid-state fermentation based on solid medium' dry weight variation.

PubMed

Mazaheri, Davood; Shojaosadati, Seyed Abbas; Zamir, Seyed Morteza; Mousavi, Seyyed Mohammad

2018-04-21

In this work, mathematical modeling of ethanol production in solid-state fermentation (SSF) has been done based on the variation in the dry weight of solid medium. This method was previously used for mathematical modeling of enzyme production; however, the model should be modified to predict the production of a volatile compound like ethanol. The experimental results of bioethanol production from the mixture of carob pods and wheat bran by Zymomonas mobilis in SSF were used for the model validation. Exponential and logistic kinetic models were used for modeling the growth of microorganism. In both cases, the model predictions matched well with the experimental results during the exponential growth phase, indicating the good ability of solid medium weight variation method for modeling a volatile product formation in solid-state fermentation. In addition, using logistic model, better predictions were obtained.

Inactivation of A currents and A channels on rat nodose neurons in culture

PubMed Central

1989-01-01

Cultured sensory neurons from nodose ganglia were investigated with whole-cell patch-clamp techniques and single-channel recordings to characterize the A current. Membrane depolarization from -40 mV holding potential activated the delayed rectifier current (IK) at potentials positive to -30 mV; this current had a sigmoidal time course and showed little or no inactivation. In most neurons, the A current was completely inactivated at the -40 mV holding potential and required hyperpolarization to remove the inactivation; the A current was isolated by subtracting the IK evoked by depolarizations from -40 mV from the total outward current evoked by depolarizations from -90 mV. The decay of the A current on several neurons had complex kinetics and was fit by the sum of three exponentials whose time constants were 10- 40 ms, 100-350 ms, and 1-3 s. At the single-channel level we found that one class of channel underlies the A current. The conductance of A channels varied with the square root of the external K concentration: it was 22 pS when exposed to 5.4 mM K externally, the increased to 40 pS when exposed to 140 mM K externally. A channels activated rapidly upon depolarization and the latency to first opening decreased with depolarization. The open time distributions followed a single exponential and the mean open time increased with depolarization. A channels inactivate in three different modes: some A channels inactivated with little reopening and gave rise to ensemble averages that decayed in 10-40 ms; other A channels opened and closed three to four times before inactivating and gave rise to ensemble averages that decayed in 100-350 ms; still other A channels opened and closed several hundred times and required seconds to inactivate. Channels gating in all three modes contributed to the macroscopic A current from the whole cell, but their relative contribution differed among neurons. In addition, A channels could go directly from the closed, or resting, state to the inactivated state without opening, and the probability for channels inactivating in this way was greater at less depolarized voltages. In addition, a few A channels appeared to go reversibly from a mode where inactivation occurred rapidly to a slow mode of inactivation. PMID:2592953

Motion of the two-control airplane in rectilinear flight after initial disturbances with introduction of controls following an exponential law

NASA Technical Reports Server (NTRS)

Klemin, Alexander

1937-01-01

An airplane in steady rectilinear flight was assumed to experience an initial disturbance in rolling or yawing velocity. The equations of motion were solved to see if it was possible to hasten recovery of a stable airplane or to secure recovery of an unstable airplane by the application of a single lateral control following an exponential law. The sample computations indicate that, for initial disturbances complex in character, it would be difficult to secure correlation with any type of exponential control. The possibility is visualized that the two-control operation may seriously impair the ability to hasten recovery or counteract instability.

The Western Africa ebola virus disease epidemic exhibits both global exponential and local polynomial growth rates.

PubMed

Chowell, Gerardo; Viboud, Cécile; Hyman, James M; Simonsen, Lone

2015-01-21

While many infectious disease epidemics are initially characterized by an exponential growth in time, we show that district-level Ebola virus disease (EVD) outbreaks in West Africa follow slower polynomial-based growth kinetics over several generations of the disease. We analyzed epidemic growth patterns at three different spatial scales (regional, national, and subnational) of the Ebola virus disease epidemic in Guinea, Sierra Leone and Liberia by compiling publicly available weekly time series of reported EVD case numbers from the patient database available from the World Health Organization website for the period 05-Jan to 17-Dec 2014. We found significant differences in the growth patterns of EVD cases at the scale of the country, district, and other subnational administrative divisions. The national cumulative curves of EVD cases in Guinea, Sierra Leone, and Liberia show periods of approximate exponential growth. In contrast, local epidemics are asynchronous and exhibit slow growth patterns during 3 or more EVD generations, which can be better approximated by a polynomial than an exponential function. The slower than expected growth pattern of local EVD outbreaks could result from a variety of factors, including behavior changes, success of control interventions, or intrinsic features of the disease such as a high level of clustering. Quantifying the contribution of each of these factors could help refine estimates of final epidemic size and the relative impact of different mitigation efforts in current and future EVD outbreaks.

The Western Africa Ebola Virus Disease Epidemic Exhibits Both Global Exponential and Local Polynomial Growth Rates

PubMed Central

Chowell, Gerardo; Viboud, Cécile; Hyman, James M; Simonsen, Lone

2015-01-01

Background: While many infectious disease epidemics are initially characterized by an exponential growth in time, we show that district-level Ebola virus disease (EVD) outbreaks in West Africa follow slower polynomial-based growth kinetics over several generations of the disease. Methods: We analyzed epidemic growth patterns at three different spatial scales (regional, national, and subnational) of the Ebola virus disease epidemic in Guinea, Sierra Leone and Liberia by compiling publicly available weekly time series of reported EVD case numbers from the patient database available from the World Health Organization website for the period 05-Jan to 17-Dec 2014. Results: We found significant differences in the growth patterns of EVD cases at the scale of the country, district, and other subnational administrative divisions. The national cumulative curves of EVD cases in Guinea, Sierra Leone, and Liberia show periods of approximate exponential growth. In contrast, local epidemics are asynchronous and exhibit slow growth patterns during 3 or more EVD generations, which can be better approximated by a polynomial than an exponential function. Conclusions: The slower than expected growth pattern of local EVD outbreaks could result from a variety of factors, including behavior changes, success of control interventions, or intrinsic features of the disease such as a high level of clustering. Quantifying the contribution of each of these factors could help refine estimates of final epidemic size and the relative impact of different mitigation efforts in current and future EVD outbreaks. PMID:25685633

Kinetics of Ni2Si growth from pure Ni and Ni(V) films on (111) and (100) Si

NASA Astrophysics Data System (ADS)

Harith, M. A.; Zhang, J. P.; Campisano, S. U.; Klaar, H.-J.

1987-01-01

The kinetics of Ni2Si growth from pure Ni and from Ni0.93V0.07 films on (111) and (100) silicon has been studied by the combination of He+ backscattering, x-ray diffraction, Auger electron spectroscopy (AES) and transmission electron microscopy (TEM) techniques. The activation energies are 1.5 and 1.0 eV for pure Ni and Ni(V) films, respectively while the pre-exponential factors in Ni(V) are 4 5 orders of magnitude smaller than in the pure Ni case. The variations in the measured rates are related to the different grain size of the growing suicide layers. The vanadium is rejected from the silicide layer and piles up at the metalsilicide interface.

First passage times for multiple particles with reversible target-binding kinetics

NASA Astrophysics Data System (ADS)

Grebenkov, Denis S.

2017-10-01

We investigate the first passage problem for multiple particles that diffuse towards a target, partially adsorb there, and then desorb after a finite exponentially distributed residence time. We search for the first time when m particles undergoing such reversible target-binding kinetics are found simultaneously on the target that may trigger an irreversible chemical reaction or a biophysical event. Even if the particles are independent, the finite residence time on the target yields an intricate temporal coupling between particles. We compute analytically the mean first passage time (MFPT) for two independent particles by mapping the original problem to higher-dimensional surface-mediated diffusion and solving the coupled partial differential equations. The respective effects of the adsorption and desorption rates on the MFPT are revealed and discussed.

Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

PubMed Central

2012-01-01

Background Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings. Results We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction–diffusion simulations, that the StrExp function can describe both, binding/barrier–limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IB’s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB’s to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments. Conclusions We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport. PMID:23148417

Live cell imaging combined with high-energy single-ion microbeam

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

Guo, Na; Du, Guanghua, E-mail: gh-du@impcas.ac.cn; Liu, Wenjing

DNA strand breaks can lead to cell carcinogenesis or cell death if not repaired rapidly and efficiently. An online live cell imaging system was established at the high energy microbeam facility at the Institute of Modern Physics to study early and fast cellular response to DNA damage after high linear energy transfer ion radiation. The HT1080 cells expressing XRCC1-RFP were irradiated with single high energy nickel ions, and time-lapse images of the irradiated cells were obtained online. The live cell imaging analysis shows that strand-break repair protein XRCC1 was recruited to the ion hit position within 20 s in themore » cells and formed bright foci in the cell nucleus. The fast recruitment of XRCC1 at the ion hits reached a maximum at about 200 s post-irradiation and then was followed by a slower release into the nucleoplasm. The measured dual-exponential kinetics of XRCC1 protein are consistent with the proposed consecutive reaction model, and the measurements obtained that the reaction rate constant of the XRCC1 recruitment to DNA strand break is 1.2 × 10{sup −3} s{sup −1} and the reaction rate constant of the XRCC1 release from the break-XRCC1 complex is 1.2 × 10{sup −2} s{sup −1}.« less

Genetic studies of cell fusion induced by herpes simplex virus type 1

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

Read, G.S.; Person, S.; Keller, P.M.

1980-07-01

Eight cell fusion-causing syn mutants were isolated from the KOS strain of herpes simplex virus type 1. Unlike the wild-type virus, the mutants produced plaques containing multinucleated cells, or syncytia. Fusion kinetics curves were established with a Coulter Counter assay for the mutants and wild-type virus in single infections of human embryonic lung (HEL) cells, for the mutants and wild-type virus in mixed infections (dominance test), and for pairs of mutants in mixed infection and proceeded with an exponential decrease in the number of small single cells. At some later time that was characteristic of the mutant, there was amore » significant reduction in the rate of fusion for all but possibly one of the mutants. Although the wild-type virus did not produce syncytial plaques, it did induce a small amount of fusion that stopped abruptly about 2 h after it started. These data are consistent with the hypothesis that both mutants and wild type induce an active fusion inducer and that the activity of this inducer is subsequently inhibited. The extent of fusion is apparently determined by the length of the interval during which the fusion inducer is active. That fusion is actively inhibited in wild-type infections is indicated by the observation that syn mutant-infected cells fused more readily with uninfected cells than with wild type-infected cells.« less

Pharmacokinetics of lidocaine and bupivacaine following subarachnoid administration in surgical patients: simultaneous investigation of absorption and disposition kinetics using stable isotopes

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

Burm, A.G.; Van Kleef, J.W.; Vermeulen, N.P.

1988-10-01

The pharmacokinetics of lidocaine and bupivacaine following subarachnoid administration were studied in 12 surgical patients using a stable isotope method. After subarachnoid administration of the agent to be evaluated, a deuterium-labelled analogue was administered intravenously. Blood samples were collected for 24 h. Plasma concentrations of the unlabelled and the deuterium-labelled local anesthetics were determined using a combination of capillary gas chromatography and mass fragmentography. Bi-exponential functions were fitted to the plasma concentration-time data of the deuterium-labelled local anesthetics. The progression of the absorption was evaluated using deconvolution. Mono- and bi-exponential functions were then fitted to the fraction absorbed versus timemore » data. The distribution and elimination half-lives of the deuterium-labelled analogues were 25 +/- 13 min (mean +/- SD) and 121 +/- 31 min for lidocaine and 19 +/- 10 min and 131 +/- 33 min for bupivacaine. The volumes of the central compartment and steady-state volumes of distribution were: lidocaine 57 +/- 10 l and 105 +/- 25 l, bupivacaine 25 +/- 6 l and 63 +/- 22 l. Total plasma clearance values averaged 0.97 +/- 0.21 l/min for lidocaine and 0.56 +/- 0.14 l/min for bupivacaine. The absorption of lidocaine could be described by a single first order absorption process, characterized by a half-life of 71 +/- 17 min in five out of six patients. The absorption of bupivacaine could be described adequately assuming two parallel first order absorption processes in all six patients. The half-lives, characterizing the fast and slow absorption processes of bupivacaine, were 50 +/- 27 min and 408 +/- 275 min, respectively. The fractions of the dose, absorbed in the fast and slow processes, were 0.35 +/- 0.17 and 0.61 +/- 0.16, respectively.« less

Alteration of the fast excitatory postsynaptic current by barium in voltage-clamped amphibian sympathetic ganglion cells.

PubMed Central

Connor, E. A.; Parsons, R. L.

1984-01-01

Barium-induced alterations in fast excitatory postsynaptic currents (e.p.s.cs) have been studied in voltage-clamped bullfrog sympathetic ganglion B cells. In the presence of 2-8 mM barium, e.p.s.c. decay was prolonged and in many cells the e.p.s.c. decay phase deviated from a single exponential function. The decay phase in these cases was more accurately described as the sum of two exponential functions. The frequency of occurrence of a complex decay increased both with increasing barium concentration and with hyperpolarization. Miniature e.p.s.c. decay also was prolonged in barium-treated cells. E.p.s.c. amplitude was not markedly affected by barium (2-8 mM) in cells voltage-clamped to -50 mV whereas at -90 mV there was a progressive increase in peak size with increasing barium concentration. In control cells the e.p.s.c.-voltage relationship was linear between -20 and -100 mV; however, this relationship became progressively non-linear with membrane hyperpolarization in barium-treated cells. The e.p.s.c. reversal potential was shifted to a more negative value in the presence of barium. There was a voltage-dependent increase in charge movement during the e.p.s.c. in barium-treated cells which was not present in control cells. We conclude that the voltage-dependent alteration in e.p.s.c. decay time course, peak amplitude and charge movement in barium-treated cells is due to a direct postsynaptic action of barium on the kinetics of receptor-channel gating in postganglionic sympathetic neurones. PMID:6333261

Excision Repair-Initiated Enzyme-Assisted Bicyclic Cascade Signal Amplification for Ultrasensitive Detection of Uracil-DNA Glycosylase.

PubMed

Wang, Li-Juan; Ren, Ming; Zhang, Qianyi; Tang, Bo; Zhang, Chun-Yang

2017-04-18

Uracil-DNA glycosylase (UDG) is an important base excision repair (BER) enzyme responsible for the repair of uracil-induced DNA lesion and the maintenance of genomic integrity, while the aberrant expression of UDG is associated with a variety of cancers. Thus, the accurate detection of UDG activity is essential to biomedical research and clinical diagnosis. Here, we develop a fluorescent method for ultrasensitive detection of UDG activity using excision repair-initiated enzyme-assisted bicyclic cascade signal amplification. This assay involves (1) UDG-actuated uracil-excision repair, (2) excision repair-initiated nicking enzyme-mediated isothermal exponential amplification, (3) ribonuclease H (RNase H)-induced hydrolysis of signal probes for generating fluorescence signal. The presence of UDG enables the removal of uracil from U·A pairs and generates an apurinic/apyrimidinic (AP) site. Endonuclease IV (Endo IV) subsequently cleaves the AP site, resulting in the break of DNA substrate. The cleaved DNA substrate functions as both a primer and a template to initiate isothermal exponential amplification, producing a large number of triggers. The resultant trigger may selectively hybridize with the signal probe which is modified with FAM and BHQ1, forming a RNA-DNA heterogeneous duplex. The subsequent hydrolysis of RNA-DNA duplex by RNase H leads to the generation of fluorescence signal. This assay exhibits ultrahigh sensitivity with a detection limit of 0.0001 U/mL, and it can even measure UDG activity at the single-cell level. Moreover, this method can be applied for the measurement of kinetic parameters and the screening of inhibitors, thereby providing a powerful tool for DNA repair enzyme-related biomedical research and clinical diagnosis.

[Estimation of the time of death based on the measurements of the eye temperature in comparison with other body sites].

PubMed

Kaliszan, Michał; Hauser, Roman

2007-01-01

A systematic two-stage study was conducted in pigs to verify the models of postmortem body temperature decrease currently employed in forensic medicine. During the investigations, temperature recordings were performed in four body sites (eyeballs, orbit soft tissues, muscles and rectums). The results of the study support the possible use of the eyeball and also the orbit soft tissues as temperature measuring sites at the early phase after death; they have narrowed the significance of rectum temperature measurements to the late stage of postmortem body temperature decrease, shown insignificant correlations between the body weight and the temperature decrease rate constant and illustrated the functional increase of the time of death estimation error as the body cools, expressed in the distinct tendency to overestimate the calculated time of death as compared to the actual one. In the second stage of the experiment, a lack of a plateau phase was demonstrated, at least from 30 min post mortem. It was also found that in the very early post mortem period, the kinetics of cooling of all the body sites studied was better described by the two-exponential model than the single exponential one. The study also showed that the weak airflow present in the experimental conditions did not practically affect the course of cooling of the investigated body sites. Eyeball temperature measurements with an infra-red laser thermometer performed during the experiment proved to be of no use for determination of the time of death. The experiments allowed for defining the so far unreported value of physiological temperature of pig eyeball as 38 degrees C.

Kinetic operational models of agonism for G-protein-coupled receptors.

PubMed

Hoare, Samuel R J; Pierre, Nicolas; Moya, Arturo Gonzalez; Larson, Brad

2018-06-07

The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, k τ ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter k τ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Absorbed dose estimates from a single measurement one to three days after the administration of 177Lu-DOTATATE/-TOC.

PubMed

Hänscheid, Heribert; Lapa, Constantin; Buck, Andreas K; Lassmann, Michael; Werner, Rudolf A

2017-01-01

To retrospectively analyze the accuracy of absorbed dose estimates from a single measurement of the activity concentrations in tumors and relevant organs one to three days after the administration of 177 Lu-DOTA-TATE/TOC assuming tissue specific effective half-lives. Activity kinetics in 54 kidneys, 30 neuroendocrine tumor lesions, 25 livers, and 27 spleens were deduced from series of planar images in 29 patients. After adaptation of mono- or bi-exponential fit functions to the measured data, it was analyzed for each fit function how precise the time integral can be estimated from fixed tissue-specific half-lives and a single measurement at 24, 48, or 72 h after the administration. For the kidneys, assuming a fixed tissue-specific half-life of 50 h, the deviations of the estimate from the actual integral were median (5 % percentile, 95 % percentile): -3 °% (-15 %>; +16 °%) for measurements after 24 h, +2 %> (-9 %>; +12 %>) for measurements after 48 h, and 0 % (-2 %; +12 %) for measurements after 72 h. The corresponding values for the other tissues, assuming fixed tissue-specific half-lives of 67 h for liver and spleen and 77 h for tumors, were +2 % (-25 %; +20 %) for measurements after 24 h, +2 °% (-16 %>; +17 %>) for measurements after 48 h, and +2 %> (-11 %>; +10 %>) for measurements after 72 h. Especially for the kidneys, which often represent the dose limiting organ, but also for liver, spleen, and neuroendocrine tumors, a meaningful absorbed dose estimate is possible from a single measurement after 2, more preferably 3 days after the administration of 177 Lu-DOTA-TATE/-TOC assuming fixed tissue specific effective half-lives. Schattauer GmbH.

Multi-step rhodopsin inactivation schemes can account for the size variability of single photon responses in Limulus ventral photoreceptors

PubMed Central

1994-01-01

Limulus ventral photoreceptors generate highly variable responses to the absorption of single photons. We have obtained data on the size distribution of these responses, derived the distribution predicted from simple transduction cascade models and compared the theory and data. In the simplest of models, the active state of the visual pigment (defined by its ability to activate G protein) is turned off in a single reaction. The output of such a cascade is predicted to be highly variable, largely because of stochastic variation in the number of G proteins activated. The exact distribution predicted is exponential, but we find that an exponential does not adequately account for the data. The data agree much better with the predictions of a cascade model in which the active state of the visual pigment is turned off by a multi-step process. PMID:8057085

Elimination kinetics of metals after an accidental exposure to welding fumes.

PubMed

Schaller, Karl H; Csanady, György; Filser, Johannes; Jüngert, Barbara; Drexler, Hans

2007-07-01

We had the opportunity to study the kinetics of metals in blood and urine samples of a flame-sprayer exposed to high accident-prone workplace exposure. We measured over 1 year, the nickel, aluminium, and chromium concentrations in blood and urine specimens after exposure. On this basis, we evaluated the corresponding half-lives. Blood and urine sampling were carried out five times after accidental exposure over a period of 1 year. The metals were analysed by graphite furnace atomic absorption spectrometry and Zeeman compensation with reliable methods. Either a mono-exponential or a bi-exponential function was fitted to the concentration-time courses of selected metals using weighted least squares non-linear regression analysis. The amount excreted in urine was calculated integrating the urinary decay curve and multiplying with the daily creatinine excretion. The first examination was carried out 15 days after exposure. The mean aluminium concentration in plasma was 8.2 microg/l and in urine, 58.4 microg/g creatinine. The mean nickel concentration in blood was 59.6 microg/l and the excretion in urine 700 microg/g creatinine. The mean chromium level in blood was 1.4 microg/l in urine, 7.4 microg/g creatinine. For the three elements, the metal concentrations in blood and urine exceeded the reference values at least in the initial phase. For nickel, the German biological threshold limit values (EKA) were exceeded. Aluminium showed a mono-exponential decay, whereas the elimination of chromium and nickel was biphasic in biological fluids of the accidentally exposed welder. The half-lives were as follows: for aluminium 140 days (urine) and 160 days (plasma); for chromium 40 and 730 days (urine); for nickel 25 and 610 days (urine) as well as 30 and 240 days (blood). The renal clearance of aluminium and nickel was about 2 l/h estimated for the last monitoring day.

The use of FTIR microscopy for evaluation of herpes viruses infection development kinetics

NASA Astrophysics Data System (ADS)

Erukhimovitch, Vitaly; Mukmanov, Igor; Talyshinsky, Marina; Souprun, Yelena; Huleihel, Mahmoud

2004-08-01

The kinetics of Herpes simplex infection development was studied using an FTIR microscopy (FTIR-M) method. The family of herpes viruses includes several members like H. simplex types I and II (HSV I, II), Varicella zoster (VZV) viruses which are involved in various human and animal infections of different parts of the body. In our previous study, we found significant spectral differences between normal uninfected cells in cultures and cells infected with herpes viruses at early stages of the infection. In the present study, cells in cultures were infected with either HSV-I or VZV and at various times post-infection they were examined either by optical microscopy or by advanced FTIR-M. Spectroscopic measurements show a consistent decrease in the intensity of the carbohydrate peak in correlation with the viral infection development, observed by optical microscopy. This decrease in cellular carbohydrate level was used as indicator for herpes viruses infection kinetics. This parameter could be used as a basis for applying a spectroscopic method for the evaluation of herpes virus infection development. Our results show also that the development kinetics of viral infection has an exponential character for these viruses.

A prominent anchoring effect on the kinetic control of drug release from mesoporous silica nanoparticles (MSNs).

PubMed

Tran, Vy Anh; Lee, Sang-Wha

2018-01-15

This work demonstrated kinetically controlled release of model drugs (ibuprofen, FITC) from well-tailored mesoporous silica nanoparticles (MSNs) depending on the surface charges and molecular sizes of the drugs. The molecular interactions between entrapped drugs and the pore walls of MSNs controlled the release of the drugs through the pore channels of MSNs. Also, polydopamine (PDA) layer-coated MSNs (MSNs@PDA) was quite effective to retard the release of large FITC, in contrast to a slight retardation effect on relatively small Ibuprofen. Of all things, FITC (Fluorescein isothiocyanate)-labeled APTMS (3-aminopropyltrimethoxysilane) (APTMS-FITC conjugates) grafted onto the MSNs generate a pinch-effect on the pore channel (so-called a prominent anchoring effect), which was highly effective in trapping (or blocking) drug molecules at the pore mouth of the MSNs. The anchored APTMS-FITC conjugates provided not only tortuous pathways to the diffusing molecules, but also sustained release of the ibuprofen over a long period of time (∼7days). The fast release kinetics was predicted by an exponential equation based on Fick's law, while the slow release kinetics was predicted by Higuchi model. Copyright © 2017 Elsevier Inc. All rights reserved.

Direct observation of a single nanoparticle-ubiquitin corona formation

NASA Astrophysics Data System (ADS)

Ding, Feng; Radic, Slaven; Chen, Ran; Chen, Pengyu; Geitner, Nicholas K.; Brown, Jared M.; Ke, Pu Chun

2013-09-01

The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation.The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of a nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheet content of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation. Electronic supplementary information (ESI) available: Experimental and computational methods as well as supporting figures. See DOI: 10.1039/c3nr02147e

The mechanism of tubulin-colchicine recognition--a kinetic study of the binding of a bicyclic colchicine analogue with a minor modification of the A ring.

PubMed

Dumortier, C; Potenziano, J L; Bane, S; Engelborghs, Y

1997-10-01

2-Methoxy-5-(2',3',4'-trimethoxy)-2,4,6-cycloheptatrien-1-one (MTC) is a colchicine analogue that lacks the B ring. 2-Methoxy-5-(2',4'-dimethoxyphenyl)-2,4,6-cycloheptatrien-1-one (MD) is an A-ring analogue of MTC, in which one methoxy group is replaced by a hydrogen atom. This paper describes the kinetic features of MDC binding to tubulin, and compares its behaviour with MTC to analyse the effect of the A-ring modification on the recognition process by tubulin. Binding is accompanied by a strong enhancement of MDC fluorescence and quenching of protein fluorescence. The kinetic and thermodynamic parameters were obtained from fluorescence stopped-flow measurements. The kinetics are described by a single exponential, indicating that this drug does not discriminate between the different tubulin isotypes. The observed pseudo-first-order rate constant of the fluorescence increase upon binding increases in a non-linear way, indicating that this ligand binds with a similar overall mechanism as colchicine and MTC, consisting of a fast initial binding of low affinity followed by a slower isomerisation step leading to full affinity. The K1 and k2 values for MDC at 25 degrees C were 540 +/- 65 M(-1) and 70 +/- 6 s(-1) respectively. From the temperature dependence, a reaction enthalpy change (deltaH(o)1) of the initial binding of 49 +/- 11 kJ/mol(-1) and an activation energy for the second step of 28 +/- 9 kJ/mol(-1) were calculated. Displacement experiments of bound MDC by MTC allowed the determination of a rate constant of reverse isomerisation of 0.60 +/- 0.07 s(-1) at 25 degrees C and the activation energy of 81 +/- 6 kJ/mol(-1). The overall binding constant was (6.3 +/- 0.2) x 10(4) M(-1) at 25 degrees C. Combination of these results with the kinetic parameters for association gives a full characterisation of the enthalpy pathway for the binding of MDC. The pathway of MDC is shown to differ considerably from that of MTC binding. Since its structural difference is located in ring A, this result indicates the use of ring A in the first step. The kinetics of the binding of MDC in the presence of some A-ring colchicine analogues (podophyllotoxin, 3',4',5'-trimethoxyacetophenone and N-acetylmescaline) and a C-ring analogue (tropolone methyl ether) suggest that the A and C rings are involved in the binding of MDC.

The dynamics of charge transfer with and without a barrier: A very simplified model of cyclic voltammetry.

PubMed

Ouyang, Wenjun; Subotnik, Joseph E

2017-05-07

Using the Anderson-Holstein model, we investigate charge transfer dynamics between a molecule and a metal surface for two extreme cases. (i) With a large barrier, we show that the dynamics follow a single exponential decay as expected; (ii) without any barrier, we show that the dynamics are more complicated. On the one hand, if the metal-molecule coupling is small, single exponential dynamics persist. On the other hand, when the coupling between the metal and the molecule is large, the dynamics follow a biexponential decay. We analyze the dynamics using the Smoluchowski equation, develop a simple model, and explore the consequences of biexponential dynamics for a hypothetical cyclic voltammetry experiment.

The Interaction of High-Speed Turbulence with Flames: Global Properties and Internal Flame Structure

DTIC Science & Technology

2009-09-28

S L, on all scales, including that of the laminar flame thickness, presents a number of both experimental and numerical challenges. Hereafter, we...fuel preconditioning, compression of the overall system, or propagation of large-scale shocks . Probing such regimes experimentally requires either...reactions are modeled using the first-order Arrhenius kinetics dY dt ≡ ẇ = −AρY exp ( − Q RT ) , (5) where A is the pre-exponential factor, Q is the

STOCK Mechanics:. a General Theory and Method of Energy Conservation with Applications on Djia

NASA Astrophysics Data System (ADS)

Tuncay, Çağlar

A new method, based on the original theory of conservation of sum of kinetic and potential energy defined for prices is proposed and applied on the Dow Jones Industrials Average (DJIA). The general trends averaged over months or years gave a roughly conserved total energy, with three different potential energies, i.e., positive definite quadratic, negative definite quadratic and linear potential energy for exponential rises (and falls), sinusoidal oscillations and parabolic trajectories, respectively. Corresponding expressions for force (impact) are also given.

The tetravalent organic cation spermine causes the gating of the IRK1 channel expressed in murine fibroblast cells.

PubMed Central

Ishihara, K; Hiraoka, M; Ochi, R

1996-01-01

1. The activation kinetics of the IRK1 channel stably expressed in L cells (a murine fibroblast cell line) were studied under the whole-cell voltage clamp. Without polyamines or Mg2+ in the pipettes, inward currents showed an exponential activation on hyperpolarization. The steep inward rectification of the currents around the reversal potential (Erev) could be described by the open-close transition of the channel with first-order kinetics. 2. When the tetravalent organic cation spermine (Spm) was added in the pipettes, the activation kinetics changed; this was explicable by the increase in the closing rate constant. The activation of the currents observed without Spm or Mg2+ in the pipettes was ascribed to the unblocking of the 'endogenous-Spm block'. 3. In the presence of the divalent cation putrescine (Put) or of Mg2+ in the pipettes, a different non-conductive state suppressed the outward currents on depolarization; the channels instantaneously changed to the open state on repolarization. As the depolarization was prolonged, this non-conductive state was replaced by the non-conductive state that shows an exponential activation on repolarization. This phenomenon was attributed to the redistribution of the channels from the Put- or Mg(2+)-blocked state to the 'endogenous Spm-blocked state' during depolarization. 4. In the presence of the trivalent cation spermidine (Spd) in the pipettes, two different non-conductive states occurred, showing a faster and a slower activation on repolarization. The rectification around Erev was mainly due to the non-conductive state showing a faster activation, which appeared to be the Spd-blocked state. During depolarization, redistribution of the channels to the 'endogenous Spm-blocked state' also occurred. 5. In the presence of Spd, Put or Mg2+ in the pipettes, the voltage dependence of the activation time constant reflecting the unblocking of the 'endogenous Spm' was shifted in the hyperpolarizing direction. 6. Our results suggest that the 'intrinsic gating' that shows the time-dependent activation on repolarization, and that is responsible for the inward rectification around Erev, reflects the blocking kinetics of the tetravalent Spm. PMID:8866861

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

PubMed Central

Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

2014-01-01

In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating the thermodynamic and kinetic quality of different pathway chemistries that produce the same molecules. PMID:24586134

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

PubMed

Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

2010-06-22

The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

The Free Energy Landscape of Small Molecule Unbinding

PubMed Central

Huang, Danzhi; Caflisch, Amedeo

2011-01-01

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding. PMID:21390201

The free energy landscape of small molecule unbinding.

PubMed

Huang, Danzhi; Caflisch, Amedeo

2011-02-01

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding.

A nonstationary Poisson point process describes the sequence of action potentials over long time scales in lateral-superior-olive auditory neurons.

PubMed

Turcott, R G; Lowen, S B; Li, E; Johnson, D H; Tsuchitani, C; Teich, M C

1994-01-01

The behavior of lateral-superior-olive (LSO) auditory neurons over large time scales was investigated. Of particular interest was the determination as to whether LSO neurons exhibit the same type of fractal behavior as that observed in primary VIII-nerve auditory neurons. It has been suggested that this fractal behavior, apparent on long time scales, may play a role in optimally coding natural sounds. We found that a nonfractal model, the nonstationary dead-time-modified Poisson point process (DTMP), describes the LSO firing patterns well for time scales greater than a few tens of milliseconds, a region where the specific details of refractoriness are unimportant. The rate is given by the sum of two decaying exponential functions. The process is completely specified by the initial values and time constants of the two exponentials and by the dead-time relation. Specific measures of the firing patterns investigated were the interspike-interval (ISI) histogram, the Fano-factor time curve (FFC), and the serial count correlation coefficient (SCC) with the number of action potentials in successive counting times serving as the random variable. For all the data sets we examined, the latter portion of the recording was well approximated by a single exponential rate function since the initial exponential portion rapidly decreases to a negligible value. Analytical expressions available for the statistics of a DTMP with a single exponential rate function can therefore be used for this portion of the data. Good agreement was obtained among the analytical results, the computer simulation, and the experimental data on time scales where the details of refractoriness are insignificant.(ABSTRACT TRUNCATED AT 250 WORDS)

Unfolding of Ubiquitin Studied by Picosecond Time-Resolved Fluorescence of the Tyrosine Residue

PubMed Central

Noronha, Melinda; Lima, João C.; Bastos, Margarida; Santos, Helena; Maçanita, António L.

2004-01-01

The photophysics of the single tyrosine in bovine ubiquitin (UBQ) was studied by picosecond time-resolved fluorescence spectroscopy, as a function of pH and along thermal and chemical unfolding, with the following results: First, at room temperature (25°C) and below pH 1.5, native UBQ shows single-exponential decays. From pH 2 to 7, triple-exponential decays were observed and the three decay times were attributed to the presence of tyrosine, a tyrosine-carboxylate hydrogen-bonded complex, and excited-state tyrosinate. Second, at pH 1.5, the water-exposed tyrosine of either thermally or chemically unfolded UBQ decays as a sum of two exponentials. The double-exponential decays were interpreted and analyzed in terms of excited-state intramolecular electron transfer from the phenol to the amide moiety, occurring in one of the three rotamers of tyrosine in UBQ. The values of the rate constants indicate the presence of different unfolded states and an increase in the mobility of the tyrosine residue during unfolding. Finally, from the pre-exponential coefficients of the fluorescence decays, the unfolding equilibrium constants (KU) were calculated, as a function of temperature or denaturant concentration. Despite the presence of different unfolded states, both thermal and chemical unfolding data of UBQ could be fitted to a two-state model. The thermodynamic parameters Tm = 54.6°C, ΔHTm = 56.5 kcal/mol, and ΔCp = 890 cal/mol//K, were determined from the unfolding equilibrium constants calculated accordingly, and compared to values obtained by differential scanning calorimetry also under the assumption of a two-state transition, Tm = 57.0°C, ΔHm= 51.4 kcal/mol, and ΔCp = 730 cal/mol//K. PMID:15454455

Tl+-induced micros gating of current indicates instability of the MaxiK selectivity filter as caused by ion/pore interaction.

PubMed

Schroeder, Indra; Hansen, Ulf-Peter

2008-04-01

Patch clamp experiments on single MaxiK channels expressed in HEK293 cells were performed at high temporal resolution (50-kHz filter) in asymmetrical solutions containing 0, 25, 50, or 150 mM Tl+ on the luminal or cytosolic side with [K+] + [Tl+] = 150 mM and 150 mM K+ on the other side. Outward current in the presence of cytosolic Tl+ did not show fast gating behavior that was significantly different from that in the absence of Tl+. With luminal Tl+ and at membrane potentials more negative than -40 mV, the single-channel current showed a negative slope resistance concomitantly with a flickery block, resulting in an artificially reduced apparent single-channel current I(app). The analysis of the amplitude histograms by beta distributions enabled the estimation of the true single-channel current and the determination of the rate constants of a simple two-state O-C Markov model for the gating in the bursts. The voltage dependence of the gating ratio R = I(true)/I(app) = (k(CO) + k(OC))/k(CO) could be described by exponential functions with different characteristic voltages above or below 50 mM Tl(+). The true single-channel current I(true) decreased with Tl+ concentrations up to 50 mM and stayed constant thereafter. Different models were considered. The most likely ones related the exponential increase of the gating ratio to ion depletion at the luminal side of the selectivity filter, whereas the influence of [Tl+] on the characteristic voltage of these exponential functions and of the value of I(true) were determined by [Tl+] at the inner side of the selectivity filter or in the cavity.

Reaction Kinetic Model of Dilute Acid-Catalyzed Hemicellulose Hydrolysis of Corn Stover under High-Solid Conditions

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

Shi, Suan; Guan, Wenjian; Kang, Li

High solid conditions are desirable in pretreatment of lignocellulosic biomass. An advanced dilute-acid pretreatment reactor has been developed at National Renewable Energy Laboratory (NREL). It is a continuous auger-driven reactor that can be operated with high-solid charge at high temperature and with short residence time resulting high productivity and high sugar concentration. Here, we investigated the kinetics of the reactions associated with dilute-acid pretreatment of corn stover, covering the reaction conditions of the NREL reactor operation: 155-185 C, 1-2 wt% sulfuric acid concentration, and 1:2 solid to liquid ratio. The experimental data were fitted to a first-order biphasic model whichmore » assumes that xylan is comprised of two different fragments: fast and slow reacting fractions. Due to the high solid loading condition, significant amount of xylose oligomers was observed during the pretreatment. We also included the oligomers as an intermediate entity in the kinetic model. The effect of acid concentration was incorporated into the pre-exponential factor of Arrhenius equation. The kinetic model with bestfit kinetic parameters has shown good agreement with experimental data. The kinetic parameter values of the proposed model were noticeably different from those previously reported. The activation energies of xylan hydrolysis are lower and the acid exponents are higher than the average of literature values. The proposed model can serve as a useful tool for design and operation of pretreatment system pertaining to corn stover.« less

Reaction Kinetic Model of Dilute Acid-Catalyzed Hemicellulose Hydrolysis of Corn Stover under High-Solid Conditions

DOE PAGES

Shi, Suan; Guan, Wenjian; Kang, Li; ...

2017-09-13

High solid conditions are desirable in pretreatment of lignocellulosic biomass. An advanced dilute-acid pretreatment reactor has been developed at National Renewable Energy Laboratory (NREL). It is a continuous auger-driven reactor that can be operated with high-solid charge at high temperature and with short residence time resulting high productivity and high sugar concentration. Here, we investigated the kinetics of the reactions associated with dilute-acid pretreatment of corn stover, covering the reaction conditions of the NREL reactor operation: 155-185 C, 1-2 wt% sulfuric acid concentration, and 1:2 solid to liquid ratio. The experimental data were fitted to a first-order biphasic model whichmore » assumes that xylan is comprised of two different fragments: fast and slow reacting fractions. Due to the high solid loading condition, significant amount of xylose oligomers was observed during the pretreatment. We also included the oligomers as an intermediate entity in the kinetic model. The effect of acid concentration was incorporated into the pre-exponential factor of Arrhenius equation. The kinetic model with bestfit kinetic parameters has shown good agreement with experimental data. The kinetic parameter values of the proposed model were noticeably different from those previously reported. The activation energies of xylan hydrolysis are lower and the acid exponents are higher than the average of literature values. The proposed model can serve as a useful tool for design and operation of pretreatment system pertaining to corn stover.« less

Clarifications regarding the use of model-fitting methods of kinetic analysis for determining the activation energy from a single non-isothermal curve.

PubMed

Sánchez-Jiménez, Pedro E; Pérez-Maqueda, Luis A; Perejón, Antonio; Criado, José M

2013-02-05

This paper provides some clarifications regarding the use of model-fitting methods of kinetic analysis for estimating the activation energy of a process, in response to some results recently published in Chemistry Central journal. The model fitting methods of Arrhenius and Savata are used to determine the activation energy of a single simulated curve. It is shown that most kinetic models correctly fit the data, each providing a different value for the activation energy. Therefore it is not really possible to determine the correct activation energy from a single non-isothermal curve. On the other hand, when a set of curves are recorded under different heating schedules are used, the correct kinetic parameters can be clearly discerned. Here, it is shown that the activation energy and the kinetic model cannot be unambiguously determined from a single experimental curve recorded under non isothermal conditions. Thus, the use of a set of curves recorded under different heating schedules is mandatory if model-fitting methods are employed.

Partitioning of monomethylmercury between freshwater algae and water.

PubMed

Miles, C J; Moye, H A; Phlips, E J; Sargent, B

2001-11-01

Phytoplankton-water monomethylmercury (MeHg) partition constants (KpI) have been determined in the laboratory for two green algae Selenastrum capricornutum and Cosmarium botrytis, the blue-green algae Schizothrix calcicola, and the diatom Thallasiosira spp., algal species that are commonly found in natural surface waters. Two methods were used to determine KpI, the Freundlich isotherm method and the flow-through/dialysis bag method. Both methods yielded KpI values of about 10(6.6) for S. capricornutum and were not significantly different. The KpI for the four algae studied were similar except for Schizothrix, which was significantly lower than S. capricornutum. The KpI for MeHg and S. capricornutum (exponential growth) was not significantly different in systems with predominantly MeHgOH or MeHgCl species. This is consistent with other studies that show metal speciation controls uptake kinetics, but the reactivity with intracellular components controls steady-state concentrations. Partitioning constants determined with exponential and stationary phase S. capricornutum cells at the same conditions were not significantly different, while the partitioning constant for exponential phase, phosphorus-limited cells was significantly lower, suggesting that P-limitation alters the ecophysiology of S. capricornutum sufficiently to impact partitioning, which may then ultimately affect mercury levels in higher trophic species.

A Parametric Study of Fine-scale Turbulence Mixing Noise

NASA Technical Reports Server (NTRS)

Khavaran, Abbas; Bridges, James; Freund, Jonathan B.

2002-01-01

The present paper is a study of aerodynamic noise spectra from model functions that describe the source. The study is motivated by the need to improve the spectral shape of the MGBK jet noise prediction methodology at high frequency. The predicted spectral shape usually appears less broadband than measurements and faster decaying at high frequency. Theoretical representation of the source is based on Lilley's equation. Numerical simulations of high-speed subsonic jets as well as some recent turbulence measurements reveal a number of interesting statistical properties of turbulence correlation functions that may have a bearing on radiated noise. These studies indicate that an exponential spatial function may be a more appropriate representation of a two-point correlation compared to its Gaussian counterpart. The effect of source non-compactness on spectral shape is discussed. It is shown that source non-compactness could well be the differentiating factor between the Gaussian and exponential model functions. In particular, the fall-off of the noise spectra at high frequency is studied and it is shown that a non-compact source with an exponential model function results in a broader spectrum and better agreement with data. An alternate source model that represents the source as a covariance of the convective derivative of fine-scale turbulence kinetic energy is also examined.

Accounting for inherent variability of growth in microbial risk assessment.

PubMed

Marks, H M; Coleman, M E

2005-04-15

Risk assessments of pathogens need to account for the growth of small number of cells under varying conditions. In order to determine the possible risks that occur when there are small numbers of cells, stochastic models of growth are needed that would capture the distribution of the number of cells over replicate trials of the same scenario or environmental conditions. This paper provides a simple stochastic growth model, accounting only for inherent cell-growth variability, assuming constant growth kinetic parameters, for an initial, small, numbers of cells assumed to be transforming from a stationary to an exponential phase. Two, basic, microbial sets of assumptions are considered: serial, where it is assume that cells transform through a lag phase before entering the exponential phase of growth; and parallel, where it is assumed that lag and exponential phases develop in parallel. The model is based on, first determining the distribution of the time when growth commences, and then modelling the conditional distribution of the number of cells. For the latter distribution, it is found that a Weibull distribution provides a simple approximation to the conditional distribution of the relative growth, so that the model developed in this paper can be easily implemented in risk assessments using commercial software packages.

Engineering entropy-driven reactions and networks catalyzed by DNA.

PubMed

Zhang, David Yu; Turberfield, Andrew J; Yurke, Bernard; Winfree, Erik

2007-11-16

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.

Time-resolved tryptophan fluorescence in photosynthetic reaction centers from Rhodobacter sphaeroides

NASA Technical Reports Server (NTRS)

Godik, V. I.; Blankenship, R. E.; Causgrove, T. P.; Woodbury, N.

1993-01-01

Tryptophan fluorescence of reaction centers isolated from Rhodobacter sphaeroides, both stationary and time-resolved, was studied. Fluorescence kinetics were found to fit best a sum of four discrete exponential components. Half of the initial amplitude was due to a component with a lifetime of congruent to 60 ps, belonging to Trp residues, capable of efficient transfer of excitation energy to bacteriochlorophyll molecules of the reaction center. The three other components seem to be emitted by Trp ground-state conformers, unable to participate in such a transfer. Under the influence of intense actinic light, photooxidizing the reaction centers, the yield of stationary fluorescence diminished by congruent to 1.5 times, while the number of the kinetic components and their life times remained practically unchanged. Possible implications of the observed effects for the primary photosynthesis events are considered.

Dissipation kinetics of bifenazate in tea under tropical conditions.

PubMed

Satheshkumar, Annamalai; Senthurpandian, Velu Kalaipandian; Shanmugaselvan, Veilumuthu Anandham

2014-02-15

Field experiments were conducted during April and May of 2011 in Valparai, Coonoor and Gudalur (Tamil Nadu, India) to determine the residues of bifenazate in black tea. From this study, residue levels of bifenazate at different harvest intervals, persistence, dissipation pattern during processing, rate constant and half-life values were calculated. Residues of bifenazate dissipated exponentially after spraying and at Gudalur trial, on the 16th day after application residues were below the maximum residue level of 0.02 mg/kg set by the European Union. However, no residues were detected in the tea brew. Regression lines drawn for bifenazate showed that it followed first order dissipation kinetics. Half-life values varied from 1.03 to 1.36 days for bifenazate and a pre-harvest interval of 16 days is suggested. Copyright © 2013 Elsevier Ltd. All rights reserved.

λ-Repressor Oligomerization Kinetics at High Concentrations Using Fluorescence Correlation Spectroscopy in Zero-Mode Waveguides

PubMed Central

Samiee, K. T.; Foquet, M.; Guo, L.; Cox, E. C.; Craighead, H. G.

2005-01-01

Fluorescence correlation spectroscopy (FCS) has demonstrated its utility for measuring transport properties and kinetics at low fluorophore concentrations. In this article, we demonstrate that simple optical nanostructures, known as zero-mode waveguides, can be used to significantly reduce the FCS observation volume. This, in turn, allows FCS to be applied to solutions with significantly higher fluorophore concentrations. We derive an empirical FCS model accounting for one-dimensional diffusion in a finite tube with a simple exponential observation profile. This technique is used to measure the oligomerization of the bacteriophage λ repressor protein at micromolar concentrations. The results agree with previous studies utilizing conventional techniques. Additionally, we demonstrate that the zero-mode waveguides can be used to assay biological activity by measuring changes in diffusion constant as a result of ligand binding. PMID:15613638

Kinetic analysis of simultaneous denitrification and biomineralization of novel Acinetobacter sp. CN86.

PubMed

Su, Jun-Feng; Shi, Jing-Xin; Huang, Ting-Lin; Ma, Fang

2016-08-15

A novel aerobic denitrification and biomineralization strain CN86 was isolated from the Qu Jiang artificial lake. Based on phylogenetic characteristics, the isolated strain was identified as Acinetobacter species. Strain CN86 was confirmed to have the ability to perform simultaneous denitrification and biomineralization. Exponential decay equation was used for the matching of kinetic processes on denitrification and biomineralization. A highest nitrate removal rate was achieved at the pH7.0, organic concentration of 1.5g/L and temperature of 30°C. An optimal hardness removal rate was obtained at the pH9.0, organic concentration of 2.0g/L and temperature of 30°C. Strain CN86 is a suitable candidate for the simultaneous removal of nitrate and hardness in groundwater treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

EasyDelta: A spreadsheet for kinetic modeling of the stable carbon isotope composition of natural gases

NASA Astrophysics Data System (ADS)

Zou, Yan-Rong; Wang, Lianyuan; Shuai, Yanhua; Peng, Ping'an

2005-08-01

A new kinetic model and an Excel © spreadsheet program for modeling the stable carbon isotope composition of natural gases is provided in this paper. The model and spreadsheet could be used to describe and predict the variances in stable carbon isotope of natural gases under both experimental and geological conditions with heating temperature or geological time. It is a user-friendly convenient tool for the modeling of isotope variation with time under experimental and geological conditions. The spreadsheet, based on experimental data, requires the input of the kinetic parameters of gaseous hydrocarbons generation. Some assumptions are made in this model: the conventional (non-isotope species) kinetic parameters represent the light isotope species; the initial isotopic value is the same for all parallel chemical reaction of gaseous hydrocarbons generation for simplicity, the re-exponential factor ratio, 13A/ 12A, is a constant, and both heavy and light isotope species have similar activation energy distribution. These assumptions are common in modeling of isotope ratios. The spreadsheet is used for searching the best kinetic parameters of the heavy isotope species to reach the minimum errors compared with experimental data, and then extrapolating isotopic changes to the thermal history of sedimentary basins. A short calculation example on the variation in δ13C values of methane is provided in this paper to show application to geological conditions.

Confirmation of monod model for biofiltration of styrene vapors from waste flue gas.

PubMed

Dehghanzadeh, Reza; Roshani, Babak; Asadi, Mahzar; Fahiminia, Mohammad; Aslhashemi, Ahmad

2012-01-01

The objective of this research was to investigate the kinetic behavior of the biofil¬tration process for the removal of styrene. A three stage compost based biofilter was inoculated with thickened activated sludge. The reaction order rate constants were obtained from continuous experiments and used as the specific growth rate for the Monod equation. The measured concentration profiles show a linear dependence on the bed height in the biofilter at higher loadings, such as 75 and 45 g m-3 h-1. This is the condition of reaction limitation for a reaction with zero-order kinetics. From the experimental data, maximum elimination capac¬ity (ECmax) was estimated to be 44, 40 and 26 g m-3 h-1 at empty bed retention times (EBRTs) of 120, 60 and 30 s, respectively. However, at lower loadings, the measured concentration profile of the biofilter is one of exponential increase, which is the condition of both reaction and diffusion limitations for a reaction with zero-order kinetics. Maximum elimination capacities found from the experimental results were the same as Monod model predictions. Both the experimental re¬sults and the model predictions showed the influence of EBRT on the removal rate of styrene, particularly for the highest loading rate. In terms of the practical applications of the proposed models have the advantage of being simpler than Monod kinetics and Monod kinetics requires a numerical solution.

Biokinetics of radiolabeled Iodophenylpentadecanoic acid (I-123-IPPA) and thallium-201 in a rabbit model of chronic myocardial infarction measured using a series of thermoluminescent dosimeters

NASA Astrophysics Data System (ADS)

Medich, David Christopher

1997-09-01

The biokinetics of Iodophenylpentadecanoic acid (123I-IPPA) during a chronic period of myocardial infarction were determined and compared to 201Tl. IPPA was assessed as a perfusion and metabolic tracer in the scintigraphic diagnosis of coronary artery disease. The myocardial clearance kinetics were measured by placing a series of thermoluminescent dosimeters (TLDs) on normal and infarcted tissue to measure the local myocardial activity content over time. The arterial blood pool activity was fit to a bi-exponential function for 201Tl and a tri-exponential function for 123I-IPPA to estimate the left ventricle contribution to TLD response. At equilibrium, the blood pool contribution was estimated experimentally to be less than 5% of the total TLD response. The method was unable to resolve the initial uptake of the imaging agent due in part to the 2 minute TLD response integration time and in part to the 30 second lag time for the first TLD placement. A noticeable disparity was observed between the tracer concentrations of IPPA in normal and ischemic tissue of approximately 2:1. The fitting parameters (representing the biokinetic eigenvalue rate constants) were related to the fundamental rate constants of a recycling biokinetic model. The myocardial IPPA content within normal tissue was elevated after approximately 130 minutes post injection. This phenomenon was observed in all but one (950215) of the IPPA TLD kinetics curves.

Time-dependent cell disintegration kinetics in lung tumors after irradiation

NASA Astrophysics Data System (ADS)

Chvetsov, Alexei V.; Palta, Jatinder J.; Nagata, Yasushi

2008-05-01

We study the time-dependent disintegration kinetics of tumor cells that did not survive radiotherapy treatment. To evaluate the cell disintegration rate after irradiation, we studied the volume changes of solitary lung tumors after stereotactic radiotherapy. The analysis is performed using two approximations: (1) tumor volume is a linear function of the total cell number in the tumor and (2) the cell disintegration rate is governed by the exponential decay with constant risk, which is defined by the initial cell number and a half-life T1/2. The half-life T1/2 is determined using the least-squares fit to the clinical data on lung tumor size variation with time after stereotactic radiotherapy. We show that the tumor volume variation after stereotactic radiotherapy of solitary lung tumors can be approximated by an exponential function. A small constant component in the volume variation does not change with time; however, this component may be the residual irregular density due to radiation fibrosis and was, therefore, subtracted from the total volume variation in our computations. Using computerized fitting of the exponent function to the clinical data for selected patients, we have determined that the average half-life T1/2 of cell disintegration is 28.2 days for squamous cell carcinoma and 72.4 days for adenocarcinoma. This model is needed for simulating the tumor volume variation during radiotherapy, which may be important for time-dependent treatment planning of proton therapy that is sensitive to density variations.

Reproducibility of onset and recovery oxygen uptake kinetics in moderately impaired patients with chronic heart failure

PubMed Central

De Vries, Wouter R.; Hoogeveen, Adwin R.; Zonderland, Maria L.; Thijssen, Eric J. M.; Schep, Goof

2007-01-01

Oxygen (O2) kinetics reflect the ability to adapt to or recover from exercise that is indicative of daily life. In patients with chronic heart failure (CHF), parameters of O2 kinetics have shown to be useful for clinical purposes like grading of functional impairment and assessment of prognosis. This study compared the goodness of fit and reproducibility of previously described methods to assess O2 kinetics in these patients. Nineteen CHF patients, New York Heart Association class II–III, performed two constant-load tests on a cycle ergometer at 50% of the maximum workload. Time constants of O2 onset- and recovery kinetics (τ) were calculated by mono-exponential modeling with four different sampling intervals (5 and 10 s, 5 and 8 breaths). The goodness of fit was expressed as the coefficient of determination (R2). Onset kinetics were also evaluated by the mean response time (MRT). Considering O2 onset kinetics, τ showed a significant inverse correlation with peak- \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} $$ \\ifmmode\\expandafter\\dot\\else\\expandafter\\.\\fi{V}{\\text{O}}_{2} $$\\end{document} (R = −0.88, using 10 s sampling intervals). The limits of agreement of both τ and MRT, however, were not clinically acceptable. O2 recovery kinetics yielded better reproducibility and goodness of fit. Using the most optimal sampling interval (5 breaths), a change of at least 13 s in τ is needed to exceed normal test-to-test variations. In conclusion, O2 recovery kinetics are more reproducible for clinical purposes than O2 onset kinetics in moderately impaired patients with CHF. It should be recognized that this observation cannot be assumed to be generalizable to more severely impaired CHF patients. PMID:17277937

Water vapor sorption properties of cellulose nanocrystals and nanofibers using dynamic vapor sorption apparatus.

PubMed

Guo, Xin; Wu, Yiqiang; Xie, Xinfeng

2017-10-27

Hygroscopic behavior is an inherent characteristic of nanocellulose which strongly affects its applications. In this study, the water vapor sorption behavior of four nanocellulose samples, such as cellulose nanocrystals and nanofibers with cellulose I and II structures (cellulose nanocrystals (CNC) I, CNC II, cellulose nanofibers (CNF) I, and CNF II) were studied by dynamic vapor sorption. The highly reproducible data including the running time, real-time sample mass, target relative humidity (RH), actual RH, and isotherm temperature were recorded during the sorption process. In analyzing these data, significant differences in the total running time, equilibrium moisture content, sorption hysteresis and sorption kinetics between these four nanocellulose samples were confirmed. It was important to note that CNC I, CNC II, CNF I, and CNF II had equilibrium moisture contents of 21.4, 28.6, 33.2, and 38.9%, respectively, at a RH of 95%. Then, the sorption kinetics behavior was accurately described by using the parallel exponential kinetics (PEK) model. Furthermore, the Kelvin-Voigt model was introduced to interpret the PEK behavior and calculate the modulus of these four nanocellulose samples.

Thermogravimetric kinetic modelling of in-situ catalytic pyrolytic conversion of rice husk to bioenergy using rice hull ash catalyst.

PubMed

Loy, Adrian Chun Minh; Gan, Darren Kin Wai; Yusup, Suzana; Chin, Bridgid Lai Fui; Lam, Man Kee; Shahbaz, Muhammad; Unrean, Pornkamol; Acda, Menandro N; Rianawati, Elisabeth

2018-08-01

The thermal degradation behaviour and kinetic parameter of non-catalytic and catalytic pyrolysis of rice husk (RH) using rice hull ash (RHA) as catalyst were investigated using thermogravimetric analysis at four different heating rates of 10, 20, 50 and 100 K/min. Four different iso conversional kinetic models such as Kissinger, Friedman, Kissinger-Akahira-Sunose (KAS) and Ozawa-Flynn-Wall (OFW) were applied in this study to calculate the activation energy (E A ) and pre-exponential value (A) of the system. The E A of non-catalytic and catalytic pyrolysis was found to be in the range of 152-190 kJ/mol and 146-153 kJ/mol, respectively. The results showed that the catalytic pyrolysis of RH had resulted in a lower E A as compared to non-catalytic pyrolysis of RH and other biomass in literature. Furthermore, the high Gibb's free energy obtained in RH implied that it has the potential to serve as a source of bioenergy production. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparative kinetic and energetic modelling of phyllosemiquinone oxidation in Photosystem I.

PubMed

Santabarbara, Stefano; Zucchelli, Giuseppe

2016-04-14

The oxidation kinetics of phyllo(semi)quinone (PhQ), which acts as an electron transfer (ET) intermediate in the Photosystem I reaction centre, are described by a minimum of two exponential phases, characterised by lifetimes in the 10-30 ns and 150-300 ns ranges. The fastest phase is considered to be dominated by the oxidation of the PhQ molecule coordinated by the PsaB reaction centre subunit (PhQB), and the slowest phase is dominated by the oxidation of the PsaA coordinated PhQ (PhQA). Testing different energetic schemes within a unified theory-based kinetic modelling approach provides reliable limit-values for some of the physical-chemical parameters controlling these ET reactions: (i) the value of ΔG(0) associated with PhQA oxidation is smaller than ∼+30 meV; (ii) the value of the total reorganisation energy (λt) likely exceeds 0.7 eV; (iii) different mean nuclear modes are coupled to PhQB and PhQA oxidation, the former being larger, and both being ≥100 cm(-1).

Empirical kinetics and their role in elucidating the utility of transition-state theory to mineral–water reactions. A comment upon, ''Evidence and Potential Implications of Exponential Tails to Concentration Versus Time Plots for the Batch Dissolution of Calcite'' by V. W. Truesdale

DOE PAGES

Icenhower, Jonathan P.

2015-06-23

Transition-state theory (TST) is a successful theory for understanding many different types of reactions, but its application to mineral-water systems has not been successful, especially as the system approaches saturation with respect to a rate-limiting phase. A number of investigators have proposed alternate frameworks for using the kinetic rate data to construct models of dissolution, including Truesdale (Aquat Geochem, 2015; this issue). This alternate approach has been resisted, in spite of self-evident discrepancies between TST expectations and the data. The failure of TST under certain circumstances is a result of the presence of metastable intermediaries or reaction layers that formmore » on the surface of reacting solids, and these phenomena are not anticipated by the current theory. Furthermore, alternate approaches, such as the shrinking object model advocated by Truesdale, represent a potentially important avenue for advancing the science of dissolution kinetics.« less

Drug Resistance and the Kinetics of Metastatic Cancer

NASA Astrophysics Data System (ADS)

Blagoev, Krastan B.

2012-02-01

Most metastatic cancers after initial response to current drug therapies develop resistance to the treatment. We present cancer data and a theory that explains the observed kinetics of tumor growth in cancer patients and using a stochastic model based on this theory we relate the kinetics of tumor growth to Kaplan-Meyer survival curves. The theory points to the tumor growth rate as the most important parameter determining the outcome of a drug treatment. The overall tumor growth or decay rate is a reflection of the balance between cell division, senescence and apoptosis and we propose that the deviation of the decay rate from exponential is a measure of the emergence of drug resistance. In clinical trials the progression free survival, the overall survival, and the shape of the Kaplan-Meyer plots are determined by the tumor growth rate probability distribution among the patients in the trial. How drug treatments modify this distribution will also be described. At the end of the talk we will discuss the connection between the theory described here and the age related cancer mortality rates in the United States.

Difference in Dwarf Galaxy Surface Brightness Profiles as a Function of Environment

NASA Astrophysics Data System (ADS)

Lee, Youngdae; Park, Hong Soo; Kim, Sang Chul; Moon, Dae-Sik; Lee, Jae-Joon; Kim, Dong-Jin; Cha, Sang-Mok

2018-05-01

We investigate surface brightness profiles (SBPs) of dwarf galaxies in field, group, and cluster environments. With deep BV I images from the Korea Microlensing Telescope Network Supernova Program, SBPs of 38 dwarfs in the NGC 2784 group are fitted by a single-exponential or double-exponential model. We find that 53% of the dwarfs are fitted with single-exponential profiles (“Type I”), while 47% of the dwarfs show double-exponential profiles; 37% of all dwarfs have smaller sizes for the outer part than the inner part (“Type II”), while 10% have a larger outer than inner part (“Type III”). We compare these results with those in the field and in the Virgo cluster, where the SBP types of 102 field dwarfs are compiled from a previous study and the SBP types of 375 cluster dwarfs are measured using SDSS r-band images. As a result, the distributions of SBP types are different in the three environments. Common SBP types for the field, the NGC 2784 group, and the Virgo cluster are Type II, Type I and II, and Type I and III profiles, respectively. After comparing the sizes of dwarfs in different environments, we suggest that since the sizes of some dwarfs are changed due to environmental effects, SBP types are capable of being transformed and the distributions of SBP types in the three environments are different. We discuss possible environmental mechanisms for the transformation of SBP types. Based on data collected at KMTNet Telescopes and SDSS.

First storage of ion beams in the Double Electrostatic Ion-Ring Experiment: DESIREE.

PubMed

Schmidt, H T; Thomas, R D; Gatchell, M; Rosén, S; Reinhed, P; Löfgren, P; Brännholm, L; Blom, M; Björkhage, M; Bäckström, E; Alexander, J D; Leontein, S; Hanstorp, D; Zettergren, H; Liljeby, L; Källberg, A; Simonsson, A; Hellberg, F; Mannervik, S; Larsson, M; Geppert, W D; Rensfelt, K G; Danared, H; Paál, A; Masuda, M; Halldén, P; Andler, G; Stockett, M H; Chen, T; Källersjö, G; Weimer, J; Hansen, K; Hartman, H; Cederquist, H

2013-05-01

We report on the first storage of ion beams in the Double ElectroStatic Ion Ring ExpEriment, DESIREE, at Stockholm University. We have produced beams of atomic carbon anions and small carbon anion molecules (C(n)(-), n = 1, 2, 3, 4) in a sputter ion source. The ion beams were accelerated to 10 keV kinetic energy and stored in an electrostatic ion storage ring enclosed in a vacuum chamber at 13 K. For 10 keV C2 (-) molecular anions we measure the residual-gas limited beam storage lifetime to be 448 s ± 18 s with two independent detector systems. Using the measured storage lifetimes we estimate that the residual gas pressure is in the 10(-14) mbar range. When high current ion beams are injected, the number of stored particles does not follow a single exponential decay law as would be expected for stored particles lost solely due to electron detachment in collision with the residual-gas. Instead, we observe a faster initial decay rate, which we ascribe to the effect of the space charge of the ion beam on the storage capacity.

Ultrafast electron-optical phonon scattering and quasiparticle lifetime in CVD-grown graphene.

PubMed

Shang, Jingzhi; Yu, Ting; Lin, Jianyi; Gurzadyan, Gagik G

2011-04-26

Ultrafast quasiparticle dynamics in graphene grown by chemical vapor deposition (CVD) has been studied by UV pump/white-light probe spectroscopy. Transient differential transmission spectra of monolayer graphene are observed in the visible probe range (400-650 nm). Kinetics of the quasiparticle (i.e., low-energy single-particle excitation with renormalized energy due to electron-electron Coulomb, electron-optical phonon (e-op), and optical phonon-acoustic phonon (op-ap) interactions) was monitored with 50 fs resolution. Extending the probe range to near-infrared, we find the evolution of quasiparticle relaxation channels from monoexponential e-op scattering to double exponential decay due to e-op and op-ap scattering. Moreover, quasiparticle lifetimes of mono- and randomly stacked graphene films are obtained for the probe photon energies continuously from 1.9 to 2.3 eV. Dependence of quasiparticle decay rate on the probe energy is linear for 10-layer stacked graphene films. This is due to the dominant e-op intervalley scattering and the linear density of states in the probed electronic band. A dimensionless coupling constant W is derived, which characterizes the scattering strength of quasiparticles by lattice points in graphene.

Interactive effects of temperature, pH, and water activity on the growth kinetics of Shiga toxin-producing Escherichia coli O104:H4 3.

PubMed

Juneja, Vijay K; Mukhopadhyay, Sudarsan; Ukuku, Dike; Hwang, Cheng-An; Wu, Vivian C H; Thippareddi, Harshavardhan

2014-05-01

The risk of non-O157 Shiga toxin-producing Escherichia coli strains has become a growing public health concern. Several studies characterized the behavior of E. coli O157:H7; however, no reports on the influence of multiple factors on E. coli O104:H4 are available. This study examined the effects and interactions of temperature (7 to 46°C), pH (4.5 to 8.5), and water activity (aw ; 0.95 to 0.99) on the growth kinetics of E. coli O104:H4 and developed predictive models to estimate its growth potential in foods. Growth kinetics studies for each of the 23 variable combinations from a central composite design were performed. Growth data were used to obtain the lag phase duration (LPD), exponential growth rate, generation time, and maximum population density (MPD). These growth parameters as a function of temperature, pH, and aw as controlling factors were analyzed to generate second-order response surface models. The results indicate that the observed MPD was dependent on the pH, aw, and temperature of the growth medium. Increasing temperature resulted in a concomitant decrease in LPD. Regression analysis suggests that temperature, pH, and aw significantly affect the LPD, exponential growth rate, generation time, and MPD of E. coli O104:H4. A comparison between the observed values and those of E. coli O157:H7 predictions obtained by using the U. S. Department of Agriculture Pathogen Modeling Program indicated that E. coli O104:H4 grows faster than E. coli O157:H7. The developed models were validated with alfalfa and broccoli sprouts. These models will provide risk assessors and food safety managers a rapid means of estimating the likelihood that the pathogen, if present, would grow in response to the interaction of the three variables assessed.

Analysis of the 22-NBD-cholesterol transfer between liposome membranes and its relation to the intermembrane exchange of 25-hydroxycholesterol.

PubMed

Ishii, Haruyuki; Shimanouchi, Toshinori; Umakoshi, Hiroshi; Walde, Peter; Kuboi, Ryoichi

2010-05-01

The transfer of 22-NBD-cholesterol (22-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-23,24-bisnor-5-cholen-3-ol) between two liposome membranes was quantitatively analyzed by using the fluorescence resonance energy transfer (FRET) method. Liposomes labeled with both 22-NBD-cholesterol and a rhodamine-labeled phosphatidylethanolamine (Rh-DHPE) were used as donor liposomes, and the 22-NBD-cholesterol transfer from these donor liposomes to acceptor liposomes prepared from same type of phosphatidylcholine was monitored. The transfer kinetics was found to be composed of a fast and a slow phase, and all kinetic measurements could be fitted with a bi-exponential model. The results obtained indicate that the 22-NBD-cholesterol transfer kinetics between liposome membranes depends on the fluidity of the liposome used and that the curvature may affect the kinetics. Furthermore, the behavior of 22-NBD-cholesterol in lipid membrane is similar to that of the oxysterol 25-hydroxycholesterol rather than cholesterol. It is proposed that 22-NBD-cholesterol can be a useful fluorescent probe to mimic the intermembrane transfer of oxidized cholesterols like 25-hydroxycholesterol, rather than that of cholesterol itself. 2010 Elsevier B.V. All rights reserved.

Optimal back-extrapolation method for estimating plasma volume in humans using the indocyanine green dilution method.

PubMed

Polidori, David; Rowley, Clarence

2014-07-22

The indocyanine green dilution method is one of the methods available to estimate plasma volume, although some researchers have questioned the accuracy of this method. We developed a new, physiologically based mathematical model of indocyanine green kinetics that more accurately represents indocyanine green kinetics during the first few minutes postinjection than what is assumed when using the traditional mono-exponential back-extrapolation method. The mathematical model is used to develop an optimal back-extrapolation method for estimating plasma volume based on simulated indocyanine green kinetics obtained from the physiological model. Results from a clinical study using the indocyanine green dilution method in 36 subjects with type 2 diabetes indicate that the estimated plasma volumes are considerably lower when using the traditional back-extrapolation method than when using the proposed back-extrapolation method (mean (standard deviation) plasma volume = 26.8 (5.4) mL/kg for the traditional method vs 35.1 (7.0) mL/kg for the proposed method). The results obtained using the proposed method are more consistent with previously reported plasma volume values. Based on the more physiological representation of indocyanine green kinetics and greater consistency with previously reported plasma volume values, the new back-extrapolation method is proposed for use when estimating plasma volume using the indocyanine green dilution method.

Involvement of α-, γ- and δ-Tocopherol Isomers from
Pumpkin (Cucurbita pepo L.) Seed Oil or Oil Mixtures in
the Biphasic DPPH˙ Disappearance Kinetics

PubMed Central

Broznić, Dalibor; Milin, Čedomila

2016-01-01

Summary The antioxidant activity of three types of pumpkin seed oil or oil mixtures (cold- -pressed, produced from roasted seed paste and salad) produced in the northern part of Croatia and the kinetics of their behaviour as free radical scavengers were investigated using DPPH˙. In addition, the involvement of oil tocopherol isomers (α-, γ- and δ-) in different steps of DPPH˙ disappearance and their impact on the rate of reaction were analysed. The kinetics of DPPH˙ disappearance is a two-step process. In the first step, rapid disappearance of DPPH˙ occurs during the first 11 min of the reaction, depending on the oil type, followed by a slower decline in the second step. To describe DPPH˙ disappearance kinetics, six mathematical models (mono- and biphasic) were tested. Our findings showed that γ- and δ-tocopherols affected DPPH˙ disappearance during the first step, and α-tocopherol in the second step of the reaction. Moreover, α-tocopherol demonstrated 30 times higher antioxidant activity than γ- and δ-tocopherols. The results indicated the biphasic double-exponential behaviour of DPPH˙ disappearance in oil samples, due to the complexity of reactions that involve different tocopherol isomers and proceed through different chemical pathways. PMID:27904410

Involvement of α-, γ- and δ-Tocopherol Isomers from
Pumpkin (Cucurbita pepo L.) Seed Oil or Oil Mixtures in
the Biphasic DPPH˙ Disappearance Kinetics.

PubMed

Broznić, Dalibor; Jurešić, Gordana Čanadi; Milin, Čedomila

2016-06-01

The antioxidant activity of three types of pumpkin seed oil or oil mixtures (cold- -pressed, produced from roasted seed paste and salad) produced in the northern part of Croatia and the kinetics of their behaviour as free radical scavengers were investigated using DPPH˙. In addition, the involvement of oil tocopherol isomers (α-, γ- and δ-) in different steps of DPPH˙ disappearance and their impact on the rate of reaction were analysed. The kinetics of DPPH˙ disappearance is a two-step process. In the first step, rapid disappearance of DPPH˙ occurs during the first 11 min of the reaction, depending on the oil type, followed by a slower decline in the second step. To describe DPPH˙ disappearance kinetics, six mathematical models (mono- and biphasic) were tested. Our findings showed that γ- and δ-tocopherols affected DPPH˙ disappearance during the first step, and α-tocopherol in the second step of the reaction. Moreover, α-tocopherol demonstrated 30 times higher antioxidant activity than γ- and δ-tocopherols. The results indicated the biphasic double-exponential behaviour of DPPH˙ disappearance in oil samples, due to the complexity of reactions that involve different tocopherol isomers and proceed through different chemical pathways.

Wealth distribution, Pareto law, and stretched exponential decay of money: Computer simulations analysis of agent-based models

NASA Astrophysics Data System (ADS)

Aydiner, Ekrem; Cherstvy, Andrey G.; Metzler, Ralf

2018-01-01

We study by Monte Carlo simulations a kinetic exchange trading model for both fixed and distributed saving propensities of the agents and rationalize the person and wealth distributions. We show that the newly introduced wealth distribution - that may be more amenable in certain situations - features a different power-law exponent, particularly for distributed saving propensities of the agents. For open agent-based systems, we analyze the person and wealth distributions and find that the presence of trap agents alters their amplitude, leaving however the scaling exponents nearly unaffected. For an open system, we show that the total wealth - for different trap agent densities and saving propensities of the agents - decreases in time according to the classical Kohlrausch-Williams-Watts stretched exponential law. Interestingly, this decay does not depend on the trap agent density, but rather on saving propensities. The system relaxation for fixed and distributed saving schemes are found to be different.

Photo-dynamics of roseoflavin and riboflavin in aqueous and organic solvents

NASA Astrophysics Data System (ADS)

Zirak, P.; Penzkofer, A.; Mathes, T.; Hegemann, P.

2009-03-01

Roseoflavin (8-dimethylamino-8-demethyl- D-riboflavin) and riboflavin in aqueous and organic solvents are studied by optical absorption spectroscopy, fluorescence spectroscopy, and fluorescence decay kinetics. Solvent polarity dependent absorption shifts are observed. The fluorescence quantum yields are solvent dependent. For roseoflavin the fluorescence decay shows a bi-exponential dependence (ps to sub-ps time constant, and 100 ps to a few ns time constant). The roseoflavin photo-dynamics is explained in terms of fast intra-molecular charge transfer (diabatic electron transfer) from the dimethylamino electron donor group to the pteridin carbonyl electron acceptor followed by intra-molecular charge recombination. The fast fluorescence component is due to direct locally-excited-state emission, and the slow fluorescence component is due to delayed locally-excited-state emission and charge transfer state emission. The fluorescence decay of riboflavin is mono-exponential. The S 1-state potential energy surface is determined by vibronic relaxation and solvation dynamics due to excited-state dipole moment changes (adiabatic optical electron transfer).

Flash spectroscopy of purple membrane.

PubMed Central

Xie, A H; Nagle, J F; Lozier, R H

1987-01-01

Flash spectroscopy data were obtained for purple membrane fragments at pH 5, 7, and 9 for seven temperatures from 5 degrees to 35 degrees C, at the magic angle for actinic versus measuring beam polarizations, at fifteen wavelengths from 380 to 700 nm, and for about five decades of time from 1 microsecond to completion of the photocycle. Signal-to-noise ratios are as high as 500. Systematic errors involving beam geometries, light scattering, absorption flattening, photoselection, temperature fluctuations, partial dark adaptation of the sample, unwanted actinic effects, and cooperativity were eliminated, compensated for, or are shown to be irrelevant for the conclusions. Using nonlinear least squares techniques, all data at one temperature and one pH were fitted to sums of exponential decays, which is the form required if the system obeys conventional first-order kinetics. The rate constants obtained have well behaved Arrhenius plots. Analysis of the residual errors of the fitting shows that seven exponentials are required to fit the data to the accuracy of the noise level. PMID:3580488

Flash spectroscopy of purple membrane.

PubMed

Xie, A H; Nagle, J F; Lozier, R H

1987-04-01

Flash spectroscopy data were obtained for purple membrane fragments at pH 5, 7, and 9 for seven temperatures from 5 degrees to 35 degrees C, at the magic angle for actinic versus measuring beam polarizations, at fifteen wavelengths from 380 to 700 nm, and for about five decades of time from 1 microsecond to completion of the photocycle. Signal-to-noise ratios are as high as 500. Systematic errors involving beam geometries, light scattering, absorption flattening, photoselection, temperature fluctuations, partial dark adaptation of the sample, unwanted actinic effects, and cooperativity were eliminated, compensated for, or are shown to be irrelevant for the conclusions. Using nonlinear least squares techniques, all data at one temperature and one pH were fitted to sums of exponential decays, which is the form required if the system obeys conventional first-order kinetics. The rate constants obtained have well behaved Arrhenius plots. Analysis of the residual errors of the fitting shows that seven exponentials are required to fit the data to the accuracy of the noise level.

Deterministic Models of Inhalational Anthrax in New Zealand White Rabbits

PubMed Central

2014-01-01

Computational models describing bacterial kinetics were developed for inhalational anthrax in New Zealand white (NZW) rabbits following inhalation of Ames strain B. anthracis. The data used to parameterize the models included bacterial numbers in the airways, lung tissue, draining lymph nodes, and blood. Initial bacterial numbers were deposited spore dose. The first model was a single exponential ordinary differential equation (ODE) with 3 rate parameters that described mucociliated (physical) clearance, immune clearance (bacterial killing), and bacterial growth. At 36 hours postexposure, the ODE model predicted 1.7×107 bacteria in the rabbit, which agreed well with data from actual experiments (4.0×107 bacteria at 36 hours). Next, building on the single ODE model, a physiological-based biokinetic (PBBK) compartmentalized model was developed in which 1 physiological compartment was the lumen of the airways and the other was the rabbit body (lung tissue, lymph nodes, blood). The 2 compartments were connected with a parameter describing transport of bacteria from the airways into the body. The PBBK model predicted 4.9×107 bacteria in the body at 36 hours, and by 45 hours the model showed all clearance mechanisms were saturated, suggesting the rabbit would quickly succumb to the infection. As with the ODE model, the PBBK model results agreed well with laboratory observations. These data are discussed along with the need for and potential application of the models in risk assessment, drug development, and as a general aid to the experimentalist studying inhalational anthrax. PMID:24527843

Ligation with Nucleic Acid Sequence–Based Amplification

PubMed Central

Ong, Carmichael; Tai, Warren; Sarma, Aartik; Opal, Steven M.; Artenstein, Andrew W.; Tripathi, Anubhav

2012-01-01

This work presents a novel method for detecting nucleic acid targets using a ligation step along with an isothermal, exponential amplification step. We use an engineered ssDNA with two variable regions on the ends, allowing us to design the probe for optimal reaction kinetics and primer binding. This two-part probe is ligated by T4 DNA Ligase only when both parts bind adjacently to the target. The assay demonstrates that the expected 72-nt RNA product appears only when the synthetic target, T4 ligase, and both probe fragments are present during the ligation step. An extraneous 38-nt RNA product also appears due to linear amplification of unligated probe (P3), but its presence does not cause a false-positive result. In addition, 40 mmol/L KCl in the final amplification mix was found to be optimal. It was also found that increasing P5 in excess of P3 helped with ligation and reduced the extraneous 38-nt RNA product. The assay was also tested with a single nucleotide polymorphism target, changing one base at the ligation site. The assay was able to yield a negative signal despite only a single-base change. Finally, using P3 and P5 with longer binding sites results in increased overall sensitivity of the reaction, showing that increasing ligation efficiency can improve the assay overall. We believe that this method can be used effectively for a number of diagnostic assays. PMID:22449695

Verification of the exponential model of body temperature decrease after death in pigs.

PubMed

Kaliszan, Michal; Hauser, Roman; Kaliszan, Roman; Wiczling, Paweł; Buczyñski, Janusz; Penkowski, Michal

2005-09-01

The authors have conducted a systematic study in pigs to verify the models of post-mortem body temperature decrease currently employed in forensic medicine. Twenty-four hour automatic temperature recordings were performed in four body sites starting 1.25 h after pig killing in an industrial slaughterhouse under typical environmental conditions (19.5-22.5 degrees C). The animals had been randomly selected under a regular manufacturing process. The temperature decrease time plots drawn starting 75 min after death for the eyeball, the orbit soft tissues, the rectum and muscle tissue were found to fit the single-exponential thermodynamic model originally proposed by H. Rainy in 1868. In view of the actual intersubject variability, the addition of a second exponential term to the model was demonstrated to be statistically insignificant. Therefore, the two-exponential model for death time estimation frequently recommended in the forensic medicine literature, even if theoretically substantiated for individual test cases, provides no advantage as regards the reliability of estimation in an actual case. The improvement of the precision of time of death estimation by the reconstruction of an individual curve on the basis of two dead body temperature measurements taken 1 h apart or taken continuously for a longer time (about 4 h), has also been proved incorrect. It was demonstrated that the reported increase of precision of time of death estimation due to use of a multiexponential model, with individual exponential terms to account for the cooling rate of the specific body sites separately, is artifactual. The results of this study support the use of the eyeball and/or the orbit soft tissues as temperature measuring sites at times shortly after death. A single-exponential model applied to the eyeball cooling has been shown to provide a very precise estimation of the time of death up to approximately 13 h after death. For the period thereafter, a better estimation of the time of death is obtained from temperature data collected from the muscles or the rectum.

Single Session Web-Based Counselling: A Thematic Analysis of Content from the Perspective of the Client

ERIC Educational Resources Information Center

Rodda, S. N.; Lubman, D. I.; Cheetham, A.; Dowling, N. A.; Jackson, A. C.

2015-01-01

Despite the exponential growth of non-appointment-based web counselling, there is limited information on what happens in a single session intervention. This exploratory study, involving a thematic analysis of 85 counselling transcripts of people seeking help for problem gambling, aimed to describe the presentation and content of online…

Statistical inference in single molecule measurements of protein adsorption

NASA Astrophysics Data System (ADS)

Armstrong, Megan J.; Tsitkov, Stanislav; Hess, Henry

2018-02-01

Significant effort has been invested into understanding the dynamics of protein adsorption on surfaces, in particular to predict protein behavior at the specialized surfaces of biomedical technologies like hydrogels, nanoparticles, and biosensors. Recently, the application of fluorescent single molecule imaging to this field has permitted the tracking of individual proteins and their stochastic contribution to the aggregate dynamics of adsorption. However, the interpretation of these results is complicated by (1) the finite time available to observe effectively infinite adsorption timescales and (2) the contribution of photobleaching kinetics to adsorption kinetics. Here, we perform a protein adsorption simulation to introduce specific survival analysis methods that overcome the first complication. Additionally, we collect single molecule residence time data from the adsorption of fibrinogen to glass and use survival analysis to distinguish photobleaching kinetics from protein adsorption kinetics.

Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions

NASA Astrophysics Data System (ADS)

Oliveira, Luiz F. L.; Fu, Christopher D.; Pfaendtner, Jim

2018-04-01

Infrequent metadynamics uses biased simulations to estimate the unbiased kinetics of a system, facilitating the calculation of rates and barriers. Here the method is applied to study intramolecular hydrogen transfer reactions involving peroxy radicals, a class of reactions that is challenging to model due to the entropic contributions of the formation of ring structures in the transition state. Using the self-consistent charge density-functional based tight-binding (DFTB) method, we applied infrequent metadynamics to the study of four intramolecular H-transfer reactions, demonstrating that the method can qualitatively reproduce these high entropic contributions, as observed in experiments and those predicted by transition state theory modeled by higher levels of theory. We also show that infrequent metadynamics and DFTB are successful in describing the relationship between transition state ring size and kinetic coefficients (e.g., activation energies and the pre-exponential factors).

Effect of composting on the thermal decomposition behavior and kinetic parameters of pig manure-derived solid waste.

PubMed

Dhyani, Vaibhav; Kumar Awasthi, Mukesh; Wang, Quan; Kumar, Jitendra; Ren, Xiuna; Zhao, Junchao; Chen, Hongyu; Wang, Meijing; Bhaskar, Thallada; Zhang, Zengqiang

2018-03-01

In this work, the influence of composting on the thermal decomposition behavior and decomposition kinetics of pig manure-derived solid wastes was analyzed using thermogravimetry. Wheat straw, biochar, zeolite, and wood vinegar were added to pig manure during composting. The composting was done in the 130 L PVC reactors with 100 L effective volume for 50 days. The activation energy of pyrolysis of samples before and after composting was calculated using Friedman's method, while the pre-exponential factor was calculated using Kissinger's equation. It was observed that composting decreased the volatile content of all the samples. The additives when added together in pig manure lead to a reduction in the activation energy of decomposition, advocating the presence of simpler compounds in the compost material in comparison with the complex feedstock. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reaction rates and prediction of thermal instability during aluminum alloy 6061 dissolution

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

McFarlane, J.; DePaoli, D. W.; Mattus, C. H.

Here, chemical kinetics of dissolution of aluminum alloy 6061 was investigated for the processing of Pu-238 for deep space missions. The rate of dissolution was measured by the heat release and appeared to be controlled by the rate of release of Al(OH) 4 – from the metal surface. Rates of reaction were measured from 273 to 365 K, giving an activation energy of 72 ± 13 kJ•(mol Al) –1 and a pre-exponential factor of 5 ± 3 × 10 9 dm 3mol –1min –1. Minor alloying elements did not appear to affect the reaction kinetics. The average heat of dissolutionmore » was –360 ± 70 kJ•(mol NaAlO 2) –1. When extrapolated to an infinitely dilute solution of aluminum, kJ•(mol NaAlO 2) –1.« less

Calculation of spontaneous emission from a V-type three-level atom in photonic crystals using fractional calculus

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

Huang, Chih-Hsien; Hsieh, Wen-Feng; Institute of Electro-Optical Science and Engineering, National Cheng Kung University, 1 Dahsueh Rd., Tainan 701, Taiwan

2011-07-15

Fractional time derivative, an abstract mathematical operator of fractional calculus, is used to describe the real optical system of a V-type three-level atom embedded in a photonic crystal. A fractional kinetic equation governing the dynamics of the spontaneous emission from this optical system is obtained as a fractional Langevin equation. Solving this fractional kinetic equation by fractional calculus leads to the analytical solutions expressed in terms of fractional exponential functions. The accuracy of the obtained solutions is verified through reducing the system into the special cases whose results are consistent with the experimental observation. With accurate physical results and avoidingmore » the complex integration for solving this optical system, we propose fractional calculus with fractional time derivative as a better mathematical method to study spontaneous emission dynamics from the optical system with non-Markovian dynamics.« less

Reaction rates and prediction of thermal instability during aluminum alloy 6061 dissolution

DOE PAGES

McFarlane, J.; DePaoli, D. W.; Mattus, C. H.

2017-11-10

Here, chemical kinetics of dissolution of aluminum alloy 6061 was investigated for the processing of Pu-238 for deep space missions. The rate of dissolution was measured by the heat release and appeared to be controlled by the rate of release of Al(OH) 4 – from the metal surface. Rates of reaction were measured from 273 to 365 K, giving an activation energy of 72 ± 13 kJ•(mol Al) –1 and a pre-exponential factor of 5 ± 3 × 10 9 dm 3mol –1min –1. Minor alloying elements did not appear to affect the reaction kinetics. The average heat of dissolutionmore » was –360 ± 70 kJ•(mol NaAlO 2) –1. When extrapolated to an infinitely dilute solution of aluminum, kJ•(mol NaAlO 2) –1.« less

Chemical Dosing and First-Order Kinetics

ERIC Educational Resources Information Center

Hladky, Paul W.

2011-01-01

College students encounter a variety of first-order phenomena in their mathematics and science courses. Introductory chemistry textbooks that discuss first-order processes, usually in conjunction with chemical kinetics or radioactive decay, stop at single, discrete dose events. Although single-dose situations are important, multiple-dose events,…

Microsecond kinetics in model single- and double-stranded amylose polymers.

PubMed

Sattelle, Benedict M; Almond, Andrew

2014-05-07

Amylose, a component of starch with increasing biotechnological significance, is a linear glucose polysaccharide that self-organizes into single- and double-helical assemblies. Starch granule packing, gelation and inclusion-complex formation result from finely balanced macromolecular kinetics that have eluded precise experimental quantification. Here, graphics processing unit (GPU) accelerated multi-microsecond aqueous simulations are employed to explore conformational kinetics in model single- and double-stranded amylose. The all-atom dynamics concur with prior X-ray and NMR data while surprising and previously overlooked microsecond helix-coil, glycosidic linkage and pyranose ring exchange are hypothesized. In a dodecasaccharide, single-helical collapse was correlated with linkages and rings transitioning from their expected syn and (4)C1 chair conformers. The associated microsecond exchange rates were dependent on proximity to the termini and chain length (comparing hexa- and trisaccharides), while kinetic features of dodecasaccharide linkage and ring flexing are proposed to be a good model for polymers. Similar length double-helices were stable on microsecond timescales but the parallel configuration was sturdier than the antiparallel equivalent. In both, tertiary organization restricted local chain dynamics, implying that simulations of single amylose strands cannot be extrapolated to dimers. Unbiased multi-microsecond simulations of amylose are proposed as a valuable route to probing macromolecular kinetics in water, assessing the impact of chemical modifications on helical stability and accelerating the development of new biotechnologies.

Structure determination and optical properties of CsSm(PO{sub 3}){sub 4}

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

Ben Hassen, N.; Ferhi, M., E-mail: ferhi.mounir@gmail.com; Horchani-Naifer, K.

2015-03-15

Graphical abstract: Projection of the CsSm(PO{sub 3}){sub 4} structure viewing along the a axis. - Highlights: • Single crystal of a new polyphosphate CsSm(PO{sub 3}){sub 4} has been synthesized. • The obtained compound has been characterized by several techniques. • The crystal structure of CsSm(PO{sub 3}){sub 4} has been resolved. • Spectroscopic properties of Sm{sup 3+} in CsSm(PO{sub 3}){sub 4} have been performed. - Abstract: A new alkali metal-rare earth polyphosphate CsSm(PO{sub 3}){sub 4} has been synthesized by flux method. The obtained compound has been characterized by means of single crystal X-ray diffraction, Fourier transform infrared (FTIR) and Raman scatteringmore » spectroscopies. It crystallizes in the monoclinic space group P2{sub 1}/n with the following unit-cell parameters: a = 10.382(2), b = 8.978(6), c = 11.205(4) Å, β = 106.398(3)° and Z = 4. The structure of CsSm(PO{sub 3}){sub 4} is an infinite three-dimensional framework made up of double spiral (PO{sub 3}){sub n} chains linked with neighboring SmO{sub 8} and CsO{sub 11} polyhedra. Spectroscopic properties of Sm{sup 3+} in this new compound including excitation, emission, and kinetic measurement have been performed. The emission spectrum shows four transitions characteristics of Sm{sup 3+} in the orange–red region by excitation wavelength at 400 nm. The decay time curve of {sup 4}G{sub 5/2} → {sup 6}H{sub 7/2} transition has been also registered and fitted to a single exponential function.« less

Influence of Natural Organic Matter on Attachment Kinetics of Salmonella Typhimurium

NASA Astrophysics Data System (ADS)

Chowdhury, I.; Zorlu, O.; Hill, J. E.; Walker, S. L.

2011-12-01

Salmonella enterica serovar Typhimurium is one of the most common and virulent bacterial pathogens, usually found in food and water. This waterborne pathogen has been attributed to causing gastroenteritis and typhoid fever, leading to 16 million cases and over half a million deaths worldwide each year. Natural organic matter (NOM) is ubiquitous in environment and previous work has shown NOM to enhance the stability and transport of bacteria cells; hence NOM will certainly interact with Salmonella and affect its transport in environment. The objective of this study was to investigate the influence of NOM (Suwannee River humic acid standard II, SRHA) on the attachment kinetics of a model Salmonella (Salmonella enterica serovar Typhimurium SA5983) to glass. The transport study was conducted in a parallel plate flow chamber using fluorescent microscope to visualize the bacterial cells, which were tagged with green fluorescent protein (GFP). The solution pH was unadjusted, and the flow rate through parallel plate channel was 0.1 mL/min to simulate groundwater conditions. Parameters varied in this study were NOM presence, ion valence (K+, Ca2+) as well as cell growth phase (mid-exponential and late-exponential growth phases). These parameters were chosen because ion valence may alter the NOM conformation and capacity for bridging, as well growth phase impacts the cellular surface chemistry. Extensive characterization of the bacterial cells was conducted including measurements of electrophoretic mobility, hydrophobicity, acidity, surface charge density and extracellular polymeric substance content. Additionally, electrokintic characterization was conducted for the glass. Preliminary results demonstrated the sensitivity of cell attachment to ionic valence and cell growth phase. Also the addition of NOM reduced the attachment of the Salmonella cells significantly under all of these conditions. Without NOM, attachment efficiencies (α) in KCl were similar at both growth phases; however, in the presence of the divalent ion, α decreased as the cells aged. In presence of NOM and KCl, α was significantly lower at late exponential phase than mid exponential phase; whereas, the opposite was observed with divalent ions. These trends indicate the complex role of NOM, which is coupled with ion valence and growth phase, in the transport of Salmonella. Detailed results will be presented along with proposed mechanisms involved in the interactions between Salmonella and NOM. These mechanisms highlight the role this important naturally occurring macromolecule plays in the fate of Salmonella. This understanding will improve our ability to predict the behavior of this pathogen in environmentally relevant conditions.

Kinetics and components of the flash photocurrent of isolated retinal rods of the larval salamander, Ambystoma tigrinum.

PubMed Central

Cobbs, W H; Pugh, E N

1987-01-01

1. Membrane currents initiated by intense, 20 microseconds flashes (photocurrents) were recorded from isolated salamander rods by combined extracellular suction electrodes and intracellular tight-seal electrodes either in current or voltage clamp mode. The magnitudes (mean +/- 2 S.E.M.) of the maximal photoresponses recorded by the suction and by the intracellular electrode respectively were 40 +/- 5 pA (n = 18) and 35 +/- 7 mV (n = 8) for current clamp at zero current; 43 +/- 9 pA and 66 +/- 13 (n = 11) pA for voltage clamp at the zero-current holding potential, -24 +/- 3 mV. 2. Photocurrents initiated by flashes isomerizing 0.1% or more of the outer segment's rhodopsin achieved a saturated velocity and were 95% complete in less than 50 ms. The effect of incrementing flash intensity above 0.1% isomerization can be described as a translation of the photocurrent along the time axis towards the origin. Within the interval 0-50 ms the latter two-thirds of the velocity-saturated photocurrent is well described as a single-exponential decay. The decay was much faster in voltage clamp (2.8 +/- 1.2 ms, n = 11) than in current clamp mode (17 +/- 5 ms, n = 17). 3. The initial third of the velocity-saturated photocurrent, occurring over the interval from the flash to the onset of exponential decay, followed about the same time course in current and voltage clamp. The time interval occupied by this initial 'latent' phase decreased with increasing flash intensity and attained an apparent minimum of about 7 ms in response to flashes isomerizing 10% or more of the rhodopsin at ca. 22 degrees C. 4. The hypothesis that the decay of outer segment light-sensitive membrane current is the same in current and voltage clamp was supported by an analysis of the difference between outer segment currents measured successively in the two recording modes. First, the tail of the difference current decayed exponentially with a time constant approximately equal to R x C, where R and C are independently estimated slope resistance and capacitance of the rod. Secondly, the integral of the difference current, when divided by outer segment capacitance, closely approximated the hyperpolarizing light response measured under current clamp. Thus, displacement current accounted for the difference between photocurrents measured in current and voltage clamp.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:2832596

Enantioselective Total Synthesis of Natural Isoflavans: Asymmetric Transfer Hydrogenation/Deoxygenation of Isoflavanones with Dynamic Kinetic Resolution.

PubMed

Keßberg, Anton; Lübken, Tilo; Metz, Peter

2018-05-02

A concise and highly enantioselective synthesis of structurally diverse isoflavans from a single chromone is described. The key transformation is a single-step conversion of racemic isoflavanones into virtually enantiopure isoflavans by domino asymmetric transfer hydrogenation/deoxygenation with dynamic kinetic resolution.

Exact simulation of integrate-and-fire models with exponential currents.

PubMed

Brette, Romain

2007-10-01

Neural networks can be simulated exactly using event-driven strategies, in which the algorithm advances directly from one spike to the next spike. It applies to neuron models for which we have (1) an explicit expression for the evolution of the state variables between spikes and (2) an explicit test on the state variables that predicts whether and when a spike will be emitted. In a previous work, we proposed a method that allows exact simulation of an integrate-and-fire model with exponential conductances, with the constraint of a single synaptic time constant. In this note, we propose a method, based on polynomial root finding, that applies to integrate-and-fire models with exponential currents, with possibly many different synaptic time constants. Models can include biexponential synaptic currents and spike-triggered adaptation currents.

Confirmation of Monod Model for Biofiltration of Styrene Vapors from Waste Flue Gas

PubMed Central

Dehghanzadeh, Reza; Roshani, Babak; Asadi, Mahzar; Fahiminia, Mohammad; AslHashemi, Ahmad

2012-01-01

Background: The objective of this research was to investigate the kinetic behavior of the biofil¬tration process for the removal of styrene. Methods: A three stage compost based biofilter was inoculated with thickened activated sludge. The reaction order rate constants were obtained from continuous experiments and used as the specific growth rate for the Monod equation. Results: The measured concentration profiles show a linear dependence on the bed height in the biofilter at higher loadings, such as 75 and 45 g m-3 h-1. This is the condition of reaction limitation for a reaction with zero-order kinetics. From the experimental data, maximum elimination capac¬ity (ECmax) was estimated to be 44, 40 and 26 g m-3 h-1 at empty bed retention times (EBRTs) of 120, 60 and 30 s, respectively. However, at lower loadings, the measured concentration profile of the biofilter is one of exponential increase, which is the condition of both reaction and diffusion limitations for a reaction with zero-order kinetics. Maximum elimination capacities found from the experimental results were the same as Monod model predictions. Both the experimental re¬sults and the model predictions showed the influence of EBRT on the removal rate of styrene, particularly for the highest loading rate. Conclusion: In terms of the practical applications of the proposed models have the advantage of being simpler than Monod kinetics and Monod kinetics requires a numerical solution. PMID:24688940

Electrochemical oxidation of COD from real textile wastewaters: Kinetic study and energy consumption.

PubMed

Zou, Jiaxiu; Peng, Xiaolan; Li, Miao; Xiong, Ying; Wang, Bing; Dong, Faqin; Wang, Bin

2017-03-01

In the present study, the electrochemical oxidation of real wastewaters discharged by textile industry was carried out using a boron-doped diamond (BDD) anode. The effect of operational variables, such as applied current density (20-100 mA·cm -2 ), NaCl concentration added to the real wastewaters (0-3 g·L -1 ), and pH value (2.0-10.0), on the kinetics of COD oxidation and on the energy consumption was carefully investigated. The obtained experimental results could be well matched with a proposed kinetic model, in which the indirect oxidation mediated by electrogenerated strong oxidants would be described through a pseudo-first-order kinetic constant k. Values of k exhibited a linear increase with increasing applied current density and decreasing pH value, and an exponential increase with NaCl concentration. Furthermore, high oxidation kinetics resulted in low specific energy consumption, but this conclusion was not suitable to the results obtained under different applied current density. Under the optimum operational conditions, it only took 3 h to complete remove the COD in the real textile wastewaters and the specific energy consumption could be as low as 11.12 kWh·kg -1  COD. The obtained results, low energy consumption and short electrolysis time, allowed to conclude that the electrochemical oxidation based on BDD anodes would have practical industrial application for the treatment of real textile wastewater. Copyright © 2016 Elsevier Ltd. All rights reserved.

Uptake, transfer and elimination kinetics of paralytic shellfish toxins in common octopus (Octopus vulgaris).

PubMed

Lopes, Vanessa M; Baptista, Miguel; Repolho, Tiago; Rosa, Rui; Costa, Pedro Reis

2014-01-01

Marine phycotoxins derived from harmful algal blooms are known to be associated with mass mortalities in the higher trophic levels of marine food webs. Bivalve mollusks and planktivorous fish are the most studied vectors of marine phycotoxins. However, field surveys recently showed that cephalopod mollusks also constitute potential vectors of toxins. Thus, here we determine, for the first time, the time course of accumulation and depuration of paralytic shellfish toxins (PSTs) in the common octopus (Octopus vulgaris). Concomitantly, the underlying kinetics of toxin transfer between tissue compartments was also calculated. Naturally contaminated clams were used to orally expose the octopus to PSTs during 6 days. Afterwards, octopus specimens were fed with non-contaminated shellfish during 10 days of depuration period. Toxins reached the highest concentrations in the digestive gland surpassing the levels in the kidney by three orders of magnitude. PSTs were not detected in any other tissue analyzed. Net accumulation efficiencies of 42% for GTX5, 36% for dcSTX and 23% for C1+2 were calculated for the digestive gland. These compounds were the most abundant toxins in both digestive gland and the contaminated shellfish diet. The small differences in relative abundance of each toxin observed between the prey and the cephalopod predator indicates low conversion rates of these toxins. The depuration period was better described using an exponential decay model comprising a single compartment - the entire viscera. It is worth noting that since octopuses' excretion and depuration rates are low, the digestive gland is able to accumulate very high toxin concentrations for long periods of time. Therefore, the present study clearly shows that O. vulgaris is a high-potential vector of PSTs during and even after the occurrence of these toxic algal blooms. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of the Kv channels of mouse carotid body chemoreceptor cells and their role in oxygen sensing

PubMed Central

Pérez-García, M Teresa; Colinas, Olaia; Miguel-Velado, Eduardo; Moreno-Domínguez, Alejandro; López-López, José Ramón

2004-01-01

As there are wide interspecies variations in the molecular nature of the O2-sensitive Kv channels in arterial chemoreceptors, we have characterized the expression of these channels and their hypoxic sensitivity in the mouse carotid body (CB). CB chemoreceptor cells were obtained from a transgenic mouse expressing green fluorescent protein (GFP) under the control of tyrosine hydroxylase (TH) promoter. Immunocytochemical identification of TH in CB cell cultures reveals a good match with GFP-positive cells. Furthermore, these cells show an increase in [Ca2+]i in response to low PO2, demonstrating their ability to engender a physiological response. Whole-cell experiments demonstrated slow-inactivating K+ currents with activation threshold around −30 mV and a bi-exponential kinetic of deactivation (τ of 6.24 ± 0.52 and 32.85 ± 4.14 ms). TEA sensitivity of the currents identified also two different components (IC50 of 17.8 ± 2.8 and 940.0 ± 14.7 μm). Current amplitude decreased reversibly in response to hypoxia, which selectively affected the fast deactivating component. Hypoxic inhibition was also abolished in the presence of low (10–50 μm) concentrations of TEA, suggesting that O2 interacts with the component of the current most sensitive to TEA. The kinetic and pharmacological profile of the currents suggested the presence of Kv2 and Kv3 channels as their molecular correlates, and we have identified several members of these two subfamilies by single-cell PCR and immunocytochemistry. This report represents the first functional and molecular characterization of Kv channels in mouse CB chemoreceptor cells, and strongly suggests that O2-sensitive Kv channels in this preparation belong to the Kv3 subfamily. PMID:15034123

Investigation of RNA Hairpin Loop Folding with Time-Resolved Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Stancik, Aaron Lee

Ribonucleic acids (RNAs) are a group of functional biopolymers central to the molecular underpinnings of life. To complete the many processes they mediate, RNAs must fold into precise three-dimensional structures. Hairpin loops are the most ubiquitous and basic structural elements present in all folded RNAs, and are the foundation upon which all complex tertiary structures are built. A hairpin loop forms when a single stranded RNA molecule folds back on itself creating a helical stem of paired bases capped by a loop. This work investigates the formation of UNCG hairpin loops with the sequence 5'-GC(UNCG)GC-3' (N = A, U, G, or C) using both equilibrium infrared (IR) and time-resolved IR spectroscopy. Equilibrium IR melting data were used to determine thermodynamic parameters. Melting temperatures ranged from 50 to 60°C, and enthalpies of unfolding were on the order of 100 kJ/mol. In the time-resolved work, temperature jumps of up to 20°C at 2.5°C increments were obtained with transient relaxation kinetics spanning nanoseconds to hundreds of microseconds. The relaxation kinetics for all of the oligomers studied were fit to first or second order exponentials. Multiple vibrational transitions were probed on each oligomer for fully folded and partially denatured structures. In the time-resolved limit, in contrast to equilibrium melting, RNA does not fold according to two-state behavior. These results are some of the first to show that RNA hairpins fold according to a rugged energy landscape, which contradicts their relatively simple nature. In addition, this work has proven that time-resolved IR spectroscopy is a powerful and novel tool for investigating the earliest events of RNA folding, the formation of the hairpin loop.

Kinetics of the iodine- and bromine-mediated transport of halide ions: demonstration of an interfacial complexation mechanism.

PubMed Central

Klotz, K H; Benz, R

1993-01-01

Stationary and kinetic experiments were performed on lipid bilayer membranes to study the mechanism of iodine- and bromine-mediated halide transport in detail. The stationary conductance data suggested that four different 1:1 complexes between I2 and Br2 and the halides I- and Br- were responsible for the observed conductance increase by iodine and bromine (I3-, I2Br-, Br2I-, and Br3-). Charge pulse experiments allowed the further elucidation of the transport mechanism. Only two of three exponential voltage relaxations predicted by the Läuger model could be resolved under all experimental conditions. This means that either the heterogeneous complexation reactions kR (association) and kD (dissociation) were too fast to be resolved or that the neutral carriers were always in equilibrium within the membrane. Experiments at different carrier and halide concentrations suggested that the translocation of the neutral carrier is much faster than the other processes involved in carrier-mediated ion transport. The model was modified accordingly. From the charge pulse data at different halide concentrations, the translocation rate constant of the complexed carriers, kAS, the dissociation constant, kD, and the total surface concentration of charged carriers, NAS, could be evaluated from one single charge pulse experiment. The association rate of the complex, kR, could be obtained in some cases from the plot of the stationary conductance data as a function of the halide concentration in the aqueous phase. The translocation rate constant, kAS, of the different complexes is a function of the image force and of the Born charging energy. It increases 5000-fold from Br3- to I3- because of an enlarged ion radius. PMID:8312500

Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

PubMed Central

Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

2012-01-01

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

PubMed

Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

2012-07-03

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

Connecting the dots across time: reconstruction of single-cell signalling trajectories using time-stamped data

NASA Astrophysics Data System (ADS)

Mukherjee, Sayak; Stewart, David; Stewart, William; Lanier, Lewis L.; Das, Jayajit

2017-08-01

Single-cell responses are shaped by the geometry of signalling kinetic trajectories carved in a multidimensional space spanned by signalling protein abundances. It is, however, challenging to assay a large number (more than 3) of signalling species in live-cell imaging, which makes it difficult to probe single-cell signalling kinetic trajectories in large dimensions. Flow and mass cytometry techniques can measure a large number (4 to more than 40) of signalling species but are unable to track single cells. Thus, cytometry experiments provide detailed time-stamped snapshots of single-cell signalling kinetics. Is it possible to use the time-stamped cytometry data to reconstruct single-cell signalling trajectories? Borrowing concepts of conserved and slow variables from non-equilibrium statistical physics we develop an approach to reconstruct signalling trajectories using snapshot data by creating new variables that remain invariant or vary slowly during the signalling kinetics. We apply this approach to reconstruct trajectories using snapshot data obtained from in silico simulations, live-cell imaging measurements, and, synthetic flow cytometry datasets. The application of invariants and slow variables to reconstruct trajectories provides a radically different way to track objects using snapshot data. The approach is likely to have implications for solving matching problems in a wide range of disciplines.

A comparison of modelling techniques used to characterise oxygen uptake kinetics during the on-transient of exercise.

PubMed

Bell, C; Paterson, D H; Kowalchuk, J M; Padilla, J; Cunningham, D A

2001-09-01

We compared estimates for the phase 2 time constant (tau) of oxygen uptake (VO2) during moderate- and heavy-intensity exercise, and the slow component of VO2 during heavy-intensity exercise using previously published exponential models. Estimates for tau and the slow component were different (P < 0.05) among models. For moderate-intensity exercise, a two-component exponential model, or a mono-exponential model fitted from 20 s to 3 min were best. For heavy-intensity exercise, a three-component model fitted throughout the entire 6 min bout of exercise, or a two-component model fitted from 20 s were best. When the time delays for the two- and three-component models were equal the best statistical fit was obtained; however, this model produced an inappropriately low DeltaVO2/DeltaWR (WR, work rate) for the projected phase 2 steady state, and the estimate of phase 2 tau was shortened compared with other models. The slow component was quantified as the difference between VO2 at end-exercise (6 min) and at 3 min (DeltaVO2 (6-3 min)); 259 ml x min(-1)), and also using the phase 3 amplitude terms (truncated to end-exercise) from exponential fits (409-833 ml x min(-1)). Onset of the slow component was identified by the phase 3 time delay parameter as being of delayed onset approximately 2 min (vs. arbitrary 3 min). Using this delay DeltaVO2 (6-2 min) was approximately 400 ml x min(-1). Use of valid consistent methods to estimate tau and the slow component in exercise are needed to advance physiological understanding.

Growth and differentiation of human lens epithelial cells in vitro on matrix

NASA Technical Reports Server (NTRS)

Blakely, E. A.; Bjornstad, K. A.; Chang, P. Y.; McNamara, M. P.; Chang, E.; Aragon, G.; Lin, S. P.; Lui, G.; Polansky, J. R.

2000-01-01

PURPOSE: To characterize the growth and maturation of nonimmortalized human lens epithelial (HLE) cells grown in vitro. METHODS: HLE cells, established from 18-week prenatal lenses, were maintained on bovine corneal endothelial (BCE) extracellular matrix (ECM) in medium supplemented with basic fibroblast growth factor (FGF-2). The identity, growth, and differentiation of the cultures were characterized by karyotyping, cell morphology, and growth kinetics studies, reverse transcription-polymerase chain reaction (RT-PCR), immunofluorescence, and Western blot analysis. RESULTS: HLE cells had a male, human diploid (2N = 46) karyotype. The population-doubling time of exponentially growing cells was 24 hours. After 15 days in culture, cell morphology changed, and lentoid formation was evident. Reverse transcription-polymerase chain reaction (RT-PCR) indicated expression of alphaA- and betaB2-crystallin, fibroblast growth factor receptor 1 (FGFR1), and major intrinsic protein (MIP26) in exponential growth. Western analyses of protein extracts show positive expression of three immunologically distinct classes of crystallin proteins (alphaA-, alphaB-, and betaB2-crystallin) with time in culture. By Western blot analysis, expression of p57(KIP2), a known marker of terminally differentiated fiber cells, was detectable in exponential cultures, and levels increased after confluence. MIP26 and gamma-crystallin protein expression was detected in confluent cultures, by using immunofluorescence, but not in exponentially growing cells. CONCLUSIONS: HLE cells can be maintained for up to 4 months on ECM derived from BCE cells in medium containing FGF-2. With time in culture, the cells demonstrate morphologic characteristics of, and express protein markers for, lens fiber cell differentiation. This in vitro model will be useful for investigations of radiation-induced cataractogenesis and other studies of lens toxicity.

A Long-Lived Oscillatory Space-Time Correlation Function of Two Dimensional Colloids

NASA Astrophysics Data System (ADS)

Kim, Jeongmin; Sung, Bong June

2014-03-01

Diffusion of a colloid in solution has drawn significant attention for a century. A well-known behavior of the colloid is called Brownian motion : the particle displacement probability distribution (PDPD) is Gaussian and the mean-square displacement (MSD) is linear with time. However, recent simulation and experimental studies revealed the heterogeneous dynamics of colloids near glass transitions or in complex environments such as entangled actin, PDPD exhibited the exponential tail at a large length instead of being Gaussian at all length scales. More interestingly, PDPD is still exponential even when MSD was still linear with time. It requires a refreshing insight on the colloidal diffusion in the complex environments. In this work, we study heterogeneous dynamics of two dimensional (2D) colloids using molecular dynamics simulations. Unlike in three dimensions, 2D solids do not follow the Lindemann melting criterion. The Kosterlitz-Thouless-Halperin-Nelson-Young theory predicts two-step phase transitions with an intermediate phase, the hexatic phase between isotropic liquids and solids. Near solid-hexatic transition, PDPD shows interesting oscillatory behavior between a central Gaussian part and an exponential tail. Until 12 times longer than translational relaxation time, the oscillatory behavior still persists even after entering the Fickian regime. We also show that multi-layered kinetic clusters account for heterogeneous dynamics of 2D colloids with the long-lived anomalous oscillatory PDPD.

Kinetic modeling of ion conduction in KcsA potassium channel.

PubMed

Mafé, Salvador; Pellicer, Julio; Cervera, Javier

2005-05-22

KcsA constitutes a potassium channel of known structure that shows both high conduction rates and selectivity among monovalent cations. A kinetic model for ion conduction through this channel that assumes rapid ion transport within the filter has recently been presented by Nelson. In a recent, brief communication, we used the model to provide preliminary explanations to the experimental current-voltage J-V and conductance-concentration g-S curves obtained for a series of monovalent ions (K(+),Tl(+), and Rb(+)). We did not assume rapid ion transport in the calculations, since ion transport within the selectivity filter could be rate limiting for ions other than native K(+). This previous work is now significantly extended to the following experimental problems. First, the outward rectification of the J-V curves in K(+) symmetrical solutions is analyzed using a generalized kinetic model. Second, the J-V and g-S curves for NH(4) (+) are obtained and compared with those of other ions (the NH(4) (+) J-V curve is qualitatively different from those of Rb(+) and Tl(+)). Third, the effects of Na(+) block on K(+) and Rb(+) currents through single KcsA channels are studied and the different blocking behavior is related to the values of the translocation rate constants characteristic of ion transport within the filter. Finally, the significantly decreased K(+) conductance caused by mutation of the wild-type channel is also explained in terms of this rate constant. In order to keep the number of model parameters to a minimum, we do not allow the electrical distance (an empirical parameter of kinetic models that controls the exponential voltage dependence of the dissociation rate) to vary with the ionic species. Without introducing the relatively high number of adjustable parameters of more comprehensive site-based models, we show that ion association to the filter is rate controlling at low concentrations, but ion dissociation from the filter and ion transport within the filter could limit conduction at high concentration. Although some experimental data from other authors were included to allow qualitative comparison with model calculations, the absolute values of the effective rate constants obtained are only tentative. However, the relative changes in these constants needed to explain qualitatively the experiments should be of significance.

Anomalous yet Brownian.

PubMed

Wang, Bo; Anthony, Stephen M; Bae, Sung Chul; Granick, Steve

2009-09-08

We describe experiments using single-particle tracking in which mean-square displacement is simply proportional to time (Fickian), yet the distribution of displacement probability is not Gaussian as should be expected of a classical random walk but, instead, is decidedly exponential for large displacements, the decay length of the exponential being proportional to the square root of time. The first example is when colloidal beads diffuse along linear phospholipid bilayer tubes whose radius is the same as that of the beads. The second is when beads diffuse through entangled F-actin networks, bead radius being less than one-fifth of the actin network mesh size. We explore the relevance to dynamic heterogeneity in trajectory space, which has been extensively discussed regarding glassy systems. Data for the second system might suggest activated diffusion between pores in the entangled F-actin networks, in the same spirit as activated diffusion and exponential tails observed in glassy systems. But the first system shows exceptionally rapid diffusion, nearly as rapid as for identical colloids in free suspension, yet still displaying an exponential probability distribution as in the second system. Thus, although the exponential tail is reminiscent of glassy systems, in fact, these dynamics are exceptionally rapid. We also compare with particle trajectories that are at first subdiffusive but Fickian at the longest measurement times, finding that displacement probability distributions fall onto the same master curve in both regimes. The need is emphasized for experiments, theory, and computer simulation to allow definitive interpretation of this simple and clean exponential probability distribution.

[CoCuMnOx Photocatalyzed Oxidation of Multi-component VOCs and Kinetic Analysis].

PubMed

Meng, Hai-long; Bo, Long-li; Liu, Jia-dong; Gao, Bo; Feng, Qi-qi; Tan, Na; Xie, Shuai

2016-05-15

Solar energy absorption coating CoCuMnOx was prepared by co-precipitation method and applied to photodegrade multi- component VOCs including toluene, ethyl acetate and acetone under visible light irradiation. The photocatalytic oxidation performance of toluene, ethyl acetate and acetone was analyzed and reaction kinetics of VOCs were investigated synchronously. The research indicated that removal rates of single-component toluene, ethyl acetate and acetone were 57%, 62% and 58% respectively under conditions of 400 mg · m⁻³ initial concentration, 120 mm illumination distance, 1 g/350 cm² dosage of CoCuMnOx and 6 h of irradiation time by 100 W tungsten halogen lamp. Due to the competition among different VOCs, removal efficiencies in three-component mixture were reduced by 5%-26% as compared with single VOC. Degradation processes of single-component VOC and three-component VOCs both fitted pseudo first order reaction kinetics, and kinetic constants of toluene, ethyl acetate and acetone were 0.002, 0.002 8 and 0.002 33 min⁻¹ respectively under single-component condition. Reaction rates of VOCs in three-component mixture were 0.49-0.88 times of single components.

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

Cooperativity in Monomeric Enzymes with Single Ligand-Binding Sites

PubMed Central

Porter, Carol M.

2011-01-01

Cooperativity is widespread in biology. It empowers a variety of regulatory mechanisms and impacts both the kinetic and thermodynamic properties of macromolecular systems. Traditionally, cooperativity is viewed as requiring the participation of multiple, spatially distinct binding sites that communicate via ligand-induced structural rearrangements; however, cooperativity requires neither multiple ligand binding events nor multimeric assemblies. An underappreciated manifestation of cooperativity has been observed in the non-Michaelis-Menten kinetic response of certain monomeric enzymes that possess only a single ligand-binding site. In this review, we present an overview of kinetic cooperativity in monomeric enzymes. We discuss the primary mechanisms postulated to give rise to monomeric cooperativity and highlight modern experimental methods that could offer new insights into the nature of this phenomenon. We conclude with an updated list of single subunit enzymes that are suspected of displaying cooperativity, and a discussion of the biological significance of this unique kinetic response. PMID:22137502

Decarboxylation of Δ 9-tetrahydrocannabinol: Kinetics and molecular modeling

NASA Astrophysics Data System (ADS)

Perrotin-Brunel, Helene; Buijs, Wim; van Spronsen, Jaap; van Roosmalen, Maaike J. E.; Peters, Cor J.; Verpoorte, Rob; Witkamp, Geert-Jan

2011-02-01

Efficient tetrahydrocannabinol (Δ 9-THC) production from cannabis is important for its medical application and as basis for the development of production routes of other drugs from plants. This work presents one of the steps of Δ 9-THC production from cannabis plant material, the decarboxylation reaction, transforming the Δ 9-THC-acid naturally present in the plant into the psychoactive Δ 9-THC. Results of experiments showed pseudo-first order reaction kinetics, with an activation barrier of 85 kJ mol -1 and a pre-exponential factor of 3.7 × 10 8 s -1. Using molecular modeling, two options were identified for an acid catalyzed β-keto acid type mechanism for the decarboxylation of Δ 9-THC-acid. Each of these mechanisms might play a role, depending on the actual process conditions. Formic acid proved to be a good model for a catalyst of such a reaction. Also, the computational idea of catalysis by water to catalysis by an acid, put forward by Li and Brill, and Churchev and Belbruno was extended, and a new direct keto-enol route was found. A direct keto-enol mechanism catalyzed by formic acid seems to be the best explanation for the observed activation barrier and the pre-exponential factor of the decarboxylation of Δ 9-THC-acid. Evidence for this was found by performing an extraction experiment with Cannabis Flos. It revealed the presence of short chain carboxylic acids supporting this hypothesis. The presented approach is important for the development of a sustainable production of Δ 9-THC from the plant.

Modeling of thermal degradation kinetics of the C-glucosyl xanthone mangiferin in an aqueous model solution as a function of pH and temperature and protective effect of honeybush extract matrix.

PubMed

Beelders, Theresa; de Beer, Dalene; Kidd, Martin; Joubert, Elizabeth

2018-01-01

Mangiferin, a C-glucosyl xanthone, abundant in mango and honeybush, is increasingly targeted for its bioactive properties and thus to enhance functional properties of food. The thermal degradation kinetics of mangiferin at pH3, 4, 5, 6 and 7 were each modeled at five temperatures ranging between 60 and 140°C. First-order reaction models were fitted to the data using non-linear regression to determine the reaction rate constant at each pH-temperature combination. The reaction rate constant increased with increasing temperature and pH. Comparison of the reaction rate constants at 100°C revealed an exponential relationship between the reaction rate constant and pH. The data for each pH were also modeled with the Arrhenius equation using non-linear and linear regression to determine the activation energy and pre-exponential factor. Activation energies decreased slightly with increasing pH. Finally, a multi-linear model taking into account both temperature and pH was developed for mangiferin degradation. Sterilization (121°C for 4min) of honeybush extracts dissolved at pH4, 5 and 7 did not cause noticeable degradation of mangiferin, although the multi-linear model predicted 34% degradation at pH7. The extract matrix is postulated to exert a protective effect as changes in potential precursor content could not fully explain the stability of mangiferin. Copyright © 2017 Elsevier Ltd. All rights reserved.

Soil erosion-runoff relationships: insights from laboratory studies

NASA Astrophysics Data System (ADS)

Mamedov, Amrakh; Warrington, David; Levy, Guy

2016-04-01

Understanding the processes and mechanisms affecting runoff generation and subsequent soil erosion in semi-arid regions is essential for the development of improved soil and water conservation management practices. Using a drip type laboratory rain simulator, we studied runoff and soil erosion, and the relationships between them, in 60 semi-arid region soils varying in their intrinsic properties (e.g., texture, organic matter) under differing extrinsic conditions (e.g., rain properties, and conditions prevailing in the field soil). Both runoff and soil erosion were significantly affected by the intrinsic soil and rain properties, and soil conditions within agricultural fields or watersheds. The relationship between soil erosion and runoff was stronger when the rain kinetic energy was higher rather than lower, and could be expressed either as a linear or exponential function. Linear functions applied to certain limited cases associated with conditions that enhanced soil structure stability, (e.g., slow wetting, amending with soil stabilizers, minimum tillage in clay soils, and short duration exposure to rain). Exponential functions applied to most of the cases under conditions that tended to harm soil stability (e.g., fast wetting of soils, a wide range of antecedent soil water contents and rain kinetic energies, conventional tillage, following biosolid applications, irrigation with water of poor quality, consecutive rain simulations). The established relationships between runoff and soil erosion contributed to a better understanding of the mechanisms governing overland flow and soil loss, and could assist in (i) further development of soil erosion models and research techniques, and (ii) the design of more suitable management practices for soil and water conservation.

Kinetic analysis of a monoclonal therapeutic antibody and its single-chain homolog by surface plasmon resonance.

PubMed

Patel, Rekha; Andrien, Bruce A

2010-01-01

Monoclonal antibodies (mAbs) and antibody fragments have become an emerging class of therapeutics since 1986. Their versatility enables them to be engineered for optimal efficiency and decreased immunogenicity, and the path to market has been set by recent regulatory approvals. One of the initial criteria for success of any protein or antibody therapeutic is to understand its binding characteristics to the target antigen. Surface plasmon resonance (SPR) has been widely used and is an important tool for ligand-antigen binding characterization. In this work, the binding kinetics of a recombinant mAb and its single-chain antibody homolog, single-chain variable fragment (scFv), was analyzed by SPR. These two proteins target the same antigen. The binding kinetics of the mAb (bivalent antibody) and scFv (monovalent scFv) for this antigen was analyzed along with an assessment of the thermodynamics of the binding interactions. Alternative binding configurations were investigated to evaluate potential experimental bias because theoretically experimental binding configuration should have no impact on binding kinetics. Self-association binding kinetics in the proteins' respective formulation solutions and antigen epitope mapping were also evaluated. Functional characterization of monoclonal and single-chain antibodies has become just as important as structural characterization in the biotechnology field.

Ascending-ramp biphasic waveform has a lower defibrillation threshold and releases less troponin I than a truncated exponential biphasic waveform.

PubMed

Huang, Jian; Walcott, Gregory P; Ruse, Richard B; Bohanan, Scott J; Killingsworth, Cheryl R; Ideker, Raymond E

2012-09-11

We tested the hypothesis that the shape of the shock waveform affects not only the defibrillation threshold but also the amount of cardiac damage. Defibrillation thresholds were determined for 11 waveforms-3 ascending-ramp waveforms, 3 descending-ramp waveforms, 3 rectilinear first-phase biphasic waveforms, a Gurvich waveform, and a truncated exponential biphasic waveform-in 6 pigs with electrodes in the right ventricular apex and superior vena cava. The ascending, descending, and rectilinear waveforms had 4-, 8-, and 16-millisecond first phases and a 3.5-millisecond rectilinear second phase that was half the voltage of the first phase. The exponential biphasic waveform had a 60% first-phase and a 50% second-phase tilt. In a second study, we attempted to defibrillate after 10 seconds of ventricular fibrillation with a single ≈30-J shock (6 pigs successfully defibrillated with 8-millisecond ascending, 8-millisecond rectilinear, and truncated exponential biphasic waveforms). Troponin I blood levels were determined before and 2 to 10 hours after the shock. The lowest-energy defibrillation threshold was for the 8-milliseconds ascending ramp (14.6±7.3 J [mean±SD]), which was significantly less than for the truncated exponential (19.6±6.3 J). Six hours after shock, troponin I was significantly less for the ascending-ramp waveform (0.80±0.54 ng/mL) than for the truncated exponential (1.92±0.47 ng/mL) or the rectilinear waveform (1.17±0.45 ng/mL). The ascending ramp has a significantly lower defibrillation threshold and at ≈30 J causes 58% less troponin I release than the truncated exponential biphasic shock. Therefore, the shock waveform affects both the defibrillation threshold and the amount of cardiac damage.

Single-channel activations and concentration jumps: comparison of recombinant NR1a/NR2A and NR1a/NR2D NMDA receptors

PubMed Central

Wyllie, David J A; Béhé, Philippe; Colquhoun, David

1998-01-01

We have expressed recombinant NR1a/NR2A and NR1a/NR2D N-methyl-D-aspartate (NMDA) receptor channels in Xenopus oocytes and made recordings of single-channel and macroscopic currents in outside-out membrane patches. For each receptor type we measured (a) the individual single-channel activations evoked by low glutamate concentrations in steady-state recordings, and (b) the macroscopic responses elicited by brief concentration jumps with high agonist concentrations, and we explore the relationship between these two sorts of observation. Low concentration (5–100 nM) steady-state recordings of NR1a/NR2A and NR1a/NR2D single-channel activity generated shut-time distributions that were best fitted with a mixture of five and six exponential components, respectively. Individual activations of either receptor type were resolved as bursts of openings, which we refer to as ‘super-clusters’. During a single activation, NR1a/NR2A receptors were open for 36 % of the time, but NR1a/NR2D receptors were open for only 4 % of the time. For both, distributions of super-cluster durations were best fitted with a mixture of six exponential components. Their overall mean durations were 35.8 and 1602 ms, respectively. Steady-state super-clusters were aligned on their first openings and averaged. The average was well fitted by a sum of exponentials with time constants taken from fits to super-cluster length distributions. It is shown that this is what would be expected for a channel that shows simple Markovian behaviour. The current through NR1a/NR2A channels following a concentration jump from zero to 1 mM glutamate for 1 ms was well fitted by three exponential components with time constants of 13 ms (rising phase), 70 ms and 350 ms (decaying phase). Similar concentration jumps on NR1a/NR2D channels were well fitted by two exponentials with means of 45 ms (rising phase) and 4408 ms (decaying phase) components. During prolonged exposure to glutamate, NR1a/NR2A channels desensitized with a time constant of 649 ms, while NR1a/NR2D channels exhibited no apparent desensitization. We show that under certain conditions, the time constants for the macroscopic jump response should be the same as those for the distribution of super-cluster lengths, though the resolution of the latter is so much greater that it cannot be expected that all the components will be resolvable in a macroscopic current. Good agreement was found for jumps on NR1a/NR2D receptors, and for some jump experiments on NR1a/NR2A. However, the latter were rather variable and some were slower than predicted. Slow decays were associated with patches that had large currents. PMID:9625862

Markov Analysis of Sleep Dynamics

NASA Astrophysics Data System (ADS)

Kim, J. W.; Lee, J.-S.; Robinson, P. A.; Jeong, D.-U.

2009-05-01

A new approach, based on a Markov transition matrix, is proposed to explain frequent sleep and wake transitions during sleep. The matrix is determined by analyzing hypnograms of 113 obstructive sleep apnea patients. Our approach shows that the statistics of sleep can be constructed via a single Markov process and that durations of all states have modified exponential distributions, in contrast to recent reports of a scale-free form for the wake stage and an exponential form for the sleep stage. Hypnograms of the same subjects, but treated with Continuous Positive Airway Pressure, are analyzed and compared quantitatively with the pretreatment ones, suggesting potential clinical applications.

Weighted Scaling in Non-growth Random Networks

NASA Astrophysics Data System (ADS)

Chen, Guang; Yang, Xu-Hua; Xu, Xin-Li

2012-09-01

We propose a weighted model to explain the self-organizing formation of scale-free phenomenon in non-growth random networks. In this model, we use multiple-edges to represent the connections between vertices and define the weight of a multiple-edge as the total weights of all single-edges within it and the strength of a vertex as the sum of weights for those multiple-edges attached to it. The network evolves according to a vertex strength preferential selection mechanism. During the evolution process, the network always holds its total number of vertices and its total number of single-edges constantly. We show analytically and numerically that a network will form steady scale-free distributions with our model. The results show that a weighted non-growth random network can evolve into scale-free state. It is interesting that the network also obtains the character of an exponential edge weight distribution. Namely, coexistence of scale-free distribution and exponential distribution emerges.

Edge Extraction by an Exponential Function Considering X-ray Transmission Characteristics

NASA Astrophysics Data System (ADS)

Kim, Jong Hyeong; Youp Synn, Sang; Cho, Sung Man; Jong Joo, Won

2011-04-01

3-D radiographic methodology has been into the spotlight for quality inspection of mass product or in-service inspection of aging product. To locate a target object in 3-D space, its characteristic contours such as edge length, edge angle, and vertices are very important. In spite of a simple geometry product, it is very difficult to get clear shape contours from a single radiographic image. The image contains scattering noise at the edges and ambiguity coming from X-Ray absorption within the body. This article suggests a concise method to extract whole edges from a single X-ray image. At the edge point of the object, the intensity of the X-ray decays exponentially as the X-ray penetrates the object. Considering this X-Ray decaying property, edges are extracted by using the least square fitting with the control of Coefficient of Determination.

Monitoring of interaction of low-frequency electric field with biological tissues upon optical clearing with optical coherence tomography.

PubMed

Peña, Adrián F; Doronin, Alexander; Tuchin, Valery V; Meglinski, Igor

2014-08-01

The influence of a low-frequency electric field applied to soft biological tissues ex vivo at normal conditions and upon the topical application of optical clearing agents has been studied by optical coherence tomography (OCT). The electro-kinetic response of tissues has been observed and quantitatively evaluated by the double correlation OCT approach, utilizing consistent application of an adaptive Wiener filtering and Fourier domain correlation algorithm. The results show that fluctuations, induced by the electric field within the biological tissues are exponentially increased in time. We demonstrate that in comparison to impedance measurements and the mapping of the temperature profile at the surface of the tissue samples, the double correlation OCT approach is much more sensitive to the changes associated with the tissues' electro-kinetic response. We also found that topical application of the optical clearing agent reduces the tissues' electro-kinetic response and is cooling the tissue, thus reducing the temperature induced by the electric current by a few degrees. We anticipate that dcOCT approach can find a new application in bioelectrical impedance analysis and monitoring of the electric properties of biological tissues, including the resistivity of high water content tissues and its variations.

Mechanism of voltage-gated channel formation in lipid membranes.

PubMed

Guidelli, Rolando; Becucci, Lucia

2016-04-01

Although several molecular models for voltage-gated ion channels in lipid membranes have been proposed, a detailed mechanism accounting for the salient features of experimental data is lacking. A general treatment accounting for peptide dipole orientation in the electric field and their nucleation and growth kinetics with ion channel formation is provided. This is the first treatment that explains all the main features of the experimental current-voltage curves of peptides forming voltage-gated channels available in the literature. It predicts a regime of weakly voltage-dependent conductance, followed by one of strong voltage-dependent conductance at higher voltages. It also predicts values of the parameters expressing the exponential dependence of conductance upon voltage and peptide bulk concentration for both regimes, in good agreement with those reported in the literature. Most importantly, the only two adjustable parameters involved in the kinetics of nucleation and growth of ion channels can be varied over broad ranges without affecting the above predictions to a significant extent. Thus, the fitting of experimental current-voltage curves stems naturally from the treatment and depends only slightly upon the choice of the kinetic parameters. Copyright © 2015 Elsevier B.V. All rights reserved.

Kinetic model of the thermal pyrolysis of chrome tanned leather treated with NaOH under different conditions using thermogravimetric analysis.

PubMed

Bañón, E; Marcilla, A; García, A N; Martínez, P; León, M

2016-02-01

The thermal decomposition of chrome tanned leather before and after a soaking treatment with NaOH was studied using thermogravimetric analysis (TGA). The effect of the solution concentration (0.2M and 0.5M) and the soaking time (5min and 15min) was evaluated. TGA experiments at four heating rates (5, 10, 15 and 20°Cmin(-1)) were run in a nitrogen atmosphere for every treatment condition. A kinetic model was developed considering the effect of the three variables studied, i.e.: the NaOH solution concentration, the soaking time and the heating rate. The proposed model for chrome tanned leather pyrolysis involves a set of four reactions, i.e.: three independent nth order reactions, yielding the corresponding products and one of them undergoing a successive cero order reaction. The model was successfully applied simultaneously to all the experimental data obtained. The evaluation of the kinetic parameters obtained (activation energy, pre-exponential factor and reaction order) allowed a better understanding of the effect of the alkali treatment on these wastes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Pixel-based approach to assess contrast-enhanced ultrasound kinetics parameters for differential diagnosis of rheumatoid arthritis.

PubMed

Rizzo, Gaia; Raffeiner, Bernd; Coran, Alessandro; Ciprian, Luca; Fiocco, Ugo; Botsios, Costantino; Stramare, Roberto; Grisan, Enrico

2015-07-01

Inflammatory rheumatic diseases are the leading causes of disability and constitute a frequent medical disorder, leading to inability to work, high comorbidity, and increased mortality. The standard for diagnosing and differentiating arthritis is based on clinical examination, laboratory exams, and imaging findings, such as synovitis, bone edema, or joint erosions. Contrast-enhanced ultrasound (CEUS) examination of the small joints is emerging as a sensitive tool for assessing vascularization and disease activity. Quantitative assessment is mostly performed at the region of interest level, where the mean intensity curve is fitted with an exponential function. We showed that using a more physiologically motivated perfusion curve, and by estimating the kinetic parameters separately pixel by pixel, the quantitative information gathered is able to more effectively characterize the different perfusion patterns. In particular, we demonstrated that a random forest classifier based on pixelwise quantification of the kinetic contrast agent perfusion features can discriminate rheumatoid arthritis from different arthritis forms (psoriatic arthritis, spondyloarthritis, and arthritis in connective tissue disease) with an average accuracy of 97%. On the contrary, clinical evaluation (DAS28), semiquantitative CEUS assessment, serological markers, or region-based parameters do not allow such a high diagnostic accuracy.

Pixel-based approach to assess contrast-enhanced ultrasound kinetics parameters for differential diagnosis of rheumatoid arthritis

PubMed Central

Rizzo, Gaia; Raffeiner, Bernd; Coran, Alessandro; Ciprian, Luca; Fiocco, Ugo; Botsios, Costantino; Stramare, Roberto; Grisan, Enrico

2015-01-01

Abstract. Inflammatory rheumatic diseases are the leading causes of disability and constitute a frequent medical disorder, leading to inability to work, high comorbidity, and increased mortality. The standard for diagnosing and differentiating arthritis is based on clinical examination, laboratory exams, and imaging findings, such as synovitis, bone edema, or joint erosions. Contrast-enhanced ultrasound (CEUS) examination of the small joints is emerging as a sensitive tool for assessing vascularization and disease activity. Quantitative assessment is mostly performed at the region of interest level, where the mean intensity curve is fitted with an exponential function. We showed that using a more physiologically motivated perfusion curve, and by estimating the kinetic parameters separately pixel by pixel, the quantitative information gathered is able to more effectively characterize the different perfusion patterns. In particular, we demonstrated that a random forest classifier based on pixelwise quantification of the kinetic contrast agent perfusion features can discriminate rheumatoid arthritis from different arthritis forms (psoriatic arthritis, spondyloarthritis, and arthritis in connective tissue disease) with an average accuracy of 97%. On the contrary, clinical evaluation (DAS28), semiquantitative CEUS assessment, serological markers, or region-based parameters do not allow such a high diagnostic accuracy. PMID:27014713

Modeling generic aspects of ideal fibril formation

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

Michel, D., E-mail: denis.michel@live.fr

Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions.more » These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term “critical concentration” is used for different things, involved in either nucleation or elongation.« less

Modeling generic aspects of ideal fibril formation

NASA Astrophysics Data System (ADS)

Michel, D.

2016-01-01

Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various intermediate forms which can be reshuffled by minor modifications of physico-chemical conditions or amino-acid sequences. To bypass this complexity, the multifaceted phenomenon of fibril formation is reduced here to its most elementary principles defined for a linear prototype of fibril. Selected generic features, including nucleation, elongation, and conformational recruitment, are modeled using minimalist hypotheses and tools, by separating equilibrium from kinetic aspects and in vitro from in vivo conditions. These reductionist approaches allow to bring out known and new rudiments, including the kinetic and equilibrium effects of nucleation, the dual influence of elongation on nucleation, the kinetic limitations on nucleation and fibril numbers, and the accumulation of complexes in vivo by rescue from degradation. Overlooked aspects of these processes are also pointed: the exponential distribution of fibril lengths can be recovered using various models because it is attributable to randomness only. It is also suggested that the same term "critical concentration" is used for different things, involved in either nucleation or elongation.

Multicomponent kinetic simulation of Bernstein–Greene–Kruskal modes associated with ion acoustic and dust-ion acoustic excitations in electron-ion and dusty plasmas

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

Hosseini Jenab, S. M., E-mail: mehdi.jenab@yahoo.com; Kourakis, I., E-mail: IoannisKourakisSci@gmail.com

2014-04-15

A series of numerical simulations based on a recurrence-free Vlasov kinetic algorithm presented earlier [Abbasi et al., Phys. Rev. E 84, 036702 (2011)] are reported. Electron-ion plasmas and three-component (electron-ion-dust) dusty, or complex, plasmas are considered, via independent simulations. Considering all plasma components modeled through a kinetic approach, the nonlinear behavior of ionic scale acoustic excitations is investigated. The focus is on Bernstein–Greene–Kruskal (BGK) modes generated during the simulations. In particular, we aim at investigating the parametric dependence of the characteristics of BGK structures, namely of their time periodicity (τ{sub trap}) and their amplitude, on the electron-to-ion temperature ratio andmore » on the dust concentration. In electron-ion plasma, an exponential relation between τ{sub trap} and the amplitude of BGK modes and the electron-to-ion temperature ratio is observed. It is argued that both characteristics, namely, the periodicity τ{sub trap} and amplitude, are also related to the size of the phase-space vortex which is associated with BGK mode creation. In dusty plasmas, BGK modes characteristics appear to depend on the dust particle density linearly.« less

[Mass Transfer Kinetics Model of Ultrasonic Extraction of Pomegranate Peel Polyphenols].

PubMed

Wang, Zhan-yi; Zhang, Li-hua; Wang, Yu-hai; Zhang, Yuan-hu; Ma, Li; Zheng, Dan-dan

2015-05-01

The dynamic mathematical model of ultrasonic extraction of polyphenols from pomegranate peel was constructed with the Fick's second law as the theoretical basis. The spherical model was selected, with mass concentrations of pomegranate peel polyphenols as the index, 50% ethanol as the extraction solvent and ultrasonic extraction as the extraction method. In different test conditions including the liquid ratio, extraction temperature and extraction time, a series of kinetic parameters were solved, such as the extraction process (k), relative raffinate rate, surface diffusion coefficient(D(S)), half life (t½) and the apparent activation energy (E(a)). With the extraction temperature increasing, k and D(S) were gradually increased with t½ decreasing,which indicated that the elevated temperature was favorable to the extraction of pomegranate peel polyphenols. The exponential equation of relative raffinate rate showed that the established numerical dynamics model fitted the extraction of pomegranate peel polyphenols, and the relationship between the reaction conditions and pomegranate peel polyphenols concentration was well reflected by the model. Based on the experimental results, a feasible and reliable kinetic model for ultrasonic extraction of polyphenols from pomegranate peel is established, which can be used for the optimization control of engineering magnifying production.

Firing patterns in the adaptive exponential integrate-and-fire model.

PubMed

Naud, Richard; Marcille, Nicolas; Clopath, Claudia; Gerstner, Wulfram

2008-11-01

For simulations of large spiking neuron networks, an accurate, simple and versatile single-neuron modeling framework is required. Here we explore the versatility of a simple two-equation model: the adaptive exponential integrate-and-fire neuron. We show that this model generates multiple firing patterns depending on the choice of parameter values, and present a phase diagram describing the transition from one firing type to another. We give an analytical criterion to distinguish between continuous adaption, initial bursting, regular bursting and two types of tonic spiking. Also, we report that the deterministic model is capable of producing irregular spiking when stimulated with constant current, indicating low-dimensional chaos. Lastly, the simple model is fitted to real experiments of cortical neurons under step current stimulation. The results provide support for the suitability of simple models such as the adaptive exponential integrate-and-fire neuron for large network simulations.

How extreme are extremes?

NASA Astrophysics Data System (ADS)

Cucchi, Marco; Petitta, Marcello; Calmanti, Sandro

2016-04-01

High temperatures have an impact on the energy balance of any living organism and on the operational capabilities of critical infrastructures. Heat-wave indicators have been mainly developed with the aim of capturing the potential impacts on specific sectors (agriculture, health, wildfires, transport, power generation and distribution). However, the ability to capture the occurrence of extreme temperature events is an essential property of a multi-hazard extreme climate indicator. Aim of this study is to develop a standardized heat-wave indicator, that can be combined with other indices in order to describe multiple hazards in a single indicator. The proposed approach can be used in order to have a quantified indicator of the strenght of a certain extreme. As a matter of fact, extremes are usually distributed in exponential or exponential-exponential functions and it is difficult to quickly asses how strong was an extreme events considering only its magnitude. The proposed approach simplify the quantitative and qualitative communication of extreme magnitude

Adult Age Differences and the Role of Cognitive Resources in Perceptual–Motor Skill Acquisition: Application of a Multilevel Negative Exponential Model

PubMed Central

Kennedy, Kristen M.; Rodrigue, Karen M.; Lindenberger, Ulman; Raz, Naftali

2010-01-01

The effects of advanced age and cognitive resources on the course of skill acquisition are unclear, and discrepancies among studies may reflect limitations of data analytic approaches. We applied a multilevel negative exponential model to skill acquisition data from 80 trials (four 20-trial blocks) of a pursuit rotor task administered to healthy adults (19–80 years old). The analyses conducted at the single-trial level indicated that the negative exponential function described performance well. Learning parameters correlated with measures of task-relevant cognitive resources on all blocks except the last and with age on all blocks after the second. Thus, age differences in motor skill acquisition may evolve in 2 phases: In the first, age differences are collinear with individual differences in task-relevant cognitive resources; in the second, age differences orthogonal to these resources emerge. PMID:20047985

On the biophysics and kinetics of toehold-mediated DNA strand displacement

PubMed Central

Srinivas, Niranjan; Ouldridge, Thomas E.; Šulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, Erik

2013-01-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. PMID:24019238

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

PubMed

Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

2013-12-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

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

Raffel, D.M.; Rosario, R.B. del; Tluczek, L.

Elimination of the {alpha}-carbon CH{sub 3} group from C-11 hydroxyephedrine (HED) yields a new radiotracer for cardiac sympathetic neurons: C-11 phenylephrine (PHEN). This small structural change has profound effects on the tracer kinetics - HED is not metabolized by neuronal monoamine oxidase (MAO), while PHEN is an excellent MAO substrate. To assess the influence of MAO metabolism and vesicular storage on PHEN kinetics a series of constant infusion studies were performed. Isolated working rat hearts were perfused under control conditions for 25 min, then switched to a second perfusate circuit containing PHEN at tracer concentrations. PHEN was infused for 10more » min then the heart switched back to normal perfusate to effect washout of PHEN. The amount of PHEN in the heart was externally measured using coinsidence detection. The data between 1 and 4 min were used to estimate an uptake constant, K{sub up} (ml/min/g wet). Washout data were fit to multiple exponentials. Several studies were done: (1) To slow MAO metabolism, the dideuterium substituted analog C-11 D{sub 2-}PHEN was made and studied as described above. (2) For both tracers, the effect of age on washout kinetics was studied as rat heart MAO levels steadily increase throughout the animal`s life. (3) The effect of MAO inhibition was studied using 100 {mu}M pargyline throughout the experiment. (4) Reserpine pretreated rats were used to assess the influence of vesicular storage on tracer kinetics.« less

Thermogravimetric and model-free kinetic studies on CO2 gasification of low-quality, high-sulphur Indian coals

NASA Astrophysics Data System (ADS)

Das, Tonkeswar; Saikia, Ananya; Mahanta, Banashree; Choudhury, Rahul; Saikia, Binoy K.

2016-10-01

Coal gasification with CO2 has emerged as a cleaner and more efficient way for the production of energy, and it offers the advantages of CO2 mitigation policies through simultaneous CO2 sequestration. In the present investigation, a feasibility study on the gasification of three low-quality, high-sulphur coals from the north-eastern region (NER) of India in a CO2 atmosphere using thermogravimetric analysis (TGA-DTA) has been made in order to have a better understanding of the physical and chemical characteristics in the process of gasification of coal. Model-free kinetics was applied to determine the activation energies (E) and pre-exponential factors (A) of the CO2 gasification process of the coals. Multivariate non-linear regression analyses were performed to find out the formal mechanisms, kinetic model, and the corresponding kinetic triplets. The results revealed that coal gasification with CO2 mainly occurs in the temperature range of 800∘-1400∘C and a maximum of at around 1100∘C. The reaction mechanisms responsible for CO2 gasification of the coals were observed to be of the ` nth order with autocatalysis (CnB)' and ` nth order (Fn) mechanism'. The activation energy of the CO2 gasification was found to be in the range 129.07-146.81 kJ mol-1.

Aqueous extraction kinetics of soluble solids, phenolics and flavonoids from sage (Salvia fruticosa Miller) leaves.

PubMed

Torun, Mehmet; Dincer, Cuneyt; Topuz, Ayhan; Sahin-Nadeem, Hilal; Ozdemir, Feramuz

2015-05-01

In the present study, aqueous extraction kinetics of total soluble solids (TSS), total phenolic content (TPC) and total flavonoid content (TFC) from Salvia fruticosa leaves were investigated throughout 150 min. of extraction period against temperature (60-80 °C), particle size (2-8 mm) and loading percentage (1-4 %). The extract yielded 25 g/100 g TSS which contained 30 g/100 g TPC and 25 g/100 g TFC. The extraction data in time course fit with reversible first order kinetic model. All tested variables showed significant effect on the estimated kinetic parameters except equilibrium concentration. Increasing the extraction temperature resulted high extraction rate constants and equilibrium concentrations of the tested variables notably above 70 °C. By using the Arrhenius relationship, activation energy of the TSS, TPC and TFC were determined as 46.11 ± 5.61, 36.80 ± 3.12 and 33.52 ± 2.23 kj/mol, respectively. By decreasing the particle size, the extraction rate constants and diffusion coefficients exponentially increased whereas equilibrium concentrations did not change significantly. The equilibrium concentrations of the tested parameters showed linear behavior with increasing the loading percentage of the sage, however; the change in extraction rates did not show linear behavior due to submerging effect of 4 % loading.

Optimal back-extrapolation method for estimating plasma volume in humans using the indocyanine green dilution method

PubMed Central

2014-01-01

Background The indocyanine green dilution method is one of the methods available to estimate plasma volume, although some researchers have questioned the accuracy of this method. Methods We developed a new, physiologically based mathematical model of indocyanine green kinetics that more accurately represents indocyanine green kinetics during the first few minutes postinjection than what is assumed when using the traditional mono-exponential back-extrapolation method. The mathematical model is used to develop an optimal back-extrapolation method for estimating plasma volume based on simulated indocyanine green kinetics obtained from the physiological model. Results Results from a clinical study using the indocyanine green dilution method in 36 subjects with type 2 diabetes indicate that the estimated plasma volumes are considerably lower when using the traditional back-extrapolation method than when using the proposed back-extrapolation method (mean (standard deviation) plasma volume = 26.8 (5.4) mL/kg for the traditional method vs 35.1 (7.0) mL/kg for the proposed method). The results obtained using the proposed method are more consistent with previously reported plasma volume values. Conclusions Based on the more physiological representation of indocyanine green kinetics and greater consistency with previously reported plasma volume values, the new back-extrapolation method is proposed for use when estimating plasma volume using the indocyanine green dilution method. PMID:25052018

Investigation of nucleation kinetics in H2SO4 vapor through modeling of gas phase kinetics coupled with particle dynamics

NASA Astrophysics Data System (ADS)

Carlsson, Philip T. M.; Zeuch, Thomas

2018-03-01

We have developed a new model utilizing our existing kinetic gas phase models to simulate experimental particle size distributions emerging in dry supersaturated H2SO4 vapor homogeneously produced by rapid oxidation of SO2 through stabilized Criegee-Intermediates from 2-butene ozonolysis. We use a sectional method for simulating the particle dynamics. The particle treatment in the model is based on first principles and takes into account the transition from the kinetic to the diffusion-limited regime. It captures the temporal evolution of size distributions at the end of the ozonolysis experiment well, noting a slight underrepresentation of coagulation effects for larger particle sizes. The model correctly predicts the shape and the modes of the experimentally observed particle size distributions. The predicted modes show an extremely high sensitivity to the H2SO4 evaporation rates of the initially formed H2SO4 clusters (dimer to pentamer), which were arbitrarily restricted to decrease exponentially with increasing cluster size. In future, the analysis presented in this work can be extended to allow a direct validation of quantum chemically predicted stabilities of small H2SO4 clusters, which are believed to initiate a significant fraction of atmospheric new particle formation events. We discuss the prospects and possible limitations of the here presented approach.

Dye-sensitized electron transfer from TiO2 to oxidized triphenylamines that follows first-order kinetics

PubMed Central

DiMarco, Brian N.; Troian-Gautier, Ludovic; Sampaio, Renato N.

2017-01-01

Two sensitizers, [Ru(bpy)2(dcb)]2+ (RuC) and [Ru(bpy)2(dpb)]2+ (RuP), where bpy is 2,2′-bipyridine, dcb is 4,4′-dicarboxylic acid-2,2′-bipyridine and dpb is 4,4′-diphosphonic acid-2,2′-bipyridine, were anchored to mesoporous TiO2 thin films and utilized to sensitize the reaction of TiO2 electrons with oxidized triphenylamines, TiO2(e–) + TPA+ → TiO2 + TPA, to visible light in CH3CN electrolytes. A family of four symmetrically substituted triphenylamines (TPAs) with formal Eo(TPA+/0) reduction potentials that spanned a 0.5 eV range was investigated. Surprisingly, the reaction followed first-order kinetics for two TPAs that provided the largest thermodynamic driving force. Such first-order reactivity indicates a strong Coulombic interaction between TPA+ and TiO2 that enables the injected electron to tunnel back in one concerted step. The kinetics for the other TPA derivatives were non-exponential and were modelled with the Kohlrausch–William–Watts (KWW) function. A Perrin-like reaction sphere model is proposed to rationalize the kinetic data. The activation energies were the same for all of the TPAs, within experimental error. The average rate constants were found to increase with the thermodynamic driving force, consistent with electron transfer in the Marcus normal region. PMID:29629161

Drift wave stabilized by an additional streaming ion or plasma population

NASA Astrophysics Data System (ADS)

Bashir, M. F.; Vranjes, J.

2015-03-01

It is shown that the universally unstable kinetic drift wave in an electron-ion plasma can very effectively be suppressed by adding an extra flowing ion (or plasma) population. The effect of the flow of the added ions is essential, their response is of the type (vp h-vf 0) exp[-(vph-vf 0) 2] , where vf 0 is the flow speed and vp h is the phase speed parallel to the magnetic field vector. The damping is strong and it is mainly due to this ion exponential term, and this remains so for vf 0

Drift wave stabilized by an additional streaming ion or plasma population.

PubMed

Bashir, M F; Vranjes, J

2015-03-01

It is shown that the universally unstable kinetic drift wave in an electron-ion plasma can very effectively be suppressed by adding an extra flowing ion (or plasma) population. The effect of the flow of the added ions is essential, their response is of the type (vph-vf0)exp[-(vph-vf0)2], where vf0 is the flow speed and vph is the phase speed parallel to the magnetic field vector. The damping is strong and it is mainly due to this ion exponential term, and this remains so for vf0

A three-ions model of electrodiffusion kinetics in a nanochannel

NASA Astrophysics Data System (ADS)

Sebechlebská, Táňa; Neogrády, Pavel; Valent, Ivan

2016-10-01

Nanoscale electrodiffusion transport is involved in many electrochemical, technological and biological processes. Developments in computer power and numerical algorithms allow for solving full time-dependent Nernst-Planck and Poisson equations without simplifying approximations. We simulate spatio-temporal profiles of concentration and electric potential changes after a potential jump in a 10 nm channel with two cations (with opposite concentration gradients and different mobilities) and one anion (of uniform concentration). The temporal dynamics shows three exponential phases and damped oscillations of the electric potential. Despite the absence of surface charges in the studied model, an asymmetric current-voltage characteristic was observed.

Mechanical Removal and Rescreening of Local Screening Charges on Ferroelectric Surfaces

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

Tong, Sheng; Park, Woon Ik; Choi, YoonYoung

2015-01-20

We report the kinetics of screening charge removal and rescreening on periodically poled lithium niobate using charge-gradient microscopy and electrostatic force microscopy (EFM). A minimum pressure needs to be applied to initiate mechanical screening charge removal, and increasing the pressure leads to further removal of charge until a threshold is reached when all screening charges are removed. We fit all rescreening EFM contrast curves under various pressures into a universal exponential decay. The findings imply that we can control the screening degree of ferroelectric surfaces by mechanical means without affecting the polarization underneath.

Mechanical Removal and Rescreening of Local Screening Charges at Ferroelectric Surfaces

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

Tong, Sheng; Park, Woon Ik; Choi, Yoon-Young

2015-01-20

In this paper, we report the kinetics of screening charge removal and rescreening on periodically poled lithium niobate using charge-gradient microscopy and electrostatic force microscopy (EFM). A minimum pressure needs to be applied to initiate mechanical screening charge removal, and increasing the pressure leads to further removal of charge until a threshold is reached when all screening charges are removed. We fit all rescreening EFM contrast curves under various pressures into a universal exponential decay. Finally, the findings imply that we can control the screening degree of ferroelectric surfaces by mechanical means without affecting the polarization underneath.

TSH-induced cyclic AMP production in an ovine thyroid cell line: OVNIS 5H.

PubMed

Fayet, G; Aouani, A; Hovsépian, S

1986-01-06

The TSH-induced cyclic AMP response was studied using a 3-year-old ovine thyroid cell line TSH-independent for growth: OVNIS 5H. The kinetics of cyclic AMP production was followed both in cell layers and in cell culture media, with or without phosphodiesterase inhibitor. It is noteworthy that following the first wave in cyclic AMP obtained within minutes, we observed later a sustained exponential increase in cyclic AMP during the 5 days following TSH stimulation. A bioassay of TSH was derived allowing measurement of 1 microU/ml TSH from a crude bTSH preparation.

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

Single-Molecule Imaging of an in Vitro-Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics

PubMed Central

2009-01-01

Many studies of RNA folding and catalysis have revealed conformational heterogeneity, metastable folding intermediates, and long-lived states with distinct catalytic activities. We have developed a single-molecule imaging approach for investigating the functional heterogeneity of in vitro-evolved RNA aptamers. Monitoring the association of fluorescently labeled ligands with individual RNA aptamer molecules has allowed us to record binding events over the course of multiple days, thus providing sufficient statistics to quantitatively define the kinetic properties at the single-molecule level. The ligand binding kinetics of the highly optimized RNA aptamer studied here displays a remarkable degree of uniformity and lack of memory. Such homogeneous behavior is quite different from the heterogeneity seen in previous single-molecule studies of naturally derived RNA and protein enzymes. The single-molecule methods we describe may be of use in analyzing the distribution of functional molecules in heterogeneous evolving populations or even in unselected samples of random sequences. PMID:19572753

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.

Evaluation of the cure kinetics of the wood/pMDI bondline

Treesearch

David P. Harper; Michael P. Wolcott; Timothy G. Rials

2001-01-01

Micro-dielectric analysis (µDEA) and differentia1 scanning calorimetry (DSC) were used to monitor cure of polymeric diphenyl-methane diisocyanate (pMDI) resin with wood strands in a saturated steam environment. A first-order autocatalyzed kinetic model was employed to determine kinetic parameters. The kinetics were found to follow an Arrhenius relation. A single ramp...

Modelling the growth kinetics of Kocuria marina DAGII as a function of single and binary substrate during batch production of β-Cryptoxanthin.

PubMed

Mitra, Ruchira; Chaudhuri, Surabhi; Dutta, Debjani

2017-01-01

In the present investigation, growth kinetics of Kocuria marina DAGII during batch production of β-Cryptoxanthin (β-CRX) was studied by considering the effect of glucose and maltose as a single and binary substrate. The importance of mixed substrate over single substrate has been emphasised in the present study. Different mathematical models namely, the Logistic model for cell growth, the Logistic mass balance equation for substrate consumption and the Luedeking-Piret model for β-CRX production were successfully implemented. Model-based analyses for the single substrate experiments suggested that the concentrations of glucose and maltose higher than 7.5 and 10.0 g/L, respectively, inhibited the growth and β-CRX production by K. marina DAGII. The Han and Levenspiel model and the Luong product inhibition model accurately described the cell growth in glucose and maltose substrate systems with a R 2 value of 0.9989 and 0.9998, respectively. The effect of glucose and maltose as binary substrate was further investigated. The binary substrate kinetics was well described using the sum-kinetics with interaction parameters model. The results of production kinetics revealed that the presence of binary substrate in the cultivation medium increased the biomass and β-CRX yield significantly. This study is a first time detailed investigation on kinetic behaviours of K. marina DAGII during β-CRX production. The parameters obtained in the study might be helpful for developing strategies for commercial production of β-CRX by K. marina DAGII.

A note on free and forced Rossby wave solutions: The case of a straight coast and a channel

NASA Astrophysics Data System (ADS)

Graef, Federico

2017-03-01

The free Rossby wave (RW) solutions in an ocean with a straight coast when the offshore wavenumber of incident (l1) and reflected (l2) wave are equal or complex are discussed. If l1 = l2 the energy streams along the coast and a uniformly valid solution cannot be found; if l1,2 are complex it yields the sum of an exponentially decaying and growing (away from the coast) Rossby wave. The channel does not admit these solutions as free modes. If the wavenumber vectors of the RWs are perpendicular to the coast, the boundary condition of no normal flow is trivially satisfied and the value of the streamfunction does not need to vanish at the coast. A solution that satisfies Kelvin's theorem of time-independent circulation at the coast is proposed. The forced RW solutions when the ocean's forcing is a single Fourier component are studied. If the forcing is resonant, i.e. a free Rossby wave (RW), the linear response will depend critically on whether the wave carries energy perpendicular to the channel or not. In the first case, the amplitude of the response is linear in the direction normal to the channel, y, and in the second it has a parabolic profile in y. Examples of these solutions are shown for channels with parameters resembling the Mozambique Channel, the Tasman Sea, the Denmark Strait and the English Channel. The solutions for the single coast are unbounded, except when the forcing is a RW trapped against the coast. If the forcing is non-resonant, exponentially decaying or trapped RWs could be excited in the coast and both the exponentially ;decaying; and exponentially ;growing; RW could be excited in the channel.

Evidence for Dynamic Chemical Kinetics at Individual Molecular Ruthenium Catalysts.

PubMed

Easter, Quinn T; Blum, Suzanne A

2018-02-05

Catalytic cycles are typically depicted as possessing time-invariant steps with fixed rates. Yet the true behavior of individual catalysts with respect to time is unknown, hidden by the ensemble averaging inherent to bulk measurements. Evidence is presented for variable chemical kinetics at individual catalysts, with a focus on ring-opening metathesis polymerization catalyzed by the second-generation Grubbs' ruthenium catalyst. Fluorescence microscopy is used to probe the chemical kinetics of the reaction because the technique possesses sufficient sensitivity for the detection of single chemical reactions. Insertion reactions in submicron regions likely occur at groups of many (not single) catalysts, yet not so many that their unique kinetic behavior is ensemble averaged. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Normal Mode Analysis on the Relaxation of AN Excited Nitromethane Molecule in Argon Bath

NASA Astrophysics Data System (ADS)

Rivera-Rivera, Luis A.; Wagner, Albert F.

2017-06-01

In our previous work [Rivera-Rivera et al. J. Chem. Phys. 142, 014303 (2015).] classical molecular dynamics simulations followed, in an Ar bath, the relaxation of nitromethane (CH_3NO_2) instantaneously excited by statistically distributing 50 kcal/mol among all its internal degrees of freedom. The 300 K Ar bath was at pressures of 10 to 400 atm. Both rotational and vibrational energies exhibited multi-exponential decay. This study explores mode-specific mechanisms at work in the decay process. With the separation of rotation and vibration developed by Rhee and Kim [J. Chem. Phys. 107, 1394 (1997).], one can show that the vibrational kinetic energy decomposes only into vibrational normal modes while the rotational and Coriolis energies decompose into both vibrational and rotational normal modes. Then the saved CH_3NO_2 positions and momenta can be converted into mode-specific energies whose decay over 1000 ps can be monitored. The results identify vibrational and rotational modes that promote/resist energy lost and drive multi-exponential behavior. In addition to mode-specificity, the results show disruption of IVR with increasing pressure.

Smoothing Polymer Surfaces by Solvent-Vapor Exposure

NASA Astrophysics Data System (ADS)

Anthamatten, Mitchell

2003-03-01

Ultra-smooth polymer surfaces are of great importance in a large body of technical applications such as optical coatings, supermirrors, waveguides, paints, and fusion targets. We are investigating a simple approach to controlling surface roughness: by temporarily swelling the polymer with solvent molecules. As the solvent penetrates into the polymer, its viscosity is lowered, and surface tension forces drive surface flattening. To investigate sorption kinetics and surface-smoothing phenomena, a series of vapor-deposited poly(amic acid) films were exposed to dimethyl sulfoxide vapors. During solvent exposure, the surface topology was continuously monitored using light interference microscopy. The resulting power spectra indicate that high-frequency defects smooth faster than low-frequency defects. This frequency dependence was studied by depositing polymer films onto a series of 2D sinusoidal surfaces and performing smoothing experiments. Results show that the amplitudes of the sinusoidal surfaces decay exponentially with solvent exposure time, and the exponential decay constants are proportional to surface frequency. This work was performed under the auspices of the U.S. Department of Energy by the University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Direct observation of molecular cooperativity near the glass transition.

PubMed

Russell, E V; Israeloff, N E

2000-12-07

The increasingly sluggish response of a supercooled liquid as it nears its glass transition (for example, refrigerated honey) is prototypical of glassy dynamics found in proteins, neural networks and superconductors. The notion that molecules rearrange cooperatively has long been postulated to explain diverging relaxation times and broadened (non-exponential) response functions near the glass transition. Recently, cooperativity was observed and analysed in colloid glasses and in simulations of binary liquids well above the glass transition. But nanometre-scale studies of cooperativity at the molecular glass transition are lacking. Important issues to be resolved include the precise form of the cooperativity and its length scale, and whether the broadened response is intrinsic to individual cooperative regions, or arises only from heterogeneity in an ensemble of such regions. Here we describe direct observations of molecular cooperativity near the glass transition in polyvinylacetate (PVAc), using nanometre-scale probing of dielectric fluctuations. Molecular clusters switched spontaneously among two to four distinct configurations, producing random telegraph noise. Our analysis of these noise signals and their power spectra reveals that individual clusters exhibit transient dynamical heterogeneity and non-exponential kinetics.

Fundamental data on the desorption of pure interstellar ices

NASA Astrophysics Data System (ADS)

Brown, Wendy A.; Bolina, Amandeep S.

2007-01-01

The desorption of molecular ices from grain surfaces is important in a number of astrophysical environments including dense molecular clouds, cometary nuclei and the surfaces and atmospheres of some planets. With this in mind, we have performed a detailed investigation of the desorption of pure water, pure methanol and pure ammonia ices from a model dust-grain surface. We have used these results to determine the desorption energy, order of desorption and the pre-exponential factor for the desorption of these molecular ices from our model surface. We find good agreement between our desorption energies and those determined previously; however, our values for the desorption orders, and hence also the pre-exponential factors, are different to those reported previously. The kinetic parameters derived from our data have been used to model desorption on time-scales relevant to astrophysical processes and to calculate molecular residence times, given in terms of population half-life as a function of temperature. These results show the importance of laboratory data for the understanding of astronomical situations whereby icy mantles are warmed by nearby stars and by other dynamical events.

A study of water uptake by selected superdisintegrants from the sub-molecular to the particulate level.

PubMed

Barmpalexis, P; Syllignaki, P; Kachrimanis, K

2018-06-01

Water diffusion through the matrix of three superdisintegrants, namely sodium starch glycolate (SSG), croscarmellose sodium (cCMC-Na) and crospovidone (cPVP), was studied at the sub-molecular level using Attenuated Total Reflectance (ATR)-FTIR spectroscopy and molecular dynamics simulations, and the results were correlated to water uptake studies conducted at the particulate level using Parallel Exponential Kinetics (PEK) modeling in dynamic moisture sorption studies and optical microscopy. ATR-FTIR studies indicated that water diffuses inside cPVP by a single fast acting process, while in SSG and cCMC-Na, a slow and a fast process acting simultaneously, were identified. The same pattern regarding the rate of water uptake for all superdisintegrants was found also at the particulate level by PEK modeling. Moreover, molecular dynamics simulation helped elucidate the hydrogen bonding patterns formed between water-SSG and water-cCMC-Na, mainly via their carboxylic oxygen atoms and secondarily via their hydroxyl groups, while cPVP formed hydrogen bonds only through carbonyl oxygen. Finally, cPVP chains showed significant flexibility during hydration, while cCMC-Na and SSG chains retain their conformation to some extent, explaining the extensive swelling observed also at the particulate level by optical microscopy hydration studies.

Treatment with pyrophosphate inhibits uremic vascular calcification

PubMed Central

O’Neill, W. Charles; Lomashvili, Koba A.; Malluche, Hartmut H.; Faugere, Marie-Claude; Riser, Bruce L.

2011-01-01

Pyrophosphate, which may be deficient in advanced renal failure, is a potent inhibitor of vascular calcification. To explore its use as a potential therapeutic, we injected exogenous pyrophosphate subcutaneously or intraperitoneally in normal rats and found that their plasma pyrophosphate concentrations peaked within 15 min. There was a single exponential decay with a half-life of 33 min. The kinetics were indistinguishable between the two routes of administration or in anephric rats. The effect of daily intraperitoneal pyrophosphate injections on uremic vascular calcification was then tested in rats fed a high-phosphate diet containing adenine for 28 days to induce uremia. Although the incidence of aortic calcification varied and was not altered by pyrophosphate, the calcium content of calcified aortas was significantly reduced by 70%. Studies were repeated in uremic rats given calcitriol to produce more consistent aortic calcification and treated with sodium pyrophosphate delivered intraperitoneally in a larger volume of glucose-containing solution to prolong plasma pyrophosphate levels. This maneuver significantly reduced both the incidence and amount of calcification. Quantitative histomorphometry of bone samples after double-labeling with calcein indicated that there was no effect of pyrophosphate on the rates of bone formation or mineralization. Thus, exogenous pyrophosphate can inhibit uremic vascular calcification without producing adverse effects on bone. PMID:21124302

Treatment with pyrophosphate inhibits uremic vascular calcification.

PubMed

O'Neill, W Charles; Lomashvili, Koba A; Malluche, Hartmut H; Faugere, Marie-Claude; Riser, Bruce L

2011-03-01

Pyrophosphate, which may be deficient in advanced renal failure, is a potent inhibitor of vascular calcification. To explore its use as a potential therapeutic, we injected exogenous pyrophosphate subcutaneously or intraperitoneally in normal rats and found that their plasma pyrophosphate concentrations peaked within 15 min. There was a single exponential decay with a half-life of 33 min. The kinetics were indistinguishable between the two routes of administration or in anephric rats. The effect of daily intraperitoneal pyrophosphate injections on uremic vascular calcification was then tested in rats fed a high-phosphate diet containing adenine for 28 days to induce uremia. Although the incidence of aortic calcification varied and was not altered by pyrophosphate, the calcium content of calcified aortas was significantly reduced by 70%. Studies were repeated in uremic rats given calcitriol to produce more consistent aortic calcification and treated with sodium pyrophosphate delivered intraperitoneally in a larger volume of glucose-containing solution to prolong plasma pyrophosphate levels. This maneuver significantly reduced both the incidence and amount of calcification. Quantitative histomorphometry of bone samples after double-labeling with calcein indicated that there was no effect of pyrophosphate on the rates of bone formation or mineralization. Thus, exogenous pyrophosphate can inhibit uremic vascular calcification without producing adverse effects on bone.

Effect of annealing ambient on anisotropic retraction of film edges during solid-state dewetting of thin single crystal films

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

Kim, Gye Hyun; Thompson, Carl V., E-mail: cthomp@mit.edu; Ma, Wen

During solid-state dewetting of thin single crystal films, film edges retract at a rate that is strongly dependent on their crystallographic orientations. Edges with kinetically stable in-plane orientations remain straight as they retract, while those with other in-plane orientations develop in-plane facets as they retract. Kinetically stable edges have retraction rates that are lower than edges with other orientations and thus determine the shape of the natural holes that form during solid-state dewetting. In this paper, measurements of the retraction rates of kinetically stable edges for single crystal (110) and (100) Ni films on MgO are presented. Relative retraction ratesmore » of kinetically stable edges with different crystallographic orientations are observed to change under different annealing conditions, and this accordingly changes the initial shapes of growing holes. The surfaces of (110) and (100) films were also characterized using low energy electron diffraction, and different surface reconstructions were observed under different ambient conditions. The observed surface structures were found to correlate with the observed changes in the relative retraction rates of the kinetically stable edges.« less

Thermoluminescence kinetics of pyrite (FeS2)

NASA Astrophysics Data System (ADS)

Silverman, A. N.; Levy, P. W.; Kierstead, J. A.

Thermoluminescence of pyrite (FeS2) was investigated to study the kinetics of single peak glow curves. The material used normally exhibits one large and four small peaks. However a glow curve can be obtained with only the large single peak that is suitable for testing thermoluminescence kinetics. Glow curves from aliquots of a single natural pyrite crystal studied in detail contain two low intensity thermoluminescence (TL) peaks at approximately 90 and 250 C, and two chemiluminescence (CL) peaks at approximately 350 and 430 C. The CL peaks are largely removable by initially heating the sample chamber under vacuum, pumping through liquid nitrogen traps, and recording glow curves immediately after helium is introduced, procedures which reduce system contaminants that react with pyrite. The shape, the variation of the temperature of the peak maximum (T(sub max)) with dose, and the retrapping to recombination cross section ratio (sigma) of the large 250 C peak are better described by the general one trap (GOT) kinetic equation, the basic equation from which the 1st and 2nd order kinetic equations are obtained as special cases, than by the 1st and 2nd order equations.

Well hydraulics in pumping tests with exponentially decayed rates of abstraction in confined aquifers

NASA Astrophysics Data System (ADS)

Wen, Zhang; Zhan, Hongbin; Wang, Quanrong; Liang, Xing; Ma, Teng; Chen, Chen

2017-05-01

Actual field pumping tests often involve variable pumping rates which cannot be handled by the classical constant-rate or constant-head test models, and often require a convolution process to interpret the test data. In this study, we proposed a semi-analytical model considering an exponentially decreasing pumping rate started at a certain (higher) rate and eventually stabilized at a certain (lower) rate for cases with or without wellbore storage. A striking new feature of the pumping test with an exponentially decayed rate is that the drawdowns will decrease over a certain period of time during intermediate pumping stage, which has never been seen before in constant-rate or constant-head pumping tests. It was found that the drawdown-time curve associated with an exponentially decayed pumping rate function was bounded by two asymptotic curves of the constant-rate tests with rates equaling to the starting and stabilizing rates, respectively. The wellbore storage must be considered for a pumping test without an observation well (single-well test). Based on such characteristics of the time-drawdown curve, we developed a new method to estimate the aquifer parameters by using the genetic algorithm.

Macromolecular Rate Theory (MMRT) Provides a Thermodynamics Rationale to Underpin the Convergent Temperature Response in Plant Leaf Respiration

NASA Astrophysics Data System (ADS)

Liang, L. L.; Arcus, V. L.; Heskel, M.; O'Sullivan, O. S.; Weerasinghe, L. K.; Creek, D.; Egerton, J. J. G.; Tjoelker, M. G.; Atkin, O. K.; Schipper, L. A.

2017-12-01

Temperature is a crucial factor in determining the rates of ecosystem processes such as leaf respiration (R) - the flux of plant respired carbon dioxide (CO2) from leaves to the atmosphere. Generally, respiration rate increases exponentially with temperature as modelled by the Arrhenius equation, but a recent study (Heskel et al., 2016) showed a universally convergent temperature response of R using an empirical exponential/polynomial model whereby the exponent in the Arrhenius model is replaced by a quadratic function of temperature. The exponential/polynomial model has been used elsewhere to describe shoot respiration and plant respiration. What are the principles that underlie these empirical observations? Here, we demonstrate that macromolecular rate theory (MMRT), based on transition state theory for chemical kinetics, is equivalent to the exponential/polynomial model. We re-analyse the data from Heskel et al. 2016 using MMRT to show this equivalence and thus, provide an explanation based on thermodynamics, for the convergent temperature response of R. Using statistical tools, we also show the equivalent explanatory power of MMRT when compared to the exponential/polynomial model and the superiority of both of these models over the Arrhenius function. Three meaningful parameters emerge from MMRT analysis: the temperature at which the rate of respiration is maximum (the so called optimum temperature, Topt), the temperature at which the respiration rate is most sensitive to changes in temperature (the inflection temperature, Tinf) and the overall curvature of the log(rate) versus temperature plot (the so called change in heat capacity for the system, ). The latter term originates from the change in heat capacity between an enzyme-substrate complex and an enzyme transition state complex in enzyme-catalysed metabolic reactions. From MMRT, we find the average Topt and Tinf of R are 67.0±1.2 °C and 41.4±0.7 °C across global sites. The average curvature (average negative) is -1.2±0.1 kJ.mol-1K-1. MMRT extends the classic transition state theory to enzyme-catalysed reactions and scales up to more complex processes including micro-organism growth rates and ecosystem processes.

Developments in Analytical Chemistry: Acoustically Levitated Drop Reactors for Enzyme Reaction Kinetics and Single-Walled Carbon Nanotube-Based Sensors for Detection of Toxic Organic Phosphonates

ERIC Educational Resources Information Center

Field, Christopher Ryan

2009-01-01

Developments in analytical chemistry were made using acoustically levitated small volumes of liquid to study enzyme reaction kinetics and by detecting volatile organic compounds in the gas phase using single-walled carbon nanotubes. Experience gained in engineering, electronics, automation, and software development from the design and…

Modeling the Transport of the "New-Horizon" Reduced Graphene Oxide-Metal Oxide Nanohybrids in Water-Saturated Porous Media.

PubMed

Wang, Dengjun; Jin, Yan; Park, Chang Min; Heo, Jiyong; Bai, Xue; Aich, Nirupam; Su, Chunming

2018-04-17

Little is known about the fate and transport of the "new-horizon" multifunctional nanohybrids in the environment. Saturated sand-packed column experiments ( n = 66) were therefore performed to investigate the transport and retention of reduced graphene oxide (RGO)-metal oxide (Fe 3 O 4 , TiO 2 , and ZnO) nanohybrids under environmentally relevant conditions (mono- and divalent electrolytes and natural organic matter). Classical colloid science principles (Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and colloid filtration theory (CFT)) and mathematical models based on the one-dimensional convection-dispersion equation were employed to describe and predict the mobility of RGO-Fe 3 O 4 , RGO-TiO 2 , and RGO-ZnO nanohybrids in porous media. Results indicate that the mobility of the three nanohybrids under varying experimental conditions is overall explainable by DLVO theory and CFT. Numerical simulations suggest that the one-site kinetic retention model (OSKRM) considering both time- and depth-dependent retention accurately approximated the breakthrough curves (BTCs) and retention profiles (RPs) of the nanohybrids concurrently; whereas, others (e.g., two-site retention model) failed to capture the BTCs and/or RPs. This is primarily because blocking BTCs and exponential/hyperexponential/uniform RPs occurred, which is within the framework of OSKRM featuring time- (for kinetic Langmuirian blocking) and depth-dependent (for exponential/hyperexponential/uniform) retention kinetics. Employing fitted parameters (maximum solid-phase retention capacity: S max = 0.0406-3.06 cm 3 /g; and first-order attachment rate coefficient: k a = 0.133-20.6 min -1 ) extracted from the OSKRM and environmentally representative physical variables (flow velocity (0.00441-4.41 cm/min), porosity (0.24-0.54), and grain size (210-810 μm)) as initial input conditions, the long-distance transport scenarios (in 500 cm long sand columns) of the three nanohybrids were predicted via forward simulation. Our findings address the existing knowledge gap regarding the impact of physicochemical factors on the transport of the next-generation, multifunctional RGO-metal oxide nanohybrids in the subsurface.

Role of N-terminal domain and accessory subunits in controlling deactivation-inactivation coupling of Kv4.2 channels.

PubMed

Barghaan, Jan; Tozakidou, Magdalini; Ehmke, Heimo; Bähring, Robert

2008-02-15

We examined the relationship between deactivation and inactivation in Kv4.2 channels. In particular, we were interested in the role of a Kv4.2 N-terminal domain and accessory subunits in controlling macroscopic gating kinetics and asked if the effects of N-terminal deletion and accessory subunit coexpression conform to a kinetic coupling of deactivation and inactivation. We expressed Kv4.2 wild-type channels and N-terminal deletion mutants in the absence and presence of Kv channel interacting proteins (KChIPs) and dipeptidyl aminopeptidase-like proteins (DPPs) in human embryonic kidney 293 cells. Kv4.2-mediated A-type currents at positive and deactivation tail currents at negative membrane potentials were recorded under whole-cell voltage-clamp and analyzed by multi-exponential fitting. The observed changes in Kv4.2 macroscopic inactivation kinetics caused by N-terminal deletion, accessory subunit coexpression, or a combination of the two maneuvers were compared with respective changes in deactivation kinetics. Extensive correlation analyses indicated that modulatory effects on deactivation closely parallel respective effects on inactivation, including both onset and recovery kinetics. Searching for the structural determinants, which control deactivation and inactivation, we found that in a Kv4.2 Delta 2-10 N-terminal deletion mutant both the initial rapid phase of macroscopic inactivation and tail current deactivation were slowed. On the other hand, the intermediate and slow phase of A-type current decay, recovery from inactivation, and tail current decay kinetics were accelerated in Kv4.2 Delta 2-10 by KChIP2 and DPPX. Thus, a Kv4.2 N-terminal domain, which may control both inactivation and deactivation, is not necessary for active modulation of current kinetics by accessory subunits. Our results further suggest distinct mechanisms for Kv4.2 gating modulation by KChIPs and DPPs.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

NASA Astrophysics Data System (ADS)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-08-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes.

PubMed

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-08-28

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

The coherent interlayer resistance of a single, rotated interface between two stacks of AB graphite

NASA Astrophysics Data System (ADS)

Habib, K. M. Masum; Sylvia, Somaia S.; Ge, Supeng; Neupane, Mahesh; Lake, Roger K.

2013-12-01

The coherent, interlayer resistance of a misoriented, rotated interface between two stacks of AB graphite is determined for a variety of misorientation angles. The quantum-resistance of the ideal AB stack is on the order of 1 to 10 mΩ μm2. For small rotation angles, the coherent interlayer resistance exponentially approaches the ideal quantum resistance at energies away from the charge neutrality point. Over a range of intermediate angles, the resistance increases exponentially with cell size for minimum size unit cells. Larger cell sizes, of similar angles, may not follow this trend. The energy dependence of the interlayer transmission is described.

On the Rate of Relaxation for the Landau Kinetic Equation and Related Models

NASA Astrophysics Data System (ADS)

Bobylev, Alexander; Gamba, Irene M.; Zhang, Chenglong

2017-08-01

We study the rate of relaxation to equilibrium for Landau kinetic equation and some related models by considering the relatively simple case of radial solutions of the linear Landau-type equations. The well-known difficulty is that the evolution operator has no spectral gap, i.e. its spectrum is not separated from zero. Hence we do not expect purely exponential relaxation for large values of time t>0. One of the main goals of our work is to numerically identify the large time asymptotics for the relaxation to equilibrium. We recall the work of Strain and Guo (Arch Rat Mech Anal 187:287-339 2008, Commun Partial Differ Equ 31:17-429 2006), who rigorously show that the expected law of relaxation is \\exp (-ct^{2/3}) with some c > 0. In this manuscript, we find an heuristic way, performed by asymptotic methods, that finds this "law of two thirds", and then study this question numerically. More specifically, the linear Landau equation is approximated by a set of ODEs based on expansions in generalized Laguerre polynomials. We analyze the corresponding quadratic form and the solution of these ODEs in detail. It is shown that the solution has two different asymptotic stages for large values of time t and maximal order of polynomials N: the first one focus on intermediate asymptotics which agrees with the "law of two thirds" for moderately large values of time t and then the second one on absolute, purely exponential asymptotics for very large t, as expected for linear ODEs. We believe that appearance of intermediate asymptotics in finite dimensional approximations must be a generic behavior for different classes of equations in functional spaces (some PDEs, Boltzmann equations for soft potentials, etc.) and that our methods can be applied to related problems.

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.

Complexation of lysozyme with adsorbed PtBS-b-SCPI block polyelectrolyte micelles on silver surface.

PubMed

Papagiannopoulos, Aristeidis; Christoulaki, Anastasia; Spiliopoulos, Nikolaos; Vradis, Alexandros; Toprakcioglu, Chris; Pispas, Stergios

2015-01-20

We present a study of the interaction of the positively charged model protein lysozyme with the negatively charged amphiphilic diblock polyelectrolyte micelles of poly(tert-butylstyrene-b-sodium (sulfamate/carboxylate)isoprene) (PtBS-b-SCPI) on the silver/water interface. The adsorption kinetics are monitored by surface plasmon resonance, and the surface morphology is probed by atomic force microscopy. The micellar adsorption is described by stretched-exponential kinetics, and the micellar layer morphology shows that the micelles do not lose their integrity upon adsorption. The complexation of lysozyme with the adsorbed micellar layers depends on the micelles arrangement and density in the underlying layer, and lysozyme follows the local morphology of the underlying roughness. When the micellar adsorbed amount is small, the layers show low capacity in protein complexation and low resistance in loading. When the micellar adsorbed amount is high, the situation is reversed. The adsorbed layers both with or without added protein are found to be irreversibly adsorbed on the Ag surface.

Influence of gamma-irradiation on the non-isothermal decomposition of calcium-gadolinium oxalate

NASA Astrophysics Data System (ADS)

Moharana, S. C.; Praharaj, J.; Bhatta, D.

Thermal decomposition of co-precipitated unirradiated and irradiated Ca-Gd oxalate has been studied by adopting differential thermal analysis (DTA) and thermogravimetric (TG) techniques. The reaction occurs through two stages corresponding to the decomposition of gadolinium oxalate (Gd-Ox) followed by that of calcium oxalate (Ca-Ox). The kinetic parameters for both the stages are calculated by using solid state reaction models and Coats-Redfern's equation. The co-precipitation as well as irradiation alter the DTA peak temperatures and the kinetic parameters of Ca-Ox. The decomposition of Gd-Ox follows the two dimensional Contracting area (R-2) mechanism, while that of Ca-Ox follows the Avrami-Erofeev (A(2)) mechanism (n =2), which are also exhibited by the co-precipitated and irradiated samples. Co-precipitation decreases the energy of activation and the pre-exponential factor of the individual components but the reverse phenomenon takes place upon irradiation of the co-precipitate. The mechanisms underlying the phenomena are explored.

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.

Kinetic Modeling of the Reaction Rate for Quartz and Carbon Black Pellet

NASA Astrophysics Data System (ADS)

Li, Fei; Tangstad, Merete

2018-06-01

The kinetic modeling for the carbothermal reduction reaction rate in quartz and carbon black pellets is studied at different temperatures, under varying CO partial pressures in ambient atmosphere, varying carbon contents, different quartz particle sizes, and different crucible opening areas. Carbon black is produced by the cracking of natural gas. The activation energy of the SiC-producing step was determined to be 594 kJ/mol. The averaged pre-exponential factor A obtained from 1898 K, 1923 K, and 1948 K (1625 °C, 1650 °C, and 1675 °C) is 2.62E+16 min-1. The reaction rate of the gas-solid interface factor, fix-C content ( X fix-C), temperature ( T), and CO partial pressure ( X CO) can be expressed as follows: {{d/pct}}{{{d}t}} = (1 - 0.40 × X_{{{fix} - C}}^{ - 0.86} × {pct}) × 2.62 × 10^{16} × \\exp ( { - 594000/RT} ) × (2.6 - 0.015 × X_{co} ).

Kinetics of alkali-based photocathode degradation

DOE PAGES

Pavlenko, Vitaly; Liu, Fangze; Hoffbauer, Mark A.; ...

2016-11-02

Here, we report on a kinetic model that describes the degradation of the quantum efficiency (QE) of Cs 3Sb and negative electron affinity (NEA) GaAs photocathodes under UHV conditions. Additionally, the generally accepted irreversible chemical change of a photocathode’s surface due to reactions with residual gases, such as O 2, CO 2, and H 2O, the model incorporates an intermediate reversible physisorption step, similar to Langmuir adsorption. Moreover, this intermediate step is needed to satisfactorily describe the strongly non-exponential QE degradation curves for two distinctly different classes of photocathodes –surface-activated and “bulk,” indicating that in both systems the QE degradationmore » results from surface damage. The recovery of the QE upon improvement of vacuum conditions is also accurately predicted by this model with three parameters (rates of gas adsorption, desorption, and irreversible chemical reaction with the surface) comprising metrics to better characterize the lifetime of the cathodes, instead of time-pressure exposure expressed in Langmuir units.« less

Kinetics of a Migration-Driven Aggregation-Fragmentation Process

NASA Astrophysics Data System (ADS)

Zhuang, You-Yi; Lin, Zhen-Quan; Ke, Jian-Hong

2003-08-01

We propose a reversible model of the migration-driven aggregation-fragmentation process with the symmetric migration rate kernels K(k;j)=K^'(k;j)=λ kj^v and the constant aggregation rates I1, I2 and fragmentation rates J1, J2. Based on the mean-field theory, we investigate the evolution behavior of the aggregate size distributions in several cases with different values of index υ. We find that the fragmentation reaction plays a more important role in the kinetic behaviors of the system than the aggregation and migration. When J1=0 and J2 =0, the aggregate size distributions ak(t) and bk(t) obey the conventional scaling law, while when J1>0 and J2>0, they obey the modified scaling law with an exponential scaling function. The total mass of either species remains conserved. The project supported by National Natural Science Foundation of China under Grant Nos. 10275048 and 10175008, and Natural Science Foundation of Zhejiang Province of China under Grant No. 102067

Electrostatic Effects in Filamentous Protein Aggregation

PubMed Central

Buell, Alexander K.; Hung, Peter; Salvatella, Xavier; Welland, Mark E.; Dobson, Christopher M.; Knowles, Tuomas P.J.

2013-01-01

Electrostatic forces play a key role in mediating interactions between proteins. However, gaining quantitative insights into the complex effects of electrostatics on protein behavior has proved challenging, due to the wide palette of scenarios through which both cations and anions can interact with polypeptide molecules in a specific manner or can result in screening in solution. In this article, we have used a variety of biophysical methods to probe the steady-state kinetics of fibrillar protein self-assembly in a highly quantitative manner to detect how it is modulated by changes in solution ionic strength. Due to the exponential modulation of the reaction rate by electrostatic forces, this reaction represents an exquisitely sensitive probe of these effects in protein-protein interactions. Our approach, which involves a combination of experimental kinetic measurements and theoretical analysis, reveals a hierarchy of electrostatic effects that control protein aggregation. Furthermore, our results provide a highly sensitive method for the estimation of the magnitude of binding of a variety of ions to protein molecules. PMID:23473495

Kinetics of methane production from the codigestion of switchgrass and Spirulina platensis algae.

PubMed

El-Mashad, Hamed M

2013-03-01

Anaerobic batch digestion of four feedstocks was conducted at 35 and 50 °C: switchgrass; Spirulina platensis algae; and two mixtures of both switchgrass and S. platensis. Mixture 1 was composed of 87% switchgrass (based on volatile solids) and 13% S. platensis. Mixture 2 was composed of 67% switchgrass and 33% S. platensis. The kinetics of methane production from these feedstocks was studied using four first order models: exponential, Gompertz, Fitzhugh, and Cone. The methane yields after 40days of digestion at 35 °C were 355, 127, 143 and 198 ml/g VS, respectively for S. platensis, switchgrass, and Mixtures 1 and 2, while the yields at 50 °C were 358, 167, 198, and 236 ml/g VS, respectively. Based on Akaike's information criterion, the Cone model best described the experimental data. The Cone model was validated with experimental data collected from the digestion of a third mixture that was composed of 83% switchgrass and 17% S. platensis. Published by Elsevier Ltd.

Water Dynamics in Egg White Peptide, Asp-His-Thr-Lys-Glu, Powder Monitored by Dynamic Vapor Sorption and LF-NMR.

PubMed

Yang, Shuailing; Liu, Xuye; Jin, Yan; Li, Xingfang; Chen, Feng; Zhang, Mingdi; Lin, Songyi

2016-03-16

Water absorbed into the bulk amorphous structure of peptides can have profound effects on their properties. Here, we elucidated water dynamics in Asp-His-Thr-Lys-Glu (DHTKE), an antioxidant peptide derived from egg white ovalbumin, using water dynamic vapor sorption (DVS) and low-field nuclear magnetic resonance (LF-NMR). The DVS results indicated that parallel exponential kinetics model fitted well to the data of sorption kinetics behavior of DHTKE. Four different proton fractions with different mobilities were identified based on the degree of interaction between peptide and water. The water could significantly change the proton distribution and structure of the sample. The different phases of moisture absorption were reflected in the T2 parameters. In addition, the combined water content was dominant in the hygroscopicity of DHTKE. This study provides an effective real-time monitoring method for water mobility and distribution in synthetic peptides, and this method may have applications in promoting peptide quality assurance.

Kinetics of lithium peroxide monohydrate thermal decomposition

NASA Astrophysics Data System (ADS)

Nefedov, Roman; Posternak, Nikolay; Ferapontov, Yuriy

2017-11-01

Topochemical dehydration of lithium peroxide was studied to determine kinetic parameters at the range of temperatures from 90°C to 147°C in non-isothermal conditions by derivatographic method. The study was conducted to select optimal conditions of lithium peroxide synthesis in dehydration reaction of triple LiOH-H2O2-H2O system in ultra-high frequency radiation field. Conditions of dehydration reaction were caused by the thermal conductivity of LiOH -H2O2-H2O system. It is determined that dehydration process runs close to the first order reaction (n=0.85±0.03). The activation energy and pre-exponential factor values were found as Eak = 86.0 ± 0.8 kJ/mol, k0 = (2.19 ± 0.16) .1011 min-1, correspondingly. It is supposed that there is a similarity between the dehydration mechanism of lithium peroxide monohydrate and peroxide hydrates of alkaline-earth metals (calcium, barium and strontium).

Temporal and spatial binning of TCSPC data to improve signal-to-noise ratio and imaging speed

NASA Astrophysics Data System (ADS)

Walsh, Alex J.; Beier, Hope T.

2016-03-01

Time-correlated single photon counting (TCSPC) is the most robust method for fluorescence lifetime imaging using laser scanning microscopes. However, TCSPC is inherently slow making it ineffective to capture rapid events due to the single photon product per laser pulse causing extensive acquisition time limitations and the requirement of low fluorescence emission efficiency to avoid bias of measurement towards short lifetimes. Furthermore, thousands of photons per pixel are required for traditional instrument response deconvolution and fluorescence lifetime exponential decay estimation. Instrument response deconvolution and fluorescence exponential decay estimation can be performed in several ways including iterative least squares minimization and Laguerre deconvolution. This paper compares the limitations and accuracy of these fluorescence decay analysis techniques to accurately estimate double exponential decays across many data characteristics including various lifetime values, lifetime component weights, signal-to-noise ratios, and number of photons detected. Furthermore, techniques to improve data fitting, including binning data temporally and spatially, are evaluated as methods to improve decay fits and reduce image acquisition time. Simulation results demonstrate that binning temporally to 36 or 42 time bins, improves accuracy of fits for low photon count data. Such a technique reduces the required number of photons for accurate component estimation if lifetime values are known, such as for commercial fluorescent dyes and FRET experiments, and improve imaging speed 10-fold.

Kinetic concepts of thermally stimulated reactions in solids

NASA Astrophysics Data System (ADS)

Vyazovkin, Sergey

Historical analysis suggests that the basic kinetic concepts of reactions in solids were inherited from homogeneous kinetics. These concepts rest upon the assumption of a single-step reaction that disagrees with the multiple-step nature of solid-state processes. The inadequate concepts inspire such unjustified anticipations of kinetic analysis as evaluating constant activation energy and/or deriving a single-step reaction mechanism for the overall process. A more adequate concept is that of the effective activation energy, which may vary with temperature and extent of conversion. The adequacy of this concept is illustrated by literature data as well as by experimental data on the thermal dehydration of calcium oxalate monohydrate and thermal decomposition of calcium carbonate, ammonium nitrate and 1,3,5,7- tetranitro-1,3,5,7-tetrazocine.

Engineering of an ultra-thin molecular superconductor by charge transfer

DOEpatents

Hla, Saw Wai; Hassanien, Abdelrahim; Kendal, Clark

2016-06-07

A method of forming a superconductive device of a single layer of (BETS).sub.2GaCl.sub.4 molecules on a substrate surface which displays a superconducting gap that increases exponentially with the length of the molecular chain is provided.

Understanding the kinetic mechanism of RNA single base pair formation

PubMed Central

Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

2016-01-01

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

Kinetic Studies of Plasma Chemical Fuel Oxidation in Nanosecond Pulsed Discharges by Single and Two Photon Laser Induced Fluorescence

DTIC Science & Technology

2013-07-01

31st ICPIG, July 14-19, 2013, Granada , Spain Kinetic Studies of Plasma Chemical Fuel Oxidation in Nanosecond Pulsed Discharges by Single and...31st) (ICPIG) Held in Granada , Spain on 14-19 July 2013 14. ABSTRACT Single and two photon Laser Induced Fluorescence (LIF) spectroscopy is used for...Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 31st ICPIG, July 14-19, 2013, Granada , Spain preheat the fuel-air mixture to the furnace

Extreme high temperature redox kinetics in ceria: exploration of the transition from gas-phase to material-kinetic limitations

DOE PAGES

Ji, Ho-Il; Davenport, Timothy C.; Gopal, Chirranjeevi Balaji; ...

2016-07-18

The redox kinetics of undoped ceria (CeO 2-δ) are investigated by the electrical conductivity relaxation method in the oxygen partial pressure range of -4.3 ≤ log(pO 2/atm) ≤ -2.0 at 1400 °C. It is demonstrated that extremely large gas flow rates, relative to the mass of the oxide, are required in order to overcome gas phase limitations and access the material kinetic properties. Using these high flow rate conditions, the surface reaction rate constant k chem is found to obey the correlation log(k chem/cm s -1) = (0.84 ± 0.02) × log(pO 2/atm) - (0.99 ± 0.05) and increases withmore » oxygen partial pressure. This increase contrasts the known behavior of the dominant defect species, oxygen vacancies and free electrons, which decrease in concentration with increasing oxygen partial pressure. For the sample geometries employed, diffusion was too fast to be detected. At low gas flow rates, the relaxation process becomes limited by the capacity of the sweep gas to supply/remove oxygen to/from the oxide. An analytical expression is derived for the relaxation in the gas-phase limited regime, and the result reveals an exponential decay profile, identical in form to that known for a surface reaction limited process. Thus, measurements under varied gas flow rates are required to differentiate between surface reaction limited and gas flow limited behavior.« less

Radical Cations and Acid Protection during Radiolysis

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

Mincher, Bruce J.; Zarzana, Christopher A.; Mezyk, Stephen P.

2016-09-09

Ligand molecules for used nuclear fuel separation schemes are exposed to high radiation fields and high concentrations of acid. Thus, an understanding of the complex interactions between extraction ligands, diluent, and acid is critical to understanding the performance of a separation process. The diglycolamides are ligands with important structural similarities to CMPO; however, previous work has shown that their radiolytic degradation has important mechanistic differences from CMPO. The DGAs do not enjoy radioprotection by HNO3 and the kinetics of DGA radiolytic degradation are different. CMPO degrades with pseudo-zero-order kinetics in linear fashion with absorbed dose while the DGAs degrade inmore » pseudo-first-order, exponential fashion. This suggests that the DGAs degrade by simple reaction with some product of direct diluent radiolysis, while CMPO degradation is probably multi-step, with a slow step that is not dependent on the CMPO concentration, and mitigated by HNO 3. It is thus believed that radio-protection and the zero-order radiolytic degradation kinetics are related, and that these phenomena are a function of either the formation of strong acid complexes with CMPO and/or to the presence of the CMPO phenyl ring. Experiments to test both these hypotheses have been designed and partially conducted. This report summarizes findings related to these phenomena for FY16, in satisfaction of milestone M3FT-16IN030104053. It also reports continued kinetic measurements for the reactions of the dodecane radical cation with solvent extraction ligands.« less

Extreme high temperature redox kinetics in ceria: exploration of the transition from gas-phase to material-kinetic limitations.

PubMed

Ji, Ho-Il; Davenport, Timothy C; Gopal, Chirranjeevi Balaji; Haile, Sossina M

2016-08-03

The redox kinetics of undoped ceria (CeO2-δ) are investigated by the electrical conductivity relaxation method in the oxygen partial pressure range of -4.3 ≤ log(pO2/atm) ≤ -2.0 at 1400 °C. It is demonstrated that extremely large gas flow rates, relative to the mass of the oxide, are required in order to overcome gas phase limitations and access the material kinetic properties. Using these high flow rate conditions, the surface reaction rate constant kchem is found to obey the correlation log(kchem/cm s(-1)) = (0.84 ± 0.02) × log(pO2/atm) - (0.99 ± 0.05) and increases with oxygen partial pressure. This increase contrasts the known behavior of the dominant defect species, oxygen vacancies and free electrons, which decrease in concentration with increasing oxygen partial pressure. For the sample geometries employed, diffusion was too fast to be detected. At low gas flow rates, the relaxation process becomes limited by the capacity of the sweep gas to supply/remove oxygen to/from the oxide. An analytical expression is derived for the relaxation in the gas-phase limited regime, and the result reveals an exponential decay profile, identical in form to that known for a surface reaction limited process. Thus, measurements under varied gas flow rates are required to differentiate between surface reaction limited and gas flow limited behavior.

Rhodopsin kinetics in the cat retina.

PubMed

Ripps, H; Mehaffey, L; Siegel, I M

1981-03-01

The bleaching and regeneration of rhodopsin in the living cat retina was studied by means of fundus reflectometry. Bleaching was effected by continuous light exposures of 1 min or 20 min, and the changes in retinal absorbance were measured at 29 wavelengths. For all of the conditions studied (fractional bleaches of from 65 to 100%), the regeneration of rhodopsin to its prebleach levels required greater than 60 min in darkness. After the 1-min exposures, the difference spectra recorded during the first 10 min of dark adaptation were dominated by photoproduct absorption, and rhodopsin regeneration kinetics were obscured by these intermediate processes. Extending the bleaching duration to 20 min gave the products of photolysis an opportunity to dissipate, and it was possible to follow the regenerative process over its full time-course. It was not possible, however, to fit these data with the simple exponential function predicted by first-order reaction kinetics. Other possible mechanisms were considered and are presented in the text. Nevertheless, the kinetics of regeneration compared favorably with the temporal changes in log sensitivity determined electrophysiologically by other investigators. Based on the bleaching curve for cat rhodopsin, the photosensitivity was determined and found to approximate closely the value obtained for human rhodopsin; i.e., the energy Ec required to bleach 1-e-1 of the available rhodopsin was 7.09 log scotopic troland-seconds (corrected for the optics of the cat eye), as compared with approximately 7.0 in man.

{phi} meson production in Au + Au and p + p collisions at {radical}s{sub NN}=200 GeV

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

Adams, J.; Adler, C.; Aggarwal, M.M.

2004-06-01

We report the STAR measurement of {psi} meson production in Au + Au and p + p collisions at {radical}s{sub NN} = 200 GeV. Using the event mixing technique, the {psi} spectra and yields are obtained at midrapidity for five centrality bins in Au+Au collisions and for non-singly-diffractive p+p collisions. It is found that the {psi} transverse momentum distributions from Au+Au collisions are better fitted with a single-exponential while the p+p spectrum is better described by a double-exponential distribution. The measured nuclear modification factors indicate that {psi} production in central Au+Au collisions is suppressed relative to peripheral collisions when scaledmore » by the number of binary collisions (). The systematics of versus centrality and the constant {psi}/K{sup -} ratio versus beam species, centrality, and collision energy rule out kaon coalescence as the dominant mechanism for {psi} production.« less

Robust Bayesian Fluorescence Lifetime Estimation, Decay Model Selection and Instrument Response Determination for Low-Intensity FLIM Imaging

PubMed Central

Rowley, Mark I.; Coolen, Anthonius C. C.; Vojnovic, Borivoj; Barber, Paul R.

2016-01-01

We present novel Bayesian methods for the analysis of exponential decay data that exploit the evidence carried by every detected decay event and enables robust extension to advanced processing. Our algorithms are presented in the context of fluorescence lifetime imaging microscopy (FLIM) and particular attention has been paid to model the time-domain system (based on time-correlated single photon counting) with unprecedented accuracy. We present estimates of decay parameters for mono- and bi-exponential systems, offering up to a factor of two improvement in accuracy compared to previous popular techniques. Results of the analysis of synthetic and experimental data are presented, and areas where the superior precision of our techniques can be exploited in Förster Resonance Energy Transfer (FRET) experiments are described. Furthermore, we demonstrate two advanced processing methods: decay model selection to choose between differing models such as mono- and bi-exponential, and the simultaneous estimation of instrument and decay parameters. PMID:27355322

Magnetic pattern at supergranulation scale: the void size distribution

NASA Astrophysics Data System (ADS)

Berrilli, F.; Scardigli, S.; Del Moro, D.

2014-08-01

The large-scale magnetic pattern observed in the photosphere of the quiet Sun is dominated by the magnetic network. This network, created by photospheric magnetic fields swept into convective downflows, delineates the boundaries of large-scale cells of overturning plasma and exhibits "voids" in magnetic organization. These voids include internetwork fields, which are mixed-polarity sparse magnetic fields that populate the inner part of network cells. To single out voids and to quantify their intrinsic pattern we applied a fast circle-packing-based algorithm to 511 SOHO/MDI high-resolution magnetograms acquired during the unusually long solar activity minimum between cycles 23 and 24. The computed void distribution function shows a quasi-exponential decay behavior in the range 10-60 Mm. The lack of distinct flow scales in this range corroborates the hypothesis of multi-scale motion flows at the solar surface. In addition to the quasi-exponential decay, we have found that the voids depart from a simple exponential decay at about 35 Mm.

Spacecraft Solar Particle Event (SPE) Shielding: Shielding Effectiveness as a Function of SPE Model as Determined with the FLUKA Radiation Transport Code

NASA Astrophysics Data System (ADS)

Koontz, S. L.; Atwell, W. A.; Reddell, B.; Rojdev, K.

2010-12-01

In the this paper, we report the results of modeling and simulation studies in which the radiation transport code FLUKA (FLUktuierende KAskade) is used to determine the changes in total ionizing dose (TID) and single-event effect (SEE) environments behind aluminum, polyethylene, carbon, and titanium shielding masses when the assumed form (i.e., Band or Exponential) of the solar particle event (SPE) kinetic energy spectra is changed. FLUKA simulations are fully three dimensional with an isotropic particle flux incident on a concentric spherical shell shielding mass and detector structure. FLUKA is a fully integrated and extensively verified Monte Carlo simulation package for the interaction and transport of high-energy particles and nuclei in matter. The effects are reported of both energetic primary protons penetrating the shield mass and secondary particle showers caused by energetic primary protons colliding with shielding mass nuclei. SPE heavy ion spectra are not addressed. Our results, in agreement with previous studies, show that use of the Exponential form of the event spectra can seriously underestimate spacecraft SPE TID and SEE environments in some, but not all, shielding mass cases. The SPE spectra investigated are taken from four specific SPEs that produced ground-level events (GLEs) during solar cycle 23 (1997-2008). GLEs are produced by highly energetic solar particle events (ESP), i.e., those that contain significant fluences of 700 MeV to 10 GeV protons. Highly energetic SPEs are implicated in increased rates of spacecraft anomalies and spacecraft failures. High-energy protons interact with Earth’s atmosphere via nuclear reaction to produce secondary particles, some of which are neutrons that can be detected at the Earth’s surface by the global neutron monitor network. GLEs are one part of the overall SPE resulting from a particular solar flare or coronal mass ejection event on the sun. The ESP part of the particle event, detected by spacecraft, is often associated with the arrival of a “shock front” at Earth some hours after the arrival of the GLE. The specific SPEs used in this analysis are those of: 1) November 6, 1997 - GLE only; 2) July 14-15, 2000 - GLE from the 14th plus ESP from the 15th; 3) November 4-6, 2001 - GLE and ESP from the 4th; and 4) October 28-29, 2003 - GLE and ESP from the 28th plus GLE from the 29th. The corresponding Band and Exponential spectra used in this paper are like those previously reported.

Nonclassical Kinetics of Clonal yet Heterogeneous Enzymes.

PubMed

Park, Seong Jun; Song, Sanggeun; Jeong, In-Chun; Koh, Hye Ran; Kim, Ji-Hyun; Sung, Jaeyoung

2017-07-06

Enzyme-to-enzyme variation in the catalytic rate is ubiquitous among single enzymes created from the same genetic information, which persists over the lifetimes of living cells. Despite advances in single-enzyme technologies, the lack of an enzyme reaction model accounting for the heterogeneous activity of single enzymes has hindered a quantitative understanding of the nonclassical stochastic outcome of single enzyme systems. Here we present a new statistical kinetics and exactly solvable models for clonal yet heterogeneous enzymes with possibly nonergodic state dynamics and state-dependent reactivity, which enable a quantitative understanding of modern single-enzyme experimental results for the mean and fluctuation in the number of product molecules created by single enzymes. We also propose a new experimental measure of the heterogeneity and nonergodicity for a system of enzymes.

Kinetics of molecular transitions with dynamic disorder in single-molecule pulling experiments

NASA Astrophysics Data System (ADS)

Zheng, Yue; Li, Ping; Zhao, Nanrong; Hou, Zhonghuai

2013-05-01

Macromolecular transitions are subject to large fluctuations of rate constant, termed as dynamic disorder. The individual or intrinsic transition rates and activation free energies can be extracted from single-molecule pulling experiments. Here we present a theoretical framework based on a generalized Langevin equation with fractional Gaussian noise and power-law memory kernel to study the kinetics of macromolecular transitions to address the effects of dynamic disorder on barrier-crossing kinetics under external pulling force. By using the Kramers' rate theory, we have calculated the fluctuating rate constant of molecular transition, as well as the experimentally accessible quantities such as the force-dependent mean lifetime, the rupture force distribution, and the speed-dependent mean rupture force. Particular attention is paid to the discrepancies between the kinetics with and without dynamic disorder. We demonstrate that these discrepancies show strong and nontrivial dependence on the external force or the pulling speed, as well as the barrier height of the potential of mean force. Our results suggest that dynamic disorder is an important factor that should be taken into account properly in accurate interpretations of single-molecule pulling experiments.

Influence of film structure on the dewetting kinetics of thin polymer films in the solvent annealing process.

PubMed

Zhang, Huanhuan; Xu, Lin; Lai, Yuqing; Shi, Tongfei

2016-06-28

On a non-wetting solid substrate, the solvent annealing process of a thin polymer film includes the swelling process and the dewetting process. Owing to difficulties in the in situ analysis of the two processes simultaneously, a quantitative study on the solvent annealing process of thin polymer films on the non-wetting solid substrate is extremely rare. In this paper, we design an experimental method by combining spectroscopic ellipsometry with optical microscopy to achieve the simultaneous in situ study. Using this method, we investigate the influence of the structure of swollen film on its dewetting kinetics during the solvent annealing process. The results show that for a thin PS film with low Mw (Mw = 4.1 kg mol(-1)), acetone molecules can form an ultrathin enriched layer between the PS film and the solid substrate during the swelling process. The presence of the acetone enriched layer accounts for the exponential kinetic behavior in the case of a thin PS film with low Mw. However, the acetone enriched layer is not observed in the case of a thin PS film with high Mw (Mw = 400 kg mol(-1)) and the slippage effect of polymer chains is valid during the dewetting process.

Fluorescence stopped-flow study of the interaction of tubulin with the antimitotic drug MDL 27048.

PubMed

Silence, K; D'Hoore, A; Engelborghs, Y; Peyrot, V; Briand, C

1992-11-17

The kinetics of the binding of MDL 27048 to tubulin have been studied by fluorescence stopped flow. The binding is accompanied by a fluorescence increase. The time course can be described by a sum of two exponentials, assumed to be due to the presence of two major tubulin isoforms. The observed rate constants depend in a nonlinear way on the concentration of MDL in pseudo-first-order conditions. This concentration dependence can be described by the presence of a fast equilibrium of low affinity, followed by an isomerization of the initial complex. The dissociation kinetics have been studied by displacement experiments, in which MTC was used as a competitive ligand. The reaction enthalpy change for the first binding equilibrium and the activation energies for the forward and reverse steps of the isomerization were determined from the temperature dependence. This was possible for the two tubulin isotype populations. The kinetics of the binding of MDL to tubulin are slowed down in the presence of 3',4',5'-trimethoxyacetophenone, a fast binding analog of the colchicine A-ring, but are not influenced by the binding of tropolone methyl ether, indicating that the binding site of MDL has the A-subsite in common with colchicine, but not the C-subsite.

Thermodynamic and kinetic characterization of polycyclic aromatic hydrocarbons in reversed-phase liquid chromatography.

PubMed

Howerton, Samuel B; McGuffin, Victoria L

2003-07-15

The retention of six polycyclic aromatic hydrocarbons (PAHs) was characterized by reversed-phase liquid chromatography. The PAHs were detected by laser-induced fluorescence at four points along an optically transparent capillary column. The profiles were characterized in space and time using an exponentially modified Gaussian equation. The resulting parameters were used to calculate the retention factors, as well as the concomitant changes in molar enthalpy and molar volume, for each PAH on monomeric (2.7 micromol/m2) and polymeric (5.4 micromol/m2) octadecylsilica. The changes in molar enthalpy become more exothermic as ring number increases and as annelation structure becomes less condensed. The changes in molar volume become more negative as ring number increases for the planar PAHs, but are positive for the nonplanar solutes. In addition, the rate constants, as well as the concomitant activation enthalpy and activation volume, are calculated for the first time. The kinetic data demonstrate that many of the PAHs exhibit very fast transitions between the mobile and stationary phases. The transition state is very high in energy, and the activation enthalpies and volumes become greater as ring number increases and as annelation structure becomes less condensed. The changes in thermodynamic and kinetic behavior are much more pronounced for the polymeric phase than for the monomeric phase.

Kinetic study of the thermal hydrolysis of Agave salmiana for mezcal production.

PubMed

Garcia-Soto, M J; Jimenez-Islas, H; Navarrete-Bolanos, J L; Rico-Martinez, R; Miranda-Lopez, R; Botello-Alvarez, J E

2011-07-13

The kinetics of the thermal hydrolysis of the fructans of Agave salmiana were determined during the cooking step of mezcal production in a pilot autoclave. Thermal hydrolysis was achieved at different temperatures and cooking times, ranging from 96 to 116 °C and from 20 to 80 h. A simple kinetic model of the depolymerization of fructans to monomers and other reducing sugars and of the degradation of reducing sugars to furans [principally 5-(hydroxymethyl)furfural, HMF] was developed. From this model, the rate constants of the reactions were calculated, as well as the pre-exponential factors and activation energies of the Arrhenius equation. The model was found to fit the experimental data well. The tradeoff between a maximum fructan hydrolysis and a critical furan concentration in allowing for the best ethanol yield during fermentation was investigated. The results indicated that the thermal hydrolysis of agave was optimal, from the point of view of ethanol yield in the ensuing fermentation, in the temperature range of 106-116 °C and the cooking range time of 6-14 h. The optimal conditions corresponded to a fructan hydrolysis of 80%, producing syrups with furan and reducing sugar concentrations of 1 ± 0.1 and 110 ± 10 g/L, respectively.

Callus Growth Kinetics of Physic Nut (Jatropha curcas L.) and Content of Fatty Acids from Crude Oil Obtained In Vitro.

PubMed

da Luz Costa, Jefferson; da Silva, André Luís Lopes; Bier, Mário César Jucoski; Brondani, Gilvano Ebling; Gollo, André Luiz; Letti, Luiz Alberto Junior; Erasmo, Eduardo Andrea Lemus; Soccol, Carlos Ricardo

2015-06-01

The callus growth kinetics allows identifying the appropriate moment for callus pealing and monitoring the accumulation of primary and secondary metabolites. The physic nut (Jatropha curcas L.) is a plant species used for biofuel production due to its high oil content; however, this plant presents a great amount of bioactive compounds which can be useful for industry. The aim of this research was to establish a calli growth curve and to evaluate the fatty acid profile of crude oil extracted from callus. The callus growth kinetics presented a sigmoid standard curve with six distinct phases: lag, exponential, linear, deceleration, stationary, and decline. Total soluble sugars were higher at the inoculation day. Reducing sugars were higher at the inoculation day and at the 80th day. The highest percentage of ethereal extract (oil content) was obtained at the 120th day of culture, reaching 18 % of crude oil from the callus. The calli produced medium-chain and long-chain fatty acids (from 10 to 18 carbon atoms). The palmitic acid was the fatty acid with the highest proportion in oil (55.4 %). The lipid profile obtained in callus oil was different from the seed oil profile.

Thermal stabilities of drops of burning thermoplastics under the UL 94 vertical test conditions.

PubMed

Wang, Yong; Zhang, Jun

2013-02-15

The properties of polymer melts will strongly affect the fire hazard of the pool induced by polymer melt flow. In this study the thermal stabilities of eight thermoplastic polymers as well as their melting drops generated under the UL 94 vertical burning test conditions were investigated by thermogravimetric experiments. It was found that the kinetic compensation effect existed for the decomposition reactions of the polymers and their drops. For polymethylmethacrylate (PMMA), high impact polystyrene (HIPS), poly(acrylonitrile-butadiene-styrene) (ABS), polyamide 6 (PA6), polypropylene (PP) and low density polyethylene (LDPE), the onset decomposition temperature and the two decomposition kinetic parameters (the pre-exponential factor and the activation energy) of the drop were less than those of the polymer. However, the onset decomposition temperature and the two kinetic parameters of PC's drop were greater than those of polycarbonate (PC). Interestingly, for polyethylenevinylacetate (EVA18) the drop hardly contained the vinyl acetate chain segments. Similarly, for the PMMA/LDPE blends and the PMMA/PP blends, when the volume fraction of PMMA was less than 50% the drop hardly contained PMMA, implying that the blend would not drip until PMMA burned away and its surface temperature approached the decomposition temperature of the continuous phase composed of LDPE or PP. Copyright © 2012 Elsevier B.V. All rights reserved.

The Distribution of Chromosomal Aberrations in Human Cells Predicted by a Generalized Time-Dependent Model of Radiation-Induced Formation of Aberrations

NASA Technical Reports Server (NTRS)

Ponomarev, Artem L.; George, K.; Cucinotta, F. A.

2011-01-01

New experimental data show how chromosomal aberrations for low- and high-LET radiation are dependent on DSB repair deficiencies in wild-type, AT and NBS cells. We simulated the development of chromosomal aberrations in these cells lines in a stochastic track-structure-dependent model, in which different cells have different kinetics of DSB repair. We updated a previously formulated model of chromosomal aberrations, which was based on a stochastic Monte Carlo approach, to consider the time-dependence of DSB rejoining. The previous version of the model had an assumption that all DSBs would rejoin, and therefore we called it a time-independent model. The chromosomal-aberrations model takes into account the DNA and track structure for low- and high-LET radiations, and provides an explanation and prediction of the statistics of rare and more complex aberrations. We compared the program-simulated kinetics of DSB rejoining to the experimentally-derived bimodal exponential curves of the DSB kinetics. We scored the formation of translocations, dicentrics, acentric and centric rings, deletions, and inversions. The fraction of DSBs participating in aberrations was studied in relation to the rejoining time. Comparisons of simulated dose dependence for simple aberrations to the experimental dose-dependence for HF19, AT and NBS cells will be made.

Electrical energy per order and current efficiency for electrochemical oxidation of p-chlorobenzoic acid with boron-doped diamond anode.

PubMed

Lanzarini-Lopes, Mariana; Garcia-Segura, Sergi; Hristovski, Kiril; Westerhoff, Paul

2017-12-01

Electrochemical oxidation (EO) is an advanced oxidation process for water treatment to mineralize organic contaminants. While proven to degrade a range of emerging pollutants in water, less attention has been given to quantify the effect of operational variables such applied current density and pollutant concentration on efficiency and energy requirements. Particular figures of merit were mineralization current efficiency (MCE) and electrical energy per order (E EO ). Linear increases of applied current exponentially decreased the MCE due to the enhancement of undesired parasitic reactions that consumed generated hydroxyl radical. E EO values ranged from 39.3 to 331.8 kW h m -3 order -1 . Increasing the applied current also enhanced the E EO due to the transition from kinetics limited by current to kinetics limited by mass transfer. Further increases in current did not influence the removal rate, but it raised the E EO requirement. The E EO requirement diminished when decreasing initial pollutant loading with the increase of the apparent kinetic rate because of the relative availability of oxidant per pollutant molecule in solution at a defined current. Oxidation by-products released were identified, and a plausible degradative pathway has been suggested. Copyright © 2017. Published by Elsevier Ltd.

CO₂ sorption kinetics of scaled-up polyethylenimine-functionalized mesoporous silica sorbent.

PubMed

Al-Marri, M J; Khader, M M; Tawfik, M; Qi, G; Giannelis, E P

2015-03-31

Two CO2 solid sorbents based on polyethylenimine, PEI (M(n) ∼ 423 and 10K), impregnated into mesoporous silica (MPS) foam prepared in kilogram quantities via a scale-up process were synthesized and systematically characterized by a range of analytical and surface techniques. The mesoporous silica sorbent impregnated with lower molecular weight PEI, PEI-423/MPS, showed higher capacity toward CO2 sorption than the sorbent functionalized with the higher molecular weight PEI (PEI-10K/MPS). On the other hand, PEI-10K/MPS exhibited higher thermal stability than PEI-423/MPS. The kinetics of CO2 adsorption on both PEI/MPS fitted well with a double-exponential model. According to this model CO2 adsorption can be divided into two steps: the first is fast and is attributed to CO2 adsorption on the sorbent surface; the second is slower and can be related to the diffusion of CO2 within and between the mesoporous particles. In contrast, the desorption process obeyed first-order kinetics with activation energies of 64.3 and 140.7 kJ mol(-1) for PEI-423/MPS and PEI-10K/MPS, respectively. These studies suggest that the selection of amine is critical as it affects not only sorbent capacity and stability but also the energy penalty associated with sorbent regeneration.

Effect of soil parameters on the kinetics of the displacement of Fe from FeEDDHA chelates by Cu.

PubMed

Schenkeveld, Walter D C; Reichwein, Arjen M; Temminghoff, Erwin J M; van Riemsdijk, Willem H

2012-06-28

In soil application, o,o-FeEDDHA (iron (3+) ethylene diamine-N,N'-bis(2-hydroxy phenyl acetic acid) complex) is the active ingredient of FeEDDHA chelate-based Fe fertilizers. The effectiveness of o,o-FeEDDHA is potentially compromised by the displacement of Fe from FeEDDHA by Cu. The actual impact of Cu competition is codetermined by the kinetics of the displacement reaction. In this study, the influence of soil parameters on the displacement kinetics has been examined in goethite suspensions. The displacement reaction predominantly takes place on the reactive surface rather than in solution. The rate at which the o,o-FeEDDHA concentration declined depended on the available reactive surface area, the Cu loading, and the FeEDDHA loading. Soil factors reducing FeEDDHA adsorption (high ionic strength, humic acid adsorption onto the goethite surface, and monovalent instead of divalent cations in the electrolyte) decreased the displacement rate. For meso o,o-FeEDDHA, the displacement rate equation was derived, which is first order in FeEDDHA loading and half order in Cu loading. For soil conditions, the equation can be simplified to an exponential decay function in meso o,o-FeEDDHA solution concentration.

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Pulsed IR Heating Studies of Single-Molecule DNA Duplex Dissociation Kinetics and Thermodynamics

PubMed Central

Holmstrom, Erik D.; Dupuis, Nicholas F.; Nesbitt, David J.

2014-01-01

Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10−11 liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20–100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation. PMID:24411254

Ordering kinetics in two-dimensional hexagonal pattern of cylinder-forming PS-b -PMMA block copolymer thin films: Dependence on the segregation strength

NASA Astrophysics Data System (ADS)

Seguini, Gabriele; Zanenga, Fabio; Laus, Michele; Perego, Michele

2018-05-01

This paper reports the experimental determination of the growth exponents and activation enthalpies for the ordering process of standing cylinder-forming all-organic polystyrene-block-poly (methyl methacrylate) block copolymer (BCP) thin films as a function of the BCP degree of polymerization (N). The maximum growth exponent of 1/3 is observed for the BCP with the lowest N at the border of the order-disorder transition. Both the growth exponents and the activation enthalpies exponentially decrease with the BCP segregation strength (χN) following the same path of the diffusivity.

Chemical networks with inflows and outflows: a positive linear differential inclusions approach.

PubMed

Angeli, David; De Leenheer, Patrick; Sontag, Eduardo D

2009-01-01

Certain mass-action kinetics models of biochemical reaction networks, although described by nonlinear differential equations, may be partially viewed as state-dependent linear time-varying systems, which in turn may be modeled by convex compact valued positive linear differential inclusions. A result is provided on asymptotic stability of such inclusions, and applied to a ubiquitous biochemical reaction network with inflows and outflows, known as the futile cycle. We also provide a characterization of exponential stability of general homogeneous switched systems which is not only of interest in itself, but also plays a role in the analysis of the futile cycle. 2009 American Institute of Chemical Engineers

Bounded energy states in homogeneous turbulent shear flow - An alternative view

NASA Technical Reports Server (NTRS)

Bernard, P. S.; Speziale, C. G.

1992-01-01

The equilibrium structure of homogeneous turbulent shear flow is investigated from a theoretical standpoint. Existing turbulence models, in apparent agreement with physical and numerical experiments, predict an unbounded exponential time growth of the turbulent kinetic energy and dissipation rate; only the anisotropy tensor and turbulent time scale reach a structural equilibrium. It is shown that if a residual vortex stretching term is maintained in the dissipation rate transport equation, then there can exist equilibrium solutions, with bounded energy states, where the turbulence production is balanced by its dissipation. Illustrative calculations are presented for a k-epsilon model modified to account for net vortex stretching.

Weight-controlled capillary viscometer

NASA Astrophysics Data System (ADS)

Digilov, Rafael M.; Reiner, M.

2005-11-01

The draining of a water column through a vertical discharge capillary tube is examined with the aid of a force sensor. The change of the mass of the liquid in the column with time is found to be not purely exponential as implied by Poiseuille's law. Using observed residuals associated with a kinetic energy correction, an approximate formula for the mass as a function of time is derived and excellent agreement with experimental data is attained. These results are verified by a viscosity test of distilled water at room temperature. A simple and inexpensive weight-controlled capillary viscometer is proposed that is especially suitable for undergraduate physics and chemistry laboratories.

CRITICAL TESTS FOR PRT REACTOR

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

Triplett, J.R.; Anderson, J.K.; Dunn, R.E.

1960-07-01

Critical teste to be performed on the Plutonium Recycle Te st Heactor are described. Exponential, approach-tocritical, critical, and substitution experiments will be carried out. These experiments include: calibration of moderator level; determination of the wori of various fuel loadings; calibration of the shim system including determination of maximum control strength of the entire system; substitution experiments to determine reflector savings, void effects, effects of H/sub 2/O and degraded D/sub 2/O coolants, and effects of loop and other material intsllations; determination of fuel-plus-coolant and moderator temperature coefficients; and kinetic experiments to determine response of the reactor to reactivity changes. (M.C.G.)

MHz gravitational waves from short-term anisotropic inflation

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

Ito, Asuka; Soda, Jiro

2016-04-18

We reveal the universality of short-term anisotropic inflation. As a demonstration, we study inflation with an exponential type gauge kinetic function which is ubiquitous in models obtained by dimensional reduction from higher dimensional fundamental theory. It turns out that an anisotropic inflation universally takes place in the later stage of conventional inflation. Remarkably, we find that primordial gravitational waves with a peak amplitude around 10{sup −26}∼10{sup −27} are copiously produced in high-frequency bands 10 MHz∼100 MHz. If we could detect such gravitational waves in future, we would be able to probe higher dimensional fundamental theory.

Side-binding proteins modulate actin filament dynamics

PubMed Central

Crevenna, Alvaro H; Arciniega, Marcelino; Dupont, Aurélie; Mizuno, Naoko; Kowalska, Kaja; Lange, Oliver F; Wedlich-Söldner, Roland; Lamb, Don C

2015-01-01

Actin filament dynamics govern many key physiological processes from cell motility to tissue morphogenesis. A central feature of actin dynamics is the capacity of filaments to polymerize and depolymerize at their ends in response to cellular conditions. It is currently thought that filament kinetics can be described by a single rate constant for each end. In this study, using direct visualization of single actin filament elongation, we show that actin polymerization kinetics at both filament ends are strongly influenced by the binding of proteins to the lateral filament surface. We also show that the pointed-end has a non-elongating state that dominates the observed filament kinetic asymmetry. Estimates of flexibility as well as effects on fragmentation and growth suggest that the observed kinetic diversity arises from structural alteration. Tuning elongation kinetics by exploiting the malleability of the filament structure may be a ubiquitous mechanism to generate a rich variety of cellular actin dynamics. DOI: http://dx.doi.org/10.7554/eLife.04599.001 PMID:25706231

Modeling the pressure inactivation of Escherichia coli and Salmonella typhimurium in sapote mamey ( Pouteria sapota (Jacq.) H.E. Moore & Stearn) pulp.

PubMed

Saucedo-Reyes, Daniela; Carrillo-Salazar, José A; Román-Padilla, Lizbeth; Saucedo-Veloz, Crescenciano; Reyes-Santamaría, María I; Ramírez-Gilly, Mariana; Tecante, Alberto

2018-03-01

High hydrostatic pressure inactivation kinetics of Escherichia coli ATCC 25922 and Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14028 ( S. typhimurium) in a low acid mamey pulp at four pressure levels (300, 350, 400, and 450 MPa), different exposure times (0-8 min), and temperature of 25 ± 2℃ were obtained. Survival curves showed deviations from linearity in the form of a tail (upward concavity). The primary models tested were the Weibull model, the modified Gompertz equation, and the biphasic model. The Weibull model gave the best goodness of fit ( R 2 adj  > 0.956, root mean square error < 0.290) in the modeling and the lowest Akaike information criterion value. Exponential-logistic and exponential decay models, and Bigelow-type and an empirical models for b'( P) and n( P) parameters, respectively, were tested as alternative secondary models. The process validation considered the two- and one-step nonlinear regressions for making predictions of the survival fraction; both regression types provided an adequate goodness of fit and the one-step nonlinear regression clearly reduced fitting errors. The best candidate model according to the Akaike theory information, with better accuracy and more reliable predictions was the Weibull model integrated by the exponential-logistic and exponential decay secondary models as a function of time and pressure (two-step procedure) or incorporated as one equation (one-step procedure). Both mathematical expressions were used to determine the t d parameter, where the desired reductions ( 5D) (considering d = 5 ( t 5 ) as the criterion of 5 Log 10 reduction (5 D)) in both microorganisms are attainable at 400 MPa for 5.487 ± 0.488 or 5.950 ± 0.329 min, respectively, for the one- or two-step nonlinear procedure.

Pulmonary Oxygen Uptake Kinetics During Exercise in Subclinical Hypothyroidism

PubMed Central

Coelho, Emerson Filipino; de Lima, Jorge Roberto Perrout; Laterza, Mateus Camaroti; Barral, Marselha Marques; Teixeira, Patrícia de Fátima dos Santos; Vaisman, Mário

2014-01-01

Background: Patients with subclinical hypothyroidism (SCH) have lower exercise tolerance, but the impact on oxygen uptake (VO2) kinetics is unknown. This study evaluated VO2 kinetics during and after a constant load submaximal exercise in SCH. Methods: The study included 19 women with SCH (thyrotropin (TSH)=6.87±2.88 μIU/mL, free thyroxine (fT4)=0.97±0.15 ng/dL) and 19 controls (TSH=2.29±0.86 μIU/mL, T4=0.99±0.11 ng/dL) aged between 20 and 55 years. Ergospirometry exercise testing was performed for six minutes with a constant load of 50 W, followed by six minutes of passive recovery. The VO2 kinetics was quantified by the mean response time (MRT), which is the exponential time constant and approximates the time needed to reach 63% of change in VO2 (ΔVO2). The O2 deficit—energy supplied by anaerobic metabolism at the onset of exercise—and O2 debit—extra energy demand during the recovery period—were calculated by the formula MRT×ΔVO2. Values are mean±standard deviation. Results: In the rest-exercise transition, patients with SCH showed slower VO2 kinetics (MRT=47±8 sec vs. 40±6 sec, p=0.004) and a higher oxygen deficit (580±102 mL vs. 477±95 mL, p=0.003) than controls respectively. In the exercise-recovery transition, patients with SCH also showed slower VO2 kinetics (MRT=54±6 sec vs. 44±6 sec, p=0.001) and a higher oxygen debit (679±105 mL vs. 572±104 mL, p=0.003). The VO2 kinetics showed a significant correlation with TSH (p<0.05). Conclusions: This study demonstrates that women with SCH have the slowest VO2 kinetics in the onset and recovery of a constant-load submaximal exercise and highlights that this impairment is already manifest in the early stage of the disease. PMID:24512502

Pulmonary oxygen uptake kinetics during exercise in subclinical hypothyroidism.

PubMed

Werneck, Francisco Zacaron; Coelho, Emerson Filipino; de Lima, Jorge Roberto Perrout; Laterza, Mateus Camaroti; Barral, Marselha Marques; Teixeira, Patrícia de Fátima Dos Santos; Vaisman, Mário

2014-06-01

Patients with subclinical hypothyroidism (SCH) have lower exercise tolerance, but the impact on oxygen uptake (VO2) kinetics is unknown. This study evaluated VO2 kinetics during and after a constant load submaximal exercise in SCH. The study included 19 women with SCH (thyrotropin (TSH)=6.87±2.88 μIU/mL, free thyroxine (fT4)=0.97±0.15 ng/dL) and 19 controls (TSH=2.29±0.86 μIU/mL, T4=0.99±0.11 ng/dL) aged between 20 and 55 years. Ergospirometry exercise testing was performed for six minutes with a constant load of 50 W, followed by six minutes of passive recovery. The VO2 kinetics was quantified by the mean response time (MRT), which is the exponential time constant and approximates the time needed to reach 63% of change in VO2 (ΔVO2). The O2 deficit-energy supplied by anaerobic metabolism at the onset of exercise-and O2 debit-extra energy demand during the recovery period-were calculated by the formula MRT×ΔVO2. Values are mean±standard deviation. In the rest-exercise transition, patients with SCH showed slower VO2 kinetics (MRT=47±8 sec vs. 40±6 sec, p=0.004) and a higher oxygen deficit (580±102 mL vs. 477±95 mL, p=0.003) than controls respectively. In the exercise-recovery transition, patients with SCH also showed slower VO2 kinetics (MRT=54±6 sec vs. 44±6 sec, p=0.001) and a higher oxygen debit (679±105 mL vs. 572±104 mL, p=0.003). The VO2 kinetics showed a significant correlation with TSH (p<0.05). This study demonstrates that women with SCH have the slowest VO2 kinetics in the onset and recovery of a constant-load submaximal exercise and highlights that this impairment is already manifest in the early stage of the disease.

Increased knee valgus alignment and moment during single-leg landing after overhead stroke as a potential risk factor of anterior cruciate ligament injury in badminton.

PubMed

Kimura, Yuka; Ishibashi, Yasuyuki; Tsuda, Eiichi; Yamamoto, Yuji; Hayashi, Yoshimitsu; Sato, Shuichi

2012-03-01

In badminton, knees opposite to the racket-hand side received anterior cruciate ligament (ACL) injuries during single-leg landing after overhead stroke. Most of them occurred in the backhand-side of the rear court. Comparing lower limb biomechanics during single-leg landing after overhead stroke between the forehand-side and backhand-side court may help explain the different injury rates depending on court position. The knee kinematics and kinetics during single-leg landing after overhead stroke following back-stepping were different between the forehand-side and backhand-side court. Controlled laboratory study. Hip, knee and ankle joint kinematic and knee kinetic data were collected for 17 right-handed female college badminton players using a 3-dimensional motion analysis system. Subjects performed single-left-legged landing after an overhead stroke following left and right back-stepping. The kinematic and kinetic data of the left lower extremities during landing were measured and compared between left and right back-steps. Hip flexion and abduction and knee valgus at the initial contact, hip and knee flexion and knee valgus at the maximum knee flexion and the maximum knee valgus moment were significantly larger for the left back-step than the right back-step (p<0.05). Significant differences in joint kinematics and kinetics of the lower extremity during single-leg landing after overhead stroke were observed between different back-step directions. Increased knee valgus angle and moment following back-stepping to the backhand-side might be related to the higher incidence of ACL injury during single-leg landing after overhead stroke.

Configurational Entropy Approach to the Kinetics of Glasses

PubMed Central

Di Marzio, Edmund A.; Yang, Arthur J. M.

1997-01-01

A kinetic theory of glasses is developed using equilibrium theory as a foundation. After establishing basic criteria for glass formation and the capability of the equilibrium entropy theory to describe the equilibrium aspects of glass formation, a minimal model for the glass kinetics is proposed. Our kinetic model is based on a trapping description of particle motion in which escapes from deep wells provide the rate-determining steps for motion. The formula derived for the zero frequency viscosity η (0,T) is log η (0,T) = B − AF(T)kT where F is the free energy and T the temperature. Contrast this to the Vogel-Fulcher law log η (0,T) = B + A/(T − Tc). A notable feature of our description is that even though the location of the equilibrium second-order transition in temperature-pressure space is given by the break in the entropy or volume curves the viscosity and its derivative are continuous through the transition. The new expression for η (0,T) has no singularity at a critical temperature Tc as in the Vogel-Fulcher law and the behavior reduces to the Arrhenius form in the glass region. Our formula for η (0,T) is discussed in the context of the concepts of strong and fragile glasses, and the experimentally observed connection of specific heat to relaxation response in a homologous series of polydimethylsiloxane is explained. The frequency and temperature dependencies of the complex viscosity η (ω< T), the diffusion coefficient D(ω< T), and the dielectric response ε (ω< T) are also obtained for our kinetic model and found to be consistent with stretched exponential behavior. PMID:27805133

Active matter beyond mean-field: ring-kinetic theory for self-propelled particles.

PubMed

Chou, Yen-Liang; Ihle, Thomas

2015-02-01

Recently, Hanke et al. [Phys. Rev. E 88, 052309 (2013)] showed that mean-field kinetic theory fails to describe collective motion in soft active colloids and that correlations must not be neglected. Correlation effects are also expected to be essential in systems of biofilaments driven by molecular motors and in swarms of midges. To obtain correlations in an active matter system from first principles, we derive a ring-kinetic theory for Vicsek-style models of self-propelled agents from the exact N-particle evolution equation in phase space. The theory goes beyond mean-field and does not rely on Boltzmann's approximation of molecular chaos. It can handle precollisional correlations and cluster formation, which are both important to understand the phase transition to collective motion. We propose a diagrammatic technique to perform a small-density expansion of the collision operator and derive the first two equations of the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy. An algorithm is presented that numerically solves the evolution equation for the two-particle correlations on a lattice. Agent-based simulations are performed and informative quantities such as orientational and density correlation functions are compared with those obtained by ring-kinetic theory. Excellent quantitative agreement between simulations and theory is found at not-too-small noises and mean free paths. This shows that there are parameter ranges in Vicsek-like models where the correlated closure of the BBGKY hierarchy gives correct and nontrivial results. We calculate the dependence of the orientational correlations on distance in the disordered phase and find that it seems to be consistent with a power law with an exponent around -1.8, followed by an exponential decay. General limitations of the kinetic theory and its numerical solution are discussed.

Time-Resolved O3 Chemical Chain Reaction Kinetics Via High-Resolution IR Laser Absorption Methods

NASA Technical Reports Server (NTRS)

Kulcke, Axel; Blackmon, Brad; Chapman, William B.; Kim, In Koo; Nesbitt, David J.

1998-01-01

Excimer laser photolysis in combination with time-resolved IR laser absorption detection of OH radicals has been used to study O3/OH(v = 0)/HO2 chain reaction kinetics at 298 K, (i.e.,(k(sub 1) is OH + 03 yields H02 + 02 and (k(sub 2) is H02 + 03 yields OH + 202). From time-resolved detection of OH radicals with high-resolution near IR laser absorption methods, the chain induction kinetics have been measured at up to an order of magnitude higher ozone concentrations ([03] less than or equal to 10(exp 17) molecules/cu cm) than accessible in previous studies. This greater dynamic range permits the full evolution of the chain induction, propagation, and termination process to be temporally isolated and measured in real time. An exact solution for time-dependent OH evolution under pseudo- first-order chain reaction conditions is presented, which correctly predicts new kinetic signatures not included in previous OH + 03 kinetic analyses. Specifically, the solutions predict an initial exponential loss (chain "induction") of the OH radical to a steady-state level ([OH](sub ss)), with this fast initial decay determined by the sum of both chain rate constants, k(sub ind) = k(sub 1) + k(sub 2). By monitoring the chain induction feature, this sum of the rate constants is determined to be k(sub ind) = 8.4(8) x 10(exp -14) cu cm/molecule/s for room temperature reagents. This is significantly higher than the values currently recommended for use in atmospheric models, but in excellent agreement with previous results from Ravishankara et al.

Enhanced Response Time of Electrowetting Lenses with Shaped Input Voltage Functions.

PubMed

Supekar, Omkar D; Zohrabi, Mo; Gopinath, Juliet T; Bright, Victor M

2017-05-16

Adaptive optical lenses based on the electrowetting principle are being rapidly implemented in many applications, such as microscopy, remote sensing, displays, and optical communication. To characterize the response of these electrowetting lenses, the dependence upon direct current (DC) driving voltage functions was investigated in a low-viscosity liquid system. Cylindrical lenses with inner diameters of 2.45 and 3.95 mm were used to characterize the dynamic behavior of the liquids under DC voltage electrowetting actuation. With the increase of the rise time of the input exponential driving voltage, the originally underdamped system response can be damped, enabling a smooth response from the lens. We experimentally determined the optimal rise times for the fastest response from the lenses. We have also performed numerical simulations of the lens actuation with input exponential driving voltage to understand the variation in the dynamics of the liquid-liquid interface with various input rise times. We further enhanced the response time of the devices by shaping the input voltage function with multiple exponential rise times. For the 3.95 mm inner diameter lens, we achieved a response time improvement of 29% when compared to the fastest response obtained using single-exponential driving voltage. The technique shows great promise for applications that require fast response times.

Production of a Biosurfactant from Torulopsis bombicola

PubMed Central

Cooper, D. G.; Paddock, D. A.

1984-01-01

Two types of carbon sources—carbohydrate and vegetable oil—are necessary to obtain large yields of biosurfactant from Torulopsis bombicola ATCC 22214. Most of the surfactant is produced in the late exponential phase of growth. It is possible to grow the yeast on a single carbon source and then add the other type of substrate, after the exponential growth phase, and cause a burst of surfactant production. This product is a mixture of glycolipids. The maximum yield is 70 g liter−1, or 35% of the weight of the substrate used. An economic comparison demonstrated that this biosurfactant could be produced significantly more cheaply than any of the previously reported microbial surfactants. PMID:16346455

Dissimilar Kinetic Behavior of Electrically Manipulated Single- and Double-Stranded DNA Tethered to a Gold Surface

PubMed Central

Rant, Ulrich; Arinaga, Kenji; Tornow, Marc; Kim, Yong Woon; Netz, Roland R.; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard

2006-01-01

We report on the electrical manipulation of single- and double-stranded oligodeoxynucleotides that are end tethered to gold surfaces in electrolyte solution. The response to alternating repulsive and attractive electric surface fields is studied by time-resolved fluorescence measurements, revealing markedly distinct dynamics for the flexible single-stranded and stiff double-stranded DNA, respectively. Hydrodynamic simulations rationalize this finding and disclose two different kinetic mechanisms: stiff polymers undergo rotation around the anchoring pivot point; flexible polymers, on the other hand, are pulled onto the attracting surface segment by segment. PMID:16473909

Dissimilar kinetic behavior of electrically manipulated single- and double-stranded DNA tethered to a gold surface.

PubMed

Rant, Ulrich; Arinaga, Kenji; Tornow, Marc; Kim, Yong Woon; Netz, Roland R; Fujita, Shozo; Yokoyama, Naoki; Abstreiter, Gerhard

2006-05-15

We report on the electrical manipulation of single- and double-stranded oligodeoxynucleotides that are end tethered to gold surfaces in electrolyte solution. The response to alternating repulsive and attractive electric surface fields is studied by time-resolved fluorescence measurements, revealing markedly distinct dynamics for the flexible single-stranded and stiff double-stranded DNA, respectively. Hydrodynamic simulations rationalize this finding and disclose two different kinetic mechanisms: stiff polymers undergo rotation around the anchoring pivot point; flexible polymers, on the other hand, are pulled onto the attracting surface segment by segment.

Kozeny-Carman permeability relationship with disintegration process predicted from early dissolution profiles of immediate release tablets.

PubMed

Kumari, Parveen; Rathi, Pooja; Kumar, Virender; Lal, Jatin; Kaur, Harmeet; Singh, Jasbir

2017-07-01

This study was oriented toward the disintegration profiling of the diclofenac sodium (DS) immediate-release (IR) tablets and development of its relationship with medium permeability k perm based on Kozeny-Carman equation. Batches (L1-L9) of DS IR tablets with different porosities and specific surface area were prepared at different compression forces and evaluated for porosity, in vitro dissolution and particle-size analysis of the disintegrated mass. The k perm was calculated from porosities and specific surface area, and disintegration profiles were predicted from the dissolution profiles of IR tablets by stripping/residual method. The disintegration profiles were subjected to exponential regression to find out the respective disintegration equations and rate constants k d . Batches L1 and L2 showed the fastest disintegration rates as evident from their bi-exponential equations while the rest of the batches L3-L9 exhibited the first order or mono-exponential disintegration kinetics. The 95% confidence interval (CI 95% ) revealed significant differences between k d values of different batches except L4 and L6. Similar results were also spotted for dissolution profiles of IR tablets by similarity (f 2 ) test. The final relationship between k d and k perm was found to be hyperbolic, signifying the initial effect of k perm on the disintegration rate. The results showed that disintegration profiling is possible because a relationship exists between k d and k perm . The later being relatable with porosity and specific surface area can be determined by nondestructive tests.

Effects of Ethanol and Other Alkanols on Transport of Acetic Acid in Saccharomyces cerevisiae

PubMed Central

Casal, Margarida; Cardoso, Helena; Leão, Cecília

1998-01-01

In glucose-grown cells of Saccharomyces cerevisiae IGC 4072, acetic acid enters only by simple diffusion of the undissociated acid. In these cells, ethanol and other alkanols enhanced the passive influx of labelled acetic acid. The influx of the acid followed first-order kinetics with a rate constant that increased exponentially with the alcohol concentration, and an exponential enhancement constant for each alkanol was estimated. The intracellular concentration of labelled acetic acid was also enhanced by alkanols, and the effect increased exponentially with alcohol concentration. Acetic acid is transported across the plasma membrane of acetic acid-, lactic acid-, and ethanol-grown cells by acetate-proton symports. We found that in these cells ethanol and butanol inhibited the transport of labelled acetic acid in a noncompetitive way; the maximum transport velocity decreased with alcohol concentration, while the affinity of the system for acetate was not significantly affected by the alcohol. Semilog plots of Vmax versus alcohol concentration yielded straight lines with negative slopes from which estimates of the inhibition constant for each alkanol could be obtained. The intracellular concentration of labelled acid was significantly reduced in the presence of ethanol or butanol, and the effect increased with the alcohol concentration. We postulate that the absence of an operational carrier for acetate in glucose-grown cells of S. cerevisiae, combined with the relatively high permeability of the plasma membrane for the undissociated acid and the inability of the organism to metabolize acetic acid, could be one of the reasons why this species exhibits low tolerance to acidic environments containing ethanol. PMID:9464405

Heart Rate and Oxygen Uptake Kinetics in Type 2 Diabetes Patients - A Pilot Study on the Influence of Cardiovascular Medication on Regulatory Processes.

PubMed

Koschate, Jessica; Drescher, Uwe; Baum, Klaus; Brinkmann, Christian; Schiffer, Thorsten; Latsch, Joachim; Brixius, Klara; Hoffmann, Uwe

2017-05-01

The aim of this pilot study was to investigate whether there are differences in heart rate and oxygen uptake kinetics in type 2 diabetes patients, considering their cardiovascular medication. It was hypothesized that cardiovascular medication would affect heart rate and oxygen uptake kinetics and that this could be detected using a standardized exercise test. 18 subjects were tested for maximal oxygen uptake. Kinetics were measured in a single test session with standardized, randomized moderate-intensity work rate changes. Time series analysis was used to estimate kinetics. Greater maxima in cross-correlation functions indicate faster kinetics. 6 patients did not take any cardiovascular medication, 6 subjects took peripherally acting medication and 6 patients were treated with centrally acting medication. Maximum oxygen uptake was not significantly different between groups. Significant main effects were identified regarding differences in muscular oxygen uptake kinetics and heart rate kinetics. Muscular oxygen uptake kinetics were significantly faster than heart rate kinetics in the group with no cardiovascular medication (maximum in cross-correlation function of muscular oxygen uptake vs. heart rate; 0.32±0.08 vs. 0.25±0.06; p=0.001) and in the group taking peripherally acting medication (0.34±0.05 vs. 0.28±0.05; p=0.009) but not in the patients taking centrally acting medication (0.28±0.05 vs. 0.30±0.07; n.s.). It can be concluded that regulatory processes for the achievement of a similar maximal oxygen uptake are different between the groups. The used standardized test provided plausible results for heart rate and oxygen uptake kinetics in a single measurement session in this patient group. © Georg Thieme Verlag KG Stuttgart · New York.

General solutions for the oxidation kinetics of polymers

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

Gillen, K.T.; Clough, R.L.; Wise, J.

1996-08-01

The simplest general kinetic schemes applicable to the oxidation of polymers are presented, discussed and analyzed in terms of the underlying kinetic assumptions. For the classic basic autoxidation scheme (BAS), which involves three bimolecular termination steps and is applicable mainly to unstabilized polymers, typical assumptions used singly or in groups include (1) long kinetic chain length, (2) a specific ratio of the termination rate constants and (3) insensitivity to the oxygen concentration (e.g., domination by a single termination step). Steady-state solutions for the rate of oxidation are given in terms of one, two, three, or four parameters, corresponding respectively tomore » three, two, one, or zero kinetic assumptions. The recently derived four-parameter solution predicts conditions yielding unusual dependencies of the oxidation rate on oxygen concentration and on initiation rate, as well as conditions leading to some unusual diffusion-limited oxidation profile shapes. For stabilized polymers, unimolecular termination schemes are typically more appropriate than bimolecular. Kinetics incorporating unimolecular termination reactions are shown to result in very simple oxidation expressions which have been experimentally verified for both radiation-initiated oxidation of an EPDM and thermoxidative degradation of nitrile and chloroprene elastomers.« less

The rational parameterization theorem for multisite post-translational modification systems.

PubMed

Thomson, Matthew; Gunawardena, Jeremy

2009-12-21

Post-translational modification of proteins plays a central role in cellular regulation but its study has been hampered by the exponential increase in substrate modification forms ("modforms") with increasing numbers of sites. We consider here biochemical networks arising from post-translational modification under mass-action kinetics, allowing for multiple substrates, having different types of modification (phosphorylation, methylation, acetylation, etc.) on multiple sites, acted upon by multiple forward and reverse enzymes (in total number L), using general enzymatic mechanisms. These assumptions are substantially more general than in previous studies. We show that the steady-state modform concentrations constitute an algebraic variety that can be parameterized by rational functions of the L free enzyme concentrations, with coefficients which are rational functions of the rate constants. The parameterization allows steady states to be calculated by solving L algebraic equations, a dramatic reduction compared to simulating an exponentially large number of differential equations. This complexity collapse enables analysis in contexts that were previously intractable and leads to biological predictions that we review. Our results lay a foundation for the systems biology of post-translational modification and suggest deeper connections between biochemical networks and algebraic geometry.

Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases

PubMed Central

Su, Yan; Guengerich, F. Peter

2016-01-01

Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. PMID:27248785

Microbial-based synthesis of highly elastomeric biodegradable poly(3-hydroxybutyrate-co-4-hydroxybutyrate) thermoplastic.

PubMed

Huong, Kai-Hee; Teh, Chin-Hoe; Amirul, A A

2017-08-01

This study reports the production of P(3HB-co-4HB) [Poly(3-hydroxybutyrate-co-4-hydroxybutyrate)] in possession of high molecular weight and elastomeric properties by Cupriavidus sp. USMAA1020 in single-stage mixed-substrate cultivation system. 1,4-butanediol and 1,6-hexanediol are found to be efficient substrate mixture that has resulted in high copolymer yield, occupying a maximum of 70wt% of the total biomass and producing higher 4HB monomer composition ranging from 31mol% to 41mol%. In substrate mixtures involving 1,6-hexanediol, cleavage of the 6-hydroxyhexanoyl-CoA produces Acetyl-CoA and 4-hydroxybutyryl-CoA. Acetyl-CoA is instrumental in initiating the cell growth in the single-stage fermentation system, preventing 4-hydroxybutyryl-CoA from being utilized via β-oxidation and retained the 4HB monomer at higher ratios. Macroscopic kinetic models of the bioprocesses have revealed that the P(3HB-co-4HB) formation appears to be in the nature of mixed-growth associated with higher formation rate during exponential growth phase; evidenced by higher growth associated constants, α, from 0.0690g/g to 0.4615g/g compared to non-growth associated constants, β, from 0.0092g/g/h to 0.0459g/g/h. The P(3HB-co-31mol% 4HB) produced from the substrate mixture exhibited high weight-average molecular weight, M w of 927kDa approaching a million Dalton, and possessed elongation at break of 1637% upon cultivation at 0.56wt% C. This is the first report on such properties for the P(3HB-co-4HB) copolymer. The copolymer is highly resistant to polymer deformation after being stretched. Copyright © 2017 Elsevier B.V. All rights reserved.

The size distribution of Pacific Seamounts

NASA Astrophysics Data System (ADS)

Smith, Deborah K.; Jordan, Thomas H.

1987-11-01

An analysis of wide-beam, Sea Beam and map-count data in the eastern and southern Pacific confirms the hypothesis that the average number of "ordinary" seamounts with summit heights h ≥ H can be approximated by the exponential frequency-size distribution: v(H) = vo e-βH. The exponential model, characterized by the single scale parameter β-1, is found to be superior to a power-law (self-similar) model. The exponential model provides a good first-order description of the summit-height distribution over a very broad spectrum of seamount sizes, from small cones (h < 300 m) to tall composite volcanoes (h > 3500 m). The distribution parameters obtained from 157,000 km of wide-beam profiles in the eastern and southern Pacific Ocean are vo = (5.4 ± 0.65) × 10-9m-2 and β = (3.5 ± 0.21) × 10-3 m-1, yielding an average of 5400 ± 650 seamounts per million square kilometers, of which 170 ± 17 are greater than one kilometer in height. The exponential distribution provides a reference for investigating the populations of not-so-ordinary seamounts, such as those on hotspot swells and near fracture zones, and seamounts in other ocean basins. If we assume that volcano height is determined by a hydraulic head proportional to the source depth of the magma column, then our observations imply an approximately exponential distribution of source depths. For reasonable values of magma and crustal densities, a volcano with the characteristic height β-1 = 285 m has an apparent source depth on the order of the crustal thickness.

Self-organized Segregation on the Grid

NASA Astrophysics Data System (ADS)

Omidvar, Hamed; Franceschetti, Massimo

2018-02-01

We consider an agent-based model with exponentially distributed waiting times in which two types of agents interact locally over a graph, and based on this interaction and on the value of a common intolerance threshold τ , decide whether to change their types. This is equivalent to a zero-temperature ising model with Glauber dynamics, an asynchronous cellular automaton with extended Moore neighborhoods, or a Schelling model of self-organized segregation in an open system, and has applications in the analysis of social and biological networks, and spin glasses systems. Some rigorous results were recently obtained in the theoretical computer science literature, and this work provides several extensions. We enlarge the intolerance interval leading to the expected formation of large segregated regions of agents of a single type from the known size ɛ >0 to size ≈ 0.134. Namely, we show that for 0.433< τ < 1/2 (and by symmetry 1/2<τ <0.567), the expected size of the largest segregated region containing an arbitrary agent is exponential in the size of the neighborhood. We further extend the interval leading to expected large segregated regions to size ≈ 0.312 considering "almost segregated" regions, namely regions where the ratio of the number of agents of one type and the number of agents of the other type vanishes quickly as the size of the neighborhood grows. In this case, we show that for 0.344 < τ ≤ 0.433 (and by symmetry for 0.567 ≤ τ <0.656) the expected size of the largest almost segregated region containing an arbitrary agent is exponential in the size of the neighborhood. This behavior is reminiscent of supercritical percolation, where small clusters of empty sites can be observed within any sufficiently large region of the occupied percolation cluster. The exponential bounds that we provide also imply that complete segregation, where agents of a single type cover the whole grid, does not occur with high probability for p=1/2 and the range of intolerance considered.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

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

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kineticsmore » resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.« less

Steps toward identifying a biogeochemical signal in non-equilibrium methane clumped isotope measurements

NASA Astrophysics Data System (ADS)

Douglas, P. M.; Eiler, J. M.; Sessions, A. L.; Dawson, K.; Walter Anthony, K. M.; Smith, D. A.; Lloyd, M. K.; Yanay, E.

2016-12-01

Microbially produced methane is a globally important greenhouse gas, energy source, and biological substrate. Methane clumped isotope measurements have recently been developed as a new analytical tool for understanding the source of methane in different environments. When methane forms in isotopic equilibrium clumped isotope values are determined by formation temperature, but in many cases microbial methane clumped isotope values deviate strongly from expected equilibrium values. Indeed, we observe a very wide range of clumped isotope values in microbial methane, which are likely strongly influenced by kinetic isotope effects, but thus far the biological and environmental parameters controlling this variability are not understood. We will present data from both culture experiments and natural environments to explore patterns of variability in non-equilibrium clumped isotope values on temporal and spatial scales. In methanogen batch cultures sampled at different time points along a growth curve we observe significant variability in clumped isotope values, with values decreasing from early to late exponential growth. Clumped isotope values then increase during stationary growth. This result is consistent with previous work suggesting that differences in the reversibility of methanogenesis related to metabolic rates control non-equilibrium clumped isotope values. Within single lakes in Alaska and Sweden we observe substantial variability in clumped isotope values on the order of 5‰. Lower clumped isotope values are associated with larger 2H isotopic fractionation between water and methane, which is also consistent with a kinetic isotope effect determined by the reversibility of methanogenesis. Finally, we analyzed a time-series clumped isotope compositions of methane emitted from two seeps in an Alaskan lake over several months. Temporal variability in these seeps is on the order of 2‰, which is much less than the observed spatial variability within the lake. Comparing carbon isotope fractionation between CO2 and CH4 with clumped isotope data suggests the temporal variability may result from changes in methane oxidation.

A means to estimate thermal and kinetic parameters of coal dust layer from hot surface ignition tests.

PubMed

Park, Haejun; Rangwala, Ali S; Dembsey, Nicholas A

2009-08-30

A method to estimate thermal and kinetic parameters of Pittsburgh seam coal subject to thermal runaway is presented using the standard ASTM E 2021 hot surface ignition test apparatus. Parameters include thermal conductivity (k), activation energy (E), coupled term (QA) of heat of reaction (Q) and pre-exponential factor (A) which are required, but rarely known input values to determine the thermal runaway propensity of a dust material. Four different dust layer thicknesses: 6.4, 12.7, 19.1 and 25.4mm, are tested, and among them, a single steady state dust layer temperature profile of 12.7 mm thick dust layer is used to estimate k, E and QA. k is calculated by equating heat flux from the hot surface layer and heat loss rate on the boundary assuming negligible heat generation in the coal dust layer at a low hot surface temperature. E and QA are calculated by optimizing a numerically estimated steady state dust layer temperature distribution to the experimentally obtained temperature profile of a 12.7 mm thick dust layer. Two unknowns, E and QA, are reduced to one from the correlation of E and QA obtained at criticality of thermal runaway. The estimated k is 0.1 W/mK matching the previously reported value. E ranges from 61.7 to 83.1 kJ/mol, and the corresponding QA ranges from 1.7 x 10(9) to 4.8 x 10(11)J/kg s. The mean values of E (72.4 kJ/mol) and QA (2.8 x 10(10)J/kg s) are used to predict the critical hot surface temperatures for other thicknesses, and good agreement is observed between measured and experimental values. Also, the estimated E and QA ranges match the corresponding ranges calculated from the multiple tests method and values reported in previous research.

Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA.

PubMed

Ren, Hang; Cheyne, Cameron G; Fleming, Aaron M; Burrows, Cynthia J; White, Henry S

2018-04-18

Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( k intra-extra ) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( k extra-intra ) remains unchanged. Both k intra-extra and k extra-intra are on the order of 1 × 10 -2 s -1 to 1 × 10 -1 s -1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H + into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for k intra-extra ( k H / k D ≈ 5) but a limited KIE for k extra-intra ( k H / k D ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.

Errors in Computing the Normalized Protein Catabolic Rate due to Use of Single-pool Urea Kinetic Modeling or to Omission of the Residual Kidney Urea Clearance.

PubMed

Daugirdas, John T

2017-07-01

The protein catabolic rate normalized to body size (PCRn) often is computed in dialysis units to obtain information about protein ingestion. However, errors can manifest when inappropriate modeling methods are used. We used a variable volume 2-pool urea kinetic model to examine the percent errors in PCRn due to use of a 1-pool urea kinetic model or after omission of residual urea clearance (Kru). When a single-pool model was used, 2 sources of errors were identified. The first, dependent on the ratio of dialyzer urea clearance to urea distribution volume (K/V), resulted in a 7% inflation of the PCRn when K/V was in the range of 6 mL/min per L. A second, larger error appeared when Kt/V values were below 1.0 and was related to underestimation of urea distribution volume (due to overestimation of effective clearance) by the single-pool model. A previously reported prediction equation for PCRn was valid, but data suggest that it should be modified using 2-pool eKt/V and V coefficients instead of single-pool values. A third source of error, this one unrelated to use of a single-pool model, namely omission of Kru, was shown to result in an underestimation of PCRn, such that each ml/minute Kru per 35 L of V caused a 5.6% underestimate in PCRn. Marked overestimation of PCRn can result due to inappropriate use of a single-pool urea kinetic model, particularly when Kt/V <1.0 (as in short daily dialysis), or after omission of residual native kidney clearance. Copyright © 2017 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Anoxic denitrification of BTEX: Biodegradation kinetics and pollutant interactions.

PubMed

Carvajal, Andrea; Akmirza, Ilker; Navia, Daniel; Pérez, Rebeca; Muñoz, Raúl; Lebrero, Raquel

2018-05-15

Anoxic mineralization of BTEX represents a promising alternative for their abatement from O 2 -deprived emissions. However, the kinetics of anoxic BTEX biodegradation and the interactions underlying the treatment of BTEX mixtures are still unknown. An activated sludge inoculum was used for the anoxic abatement of single, dual and quaternary BTEX mixtures, being acclimated prior performing the biodegradation kinetic tests. The Monod model and a Modified Gompertz model were then used for the estimation of the biodegradation kinetic parameters. Results showed that both toluene and ethylbenzene are readily biodegradable under anoxic conditions, whereas the accumulation of toxic metabolites resulted in partial xylene and benzene degradation when present both as single components or in mixtures. Moreover, the supplementation of an additional pollutant always resulted in an inhibitory competition, with xylene inducing the highest degree of inhibition. The Modified Gompertz model provided an accurate fitting for the experimental data for single and dual substrate experiments, satisfactorily representing the antagonistic pollutant interactions. Finally, microbial analysis suggested that the degradation of the most biodegradable compounds required a lower microbial specialization and diversity, while the presence of the recalcitrant compounds resulted in the selection of a specific group of microorganisms. Copyright © 2018 Elsevier Ltd. All rights reserved.