Three-Dimensional Direct Numerical Simulation of Methane-Air Turbulent Premixed Flames with Reduced Kinetic Mechanism

NASA Astrophysics Data System (ADS)

Tanahashi, Mamoru; Kikuta, Satoshi; Miyauchi, Toshio

2004-11-01

Three-dimensional DNS of methane-air turbulent premixed flames have been conducted to investigate local extinction mechanism of turbulent premixed flames. A reduced kinetic mechanism (MeCH-19), which is created from GRI-Mech. 2.11 and includes 23 reactive species and 19 step reactions, are used to simulate CH_4-O_2-N2 reaction in turbulence. The effectiveness of this reduced kinetic mechanism has been conformed by preliminary two-dimensional DNS with the reduced kinetic mechanism and two detailed kinetic mechanisms; GRI-Mech. 2.11 and Miller & Bowman. Flame structures of methane-air turbulent premixed flames are compared with those of hydrogen-air turbulent premixed flames which have been obtained by 3D-DNS with a detailed kinetic mechanism in our previous study. Local extinctions occur in methane-air turbulent premixed flames, whereas no extinction is observed for hydrogen-air flames in nearly same turbulence condition. The local extinction mechanism is discussed based on eddy/flame interaction in small scales.

Is cancer a pure growth curve or does it follow a kinetics of dynamical structural transformation?

PubMed

González, Maraelys Morales; Joa, Javier Antonio González; Cabrales, Luis Enrique Bergues; Pupo, Ana Elisa Bergues; Schneider, Baruch; Kondakci, Suleyman; Ciria, Héctor Manuel Camué; Reyes, Juan Bory; Jarque, Manuel Verdecia; Mateus, Miguel Angel O'Farril; González, Tamara Rubio; Brooks, Soraida Candida Acosta; Cáceres, José Luis Hernández; González, Gustavo Victoriano Sierra

2017-03-07

Unperturbed tumor growth kinetics is one of the more studied cancer topics; however, it is poorly understood. Mathematical modeling is a useful tool to elucidate new mechanisms involved in tumor growth kinetics, which can be relevant to understand cancer genesis and select the most suitable treatment. The classical Kolmogorov-Johnson-Mehl-Avrami as well as the modified Kolmogorov-Johnson-Mehl-Avrami models to describe unperturbed fibrosarcoma Sa-37 tumor growth are used and compared with the Gompertz modified and Logistic models. Viable tumor cells (1×10 5 ) are inoculated to 28 BALB/c male mice. Modified Gompertz, Logistic, Kolmogorov-Johnson-Mehl-Avrami classical and modified Kolmogorov-Johnson-Mehl-Avrami models fit well to the experimental data and agree with one another. A jump in the time behaviors of the instantaneous slopes of classical and modified Kolmogorov-Johnson-Mehl-Avrami models and high values of these instantaneous slopes at very early stages of tumor growth kinetics are observed. The modified Kolmogorov-Johnson-Mehl-Avrami equation can be used to describe unperturbed fibrosarcoma Sa-37 tumor growth. It reveals that diffusion-controlled nucleation/growth and impingement mechanisms are involved in tumor growth kinetics. On the other hand, tumor development kinetics reveals dynamical structural transformations rather than a pure growth curve. Tumor fractal property prevails during entire TGK.

Structural and silver/vanadium ratio effects on silver vanadium phosphorous oxide solution formation kinetics: impact on battery electrochemistry.

PubMed

Bock, David C; Takeuchi, Kenneth J; Marschilok, Amy C; Takeuchi, Esther S

2015-01-21

The detailed understanding of non-faradaic parasitic reactions which diminish battery calendar life is essential to the development of effective batteries for use in long life applications. The dissolution of cathode materials including manganese, cobalt and vanadium oxides in battery systems has been identified as a battery failure mechanism, yet detailed dissolution studies including kinetic analysis are absent from the literature. The results presented here provide a framework for the quantitative and kinetic analyses of the dissolution of cathode materials which will aid the broader community in more fully understanding this battery failure mechanism. In this study, the dissolution of silver vanadium oxide, representing the primary battery powering implantable cardioverter defibrillators (ICD), is compared with the dissolution of silver vanadium phosphorous oxide (Ag(w)VxPyOz) materials which were targeted as alternatives to minimize solubility. This study contains the first kinetic analyses of silver and vanadium solution formation from Ag0.48VOPO4·1.9H2O and Ag2VP2O8, in a non-aqueous battery electrolyte. The kinetic results are compared with those of Ag2VO2PO4 and Ag2V4O11 to probe the relationships among crystal structure, stoichiometry, and solubility. For vanadium, significant dissolution was observed for Ag2V4O11 as well as for the phosphate oxide Ag0.49VOPO4·1.9H2O, which may involve structural water or the existence of multiple vanadium oxidation states. Notably, the materials from the SVPO family with the lowest vanadium solubility are Ag2VO2PO4 and Ag2VP2O8. The low concentrations and solution rates coupled with their electrochemical performance make these materials interesting alternatives to Ag2V4O11 for the ICD application.

The effects of kinetic structure and micrograph content on achievement in reading micrographs by college biology students

NASA Astrophysics Data System (ADS)

Johnson, Virginia Abbott; Lockard, J. David

The effects of kinetic structure and micrograph content on student achievement of reading micrograph skills were examined. The purpose of the study was to determine which form of kinetic structure, high or low, and/or micrograph content, unified or varied, was most effective and if there were any interactive effects. Randomly assigned to four treatment groups, 100 introductory college biology students attended three audiovisual presentations and practice sessions on reading light, transmission electron, and scanning electron micrographs. The micrograph skills test, administered at two points in time, assessed knowledge acquisition and retention. The test measured general concept skills and actual reading micrograph skills separately. All significant tests were considered with an = 0.05. High kinetic structure was found to be more effective than low kinetic structure in developing general concepts about micrographs. This finding supports Anderson's kinetic theory research. High kinetic structure instruction does not affect actual reading micrograph skills, but micrograph content does. Unified micrograph content practice sessions were more effective than varied micrograph content practice sessions. More attention should be given to the visual components of perceptual learning tasks.

From kinetic-structure analysis to engineering crystalline fiber networks in soft materials.

PubMed

Wang, Rong-Yao; Wang, Peng; Li, Jing-Liang; Yuan, Bing; Liu, Yu; Li, Li; Liu, Xiang-Yang

2013-03-07

Understanding the role of kinetics in fiber network microstructure formation is of considerable importance in engineering gel materials to achieve their optimized performances/functionalities. In this work, we present a new approach for kinetic-structure analysis for fibrous gel materials. In this method, kinetic data is acquired using a rheology technique and is analyzed in terms of an extended Dickinson model in which the scaling behaviors of dynamic rheological properties in the gelation process are taken into account. It enables us to extract the structural parameter, i.e. the fractal dimension, of a fibrous gel from the dynamic rheological measurement of the gelation process, and to establish the kinetic-structure relationship suitable for both dilute and concentrated gelling systems. In comparison to the fractal analysis method reported in a previous study, our method is advantageous due to its general validity for a wide range of fractal structures of fibrous gels, from a highly compact network of the spherulitic domains to an open fibrous network structure. With such a kinetic-structure analysis, we can gain a quantitative understanding of the role of kinetic control in engineering the microstructure of the fiber network in gel materials.

Predicting kinetics of polymorphic transformations from structure mapping and coordination analysis

NASA Astrophysics Data System (ADS)

Stevanović, Vladan; Trottier, Ryan; Musgrave, Charles; Therrien, Félix; Holder, Aaron; Graf, Peter

2018-03-01

To extend materials design and discovery into the space of metastable polymorphs, rapid and reliable assessment of transformation kinetics to lower energy structures is essential. Herein we focus on diffusionless polymorphic transformations and investigate routes to assess their kinetics using solely crystallographic arguments. As part of this investigation we developed a general algorithm to map crystal structures onto each other, and ascertain the low-energy (fast-kinetics) transformation pathways between them. Pathways with minimal dissociation of chemical bonds, along which the number of bonds (in ionic systems the first-shell coordination) does not decrease below that in the end structures, are shown to always be the fast-kinetics pathways. These findings enable the rapid assessment of the kinetics of polymorphic transformation and the identification of long-lived metastable structures. The utility is demonstrated on a number of transformations including those between high-pressure SnO2 phases, which lack a detailed atomic-level understanding.

Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time.

PubMed

Kamgar-Parsi, Kian; Hong, Liu; Naito, Akira; Brooks, Charles L; Ramamoorthy, Ayyalusamy

2017-09-08

The role of the peptide hormone calcitonin in skeletal protection has led to its use as a therapeutic for osteoporosis. However, calcitonin aggregation into amyloid fibrils limits its therapeutic efficacy, necessitating a modification of calcitonin's aggregation kinetics. Here, we report a direct relationship between human calcitonin (hCT) concentration and aggregation lag time. This kinetic trend was contrary to the conventional understanding of amyloid aggregation and persisted over a range of aggregation conditions, as confirmed by thioflavin-T kinetics assays, CD spectroscopy, and transmission EM. Dynamic light scattering, 1 H NMR experiments, and seeded thioflavin-T assay results indicated that differences in initial peptide species contribute to this trend more than variations in the primary nucleus formation rate. On the basis of kinetics modeling results, we propose a mechanism whereby a structural conversion of hCT monomers is needed before incorporation into the fibril. Our kinetic mechanism recapitulates the experimentally observed relationship between peptide concentration and lag time and represents a novel mechanism in amyloid aggregation. Interestingly, hCT at low pH and salmon calcitonin (sCT) exhibited the canonical inverse relationship between concentration and lag time. Comparative studies of hCT and sCT with molecular dynamics simulations and CD indicated an increased α-helical structure in sCT and low-pH hCT monomers compared with neutral-pH hCT, suggesting that α-helical monomers represent a growth-competent species, whereas unstructured random coil monomers represent a growth-incompetent species. Our finding that initial monomer concentration is positively correlated with lag time in hCT aggregation could help inform future efforts for improving therapeutic applications of CT. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

ATP regulation of the ligand-binding properties in temperate and cold-adapted haemoglobins. X-ray structure and ligand-binding kinetics in the sub-Antarctic fish Eleginops maclovinus.

PubMed

Coppola, Daniela; Abbruzzetti, Stefania; Nicoletti, Francesco; Merlino, Antonello; Gambacurta, Alessandra; Giordano, Daniela; Howes, Barry D; De Sanctis, Giampiero; Vitagliano, Luigi; Bruno, Stefano; di Prisco, Guido; Mazzarella, Lelio; Smulevich, Giulietta; Coletta, Massimo; Viappiani, Cristiano; Vergara, Alessandro; Verde, Cinzia

2012-10-30

The major haemoglobin of the sub-Antarctic fish Eleginops maclovinus was structurally and functionally characterised with the aim to compare molecular environmental adaptations in the O(2)-transport system of sub-Antarctic fishes of the suborder Notothenioidei with those of their high-latitude relatives. Ligand-binding kinetics of the major haemoglobin of E. maclovinus indicated strong stabilisation of the liganded quaternary T state, enhanced in the presence of the physiological allosteric effector ATP, compared to that of high-Antarctic Trematomus bernacchii. The activation enthalpy for O(2) dissociation was dramatically lower than that in T. bernacchii haemoglobin, suggesting remarkable differences in temperature sensitivity and structural changes associated with O(2) release and exit from the protein. The haemoglobin functional properties, together with the X-ray structure of the CO form at 1.49 Å resolution, the first of a temperate notothenioid, strongly support the hypothesis that in E. maclovinus, whose life-style varies according to changes in habitat, the mechanisms that regulate O(2) affinity and the ATP-induced Root effect differ from those of high-Antarctic Notothenioids.

Plate with decentralised velocity feedback loops: Power absorption and kinetic energy considerations

NASA Astrophysics Data System (ADS)

Gardonio, P.; Miani, S.; Blanchini, F.; Casagrande, D.; Elliott, S. J.

2012-04-01

This paper is focused on the vibration effects produced by an array of decentralised velocity feedback loops that are evenly distributed over a rectangular thin plate to minimise its flexural response. The velocity feedback loops are formed by collocated ideal velocity sensor and point force actuator pairs, which are unconditionally stable and produce 'sky-hook' damping on the plate. The study compares how the overall flexural vibration of the plate and the local absorption of vibration power by the feedback loops vary with the control gains. The analysis is carried out both considering a typical frequency-domain formulation based on kinetic energy and structural power physical quantities, which is normally used to study vibration and noise problems, and a time-domain formulation also based on kinetic energy and structural power, which is usually implemented to investigate control problems. The time-domain formulation shows to be much more computationally efficient and robust with reference to truncation errors. Thus it has been used to perform a parametric study to assess if, and under which conditions, the minimum of the kinetic energy and the maximum of the absorbed power cost functions match with reference to: (a) the number of feedback control loops, (b) the structural damping in the plate, (c) the mutual distance of a pair of control loops and (d) the mutual gains implemented in a pair of feedback loops.

Biosorption of six basic and acidic dyes on brown alga Sargassum ilicifolium: optimization, kinetic and isotherm studies.

PubMed

Tabaraki, Reza; Sadeghinejad, Negar

2017-06-01

Biosorption of Methyl Blue (MB), Fuchsin Acid (FA), Rhodamine B (RB), Methylene Blue (MEB), Bromocresol purple (BC) and Methyl Orange (MO) onto Sargassum ilicifolium was studied in a batch system. Effect of dye structure on biosorption by Sargassum ilicifolium was studied to define the correlation between chemical structure and biosorption capacity. Different dye groups such as triarylmethane (MB, FA and BC), monoazo (MO), thiazine (MEB) and xanthene (RB) were studied. At optimum experimental conditions for each dye, biosorption capacity was determined and compared. The results indicate that the chemical structure (triarylmethane, monoazo, thiazine, xanthene), number of sulfonic groups, basicity (element of chromophore group: S, N, O) and molecular weight of dye molecules influence their biosorption capacity. Experimental parameters such as biosorbent dose, pH, contact time, and initial dye concentration were optimized for each dye. The biosorption kinetic data were successfully described by the pseudo second-order model. The biosorption results were also analyzed by the Langmuir and Freundlich isotherms. Finally, biosorption capacities obtained using Sargassum ilicifolium were compared with the ones presented in the literature.

The general theory of multistage geminate reactions of isolated pairs of reactants. III. Two-stage reversible dissociation in geminate reaction A + A ↔ C ↔ B + B.

PubMed

Kipriyanov, Alexey A; Kipriyanov, Alexander A; Doktorov, Alexander B

2016-04-14

Specific two-stage reversible reaction A + A ↔ C ↔ B + B of the decay of species C reactants by two independent transition channels is considered on the basis of the general theory of multistage reactions of isolated pairs of reactants. It is assumed that at the initial instant of time, the reacting system contains only reactants C. The employed general approach has made it possible to consider, in the general case, the inhomogeneous initial distribution of reactants, and avoid application of model concepts of a reaction system structure (i.e., of the structure of reactants and their molecular mobility). Slowing of multistage reaction kinetics as compared to the kinetics of elementary stages is established and physically interpreted. To test approximations (point approximation) used to develop a universal kinetic law, a widely employed specific model of spherical particles with isotropic reactivity diffusing in solution is applied. With this particular model as an example, ultimate kinetics of chemical conversion of reactants is investigated. The question concerning the depths of chemical transformation at which long-term asymptotes are reached is studied.

The general theory of multistage geminate reactions of isolated pairs of reactants. III. Two-stage reversible dissociation in geminate reaction A + A↔C↔B + B

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

Kipriyanov, Alexey A.; Kipriyanov, Alexander A.; Doktorov, Alexander B.

2016-04-14

Specific two-stage reversible reaction A + A↔C↔B + B of the decay of species C reactants by two independent transition channels is considered on the basis of the general theory of multistage reactions of isolated pairs of reactants. It is assumed that at the initial instant of time, the reacting system contains only reactants C. The employed general approach has made it possible to consider, in the general case, the inhomogeneous initial distribution of reactants, and avoid application of model concepts of a reaction system structure (i.e., of the structure of reactants and their molecular mobility). Slowing of multistage reactionmore » kinetics as compared to the kinetics of elementary stages is established and physically interpreted. To test approximations (point approximation) used to develop a universal kinetic law, a widely employed specific model of spherical particles with isotropic reactivity diffusing in solution is applied. With this particular model as an example, ultimate kinetics of chemical conversion of reactants is investigated. The question concerning the depths of chemical transformation at which long-term asymptotes are reached is studied.« less

Comparative Analysis of Binding Kinetics and Thermodynamics of Dipeptidyl Peptidase-4 Inhibitors and Their Relationship to Structure.

PubMed

Schnapp, Gisela; Klein, Thomas; Hoevels, Yvette; Bakker, Remko A; Nar, Herbert

2016-08-25

The binding kinetics and thermodynamics of dipeptidyl peptidase (DPP)-4 inhibitors (gliptins) were investigated using surface plasmon resonance and isothermal titration calorimetry. Binding of gliptins to DPP-4 is a rapid electrostatically driven process. Off-rates were generally slow partly because of reversible covalent bond formation by some gliptins, and partly because of strong and extensive interactions. Binding of all gliptins is enthalpy-dominated due to strong ionic interactions and strong solvent-shielded hydrogen bonds. Using a congeneric series of molecules which represented the intermediates in the lead optimization program of linagliptin, the onset of slow binding kinetics and development of the thermodynamic repertoire were analyzed in the context of incremental changes of the chemical structures. All compounds rapidly associated, and therefore the optimization of affinity and residence time is highly correlated. The major contributor to the increasing free energy of binding was a strong increase of binding enthalpy, whereas entropic contributions remained low and constant despite significant addition of lipophilicity.

Enzymolysis kinetics and structural characteristics of rice protein with energy-gathered ultrasound and ultrasound assisted alkali pretreatments.

PubMed

Li, Suyun; Yang, Xue; Zhang, Yanyan; Ma, Haile; Qu, Wenjuan; Ye, Xiaofei; Muatasim, Rahma; Oladejo, Ayobami Olayemi

2016-07-01

This research investigated the structural characteristics and enzymolysis kinetics of rice protein which was pretreated by energy-gathered ultrasound and ultrasound assisted alkali. The structural characteristics of rice protein before and after the pretreatment were performed with surface hydrophobicity and Fourier transform infrared (FTIR). There was an increase in the intensity of fluorescence spectrum and changes in functional groups after the pretreatment on rice protein compared with the control (without ultrasound and ultrasound assisted alkali processed), thus significantly enhancing efficiency of the enzymatic hydrolysis. A simplified kinetic equation for the enzymolysis model with the impeded reaction of enzyme was deduced to successfully describe the enzymatic hydrolysis of rice protein by different pretreatments. The initial observed rate constants (Kin,0) as well as ineffective coefficients (kimp) were proposed and obtained based on the experimental observation. The results showed that the parameter of kin,0 increased after ultrasound and ultrasound assisted alkali pretreatments, which proved the effects of the pretreatments on the substrate enhancing the enzymolysis process and had relation to the structure changes of the pretreatments on the substrate. Furthermore, the applicability of the simplified model was demonstrated by the enzymatic hydrolysis process for other materials. Copyright © 2015 Elsevier B.V. All rights reserved.

Alternative S2 Hinge Regions of the Myosin Rod Affect Myofibrillar Structure and Myosin Kinetics

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

Miller, Mark S.; Dambacher, Corey M.; Knowles, Aileen F.

2009-07-01

The subfragment 2/light meromyosin 'hinge' region has been proposed to significantly contribute to muscle contraction force and/or speed. Transgenic replacement of the endogenous fast muscle isovariant hinge A (exon 15a) in Drosophila melanogaster indirect flight muscle with the slow muscle hinge B (exon 15b) allows examination of the structural and functional changes when only this region of the myosin molecule is different. Hinge B was previously shown to increase myosin rod length, increase A-band and sarcomere length, and decrease flight performance compared to hinge A. We applied additional measures to these transgenic lines to further evaluate the consequences of modifyingmore » this hinge region. Structurally, the longer A-band and sarcomere lengths found in the hinge B myofibrils appear to be due to the longitudinal addition of myosin heads. Functionally, hinge B, although a significant distance from the myosin catalytic domain, alters myosin kinetics in a manner consistent with this region increasing myosin rod length. These structural and functional changes combine to decrease whole fly wing-beat frequency and flight performance. Our results indicate that this hinge region plays an important role in determining myosin kinetics and in regulating thick and thin filament lengths as well as sarcomere length.« less

Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics

PubMed Central

Hata, Hiroaki; Kitajima, Tetsuro

2018-01-01

Abstract Nucleic acid secondary structure plays an important role in nucleic acid–nucleic acid recognition/hybridization processes, and is also a vital consideration in DNA nanotechnology. Although the influence of stable secondary structures on hybridization kinetics has been characterized, unstable secondary structures, which show positive ΔG° with self-folding, can also form, and their effects have not been systematically investigated. Such thermodynamically unfavorable secondary structures should not be ignored in DNA hybridization kinetics, especially under isothermal conditions. Here, we report that positive ΔG° secondary structures can change the hybridization rate by two-orders of magnitude, despite the fact that their hybridization obeyed second-order reaction kinetics. The temperature dependence of hybridization rates showed non-Arrhenius behavior; thus, their hybridization is considered to be nucleation limited. We derived a model describing how ΔG° positive secondary structures affect hybridization kinetics in stopped-flow experiments with 47 pairs of oligonucleotides. The calculated hybridization rates, which were based on the model, quantitatively agreed with the experimental rate constant. PMID:29220504

Toroidal Alfvén eigenmode triggered by trapped anisotropic energetic particles in a toroidal resistive plasma with free boundary

NASA Astrophysics Data System (ADS)

Yang, S. X.; Hao, G. Z.; Liu, Y. Q.; Wang, Z. X.; Hu, Y. J.; Zhu, J. X.; He, H. D.; Wang, A. K.

2018-04-01

The toroidal Alfvén eigenmode (TAE), excited by trapped energetic particles (EPs), is numerically investigated in a tokamak plasma, using the non-perturbative magnetohydrodynamic-kinetic hybrid formulation based MARS-K code (Liu et al 2008 Phys. Plasmas 15 112503). Compared with the fixed boundary condition at the plasma edge, a free boundary enhances the critical value of the EPs kinetic contribution for driving the TAE. Free boundary also induces finite perturbations at the plasma edge as expected. An anisotropic distribution of EPs, in the particle pitch angle space, strongly enhances the instability and results in a more global mode structure, compared with the isotropic case. The plasma resistivity is also found to play a role in the EPs-destabilized TAE. In particular, the mode stability domain is mapped out, in the 2D parameter space of the plasma resistivity and a quantity defining the width of the particle distribution in pitch angle (for anisotropic distribution). A resonance layer in the poloidal mode structure, with the layer width increasing with the plasma resistivity, appears at the large width of the particle distribution in pitch angle space. A mode conversion, from the modified ideal kink by the EPs kinetic effect to the TAE, is also observed while increasing the birth energy of EPs. Computational results suggest that the TAE mode structure can be modified by certain key plasma parameters, such as the EPs kinetic contribution, the equilibrium pressure, the plasma resistivity, the distribution of EPs, as well as the birth energy of EPs. Such modification of the eigenmode structure can only be obtained following the non-perturbative hybrid approach (Wang et al 2013 Phys. Rev. Lett. 111 145003, Wang et al 2015 Phys. Plasmas 22 022509), as adopted in this study. More importantly, numerical results show that near the marginal stability point, the dominant poloidal harmonics of the TAE overlap with each other, and are localized at the tip positions of the Alfvén continua. This kind of TAE structure in high beta plasma with unstable ideal kink is substantially different from that of the conventional TAE.

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II

NASA Astrophysics Data System (ADS)

Nemtseva, Elena V.; Lashchuk, Olesya O.; Gerasimova, Marina A.; Melnik, Tatiana N.; Nagibina, Galina S.; Melnik, Bogdan S.

2018-01-01

In most cases, intermediate states of multistage folding proteins are not ‘visible’ under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II.

PubMed

Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S

2017-12-21

In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Simulation of Decomposition Kinetics of Supercooled Austenite in Powder Steel

NASA Astrophysics Data System (ADS)

Tsyganova, M. S.; Ivashko, A. G.; Polyshuk, I. N.; Nabatov, R. I.; Tsyganova, A. I.

2017-10-01

To approve heat treatment of steel modes, quantitative data on austenite decomposition are required. Gaining these data experimentally appears to be extremely complicated. In present work, few approaches to simulate the phase transformation process are proposed considering structure characteristics of powder steels. Results of comparative analysis of these approaches are also given. Predicting the transformation kinetics by simulation is verified for PK40N2M (0.38% C, 2.10% Ni, 0.40% Mo) steel with 3% porosity and PK80 (0.80% C) steel with different porosity using published experimental data.

Kinetic Equations for Describing the Liquid-Glass Transition in Polymers

NASA Astrophysics Data System (ADS)

Aksenov, V. L.; Tropin, T. V.; Schmelzer, J. V. P.

2018-01-01

We present a theoretical approach based on nonequilibrium thermodynamics and used to describe the kinetics of the transition from the liquid to the glassy state (glass transition). In the framework of this approach, we construct kinetic equations describing the time and temperature evolution of the structural parameter. We discuss modifications of the equations required for taking the nonexponential, nonlinear character of the relaxation in the vitrification region into account. To describe the formation of polymer glasses, we present modified expressions for the system relaxation time. We compare the obtained results with experimental data, measurements of the polystyrene glass transition for different cooling rates using the method of differential scanning calorimetry. We discuss prospects for developing a method for describing the polymer glass transition.

Influence of Pyrethroid Insecticides on Sodium and Calcium Influx in Neocortical Neurons

EPA Science Inventory

Pyrethroid insecticides bind to voltage-gated sodium channels and modify their gating kinetics, thereby disrupting neuronal function. Using murine neocortical neurons in primary culture, we have compared the ability of 11 structurally diverse pyrethroid insecticides to evoke Na+ ...

Comparative kinetic analysis on thermal degradation of some cephalosporins using TG and DSC data

PubMed Central

2013-01-01

Background The thermal decomposition of cephalexine, cefadroxil and cefoperazone under non-isothermal conditions using the TG, respectively DSC methods, was studied. In case of TG, a hyphenated technique, including EGA, was used. Results The kinetic analysis was performed using the TG and DSC data in air for the first step of cephalosporin’s decomposition at four heating rates. The both TG and DSC data were processed according to an appropriate strategy to the following kinetic methods: Kissinger-Akahira-Sunose, Friedman, and NPK, in order to obtain realistic kinetic parameters, even if the decomposition process is a complex one. The EGA data offer some valuable indications about a possible decomposition mechanism. The obtained data indicate a rather good agreement between the activation energy’s values obtained by different methods, whereas the EGA data and the chemical structures give a possible explanation of the observed differences on the thermal stability. A complete kinetic analysis needs a data processing strategy using two or more methods, but the kinetic methods must also be applied to the different types of experimental data (TG and DSC). Conclusion The simultaneous use of DSC and TG data for the kinetic analysis coupled with evolved gas analysis (EGA) provided us a more complete picture of the degradation of the three cephalosporins. It was possible to estimate kinetic parameters by using three different kinetic methods and this allowed us to compare the Ea values obtained from different experimental data, TG and DSC. The thermodegradation being a complex process, the both differential and integral methods based on the single step hypothesis are inadequate for obtaining believable kinetic parameters. Only the modified NPK method allowed an objective separation of the temperature, respective conversion influence on the reaction rate and in the same time to ascertain the existence of two simultaneous steps. PMID:23594763

Impact of polymer structure and composition on fully resorbable endovascular scaffold performance

PubMed Central

Ferdous, Jahid; Kolachalama, Vijaya B.; Shazly, Tarek

2014-01-01

Fully erodible endovascular scaffolds are being increasingly considered for the treatment of obstructive arterial disease owing to their potential to mitigate long-term risks associated with permanent alternatives. While complete scaffold erosion facilitates vessel healing, generation and release of material degradation by-products from candidate materials such as poly-l-lactide (PLLA) may elicit local inflammatory responses that limit implant efficacy. We developed a computational framework to quantify how the compositional and structural parameters of PLLA-based fully erodible endovascular scaffolds affect degradation kinetics, erosion kinetics and the transient accumulation of material by-products within the arterial wall. Parametric studies reveal that, while some material properties have similar effects on these critical processes, others induce qualitatively opposing responses. For example, scaffold degradation is only mildly responsive to changes in either PLLA polydispersity or the initial degree of crystallinity, while the erosion kinetics is comparatively sensitive to crystallinity. Moreover, lactide doping can effectively tune both scaffold degradation and erosion, but a concomitant increase in local byproduct accumulation raises concerns about implant safety. Optimized erodible endovascular scaffolds must precisely balance therapeutic function and biological response over the implant lifetime, where compositional and structural parameters will have differential effects on implant performance. PMID:23261926

Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

NASA Astrophysics Data System (ADS)

Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

2015-09-01

Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

Alteration of biomacromolecule in corn by steam flaking in relation to biodegradation kinetics in ruminant, revealed with vibrational molecular spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-02-01

Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (P < 0.01) rumen degradable DM (RDDM) and starch (RDSt), but decreased (P < 0.01) rumen degradable protein (RDP). (3) Molecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (P < 0.01), but protein amides associated molecular spectral intensities were lower (P < 0.01) in SFC. (4). The molecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (P < 0.10) associated with RDDM and RDSt and protein amide spectral intensities were positively (P < 0.10) associated with RDP. This results indicated that the steam flaking induced molecular structure changes had an interactive relationship with rumen degradation kinetics.

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

PubMed Central

2017-01-01

Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful tools for characterizing the dynamic response of metabolic networks. Central to linear analysis methods are two key matrices: the Jacobian matrix (J) and the modal matrix (M-1) arising from its eigendecomposition. The modal matrix M-1 contains dynamically independent motions of the kinetic model near a reference state, and it is sparse in practice for metabolic networks. However, connecting the structure of M-1 to the kinetic properties of the underlying reactions is non-trivial. In this study, we analyze the relationship between J, M-1, and the kinetic properties of the underlying network for kinetic models of metabolism. Specifically, we describe the origin of mode sparsity structure based on features of the network stoichiometric matrix S and the reaction kinetic gradient matrix G. First, we show that due to the scaling of kinetic parameters in real networks, diagonal dominance occurs in a substantial fraction of the rows of J, resulting in simple modal structures with clear biological interpretations. Then, we show that more complicated modes originate from topologically-connected reactions that have similar reaction elasticities in G. These elasticities represent dynamic equilibrium balances within reactions and are key determinants of modal structure. The work presented should prove useful towards obtaining an understanding of the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions. PMID:29267329

Photoluminescence Characteristics of Yag:Ce, Gd Based Phosphors with Different Prehistories

NASA Astrophysics Data System (ADS)

Lisitsyn, V. M.; Soshchin, N. P.; Yang yang, Yu; Stepanov, S. A.; Lisitsyna, L. A.; Tulegenova, A. T.; Abdullin, Kh. A.

2017-09-01

Luminescence characteristics of yttrium-aluminum garnet based phosphor samples differed by their elemental composition and prehistory of synthesis are studied. The morphology, structure, and elemental composition of phosphor samples, their excitation and emission spectra, efficiency of phosphor conversion of chip emission, and kinetics of luminescence decay are measured. The emission characteristics of phosphors are compared with their structural properties and elemental composition.

Kinetic scale structure of low-frequency waves and fluctuations

NASA Astrophysics Data System (ADS)

Lopez Herrera, R. A.; Figueroa-Vinas, A.; Araneda, J. A.; Yoon, P. H.

2017-12-01

The dissipation of solar wind turbulence at kinetic scales is believed to be important for heating the corona and accelerating the wind. Linear Vlasov kinetic theory is a useful tool in identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, ion-acoustic (or kinetic slow mode), and their possible roles in the dissipation. However, kinetic mode structure near the vicinity of ion cyclotron modes is not clearly understood. The present poster aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion Bernstein versus quasi modes. The spontaneous emission theory and simulation also confirm the findings of Vlasov theory in that the kinetic Alfvén wave can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave-particle interactions.

Pathways for Ethanol Dehydrogenation and Dehydration Catalyzed by Ceria (111) and (100) Surfaces

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

Beste, Ariana; Steven Overbury

2015-01-08

We have performed computations to better understand how surface structure affects selectivity in dehydrogenation and dehydration reactions of alcohols. Ethanol reactions on the (111) and (100) ceria surfaces were studied starting from the dominant surface species, ethoxy. We used DFT (PBE+U) to explore reaction pathways leading to ethylene and acetaldehyde and calculated estimates of rate constants employing transition state theory. To assess pathway contributions, we carried out kinetic analysis. Our results show that intermediate and transition state structures are stabilized on the (100) surface compared to the (111) surface. Formation of acetaldehyde over ethylene is kinetically and thermodynamically preferred onmore » both surfaces. Our results are consistent with temperature programmed surface reaction and steady-state experiments, where acetaldehyde was found as the main product and evidence was presented that ethylene formation at higher temperature originates from changes in adsorbate and surface structure.« less

Structure sensitivity in oxide catalysis: First-principles kinetic Monte Carlo simulations for CO oxidation at RuO 2(111)

DOE PAGES

Wang, Tongyu; Reuter, Karsten

2015-11-24

We present a density-functional theory based kinetic Monte Carlo study of CO oxidation at the (111) facet of RuO 2. We compare the detailed insight into elementary processes, steady-state surface coverages, and catalytic activity to equivalent published simulation data for the frequently studied RuO 2(110) facet. Qualitative differences are identified in virtually every aspect ranging from binding energetics over lateral interactions to the interplay of elementary processes at the different active sites. Nevertheless, particularly at technologically relevant elevated temperatures, near-ambient pressures and near-stoichiometric feeds both facets exhibit almost identical catalytic activity. As a result, these findings challenge the traditional definitionmore » of structure sensitivity based on macroscopically observable turnover frequencies and prompt scrutiny of the applicability of structure sensitivity classifications developed for metals to oxide catalysis.« less

An Investigation of Hall Currents Associated with Tripolar Magnetic Fields During Magnetospheric Kelvin Helmholtz Waves

NASA Astrophysics Data System (ADS)

Sturner, A. P.; Eriksson, S.; Newman, D. L.; Lapenta, G.; Gershman, D. J.; Plaschke, F.; Ergun, R.; Wilder, F. D.; Torbert, R. B.; Giles, B. L.; Strangeway, R. J.; Russell, C. T.; Burch, J. L.

2016-12-01

Kinetic simulations and observations of magnetic reconnection suggest the Hall term of Ohm's Law is necessary for understanding fast reconnection in the Earth's magnetosphere. During high (>1) guide field plasma conditions in the solar wind and in Earth's magnetopause, tripolar variations in the guide magnetic field are often observed during current sheet crossings, and have been linked to reconnection Hall magnetic fields. Two proposed mechanisms for these tripolar variations are the presence of multiple nearby X-lines and magnetic island coalescence. We present results of an investigation into the structure of the electron currents supporting tripolar guide magnetic field variations during Kelvin-Helmholtz wave current sheet crossings using the Magnetosphere Multiscale (MMS) Mission, and compare with bipolar magnetic field structures and with kinetic simulations to understand how these tripolar structures may be used as tracers for magnetic islands.

Structure sensitivity in oxide catalysis: First-principles kinetic Monte Carlo simulations for CO oxidation at RuO{sub 2}(111)

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

Wang, Tongyu; Reuter, Karsten, E-mail: karsten.reuter@ch.tum.de; SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory and Stanford University, 443 Via Ortega, Stanford, California 94035-4300

2015-11-28

We present a density-functional theory based kinetic Monte Carlo study of CO oxidation at the (111) facet of RuO{sub 2}. We compare the detailed insight into elementary processes, steady-state surface coverages, and catalytic activity to equivalent published simulation data for the frequently studied RuO{sub 2}(110) facet. Qualitative differences are identified in virtually every aspect ranging from binding energetics over lateral interactions to the interplay of elementary processes at the different active sites. Nevertheless, particularly at technologically relevant elevated temperatures, near-ambient pressures and near-stoichiometric feeds both facets exhibit almost identical catalytic activity. These findings challenge the traditional definition of structure sensitivitymore » based on macroscopically observable turnover frequencies and prompt scrutiny of the applicability of structure sensitivity classifications developed for metals to oxide catalysis.« less

Sacrificial bonds and hidden length in biomaterials: A kinetic constitutive description of strength and toughness in bone

NASA Astrophysics Data System (ADS)

Lieou, Charles K. C.; Elbanna, Ahmed E.; Carlson, Jean M.

2013-07-01

Sacrificial bonds and hidden length in structural molecules account for the greatly increased fracture toughness of biological materials compared to synthetic materials without such structural features by providing a molecular-scale mechanism for energy dissipation. One example is in the polymeric glue connection between collagen fibrils in animal bone. In this paper we propose a simple kinetic model that describes the breakage of sacrificial bonds and the release of hidden length, based on Bell's theory. We postulate a master equation governing the rates of bond breakage and formation. This enables us to predict the mechanical behavior of a quasi-one-dimensional ensemble of polymers at different stretching rates. We find that both the rupture peak heights and maximum stretching distance increase with the stretching rate. In addition, our theory naturally permits the possibility of self-healing in such biological structures.

Comparison of shock structure solutions using independent continuum and kinetic theory approaches

NASA Technical Reports Server (NTRS)

Fiscko, Kurt A.; Chapman, Dean R.

1988-01-01

A vehicle traversing the atmosphere will experience flight regimes at high altitudes in which the thickness of a hypersonic shock wave is not small compared to the shock standoff distance from the hard body. When this occurs, it is essential to compute accurate flow field solutions within the shock structure. In this paper, one-dimensional shock structure is investigated for various monatomic gases from Mach 1.4 to Mach 35. Kinetic theory solutions are computed using the Direct Simulation Monte Carlo method. Steady-state solutions of the Navier-Stokes equations and of a slightly truncated form of the Burnett equations are determined by relaxation to a steady state of the time-dependent continuum equations. Monte Carlo results are in excellent agreement with published experimental data and are used as bases of comparison for continuum solutions. For a Maxwellian gas, the truncated Burnett equations are shown to produce far more accurate solutions of shock structure than the Navier-Stokes equations.

Dissecting structural and electronic effects in inducible nitric oxide synthase.

PubMed

Hannibal, Luciana; Page, Richard C; Haque, Mohammad Mahfuzul; Bolisetty, Karthik; Yu, Zhihao; Misra, Saurav; Stuehr, Dennis J

2015-04-01

Nitric oxide synthases (NOSs) are haem-thiolate enzymes that catalyse the conversion of L-arginine (L-Arg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide a hydrogen bond for oxygen activation (O-O scission). We present a study of native iNOS compared with iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to those of their native counterparts. Single turnover reactions catalysed by iNOSoxy with L-Arg (first reaction step) or N-hydroxy-L-arginine (second reaction step) showed that mesohaem substitution triggered higher rates of Fe(II)O₂ conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared with the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency towards NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations.

DISSECTING STRUCTURAL AND ELECTRONIC EFFECTS IN INDUCIBLE NITRIC OXIDE SYNTHASE

PubMed Central

Hannibal, Luciana; Page, Richard C.; Haque, Mohammad Mahfuzul; Bolisetty, Karthik; Yu, Zhihao; Misra, Saurav; Stuehr, Dennis J.

2015-01-01

Nitric oxide synthases (NOS) are haem-thiolate enzymes that catalyse the conversion of L-Arginine (LArg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide an H-bond for oxygen activation (O-O scission). We present a comparative study of native iNOS versus iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to their native counterparts. Single turnover reactions catalysed by iNOSoxy with LArg (first reaction step) or N-hydroxyarginine (second reaction step) showed that mesohaem substitution triggered faster rates of FeIIO2 conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared to the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency toward NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations. PMID:25608846

Stretched-to-compressed-exponential crossover observed in the electrical degradation kinetics of some spinel-metallic screen-printed structures

NASA Astrophysics Data System (ADS)

Balitska, V.; Shpotyuk, O.; Brunner, M.; Hadzaman, I.

2018-02-01

Thermally-induced (170 °C) degradation-relaxation kinetics is examined in screen-printed structures composed of spinel Cu0.1Ni0.1Co1.6Mn1.2O4 ceramics with conductive Ag or Ag-Pd layered electrodes. Structural inhomogeneities due to Ag and Ag-Pd diffusants in spinel phase environment play a decisive role in non-exponential kinetics of negative relative resistance drift. If Ag migration in spinel is inhibited by Pd addition due to Ag-Pd alloy, the kinetics attains stretched exponential behavior with ∼0.58 exponent, typical for one-stage diffusion in structurally-dispersive media. Under deep Ag penetration into spinel ceramics, as for thick films with Ag-layered electrodes, the degradation kinetics drastically changes, attaining features of two-step diffusing process governed by compressed-exponential dependence with power index of ∼1.68. Crossover from stretched- to compressed-exponential kinetics in spinel-metallic structures is mapped on free energy landscape of non-barrier multi-well system under strong perturbation from equilibrium, showing transition with a character downhill scenario resulting in faster than exponential decaying.

RNA folding: structure prediction, folding kinetics and ion electrostatics.

PubMed

Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

2015-01-01

Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

Thermodynamics, kinetics, and catalytic effect of dehydrogenation from MgH2 stepped surfaces and nanocluster: a DFT study

NASA Astrophysics Data System (ADS)

Reich, Jason; Wang, Linlin; Johnson, Duane

2013-03-01

We detail the results of a Density Functional Theory (DFT) based study of hydrogen desorption, including thermodynamics and kinetics with(out) catalytic dopants, on stepped (110) rutile and nanocluster MgH2. We investigate competing configurations (optimal surface and nanoparticle configurations) using simulated annealing with additional converged results at 0 K, necessary for finding the low-energy, doped MgH2 nanostructures. Thermodynamics of hydrogen desorption from unique dopant sites will be shown, as well as activation energies using the Nudged Elastic Band algorithm. To compare to experiment, both stepped structures and nanoclusters are required to understanding and predict the effects of ball milling. We demonstrate how these model systems relate to the intermediary sized structures typically seen in ball milling experiments.

Molecular-dynamics study of solid-liquid interface migration in fcc metals

NASA Astrophysics Data System (ADS)

Mendelev, M. I.; Rahman, M. J.; Hoyt, J. J.; Asta, M.

2010-10-01

In order to establish a link between various structural and kinetic properties of metals and the crystal-melt interfacial mobility, free-solidification molecular-dynamics simulations have been performed for a total of nine embedded atom method interatomic potentials describing pure Al, Cu and Ni. To fully explore the space of materials properties three new potentials have been developed. The new potentials are based on a previous description of Al, but in each case the liquid structure, the melting point and/or the latent heat are varied considerably. The kinetic coefficient, μ, for all systems has been compared with several theoretical predictions. It is found that at temperatures close to the melting point the magnitude of μ correlates well with the value of the diffusion coefficient in the liquid.

Kinetic Scale Structure of Low-frequency Waves and Fluctuations

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

López, Rodrigo A.; Yoon, Peter H.; Viñas, Adolfo F.

The dissipation of solar wind turbulence at kinetic scales is believed to be important for the heating of the corona and for accelerating the wind. The linear Vlasov kinetic theory is a useful tool for identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, and ion-acoustic (or kinetic slow), and their possible roles in the dissipation. However, the kinetic mode structure in the vicinity of ion-cyclotron modes is not clearly understood. The present paper aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. Themore » theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion-Bernstein modes versus quasi-modes. The spontaneous emission theory and simulation also confirm the findings of the Vlasov theory in that the kinetic Alfvén waves can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high-beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave–particle interactions.« less

Mechanistic Study of Oxygen Atom Transfer Catalyzed by Rhenium Compounds

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

Shan, Xiaopeng

2003-01-01

Two ionic and one neutral methyl(oxo)rhenium(V) compounds were synthesized and structurally characterized. They were compared in reactivity towards the ligands triphenylphosphane, pyridines, pyridine N-oxides. Assistance from Broensted bases was found on ligand displacement of ionic rhenium compounds as well as nucleophile assistance on oxidation of all compounds. From the kinetic data, crystal structures, and an analysis of the intermediates, a structural formula of PicH +3 - and mechanisms of ligand displacement and oxidation were proposed.

Kinetics of Corrosion Inhibition of Aluminum in Acidic Media by Water-Soluble Natural Polymeric Pectates as Anionic Polyelectrolyte Inhibitors.

PubMed

Hassan, Refat M; Zaafarany, Ishaq A

2013-06-17

Corrosion inhibition of aluminum (Al) in hydrochloric acid by anionic polyeletrolyte pectates (PEC) as a water-soluble natural polymer polysaccharide has been studied using both gasometric and weight loss techniques. The results drawn from these two techniques are comparable and exhibit negligible differences. The inhibition efficiency was found to increase with increasing inhibitor concentration and decrease with increasing temperature. The inhibition action of PEC on Al metal surface was found to obey the Freundlich isotherm. Factors such as the concentration and geometrical structure of the inhibitor, concentration of the corrosive medium, and temperature affecting the corrosion rates were examined. The kinetic parameters were evaluated and a suitable corrosion mechanism consistent with the kinetic results is discussed in the paper.

Kinetics of Corrosion Inhibition of Aluminum in Acidic Media by Water-Soluble Natural Polymeric Pectates as Anionic Polyelectrolyte Inhibitors

PubMed Central

Hassan, Refat M.; Zaafarany, Ishaq A.

2013-01-01

Corrosion inhibition of aluminum (Al) in hydrochloric acid by anionic polyeletrolyte pectates (PEC) as a water-soluble natural polymer polysaccharide has been studied using both gasometric and weight loss techniques. The results drawn from these two techniques are comparable and exhibit negligible differences. The inhibition efficiency was found to increase with increasing inhibitor concentration and decrease with increasing temperature. The inhibition action of PEC on Al metal surface was found to obey the Freundlich isotherm. Factors such as the concentration and geometrical structure of the inhibitor, concentration of the corrosive medium, and temperature affecting the corrosion rates were examined. The kinetic parameters were evaluated and a suitable corrosion mechanism consistent with the kinetic results is discussed in the paper. PMID:28809282

Hybrid simulations of magnetic reconnection with kinetic ions and fluid electron pressure anisotropy

DOE PAGES

Le, A.; Daughton, W.; Karimabadi, H.; ...

2016-03-16

We present the first hybrid simulations with kinetic ions and recently developed equations of state for the electron fluid appropriate for reconnection with a guide field. The equations of state account for the main anisotropy of the electron pressure tensor.Magnetic reconnection is studied in two systems, an initially force-free current sheet and a Harris sheet. The hybrid model with the equations of state is compared to two other models, hybrid simulations with isothermal electrons and fully kinetic simulations. Including the anisotropicequations of state in the hybrid model provides a better match to the fully kinetic model. In agreement with fullymore » kinetic results, the main feature captured is the formation of an electron current sheet that extends several ion inertial lengths. This electron current sheet modifies the Hall magnetic field structure near the X-line, and it is not observed in the standard hybrid model with isotropic electrons. The saturated reconnection rate in this regime nevertheless remains similar in all three models. Here, implications for global modeling are discussed.« less

Different thermostabilities of sarcoplasmic reticulum (Ca2+ + Mg2+)-ATPases from rabbit and trout muscles.

PubMed

de Toledo, F G; Albuquerque, M C; Goulart, B H; Chini, E N

1995-05-01

Trout and rabbit (Ca2+ + Mg2+)-ATPases from sarcoplasmic reticulum were compared for differences in thermal inactivation and susceptibility to trypsin digestion. The trout ATPase is more heat-sensitive than the rabbit ATPase and is stabilized by Ca2+, Na+, K+ and nucleotides. Solubilization of both ATPases shows that the two ATPases have different protein-intrinsic inactivation kinetics. When digested by trypsin, the two ATPases display different cleavage patterns. The present results indicate that the trout and rabbit ATPases have dissimilarities in protein structure that may explain the differences in thermal inactivation kinetics.

Lipo-Protein Emulsion Structure in the Diet Affects Protein Digestion Kinetics, Intestinal Mucosa Parameters and Microbiota Composition.

PubMed

Oberli, Marion; Douard, Véronique; Beaumont, Martin; Jaoui, Daphné; Devime, Fabienne; Laurent, Sandy; Chaumontet, Catherine; Mat, Damien; Le Feunteun, Steven; Michon, Camille; Davila, Anne-Marie; Fromentin, Gilles; Tomé, Daniel; Souchon, Isabelle; Leclerc, Marion; Gaudichon, Claire; Blachier, François

2018-01-01

Food structure is a key factor controlling digestion and nutrient absorption. We test the hypothesis that protein emulsion structure in the diet may affect digestive and absorptive processes. Rats (n = 40) are fed for 3 weeks with two diets chemically identical but based on lipid-protein liquid-fine (LFE) or gelled-coarse (GCE) emulsions that differ at the macro- and microstructure levels. After an overnight fasting, they ingest a 15 N-labeled LFE or GCE test meal and are euthanized 0, 15 min, 1 h, and 5 h later. 15 N enrichment in intestinal contents and blood are measured. Gastric emptying, protein digestion kinetics, 15 N absorption, and incorporation in blood protein and urea are faster with LFE than GCE. At 15 min time point, LFE group shows higher increase in GIP portal levels than GCE. Three weeks of dietary adaptation leads to higher expression of cationic amino acid transporters in ileum of LFE compared to GCE. LFE diet raises cecal butyrate and isovalerate proportion relative to GCE, suggesting increased protein fermentation. LFE diet increases fecal Parabacteroides relative abundance but decreases Bifidobacterium, Sutterella, Parasutterella genera, and Clostridium cluster XIV abundance. Protein emulsion structure regulates digestion kinetics and gastrointestinal physiology, and could be targeted to improve food health value. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermittency, coherent structures and dissipation in plasma turbulence

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

Wan, M.; Matthaeus, W. H.; Parashar, T. N.

Collisionless dissipation in turbulent plasmas such as the solar wind and the solar corona has been an intensively studied subject recently, with new insights often emerging from numerical simulation. Here we report results from high resolution, fully kinetic simulations of plasma turbulence in both two (2D) and three (3D) dimensions, studying the relationship between intermittency and dissipation. The simulations show development of turbulent coherent structures, characterized by sheet-like current density structures spanning a range of scales. An approximate dissipation measure is employed, based on work done by the electromagnetic field in the local electron fluid frame. This surrogate dissipation measuremore » is highly concentrated in small subvolumes in both 2D and 3D simulations. Fully kinetic simulations are also compared with magnetohydrodynamics (MHD) simulations in terms of coherent structures and dissipation. The interesting result emerges that the conditional averages of dissipation measure scale very similarly with normalized current density J in 2D and 3D particle-in-cell and in MHD. To the extent that the surrogate dissipation measure is accurate, this result implies that on average dissipation scales as ∼J{sup 2} in turbulent kinetic plasma. Multifractal intermittency is seen in the inertial range in both 2D and 3D, but at scales ∼ion inertial length, the scaling is closer to monofractal.« less

A comparison of the lung clearance kinetics of solid lipid nanoparticles and liposomes by following the 3H-labelled structural lipids after pulmonary delivery in rats.

PubMed

Haque, Shadabul; Whittaker, Michael; McIntosh, Michelle P; Pouton, Colin W; Phipps, Simon; Kaminskas, Lisa M

2018-04-01

The utility of biodegradable nanosized drug carriers for the local and controlled delivery of therapeutics to the lungs has prompted significant interest in the development of inhalable nanomedicines. Still, little is known about how these systems are cleared from the lungs, including the kinetics of the structural lipids. Most preclinical and clinical studies to date have evaluated the lung clearance of loaded drugs, which in many cases poorly reflects the kinetics of the nanocarrier, or the bulk-labelled particles. This study therefore aimed to describe and compare the pulmonary pharmacokinetic behaviour and patterns of lung clearance of two commonly explored inhalable nanocarriers (anionic ∼150 nm liposomes and solid lipid nanoparticles [SLNs]) in rats by following the 3 H-labelled structural lipids (phosphatidylcholine and tristearin respectively). The data showed that SLNs and liposomes were cleared from the lungs at similar rates, despite SLNs being deposited after intratracheal instillation in the upper respiratory track, and primarily via the mucociliary escalator, but this process was more pronounced for SLNs. Structural lipids were mainly associated with plasma proteins rather than nanocarrier in plasma. The lipids also exhibit prolonged lung exposure and are associated with the lung tissue (rather than BALF) over 2 weeks. Copyright © 2018 Elsevier B.V. All rights reserved.

Structure, recognition and adaptive binding in RNA aptamer complexes.

PubMed

Patel, D J; Suri, A K; Jiang, F; Jiang, L; Fan, P; Kumar, R A; Nonin, S

1997-10-10

Novel features of RNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of RNA aptamers that bind cofactors, aminoglycoside antibiotics, amino acids and peptides with high affinity and specificity. This review presents the solution structures of RNA aptamer complexes with adenosine monophosphate, flavin mononucleotide, arginine/citrulline and tobramycin together with an example of hydrogen exchange measurements of the base-pair kinetics for the AMP-RNA aptamer complex. A comparative analysis of the structures of these RNA aptamer complexes yields the principles, patterns and diversity associated with RNA architecture, molecular recognition and adaptive binding associated with complex formation.

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.

Catecholase activity of dicopper(II)-bispidine complexes: stabilities and structures of intermediates, kinetics and reaction mechanism.

PubMed

Born, Karin; Comba, Peter; Daubinet, André; Fuchs, Alexander; Wadepohl, Hubert

2007-01-01

A mechanism for the oxidation of 3,5-di-tert-butylcatechol (dtbc) with dioxygen to the corresponding quinone (dtbq), catalyzed by bispidine-dicopper complexes (bispidines are various mono- and dinucleating derivatives of 3,7-diazabicyclo[3.3.1]nonane with bis-tertiary-amine-bispyridyl or bis-tertiary-amine-trispyridyl donor sets), is proposed on the basis of (1) the stoichiometry of the reaction as well as the stabilities and structures [X-ray, density functional theory (B3LYP, TZV)] of the bispidine-dicopper(II)-3,4,5,6-tetrachlorcatechol intermediates, (2) formation kinetics and structures (molecular mechanics, MOMEC) of the end-on peroxo-dicopper(II) complexes and (3) kinetics of the stoichiometric (anaerobic) and catalytic (aerobic) copper-complex-assisted oxidation of dtbc. This involves (1) the oxidation of the dicopper(I) complexes with dioxygen to the corresponding end-on peroxo-dicopper(II) complexes, (2) coordination of dtbc as a bridging ligand upon liberation of H(2)O(2) and (3) intramolecular electron transfer to produce dtbq, which is liberated, and the dicopper(I) catalyst. Although the bispidine complexes have reactivities comparable to those of recently published catalysts with macrocyclic ligands, which seem to reproduce the enzyme-catalyzed process in various reaction sequences, a strikingly different oxidation mechanism is derived from the bispidine-dicopper-catalyzed reaction.

Measuring and modelling the structure of chocolate

NASA Astrophysics Data System (ADS)

Le Révérend, Benjamin J. D.; Fryer, Peter J.; Smart, Ian; Bakalis, Serafim

2015-01-01

The cocoa butter present in chocolate exists as six different polymorphs. To achieve the desired crystal form (βV), traditional chocolate manufacturers use relatively slow cooling (<2°C/min). A newer generation of rapid cooling systems has been suggested requiring further understanding of fat crystallisation. To allow better control and understanding of these processes and newer rapid cooling processes, it is necessary to understand both heat transfer and crystallization kinetics. The proposed model aims to predict the temperature in the chocolate products during processing as well as the crystal structure of cocoa butter throughout the process. A set of ordinary differential equations describes the kinetics of fat crystallisation. The parameters were obtained by fitting the model to a set of DSC curves. The heat transfer equations were coupled to the kinetic model and solved using commercially available CFD software. A method using single crystal XRD was developed using a novel subtraction method to quantify the cocoa butter structure in chocolate directly and results were compared to the ones predicted from the model. The model was proven to predict phase change temperature during processing accurately (±1°C). Furthermore, it was possible to correctly predict phase changes and polymorphous transitions. The good agreement between the model and experimental data on the model geometry allows a better design and control of industrial processes.

Computer simulation of structural modifications induced by highly energetic ions in uranium dioxide

NASA Astrophysics Data System (ADS)

Sasajima, Y.; Osada, T.; Ishikawa, N.; Iwase, A.

2013-11-01

The structural modification caused by the high-energy-ion irradiation of single-crystalline uranium dioxide was simulated by the molecular dynamics method. As the initial condition, high kinetic energy was supplied to the individual atoms within a cylindrical region of nanometer-order radius located in the center of the specimen. The potential proposed by Basak et al. [C.B. Basak, A.K. Sengupta, H.S. Kamath, J. Alloys Compd. 360 (2003) 210-216] was utilized to calculate interaction between atoms. The supplied kinetic energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it dissipated in the specimen. The amorphous track radius Ra was determined as a function of the effective stopping power gSe, i.e., the kinetic energy of atoms per unit length created by ion irradiation (Se: electronic stopping power, g: energy transfer ratio from stopping power to lattice vibration energy). It was found that the relationship between Ra and gSe follows the relation Ra2=aln(gS)+b. Compared to the case of Si and β-cristobalite single crystals, it was harder to produce amorphous track because of the long range interaction between U atoms.

Comparison of four kinds of extraction techniques and kinetics of microwave-assisted extraction of vanillin from Vanilla planifolia Andrews.

PubMed

Dong, Zhizhe; Gu, Fenglin; Xu, Fei; Wang, Qinghuang

2014-04-15

Vanillin yield, microscopic structure, antioxidant activity and overall odour of vanilla extracts obtained by different treatments were investigated. MAE showed the strongest extraction power, shortest time and highest antioxidant activity. Maceration gave higher vanillin yields than UAE and PAE, similar antioxidant activity with UAE, but longer times than UAE and PAE. Overall odour intensity of different vanilla extracts obtained by UAE, PAE and MAE were similar, while higher than maceration extracts. Then, powered vanilla bean with a sample/solvent ratio of 4 g/100 mL was selected as the optimum condition for MAE. Next, compared with other three equations, two-site kinetic equation with lowest RMSD and highest R²(adj) was shown to be more suitable in describing the kinetics of vanillin extraction. By fitting the parameters C(eq), k₁, k₂, and f, a kinetics model was constructed to describe vanillin extraction in terms of irradiation power, ethanol concentration, and extraction time. Copyright © 2013 Elsevier Ltd. All rights reserved.

Influence of chemical composition of zirconium alloy E110 on embrittlement under LOCA conditions - Part 1: Oxidation kinetics and macrocharacteristics of structure and fracture

NASA Astrophysics Data System (ADS)

Nikulin, S. A.; Rozhnov, A. B.; Belov, V. A.; Li, E. V.; Glazkina, V. S.

2011-11-01

Exploratory investigations of the influence of alloying and impurity content in the E110 alloy cladding tubes on the behavior under conditions of Loss of Coolant Accidents (LOCA) has been performed. Three alloys of E110 type have been tested: E110 alloy of nominal composition Zr-1%Nb (E110), E110 alloy of modified composition Zr-1%Nb-0.12%Fe-0.13%O (E110M), E110 alloy of nominal composition Zr-1%Nb with reduced impurity content (E110G). Alloys E110 and E110M were manufactured on the electrolytic basis and alloy E110G was manufactured on the basis of zirconium sponge. The high temperature oxidation tests in steam ( T = 1100 °C, 18% of equivalent cladding reacted (ECR)) have been conducted, kinetics of oxidation was investigated. Quantitative research of structure and fracture macrocharacteristics was performed by means of optical and electron microscopy. The results received were compared with the residual ductility of specimens. The results of the investigation showed the existence of "breakaway oxidation" kinetics and white spalling oxide in E110 and E110M alloys while the specimen oxidation kinetics in E110G alloy was characterized by a parabolic law and specimens had a dense black oxide. Oxygen and iron alloying in the E110 alloy positively changed the macrocharacteristics of structure and fracture. However, in general, it did not improve the resistance to embrittlement in LOCA conditions apparently because of a strong impurity influence caused by electrolytic process of zirconium production.

Evolution of Nano-structured Quasicrystals from Amorphous alloys

NASA Astrophysics Data System (ADS)

Xing, L. Q.; Kelton, K. F.

2002-03-01

Ta shows a significant effect on the precipitation of quasicrystals in (Zr_1-xTa_x)_64Cu_18Ni_8Al_10 amorphous alloys. The amorphous alloy made without Ta forms precipitates of tetragonal Zr_2Cu primary phases upon annealing. The addition of a small amount of Ta ( ~ 3 at%) to the alloy initiates the precipitation of primary icosahedral quasicrystal phases. Moreover, as the Ta concentration increases, the size of the precipitates decreases dramatically. To study the effect of Ta in this alloy system and to understand the mechanism for the precipitation of nano-structured quasicrystals, we have investigated the crystallization characteristics of the alloys made with different Ta concentration using DSC, checked the structures of the annealed samples with TEM and X-ray diffraction, and analyzed the kinetics of the crystallization processes. The kinetic parameter and the measured crystal size distribution will be compared with theoretical predictions from conventional nucleation and growth model and from a new model for nucleation that couples the long-range diffusion flux with the interfacial attachment processes.

Morphological Transformation between Nanocoils and Nanoribbons via Defragmentation Structural Rearrangement or Fragmentation-recombination Mechanism

NASA Astrophysics Data System (ADS)

Zhang, Yibin; Zheng, Yingxuan; Xiong, Wei; Peng, Cheng; Zhang, Yifan; Duan, Ran; Che, Yanke; Zhao, Jincai

2016-06-01

Kinetic control over the assembly pathways towards novel metastable functional materials or far-from-equilibrium systems has been much less studied compared to the thermodynamic equilibrium self-assembly. Herein, we report the distinct morphological transformation between nanocoils and nanoribbons in the self-assembly of unsymmetric perylene diimide (PDI) molecules. We demonstrate that the morphological transformation of the kinetically trapped assemblies into the thermodynamically stable forms proceeds via two distinct mechanisms, i.e., a direct structural rearrangement (molecule 1 or 2) and a fragmentation-recombination mechanism (molecule 4), respectively. The subtle interplay of the steric hindrance of the bulky substituents and the flexibility of the linker structure between the bulky moiety and the perylene core was demonstrated to enable the effective modulation of the energetic landscape of the assemblies and thus modulation of the assembly pathways. Herein, our work presents a new approach to control the self-assembly pathways and thereby can be used to achieve novel far-from-equilibrium systems.

Computational study of RNA folding kinetics and thermodynamics

NASA Astrophysics Data System (ADS)

Morgan, Steven Robert

RNA in its many forms is involved in the processes of protein manufacture, gene splicing, catalysis and gene regulation. It is also the store of genetic information in some viruses. The function of the RNA is determined by its structure, and it is the purpose of this thesis to investigate kinetic and thermodynamic properties of RNA secondary structures in order to obtain a better understanding of their formation and function. Our main tenet is that kinetic formation of RNA structure is necessary to explain features found in natural RNA structures, as well as aspects of the biological function of RNA. Firstly we show that examination of the energies of fragments of RNA secondary structure provides evidence for kinetic formation of structure. Local regions of RNA of length less than about 100 nucleotides adopt a conformation with energy near or equal to the minimum possible for those regions, whilst the energies of larger domains are much further from the their respective minima. This is consistent with the patterns that would be expected if RNA structure is folded Idneticatic during transcription. A Monte-Carlo algorithm is then used to model the kinetic folding of RNA during transcriptional growth. The algorithm is capable of finding the correct structure of a natural RNA for which the minimum free energy approach is unsuccessful. In the viral phage MS2 Idneticatic formed RNA structure plays an important role in the regulation of gene expression. The folding algorithm can accurately model this by IdneticaUy controlling access to the gene initiation region. The algorithm is also successfully used to model the control of replication in the ColEl plasmid. Taking a different approach, we then use a simplified model of RNA secondary structure to investigate the size of energy barriers between degenerate minimum energy structures. This model has much in common with physical systems such as spin glasses, and in fact shows similar behaviour to these systems in that energy barriers between structures grow quickly with the length of the RNA sequence. These barriers will serve to trap RNA in non-optimal structures. Together these studies demonstrate the necessity of studying RNA secondary structure from a kinetic point of view, and provide clear directions in which further work may be taken. Kinetic models of RNA secondary structure should continue to prove useful in modelling the structure and function of RNA.

Effect of cationic substitution on the double-well hydrogen-bond potential in [K1-x(NH4)x]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study.

PubMed

Choudhury, R R; Chitra, R; Selezneva, E V; Makarova, I P

2017-10-01

The structure of the mixed crystal [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K 3 H(SO 4 ) 2 . The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K + with NH 4 + has a significant influence on the short strong hydrogen bond connecting the two SO 4 2- ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 are much faster than in K 3 H(SO 4 ) 2 ; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.

PubMed

Gsponer, Joerg; Hopearuoho, Harri; Whittaker, Sara B-M; Spence, Graham R; Moore, Geoffrey R; Paci, Emanuele; Radford, Sheena E; Vendruscolo, Michele

2006-01-03

We present a detailed structural characterization of the intermediate state populated during the folding and unfolding of the bacterial immunity protein Im7. We achieve this result by incorporating a variety of experimental data available for this species in molecular dynamics simulations. First, we define the structure of the exchange-competent intermediate state of Im7 by using equilibrium hydrogen-exchange protection factors. Second, we use this ensemble to predict Phi-values and compare the results with the experimentally determined Phi-values of the kinetic refolding intermediate. Third, we predict chemical-shift measurements and compare them with the measured chemical shifts of a mutational variant of Im7 for which the kinetic folding intermediate is the most stable state populated at equilibrium. Remarkably, we found that the properties of the latter two species are predicted with high accuracy from the exchange-competent intermediate that we determined, suggesting that these three states are characterized by a similar architecture in which helices I, II, and IV are aligned in a native-like, but reorganized, manner. Furthermore, the structural ensemble that we obtained enabled us to rationalize the results of tryptophan fluorescence experiments in the WT protein and a series of mutational variants. The results show that the integration of diverse sets of experimental data at relatively low structural resolution is a powerful approach that can provide insights into the structural organization of this conformationally heterogeneous three-helix intermediate with unprecedented detail and highlight the importance of both native and non-native interactions in stabilizing its structure.

Insulation-resistance degradation kinetics of bulk BaTi1-ξAξO3-Δ and defect-chemical origin of acceptor-type(A) and doping-level(ξ) effect

NASA Astrophysics Data System (ADS)

Kwon, Hyung-Soon; Yoon, Seok-Hyun; Yoo, Han-Ill

2016-07-01

Dearth of the reproducible, consistent observations on insulation-resistance (IR) degradation kinetics of bulk dielectric BaTiO3 may be attributed to their conventional measurement method, two-probe potentiostatic, which would be by no means free from the electrode effect for a finite- dimension specimen in particular. We hereby measured the IR-degradation kinetics galvanostatically by using a series of inner probes on bulk BaTi1-ξAξO3-Δ (A = Al, Mn; ξ = 0.001, 0.003, 0.010) with their high-temperature (1000 °C) equilibrium ionic-defect-structure in air being frozen-in at 250 °C and compared with the kinetics as calculated on the basis of the electromigration of frozen-in oxygen vacancies ( cV o ) in association with the A-ionization or hole-trapping equilibria. It has turned out that the calculated depict sufficiently precisely all the as-observed kinetics as well as the effects of acceptor type(A) and doping level(ξ), thus, quantitatively establishing the correlation between the frozen-in ionic-defect-structure and IR-degradation kinetics with new insights into the degradation inner-workings: IR-degradation is triggered as soon as the oxygen vacancy concentration at the cathode reaches that corresponding to the insulator-to-semiconductor transition ( cV S / I ) and proceeds with the front of just-turned, n-type semiconducting region ( c V = cV S / I ) moving towards the anode at a fixed velocity. The healthy lifetime of the dielectric is, thus, essentially the time duration for the cathode to achieve cV S / I from cV o , and the final stage of degradation is approximated to be the length fraction χs of the semiconductor such that χs = cV o / cV S / I . A new suggestion is finally made to further suppress the IR degradation kinetics of the bulk dielectric BaTiO3.

SR2067 reveals a unique kinetic and structural signature for PPARγ partial agonism

DOE PAGES

van Marrewijk, Laura M.; Polyak, Steven W.; Hijnen, Marcel; ...

2015-11-18

Here, synthetic full agonists of PPARγ have been prescribed for the treatment of diabetes due to their ability to regulate glucose homeostasis and insulin sensitization. While the use of full agonists of PPARγ has been hampered due to severe side effects, partial agonists have shown promise due to their decreased incidence of such side effects in preclinical models. No kinetic information has been forthcoming in regard to the mechanism of full versus partial agonism of PPARγ to date. In this paper, we describe the discovery of a partial agonist, SR2067. A co-crystal structure obtained at 2.2 Å resolution demonstrates thatmore » interactions with the β-sheet are driven exclusively via hydrophobic interactions mediated through a naphthalene group, an observation that is unique from other partial agonists. Finally, surface plasmon resonance revealed that SR2067 binds to the receptor with higher affinity (K D = 513 nM) as compared to that of full agonist rosiglitazone, yet it has a much slower off rate compared to that of rosiglitazone.« less

A Monte Carlo approach to the microdosimetric kinetic model to account for dose rate time structure effects in ion beam therapy with application in treatment planning simulations.

PubMed

Manganaro, Lorenzo; Russo, Germano; Cirio, Roberto; Dalmasso, Federico; Giordanengo, Simona; Monaco, Vincenzo; Muraro, Silvia; Sacchi, Roberto; Vignati, Anna; Attili, Andrea

2017-04-01

Advanced ion beam therapeutic techniques, such as hypofractionation, respiratory gating, or laser-based pulsed beams, have dose rate time structures which are substantially different from those found in conventional approaches. The biological impact of the time structure is mediated through the β parameter in the linear quadratic (LQ) model. The aim of this study was to assess the impact of changes in the value of the β parameter on the treatment outcomes, also accounting for noninstantaneous intrafraction dose delivery or fractionation and comparing the effects of using different primary ions. An original formulation of the microdosimetric kinetic model (MKM) is used (named MCt-MKM), in which a Monte Carlo (MC) approach was introduced to account for the stochastic spatio-temporal correlations characteristic of the irradiations and the cellular repair kinetics. A modified version of the kinetic equations, validated on experimental cell survival in vitro data, was also introduced. The model, trained on the HSG cells, was used to evaluate the relative biological effectiveness (RBE) for treatments with acute and protracted fractions. Exemplary cases of prostate cancer irradiated with different ion beams were evaluated to assess the impact of the temporal effects. The LQ parameters for a range of cell lines (V79, HSG, and T1) and ion species (H, He, C, and Ne) were evaluated and compared with the experimental data available in the literature, with good results. Notably, in contrast to the original MKM formulation, the MCt-MKM explicitly predicts an ion and LET-dependent β compatible with observations. The data from a split-dose experiment were used to experimentally determine the value of the parameter related to the cellular repair kinetics. Concerning the clinical case considered, an RBE decrease was observed, depending on the dose, ion, and LET, exceeding up to 3% of the acute value in the case of a protraction in the delivery of 10 min. The intercomparison between different ions shows that the clinical optimality is strongly dependent on a complex interplay between the different physical and biological quantities considered. The present study provides a framework for exploiting the temporal effects of dose delivery. The results show the possibility of optimizing the treatment outcomes accounting for the correlation between the specific dose rate time structure and the spatial characteristic of the LET distribution, depending on the ion type used. © 2017 American Association of Physicists in Medicine.

Clustering of low-valence particles: structure and kinetics.

PubMed

Markova, Olga; Alberts, Jonathan; Munro, Edwin; Lenne, Pierre-François

2014-08-01

We compute the structure and kinetics of two systems of low-valence particles with three or six freely oriented bonds in two dimensions. The structure of clusters formed by trivalent particles is complex with loops and holes, while hexavalent particles self-organize into regular and compact structures. We identify the elementary structures which compose the clusters of trivalent particles. At initial stages of clustering, the clusters of trivalent particles grow with a power-law time dependence. Yet at longer times fusion and fission of clusters equilibrates and clusters form a heterogeneous phase with polydispersed sizes. These results emphasize the role of valence in the kinetics and stability of finite-size clusters.

Electron Heating at Kinetic Scales in Magnetosheath Turbulence

NASA Technical Reports Server (NTRS)

Chasapis, Alexandros; Matthaeus, W. H.; Parashar, T. N.; Lecontel, O.; Retino, A.; Breuillard, H.; Khotyaintsev, Y.; Vaivads, A.; Lavraud, B.; Eriksson, E.;

Human-murine transthyretin heterotetramers are kinetically stable and non-amyloidogenic. A lesson in the generation of transgenic models of diseases involving oligomeric proteins.

PubMed

Reixach, Natàlia; Foss, Ted R; Santelli, Eugenio; Pascual, Jaime; Kelly, Jeffery W; Buxbaum, Joel N

2008-01-25

The transthyretin amyloidoses appear to be caused by rate-limiting tetramer dissociation and partial monomer unfolding of the human serum protein transthyretin, resulting in aggregation and extracellular deposition of amorphous aggregates and amyloid fibrils. Mice transgenic for few copies of amyloid-prone human transthyretin variants, including the aggressive L55P mutant, failed to develop deposits. Silencing the murine transthyretin gene in the presence of the L55P human gene resulted in enhanced tissue deposition. To test the hypothesis that the murine protein interacted with human transthyretin, preventing the dissociation and partial unfolding required for amyloidogenesis, we produced recombinant murine transthyretin and human/murine transthyretin heterotetramers and compared their structures and biophysical properties to recombinant human transthyretin. We found no significant differences between the crystal structures of murine and human homotetramers. Murine transthyretin is not amyloidogenic because the native homotetramer is kinetically stable under physiologic conditions and cannot dissociate into partially unfolded monomers, the misfolding and aggregation precursor. Heterotetramers composed of murine and human subunits are also kinetically stable. These observations explain the lack of transthyretin deposition in transgenics carrying a low copy number of human transthyretin genes. The incorporation of mouse subunits into tetramers otherwise composed of human amyloid-prone transthyretin subunits imposes kinetic stability, preventing dissociation and subsequent amyloidogenesis.

The Influence of Kinetic Structure in Films on Biology Students' Achievement and Attitude.

ERIC Educational Resources Information Center

Simmons, Ellen Stephanie

1980-01-01

Tested and supported was the hypothesis that students receiving high-structured film narrations will acquire more knowledge and will respond more favorably than those receiving low-structured film narrations. Results contribute additional data to evidence supporting the need for critical application of the kinetic structure theory in evaluating…

Report on the Implementation of Homogeneous Nucleation Scheme in MARMOT-based Phase Field Simulation

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

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2013-09-30

In this report, we summarized our effort in developing mesoscale phase field models for predicting precipitation kinetics in alloys during thermal aging and/or under irradiation in nuclear reactors. The first part focused on developing a method to predict the thermodynamic properties of critical nuclei such as the sizes and concentration profiles of critical nuclei, and nucleation barrier. These properties are crucial for quantitative simulations of precipitate evolution kinetics with phase field models. Fe-Cr alloy was chosen as a model alloy because it has valid thermodynamic and kinetic data as well as it is an important structural material in nuclear reactors.more » A constrained shrinking dimer dynamics (CSDD) method was developed to search for the energy minimum path during nucleation. With the method we are able to predict the concentration profiles of the critical nuclei of Cr-rich precipitates and nucleation energy barriers. Simulations showed that Cr concentration distribution in the critical nucleus strongly depends on the overall Cr concentration as well as temperature. The Cr concentration inside the critical nucleus is much smaller than the equilibrium concentration calculated by the equilibrium phase diagram. This implies that a non-classical nucleation theory should be used to deal with the nucleation of Cr precipitates in Fe-Cr alloys. The growth kinetics of both classical and non-classical nuclei was investigated by the phase field approach. A number of interesting phenomena were observed from the simulations: 1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; 2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics. 3) a critical classical nucleus grows faster at the earlier growth stage than the non-classical nucleus. All of these results demonstrated that it is critical to introduce the correct critical nuclei into phase field modeling in order to correctly capture the kinetics of precipitation. In most alloys the matrix phase and precipitate phase have different concentrations as well as different crystal structures. For example, Cu precipitates in FeCu alloys have fcc crystal structure while the matrix Fe-Cu solid solution has bcc structure at low temperature. The WBM model and KimS model, where both concentrations and order parameters are chosen to describe the microstructures, are commonly used to model precipitations in such alloys. The WBM and KimS models have not been implemented into Marmot yet. In the second part of this report, we focused on implementing the WBM and KimS models into Marmot. The Fe-Cu alloys, which are important structure materials in nuclear reactors, was taken as the model alloys to test the models.« less

Comparison of stabilization by Vitamin E and 2,6-di-tert-butylphenols during polyethylene radio-thermal-oxidation

NASA Astrophysics Data System (ADS)

Richaud, Emmanuel

2014-10-01

This paper reports a compilation of data for PE+Vitamin E and 2,6-di-tert-butylphenols oxidation in radio-thermal ageing. Data unambiguously show that Vitamin E reacts with Prad and POOrad whereas 2,6-di-tert-butyl phenols only react with POOrad. Kinetic parameters of the stabilization reactions for both kinds of antioxidants were tentatively extracted from phenol depletion curves, and discussed regarding the structure of the stabilizer. They were also used for completing an existing kinetic model used for predicting the stabilization by antioxidants. This one permits to compare the efficiency of stabilizer with dose rate or sample thickness.

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations.

PubMed

Bernetti, Mattia; Masetti, Matteo; Pietrucci, Fabio; Blackledge, Martin; Jensen, Malene Ringkjobing; Recanatini, Maurizio; Mollica, Luca; Cavalli, Andrea

2017-10-19

Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev N TAIL , a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics. To validate our simulation strategy, we compared the predicted NMR properties against available experimental data. Our simulations reveal a rough free-energy surface comprising multiple local minima, which are separated by low energy barriers. Moreover, we identified interconversion rates between the main kinetic states, which lie in the sub-μs time scales, as suggested in previous works for Sev N TAIL . Therefore, the emerging picture is in agreement with the atomic-level properties possessed by the free IDP in solution. By providing both a thermodynamic and kinetic characterization of this IDP test case, our study demonstrates how computational methods can be effective tools for studying this challenging class of proteins.

Parameter estimation in tree graph metabolic networks.

PubMed

Astola, Laura; Stigter, Hans; Gomez Roldan, Maria Victoria; van Eeuwijk, Fred; Hall, Robert D; Groenenboom, Marian; Molenaar, Jaap J

2016-01-01

We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis-Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

Kinetic theory of age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Greenman, Chris D.; Chou, Tom

2016-01-01

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but are unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Stochastic theories that treat semi-Markov age-dependent processes using, e.g., the Bellman-Harris equation do not resolve a population's age structure and are unable to quantify population-size dependencies. Conversely, current theories that include size-dependent population dynamics (e.g., mathematical models that include carrying capacity such as the logistic equation) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new, fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a Bogoliubov--Born--Green--Kirkwood--Yvon-like hierarchy. Explicit solutions are derived in three limits: no birth, no death, and steady state. These are then compared with their corresponding mean-field results. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution.

Stability and kinetics of G-quadruplex structures

PubMed Central

Lane, Andrew N.; Chaires, J. Brad; Gray, Robert D.; Trent, John O.

2008-01-01

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence. PMID:18718931

Agent-based modeling of porous scaffold degradation and vascularization: Optimal scaffold design based on architecture and degradation dynamics.

PubMed

Mehdizadeh, Hamidreza; Bayrak, Elif S; Lu, Chenlin; Somo, Sami I; Akar, Banu; Brey, Eric M; Cinar, Ali

2015-11-01

A multi-layer agent-based model (ABM) of biomaterial scaffold vascularization is extended to consider the effects of scaffold degradation kinetics on blood vessel formation. A degradation model describing the bulk disintegration of porous hydrogels is incorporated into the ABM. The combined degradation-angiogenesis model is used to investigate growing blood vessel networks in the presence of a degradable scaffold structure. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support results in failure for the material. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as a way to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric parameters and degradation behavior of scaffolds, and enables easy refinement of the model as new knowledge about the underlying biological phenomena becomes available. This paper proposes a multi-layer agent-based model (ABM) of biomaterial scaffold vascularization integrated with a structural-kinetic model describing bulk degradation of porous hydrogels to consider the effects of scaffold degradation kinetics on blood vessel formation. This enables the assessment of scaffold characteristics and in particular the disintegration characteristics of the scaffold on angiogenesis. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support by scaffold disintegration results in failure of the material and disruption of angiogenesis. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as away to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric and degradation characteristics of tissue engineering scaffolds. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Polymorphism in molecular solids: an extraordinary system of red, orange, and yellow crystals.

PubMed

Yu, Lian

2010-09-21

Diamond and graphite are polymorphs of each other: they have the same composition but different structures and properties. Many other substances exhibit polymorphism: inorganic and organic, natural and manmade. Polymorphs are encountered in studies of crystallization, phase transition, materials synthesis, and biomineralization and in the manufacture of specialty chemicals. Polymorphs can provide valuable insights into crystal packing and structure-property relationships. 5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, known as ROY for its red, orange, and yellow crystals, has seven polymorphs with solved structures, the largest number in the Cambridge Structural Database. First synthesized by medicinal chemists, ROY has attracted attention from solid-state chemists because it demonstrates the remarkable diversity possible in organic solids. Many structures of ROY polymorphs and their thermodynamic properties are known, making ROY an important model system for testing computational models. Though not the most polymorphic substance on record, ROY is extraordinary in that many of its polymorphs can crystallize simultaneously from the same liquid and are kinetically stable under the same conditions. Studies of ROY polymorphs have revealed a new crystallization mechanism that invalidates the common view that nucleation defines the polymorph of crystallization. A slow-nucleating polymorph can still dominate the product if it grows rapidly and nucleates on another polymorph. Studies of ROY have also helped understand a new, surprisingly fast mode of crystal growth in organic liquids cooled to the glass transition temperature. This growth mode exists only for those polymorphs that have more isotropic, and perhaps more liquid-like, packing. The rich polymorphism of ROY results from a combination of favorable thermodynamics and kinetics. Not only must there be many polymorphs of comparable energies or free energies, many polymorphs must be kinetically stable and crystallize at comparable rates to be observed. This system demonstrates the unique insights that polymorphism provides into solid-state structures and properties, as well as the inadequacy of our current understanding of the phenomenon. Despite many studies of ROY, it is still impossible to predict the next molecule that is equally or more polymorphic. ROY is a lucky gift from medicinal chemists.

Structure of Kinetic Alfvén Waves of Small Transverse Scale

NASA Astrophysics Data System (ADS)

Morales, G. J.; Maggs, J. E.

1996-11-01

This analytical study illustrates the spatial pattern of kinetic Alfvén waves excited by a current-modulating disk whose dimension R transverse to the confining magnetic field is comparable to cs / Ω_i. The radial structure of the wave azimuthal magnetic field consists of 3 regions: a Bessel function behavior for r < R, a near null at r ~ R, and a driven Airy pattern for r >> R. The pattern spreads at an angle given by tan θ = (ω/Ω_i)(c_s/V_A)/(2 \\cdot 6), where ω is the modulation frequency and VA the Alfvén speed. This arises because there is a maximum value at finite k_⊥ for the ratio of the perpendicular to parallel group velocity, which differs from the cone spreading(G.J. Morales, R.S. Loritsch, and J.E. Maggs, Phys. Plasmas) 1, 3765 (1994) associated with inertial Alfvén waves. Sponsored by ONR

Kinetic Study of Laboratory Mutants of NDM-1 Metallo-β-Lactamase and the Importance of an Isoleucine at Position 35

PubMed Central

Marcoccia, Francesca; Bottoni, Carlo; Sabatini, Alessia; Colapietro, Martina; Mercuri, Paola Sandra; Galleni, Moreno; Kerff, Frédéric; Matagne, André; Celenza, Giuseppe; Amicosante, Gianfranco

2016-01-01

Two laboratory mutants of NDM-1 were generated by replacing the isoleucine at position 35 with threonine and serine residues: the NDM-1I35T and NDM-1I35S enzymes. These mutants were well characterized, and their kinetic parameters were compared with those of the NDM-1 wild type. The kcat, Km, and kcat/Km values calculated for the two mutants were slightly different from those of the wild-type enzyme. Interestingly, the kcat/Km of NDM-1I35S for loracarbef was about 14-fold higher than that of NDM-1. Far-UV circular dichroism (CD) spectra of NDM-1 and NDM-1I35T and NDM-1I35S enzymes suggest local structural rearrangements in the secondary structure with a marked reduction of α-helix content in the mutants. PMID:26856833

Toehold-Mediated Displacement of an Adenosine-Binding Aptamer from a DNA Duplex by its Ligand.

PubMed

Monserud, Jon H; Macri, Katherine M; Schwartz, Daniel K

2016-10-24

DNA is increasingly used to engineer dynamic nanoscale circuits, structures, and motors, many of which rely on DNA strand-displacement reactions. The use of functional DNA sequences (e.g., aptamers, which bind to a wide range of ligands) in these reactions would potentially confer responsiveness on such devices, and integrate DNA computation with highly varied molecular stimuli. By using high-throughput single-molecule FRET methods, we compared the kinetics of a putative aptamer-ligand and aptamer-complement strand-displacement reaction. We found that the ligands actively disrupted the DNA duplex in the presence of a DNA toehold in a similar manner to complementary DNA, with kinetic details specific to the aptamer structure, thus suggesting that the DNA strand-displacement concept can be extended to functional DNA-ligand systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetic resolution of sec-alcohols catalysed by Candida antarctica lipase B displaying Pichia pastoris whole-cell biocatalyst.

PubMed

Zhang, Kun; Pan, Zhiyou; Diao, Zhoujian; Liang, Shuli; Han, Shuangyan; Zheng, Suiping; Lin, Ying

2018-03-01

Kinetic resolution of sec-alcohols is a green process with biocatalyst. Candida antarctica lipase B (CALB) displayed on Pichia pastoris cell-surface (Pp-CALB) was characterized in kinetic resolution of sec-alcohols with different structures. The reaction parameters including acyl donors, molar ratio of substrates, solvents and temperatures were examined with 2-octanol as model substrate. 47.4% molar conversion of 2-octanol and 99.7% ee p were obtained after a 5h reaction with Pp-CALB, and 90% of its original activity still remained after being reused for 10 cycles. Pp-CALB was then used to several sec-alcohols and it showed great enzymatic activity and enantioselectivity to all tested sec-alcohols, more than 93.1% of ee p . The enantioselective characteristics of Pp-CALB catalysed sec-alcohols with different structures were compared with Novozyme 435 which was almost the same. Solvent free system as one way of green chemistry was applied to Pp-CALB and Pp-CALB showed great catalytic activity and enantioselectivity. Pp-CALB was potential biocatalyst of high enzymatic activity and enantioselectivity using in resolution of sec-alcohols. Copyright © 2017. Published by Elsevier Inc.

Adsorption of fibrinogen on a biomedical-grade stainless steel 316LVM surface: a PM-IRRAS study of the adsorption thermodynamics, kinetics and secondary structure changes.

PubMed

Desroches, Marie-Josee; Omanovic, Sasha

2008-05-14

Polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS) was employed to investigate the interaction of serum protein fibrinogen with a biomedical-grade 316LVM stainless steel surface, in terms of the adsorption thermodynamics, kinetics and secondary structure changes of the protein. Apparent Gibbs energy of adsorption values indicated a highly spontaneous and strong adsorption of fibrinogen onto the surface. The kinetics of fibrinogen adsorption were successfully modeled using a pseudo first-order kinetic model. Deconvolution of the amide I bands indicated that the adsorption of fibrinogen on 316LVM results in significant changes in the protein's secondary structure that occur predominantly within the first minute of adsorption. Among the investigated structures, the alpha-helix structure undergoes the smallest changes, while the beta-sheet and beta-turns structures undergo significant changes. It was shown that lateral interactions between the adsorbed molecules do not play a role in controlling the secondary structure changes. An increase in temperature induced changes in the secondary structure of the protein, characterized by a loss of the alpha-helical content and its transformation into the beta-turns structure.

Functional mechanism of C-terminal tail in the enzymatic role of porcine testicular carbonyl reductase: a combined experiment and molecular dynamics simulation study of the C-terminal tail in the enzymatic role of PTCR.

PubMed

Son, Minky; Bang, Woo Young; Park, Chanin; Lee, Yuno; Kwon, Seul Gi; Kim, Sam Woong; Kim, Chul Wook; Lee, Keun Woo

2014-01-01

Porcine testicular carbonyl reductase, PTCR which is one of the short chain dehydrogenases/reductases (SDR) superfamily catalyzes the NADPH-dependent reduction of carbonyl compounds including steroids and prostaglandins. Previously we reported C-terminal tail of PTCR was deleted due to a nonsynonymous single nucleotide variation (nsSNV). Here we identified from kinetic studies that the enzymatic properties for 5α-dihydrotestosterone (5α-DHT) were different between wild-type and C-terminal-deleted PTCRs. Compared to wild-type PTCR, C-terminal-deleted PTCR has much higher reduction rate. To investigate structural difference between wild-type and C-terminal-deleted PTCRs upon 5α-DHT binding, we performed molecular dynamics simulations for two complexes. Using trajectories, molecular interactions including hydrogen bonding patterns, distance between 5α-DHT and catalytic Tyr193, and interaction energies are analyzed and compared. During the MD simulation time, the dynamic behavior of C-terminal tail in wild-type PTCR is also examined using essential dynamics analysis. The results of our simulations reveal that the binding conformation of 5α-DHT in C-terminal-deleted PTCR is more favorable for reduction reaction in PTCR, which shows strong agreement with kinetic data. These structural findings provide valuable information to understand substrate specificity of PTCR and further kinetic properties of enzymes belonging to the SDR superfamily.

Functional Mechanism of C-Terminal Tail in the Enzymatic Role of Porcine Testicular Carbonyl Reductase: A Combined Experiment and Molecular Dynamics Simulation Study of the C-Terminal Tail in the Enzymatic Role of PTCR

PubMed Central

Park, Chanin; Lee, Yuno; Kwon, Seul Gi; Kim, Sam Woong; Kim, Chul Wook; Lee, Keun Woo

2014-01-01

Porcine testicular carbonyl reductase, PTCR which is one of the short chain dehydrogenases/reductases (SDR) superfamily catalyzes the NADPH-dependent reduction of carbonyl compounds including steroids and prostaglandins. Previously we reported C- terminal tail of PTCR was deleted due to a nonsynonymous single nucleotide variation (nsSNV). Here we identified from kinetic studies that the enzymatic properties for 5α-dihydrotestosterone (5α-DHT) were different between wild-type and C-terminal-deleted PTCRs. Compared to wild-type PTCR, C-terminal-deleted PTCR has much higher reduction rate. To investigate structural difference between wild-type and C-terminal-deleted PTCRs upon 5α-DHT binding, we performed molecular dynamics simulations for two complexes. Using trajectories, molecular interactions including hydrogen bonding patterns, distance between 5α-DHT and catalytic Tyr193, and interaction energies are analyzed and compared. During the MD simulation time, the dynamic behavior of C-terminal tail in wild-type PTCR is also examined using essential dynamics analysis. The results of our simulations reveal that the binding conformation of 5α-DHT in C-terminal-deleted PTCR is more favorable for reduction reaction in PTCR, which shows strong agreement with kinetic data. These structural findings provide valuable information to understand substrate specificity of PTCR and further kinetic properties of enzymes belonging to the SDR superfamily. PMID:24646606

Formation of collisionless shocks in magnetized plasma interaction with kinetic-scale obstacles

DOE PAGES

Cruz, F.; Alves, E. P.; Bamford, R. A.; ...

2017-02-06

We investigate the formation of collisionless magnetized shocks triggered by the interaction between magnetized plasma flows and miniature-sized (order of plasma kinetic-scales) magnetic obstacles resorting to massively parallel, full particle-in-cell simulations, including the electron kinetics. The critical obstacle size to generate a compressed plasma region ahead of these objects is determined by independently varying the magnitude of the dipolar magnetic moment and the plasma magnetization. Here we find that the effective size of the obstacle depends on the relative orientation between the dipolar and plasma internal magnetic fields, and we show that this may be critical to form a shockmore » in small-scale structures. We also study the microphysics of the magnetopause in different magnetic field configurations in 2D and compare the results with full 3D simulations. Finally, we evaluate the parameter range where such miniature magnetized shocks can be explored in laboratory experiments.« less

The myosin converter domain modulates muscle performance.

PubMed

Swank, Douglas M; Knowles, Aileen F; Suggs, Jennifer A; Sarsoza, Floyd; Lee, Annie; Maughan, David W; Bernstein, Sanford I

2002-04-01

Myosin is the molecular motor that powers muscle contraction as a result of conformational changes during its mechanochemical cycle. We demonstrate that the converter, a compact structural domain that differs in sequence between Drosophila melanogaster myosin isoforms, dramatically influences the kinetic properties of myosin and muscle fibres. Transgenic replacement of the converter in the fast indirect flight muscle with the converter from an embryonic muscle slowed muscle kinetics, forcing a compensatory reduction in wing beat frequency to sustain flight. Conversely, replacing the embryonic converter with the flight muscle converter sped up muscle kinetics and increased maximum power twofold, compared to flight muscles expressing the embryonic myosin isoform. The substitutions also dramatically influenced in vitro actin sliding velocity, suggesting that the converter modulates a rate-limiting step preceding cross-bridge detachment. Our integrative analysis demonstrates that isoform-specific differences in the myosin converter allow different muscle types to meet their specific locomotion demands.

Role of small oligomers on the amyloidogenic aggregation free-energy landscape.

PubMed

He, Xianglan; Giurleo, Jason T; Talaga, David S

2010-01-08

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.

Electron Heating at Kinetic Scales in Magnetosheath Turbulence

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

Chasapis, Alexandros; Matthaeus, W. H.; Parashar, T. N.

2017-02-20

We present a statistical study of coherent structures at kinetic scales, using data from the Magnetospheric Multiscale mission in the Earth’s magnetosheath. We implemented the multi-spacecraft partial variance of increments (PVI) technique to detect these structures, which are associated with intermittency at kinetic scales. We examine the properties of the electron heating occurring within such structures. We find that, statistically, structures with a high PVI index are regions of significant electron heating. We also focus on one such structure, a current sheet, which shows some signatures consistent with magnetic reconnection. Strong parallel electron heating coincides with whistler emissions at themore » edges of the current sheet.« less

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

PubMed

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

Identification of a key structural element for protein folding within beta-hairpin turns.

PubMed

Kim, Jaewon; Brych, Stephen R; Lee, Jihun; Logan, Timothy M; Blaber, Michael

2003-05-09

Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a naturally high frequency of occurrence due to favorable contributions to stability and folding. Non-Gly residues located near the left-handed alpha-helical region (L-alpha) of the Ramachandran plot are a potential indicator of structural strain. Although many investigators have studied mutations at such positions, no consistent energetic or kinetic contributions to stability or folding have been elucidated. Here we report a study of the effects of Gly, Ala and Asn substitutions found within the L-alpha region at a characteristic position in defined beta-hairpin turns within human acidic fibroblast growth factor, and demonstrate consistent effects upon stability and folding kinetics. The thermodynamic and kinetic data are compared to available data for similar mutations in other proteins, with excellent agreement. The results have identified that Gly at the i+3 position within a subset of beta-hairpin turns is a key contributor towards increasing the rate of folding to the native state of the polypeptide while leaving the rate of unfolding largely unchanged.

Implication of using different carbon sources for denitrification in wastewater treatments.

PubMed

Cherchi, Carla; Onnis-Hayden, Annalisa; El-Shawabkeh, Ibrahim; Gu, April Z

2009-08-01

Application of external carbon sources for denitrification becomes necessary for wastewater treatment plants that have to meet very stringent effluent nitrogen limits (e.g., 3 to 5 mgTN/L). In this study, we evaluated and compared three carbon sources--MicroC (Environmental Operating Solutions, Bourne, Massachusetts), methanol, and acetate-in terms of their denitrification rates and kinetics, effect on overall nitrogen removal performance, and microbial community structure of carbon-specific denitrifying enrichments. Denitrification rates and kinetics were determined with both acclimated and non-acclimated biomass, obtained from laboratory-scale sequencing batch reactor systems or full-scale plants. The results demonstrate the feasibility of the use of MicroC for denitrification processes, with maximum denitrification rates (k(dmax)) of 6.4 mgN/gVSSh and an observed yield of 0.36 mgVSS/mgCOD. Comparable maximum nitrate uptake rates were found with methanol, while acetate showed a maximum denitrification rate nearly twice as high as the others. The maximum growth rates measured at 20 degrees C for MicroC and methanol were 3.7 and 1.2 day(-1), respectively. The implications resulting from the differences in the denitrification rates and kinetics of different carbon sources on the full-scale nitrogen removal performance, under various configurations and operational conditions, were assessed using Biowin (EnviroSim Associates, Ltd., Flamborough, Ontario, Canada) simulations for both pre- and post-denitrification systems. Examination of microbial population structures using Automated Ribosomal Intergenic Spacer Analysis (ARISA) throughout the study period showed dynamic temporal changes and distinct microbial community structures of different carbon-specific denitrifying cultures. The ability of a specific carbon-acclimated denitrifying population to instantly use other carbon source also was investigated, and the chemical-structure-associated behavior patterns observed suggested that the complex biochemical pathways/enzymes involved in the denitrification process depended on the carbon sources used.

Macroscopic kinetics of pentameric ligand gated ion channels: comparisons between two prokaryotic channels and one eukaryotic channel.

PubMed

Laha, Kurt T; Ghosh, Borna; Czajkowski, Cynthia

2013-01-01

Electrochemical signaling in the brain depends on pentameric ligand-gated ion channels (pLGICs). Recently, crystal structures of prokaryotic pLGIC homologues from Erwinia chrysanthemi (ELIC) and Gloeobacter violaceus (GLIC) in presumed closed and open channel states have been solved, which provide insight into the structural mechanisms underlying channel activation. Although structural studies involving both ELIC and GLIC have become numerous, thorough functional characterizations of these channels are still needed to establish a reliable foundation for comparing kinetic properties. Here, we examined the kinetics of ELIC and GLIC current activation, desensitization, and deactivation and compared them to the GABAA receptor, a prototypic eukaryotic pLGIC. Outside-out patch-clamp recordings were performed with HEK-293T cells expressing ELIC, GLIC, or α1β2γ2L GABAA receptors, and ultra-fast ligand application was used. In response to saturating agonist concentrations, we found both ELIC and GLIC current activation were two to three orders of magnitude slower than GABAA receptor current activation. The prokaryotic channels also had slower current desensitization on a timescale of seconds. ELIC and GLIC current deactivation following 25 s pulses of agonist (cysteamine and pH 4.0 buffer, respectively) were relatively fast with time constants of 24.9 ± 5.1 ms and 1.2 ± 0.2 ms, respectively. Surprisingly, ELIC currents evoked by GABA activated very slowly with a time constant of 1.3 ± 0.3 s and deactivated even slower with a time constant of 4.6 ± 1.2 s. We conclude that the prokaryotic pLGICs undergo similar agonist-mediated gating transitions to open and desensitized states as eukaryotic pLGICs, supporting their use as experimental models. Their uncharacteristic slow activation, slow desensitization and rapid deactivation time courses are likely due to differences in specific structural elements, whose future identification may help uncover mechanisms underlying pLGIC gating transitions.

Structure/function analysis of cotton-based peptide-cellulose conjugates: spatiotemporal/kinetic assessment of protease aerogels compared to nanocrystalline and paper cellulose

USDA-ARS?s Scientific Manuscript database

The growing incidence of chronic wounds in the world population has prompted increased interest in chronic wound dressings with protease-modulating activity and protease point of care sensors to treat and enable monitoring of elevated protease-based wound pathology. However, the overall design featu...

Comparison of detailed and reduced kinetics mechanisms of silane oxidation in the basis of detonation wave structure problem

NASA Astrophysics Data System (ADS)

Fedorov, A. V.; Tropin, D. A.; Fomin, P. A.

2018-03-01

The paper deals with the problem of the structure of detonation waves in the silane-air mixture within the framework of mathematical model of a nonequilibrium gas dynamics. Detailed kinetic scheme of silane oxidation as well as the newly developed reduced kinetic model of detonation combustion of silane are used. On its basis the detonation wave (DW) structure in stoichiometric silane - air mixture and dependences of Chapman-Jouguet parameters of mixture on stoichiometric ratio between the fuel (silane) and an oxidizer (air) were obtained.

Thermodynamics and kinetics of vesicles formation processes.

PubMed

Guida, Vincenzo

2010-12-15

Vesicles are hollow aggregates, composed of bilayers of amphiphilic molecules, dispersed into and filled with a liquid solvent. These aggregates can be formed either as equilibrium or as out of equilibrium meta-stable structures and they exhibit a rich variety of different morphologies. The surprising richness of structures, the vast range of industrial applications and the presence of vesicles in a number of biological systems have attracted the interest of numerous researchers and scientists. In this article, we review both the thermodynamics and the kinetics aspects of the phenomena of formation of vesicles. We start presenting the thermodynamics of bilayer membranes formation and deformation, with the aim of deriving the conditions for the existence of equilibrium vesicles. Specifically, we use the results from continuum thermodynamics to discuss the possibility of formation of stable equilibrium vesicles, from both mixed amphiphiles and single component systems. We also link the bilayer membrane properties to the molecular structure of the starting amphiphiles. In the second part of this article, we focus on the dynamics and kinetics of vesiculation. We review the process of vesicles formation both from planar lamellar phase under shear and from isotropic micelles. In order to clarify the physical mechanisms of vesicles formation, we continuously draw a parallel between emulsification and vesiculation processes. Specifically, we compare the experimental results, the driving forces and the relative scaling laws identified for the two processes. Describing the dynamics of vesicles formation, we also discuss why non equilibrium vesicles can be formed by kinetics control and why they are meta-stable. Understanding how to control the properties, the stability and the formation process of vesicles is of fundamental importance for a vast number of industrial applications. Copyright © 2009. Published by Elsevier B.V.

Insights into Kinetics of Agitation-Induced Aggregation of Hen Lysozyme under Heat and Acidic Conditions from Various Spectroscopic Methods

PubMed Central

Chaari, Ali; Fahy, Christine; Chevillot-Biraud, Alexandre; Rholam, Mohamed

2015-01-01

Protein misfolding and amyloid formation are an underlying pathological hallmark in a number of prevalent diseases of protein aggregation ranging from Alzheimer’s and Parkinson’s diseases to systemic lysozyme amyloidosis. In this context, we have used complementary spectroscopic methods to undertake a systematic study of the self-assembly of hen egg-white lysozyme under agitation during a prolonged heating in acidic pH. The kinetics of lysozyme aggregation, monitored by Thioflavin T fluorescence, dynamic light scattering and the quenching of tryptophan fluorescence by acrylamide, is described by a sigmoid curve typical of a nucleation-dependent polymerization process. Nevertheless, we observe significant differences between the values deduced for the kinetic parameters (lag time and aggregation rate). The fibrillation process of lysozyme, as assessed by the attenuated total reflection-Fourier transform infrared spectroscopy, is accompanied by an increase in the β-sheet conformation at the expense of the α-helical conformation but the time-dependent variation of the content of these secondary structures does not evolve as a gradual transition. Moreover, the tryptophan fluorescence-monitored kinetics of lysozyme aggregation is described by three phases in which the temporal decrease of the tryptophan fluorescence quantum yield is of quasilinear nature. Finally, the generated lysozyme fibrils exhibit a typical amyloid morphology with various lengths (observed by atomic force microscopy) and contain exclusively the full-length protein (analyzed by highly performance liquid chromatography). Compared to the data obtained by other groups for the formation of lysozyme fibrils in acidic pH without agitation, this work provides new insights into the structural changes (local, secondary, oligomeric/fibrillar structures) undergone by the lysozyme during the agitation-induced formation of fibrils. PMID:26571264

Ultrasound assisted enzymatic depolymerization of aqueous guar gum solution.

PubMed

Prajapat, Amrutlal L; Subhedar, Preeti B; Gogate, Parag R

2016-03-01

The present work investigates the effectiveness of application of low intensity ultrasonic irradiation for the intensification of enzymatic depolymerization of aqueous guar gum solution. The extent of depolymerization of guar gum has been analyzed in terms of intrinsic viscosity reduction. The effect of ultrasonic irradiation on the kinetic and thermodynamic parameters related to the enzyme activity as well as the intrinsic viscosity reduction of guar gum using enzymatic approach has been evaluated. The kinetic rate constant has been found to increase with an increase in the temperature and cellulase loading. It has been observed that application of ultrasound not only enhances the extent of depolymerization but also reduces the time of depolymerization as compared to conventional enzymatic degradation technique. In the presence of cellulase enzyme, the maximum extent of depolymerization of guar gum has been observed at 60 W of ultrasonic rated power and ultrasonic treatment time of 30 min. The effect of ultrasound on the kinetic and thermodynamic parameters as well as the molecular structure of cellulase enzyme was evaluated with the help of the chemical reaction kinetics model and fluorescence spectroscopy. Application of ultrasound resulted in a reduction in the thermodynamic parameters of activation energy (Ea), enthalpy (ΔH), entropy (ΔS) and free energy (ΔG) by 47%, 50%, 65% and 1.97%, respectively. The changes in the chemical structure of guar gum treated using ultrasound assisted enzymatic approach in comparison to the native guar gum were also characterized by FTIR. The results revealed that enzymatic depolymerization of guar gum resulted in a polysaccharide with low degree of polymerization, viscosity and consistency index without any change in the core chemical structure which could make it useful for incorporation in food products. Copyright © 2015 Elsevier B.V. All rights reserved.

Reactibodies generated by kinetic selection couple chemical reactivity with favorable protein dynamics

PubMed Central

Smirnov, Ivan; Carletti, Eugénie; Kurkova, Inna; Nachon, Florian; Nicolet, Yvain; Mitkevich, Vladimir A.; Débat, Hélène; Avalle, Bérangère; Belogurov, Alexey A.; Kuznetsov, Nikita; Reshetnyak, Andrey; Masson, Patrick; Tonevitsky, Alexander G.; Ponomarenko, Natalia; Makarov, Alexander A.; Friboulet, Alain; Tramontano, Alfonso; Gabibov, Alexander

2011-01-01

Igs offer a versatile template for combinatorial and rational design approaches to the de novo creation of catalytically active proteins. We have used a covalent capture selection strategy to identify biocatalysts from within a human semisynthetic antibody variable fragment library that uses a nucleophilic mechanism. Specific phosphonylation at a single tyrosine within the variable light-chain framework was confirmed in a recombinant IgG construct. High-resolution crystallographic structures of unmodified and phosphonylated Fabs display a 15-Å-deep two-chamber cavity at the interface of variable light (VL) and variable heavy (VH) fragments having a nucleophilic tyrosine at the base of the site. The depth and structure of the pocket are atypical of antibodies in general but can be compared qualitatively with the catalytic site of cholinesterases. A structurally disordered heavy chain complementary determining region 3 loop, constituting a wall of the cleft, is stabilized after covalent modification by hydrogen bonding to the phosphonate tropinol moiety. These features and presteady state kinetics analysis indicate that an induced fit mechanism operates in this reaction. Mutations of residues located in this stabilized loop do not interfere with direct contacts to the organophosphate ligand but can interrogate second shell interactions, because the H3 loop has a conformation adjusted for binding. Kinetic and thermodynamic parameters along with computational docking support the active site model, including plasticity and simple catalytic components. Although relatively uncomplicated, this catalytic machinery displays both stereo- and chemical selectivity. The organophosphate pesticide paraoxon is hydrolyzed by covalent catalysis with rate-limiting dephosphorylation. This reactibody is, therefore, a kinetically selected protein template that has enzyme-like catalytic attributes. PMID:21896761

Chemical Kinetic Influences of Alkyl Chain Structure on the High Pressure and Temperature Oxidation of a Representative Unsaturated Biodiesel: Methyl Nonenoate.

PubMed

Fridlyand, Aleksandr; Goldsborough, S Scott; Brezinsky, Kenneth

2015-07-16

The high pressure and temperature oxidation of methyl trans-2-nonenoate, methyl trans-3-nonenoate, 1-octene, and trans-2-octene are investigated experimentally to probe the influence of the double bond position on the chemical kinetics of long esters and alkenes. Single pulse shock tube experiments are performed in the ranges p = 3.8-6.2 MPa and T = 850-1500 K, with an average reaction time of 2 ms. Gas chromatographic measurements indicate increased reactivity for trans-2-octene compared to 1-octene, whereas both methyl nonenoate isomers have reactivities similar to that of 1-octene. A difference in the yield of stable intermediates is observed for the octenes when compared to the methyl nonenoates. Chemical kinetic models are developed with the aid of the Reaction Mechanism Generator to interpret the experimental results. The models are created using two different base chemistry submodels to investigate the influence of the foundational chemistry (i.e., C0-C4), whereas Monte Carlo simulations are performed to examine the quality of agreement with the experimental results. Significant uncertainties are found in the chemistry of unsaturated esters with the double bonds located close to the ester groups. This work highlights the importance of the foundational chemistry in predictive chemical kinetics of biodiesel combustion at engine relevant conditions.

Photo-Darkening Kinetics and Structural Anisotropic Modifications in the Chalcogenide Glass Arsenic Trisulfide: a Study of Kinetic X-Ray Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Jay Min

1990-08-01

The purpose of the study is to investigate the mechanisms involved with photo-induced atomic structural modifications in the chalcogenide glass As_2 S_3. This glass exhibits the reversible effects of photo-darkening followed by thermal bleaching. We observed the time behavior of photo-induced properties under the influence of linearly polarized band -gap light. In a macroscopic optical investigation, we monitor optical changes in the photo-darkening process, and in a local structural probe we study kinetic (or time -resolved dispersive) x-ray absorption spectroscopy. Our observations center on kinetic phenomena and structural modifications induced by polarized excitation of lone-pair orbitals in the chalcogenide glass. Experimental results include the following observations: (i) The polarity of the optically induced anisotropy is critically dependent on the intensity and the polarization of the band-gap irradiation beam. (ii) The near edge peak height in x-ray absorption spectra shows subtle but sensitive change during the photo-darkening process. (iii) Photon intensity dependent dichroic kinetics reflect a connection between the optically probed macroscopic property and the x-ray probed local anisotropic structure. Analysis of the x-ray absorption results includes a computer simulation of the polarized absorption spectra. These results suggest that specific structural units tend to orient themselves with respect to the photon polarization. A substantial part of the analysis involves a major effort in dealing with the x-ray kinetic data manipulation and the experimental difficulties caused by a synchrotron instability problem. Based on our observations, we propose a possible mechanism for the observed photo-structural modifications. Through a model of computer relaxed photo-darkening kinetics, we support the notion that a twisting of a specific intermediate range order structure is responsible for local directional variations and global network distortions. In the course of this study, we refine knowledge of intermediate range order structural configurations and the bistabilities related to these configurations. The importance of the lone-pair orbital interactions in the chalcogenide glassy network is underscored.

Structural aspects of digestion of medium chain triglycerides studied in real time using sSAXS and Cryo-TEM.

PubMed

Phan, Stephanie; Hawley, Adrian; Mulet, Xavier; Waddington, Lynne; Prestidge, Clive A; Boyd, Ben J

2013-12-01

The purpose of this study was to investigate the colloidal structures formed on digestion of medium chain triglyceride (MCT) with a specific objective of identifying and characterizing a previously reported vesicular phase, which has been linked to supersaturation and anomalous digestion kinetics, and to evaluate the influence of lipid mass and enzyme inhibition on self assembled structure. MCT was digested in vitro and nanostructure was monitored in real time using synchrotron small angle X-ray scattering (sSAXS), and morphology was studied using cryogenic transmission electron microscopy (cryo-TEM). Formation of the putative vesicular phase formed on digestion of MCT was confirmed and its structural attributes were determined. Vesicle formation was dependent on lipid mass and bile salt concentration. The use of enzyme inhibitor for offline analysis of lipolysis samples did influence structural aspects of the digestion medium when compared to real time evaluation. The formation of a vesicular phase was directly linked to the kinetics of lipid digestion. Vesicle formation is linked to lipid mass, or more specifically the ratio of lipid to bile salts present in the digestion mixture. Inhibition of lipase to halt digestion during sampling for offline analysis must be done with caution as structural aspects were shown to differ for the MCT digests with and without inhibitor present.

Use of reduction rate as a quantitative knob for controlling the twin structure and shape of palladium nanocrystals.

PubMed

Wang, Yi; Peng, Hsin-Chieh; Liu, Jingyue; Huang, Cheng Zhi; Xia, Younan

2015-02-11

Kinetic control is a powerful means for maneuvering the twin structure and shape of metal nanocrystals and thus optimizing their performance in a variety of applications. However, there is only a vague understanding of the explicit roles played by reaction kinetics due to the lack of quantitative information about the kinetic parameters. With Pd as an example, here we demonstrate that kinetic parameters, including rate constant and activation energy, can be derived from spectroscopic measurements and then used to calculate the initial reduction rate and further have this parameter quantitatively correlated with the twin structure of a seed and nanocrystal. On a quantitative basis, we were able to determine the ranges of initial reduction rates required for the formation of nanocrystals with a specific twin structure, including single-crystal, multiply twinned, and stacking fault-lined. This work represents a major step forward toward the deterministic syntheses of colloidal noble-metal nanocrystals with specific twin structures and shapes.

Kinetics of the LOV domain of ZEITLUPE determine its circadian function in Arabidopsis

PubMed Central

Pudasaini, Ashutosh; Shim, Jae Sung; Song, Young Hun; Shi, Hua; Kiba, Takatoshi; Somers, David E; Imaizumi, Takato; Zoltowski, Brian D

2017-01-01

A LOV (Light, Oxygen, or Voltage) domain containing blue-light photoreceptor ZEITLUPE (ZTL) directs circadian timing by degrading clock proteins in plants. Functions hinge upon allosteric differences coupled to the ZTL photocycle; however, structural and kinetic information was unavailable. Herein, we tune the ZTL photocycle over two orders of magnitude. These variants reveal that ZTL complexes with targets independent of light, but dictates enhanced protein degradation in the dark. In vivo experiments definitively show photocycle kinetics dictate the rate of clock component degradation, thereby impacting circadian period. Structural studies demonstrate that photocycle dependent activation of ZTL depends on an unusual dark-state conformation of ZTL. Crystal structures of ZTL LOV domain confirm delineation of structural and kinetic mechanisms and identify an evolutionarily selected allosteric hinge differentiating modes of PAS/LOV signal transduction. The combined biochemical, genetic and structural studies provide new mechanisms indicating how PAS/LOV proteins integrate environmental variables in complex networks. DOI: http://dx.doi.org/10.7554/eLife.21646.001 PMID:28244872

The first mammalian aldehyde oxidase crystal structure: insights into substrate specificity.

PubMed

Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T P; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

2012-11-23

Aldehyde oxidases have pharmacological relevance, and AOX3 is the major drug-metabolizing enzyme in rodents. The crystal structure of mouse AOX3 with kinetics and molecular docking studies provides insights into its enzymatic characteristics. Differences in substrate and inhibitor specificities can be rationalized by comparing the AOX3 and xanthine oxidase structures. The first aldehyde oxidase structure represents a major advance for drug design and mechanistic studies. Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity.

RNA folding kinetics using Monte Carlo and Gillespie algorithms.

PubMed

Clote, Peter; Bayegan, Amir H

2018-04-01

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time for a K-step trajectory of the Monte Carlo algorithm is equal to [Formula: see text] times that of the Gillespie algorithm, where [Formula: see text] denotes the Boltzmann expected network degree. If the network is regular (i.e. every node has the same degree), then the mean first passage time (MFPT) computed by the Monte Carlo algorithm is equal to MFPT computed by the Gillespie algorithm multiplied by [Formula: see text]; however, this is not true for non-regular networks. In particular, RNA secondary structure folding kinetics, as computed by the Monte Carlo algorithm, is not equal to the folding kinetics, as computed by the Gillespie algorithm, although the mean first passage times are roughly correlated. Simulation software for RNA secondary structure folding according to the Monte Carlo and Gillespie algorithms is publicly available, as is our software to compute the expected degree of the network of secondary structures of a given RNA sequence-see http://bioinformatics.bc.edu/clote/RNAexpNumNbors .

Theoretical study of the gas-phase structures of sodiated and cesiated leucine and isoleucine: zwitterionic structure disfavored in kinetic method experiments.

PubMed

Rozman, Marko

2005-10-01

The most stable charge-solvated (CS) and zwitterionic (ZW) structures of sodiated and cesiated leucine and isoleucine were studied by density functional theory methods. According to the Boltzmann distribution in gas phase, both forms of LeuNa+ and IleNa+ exist, but in LeuCs+ and IleCs+, the ZW forms are dominant. Results for the sodiated compounds are consistent with the relationship found between decrease in relative stability of CS versus ZW form and aliphatic amino acid side chain length. The observed degeneracy in energy for IleNa+ conformers is at odds with kinetic method results. Additional calculations showed that kinetic method structural determinations for IleNa+ do not reflect relative order of populations in the lowest energy conformers. Since complexation of cationized amino acids into ion-bound dimers disfavors ZW structure by approximately 8 kJ mol(-1), it is suggested that for energy close conformers of sodium-cationized amino acids, the kinetic method may not be reliable for structural determinations. Copyright (c) 2005 John Wiley & Sons, Ltd.

Relationships between molecular structure and kinetic and thermodynamic controls in lipid systems. Part II: Phase behavior and transformation paths of SSS, PSS and PPS saturated triacylglycerols--effect of chain length mismatch.

PubMed

Bouzidi, Laziz; Narine, Suresh S

2012-01-01

The kinetic phase behavior and phase transformation paths of purified tristearoylglycerol (SSS), 3-palmitoyl-1,2-distearoyl-sn-glycerol (PSS) and 1,2-dipalmitoyl-3-stearoyl-sn-glycerol (PPS) were investigated in terms of polymorphism, crystallization and melting. The details of the phase transformation paths were obtained using the heating cycles of two sets of experiments: (a) cooling rate was varied and heating rate fixed and (b) cooling rate was fixed and heating rate varied. Kinetic effects were manifest in all measured properties, underscoring the complexity of the phase transformation paths for each TAG, and the intricate thermodynamics-molecular relationships. For the first time, XRD data obtained for SSS, PSS and PPS TAGs, cooled at rates higher than 0.5°C/min, suggested the formation of a transient structure similar to the so-called α(2)-phase which has been observed in mixed saturated-unsaturated TAGs quenched from the melt. The more stable phases (β' in PSS and PPS, and β in SSS) were only observed for cooling rates lower than 1.0°C/min. The kinetic and thermodynamic differences observed in the crystallization, structure and melting of SSS, PSS and PPS are proposed to be mainly due to the disturbances introduced at the "terrace" level via methyl-end group interactions, i.e., the missing of two or four CH(2) groups compared to SSS. The symmetrical SSS with a relatively flat "terrace" crystallizes preferably in the most stable β-form. Two missing CH(2) groups at the sn-1 position (PSS) introduces enough structural disturbances to promote the relative prevalence and persistence of the β'-phase, and four missing CH(2) groups at the sn-1 and sn-2 positions (PPS) is relatively too large of a disturbance and therefore favors the α-form. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Difference in postprandial GLP-1 response despite similar glucose kinetics after consumption of wheat breads with different particle size in healthy men.

PubMed

Eelderink, Coby; Noort, Martijn W J; Sozer, Nesli; Koehorst, Martijn; Holst, Jens J; Deacon, Carolyn F; Rehfeld, Jens F; Poutanen, Kaisa; Vonk, Roel J; Oudhuis, Lizette; Priebe, Marion G

2017-04-01

Underlying mechanisms of the beneficial health effects of low glycemic index starchy foods are not fully elucidated yet. We varied the wheat particle size to obtain fiber-rich breads with a high and low glycemic response and investigated the differences in postprandial glucose kinetics and metabolic response after their consumption. Ten healthy male volunteers participated in a randomized, crossover study, consuming 13 C-enriched breads with different structures; a control bread (CB) made from wheat flour combined with wheat bran, and a kernel bread (KB) where 85 % of flour was substituted with broken wheat kernels. The structure of the breads was characterized extensively. The use of stable isotopes enabled calculation of glucose kinetics: rate of appearance of exogenous glucose, endogenous glucose production, and glucose clearance rate. Additionally, postprandial plasma concentrations of glucose, insulin, glucagon, incretins, cholecystokinin, and bile acids were analyzed. Despite the attempt to obtain a bread with a low glycemic response by replacing flour by broken kernels, the glycemic response and glucose kinetics were quite similar after consumption of CB and KB. Interestingly, the glucagon-like peptide-1 (GLP-1) response was much lower after KB compared to CB (iAUC, P < 0.005). A clear postprandial increase in plasma conjugated bile acids was observed after both meals. Substitution of 85 % wheat flour by broken kernels in bread did not result in a difference in glucose response and kinetics, but in a pronounced difference in GLP-1 response. Thus, changing the processing conditions of wheat for baking bread can influence the metabolic response beyond glycemia and may therefore influence health.

Kinetic control of TolC recruitment by multidrug efflux complexes.

PubMed

Tikhonova, Elena B; Dastidar, Vishakha; Rybenkov, Valentin V; Zgurskaya, Helen I

2009-09-22

In Gram-negative pathogens, multidrug efflux pumps that provide clinically significant levels of antibiotic resistance function as three-component complexes. They are composed of the inner membrane transporters belonging to one of three superfamilies of proteins, RND, ABC, or MF; periplasmic proteins belonging to the membrane fusion protein (MFP) family; and outer membrane channels exemplified by the Escherichia coli TolC. The three-component complexes span the entire two-membrane envelope of Gram-negative bacteria and expel toxic molecules from the cytoplasmic membrane to the medium. The architecture of these complexes is expected to vary significantly because of the structural diversity of the inner membrane transporters. How the three-component pumps are assembled, their architecture, and their dynamics remain unclear. In this study, we reconstituted interactions and compared binding kinetics of the E. coli TolC with AcrA, MacA, and EmrA, the periplasmic MFPs that function in multidrug efflux with transporters from the RND, ABC, and MF superfamilies, respectively. By using surface plasmon resonance, we demonstrate that TolC interactions with MFPs are highly dynamic and sensitive to pH. The affinity of TolC to MFPs decreases in the order MacA > EmrA > AcrA. We further show that MFPs are prone to oligomerization, but differ dramatically from each other in oligomerization kinetics and stability of oligomers. The propensity of MFPs to oligomerize correlates with the stability of MFP-TolC complexes and structural features of inner membrane transporters. We propose that recruitment of TolC by various MFPs is determined not only by kinetics of MFP-TolC interactions but also by oligomerization kinetics of MFPs and pH.

Dynamic Recrystallization Behavior of Zr-1Sn-0.3Nb Alloy During Hot Rolling Process

NASA Astrophysics Data System (ADS)

Zhao, Siyu; Liu, Huiqun; Lin, Gaoyong; Jiang, Yilan; Xun, Jian

2017-11-01

Zirconium alloys are advanced materials with properties that are greatly affected by their crystalline structure. To investigate this, sheets of Zr-1Sn-0.3Nb alloy were hot rolled with different reductions (10%, 30%, 50%, and 60%) at 1023 K and 1073 K to investigate the alloy's dynamic recrystallization behavior. Recrystallization kinetics was observed via electron backscattering diffraction and transmission electron microscopy, and the results were compared with estimates based on the Johnson-Mehl-Avrami-Kolmogorov (JMAK) equation. The values of the JMAK exponent n and k increased with the rolling temperature. The estimates and microstructural observations of dynamic recrystallization (DRX) kinetics were in good agreement.

KEEN Wave Simulations: Comparing various PIC to various fixed grid Vlasov to Phase-Space Adaptive Sparse Tiling & Effective Lagrangian (PASTEL) Techniques

NASA Astrophysics Data System (ADS)

Afeyan, Bedros; Larson, David; Shadwick, Bradley; Sydora, Richard

2017-10-01

We compare various ways of solving the Vlasov-Poisson and Vlasov-Maxwell equations on rather demanding nonlinear kinetic phenomena associated with KEEN and KEEPN waves. KEEN stands for Kinetic, Electrostatic, Electron Nonlinear, and KEEPN, for electron-positron or pair plasmas analogs. Because these self-organized phase space structures are not steady-state, or single mode, or fluid or low order moment equation limited, typical techniques with low resolution or too much noise will distort the answer too much, too soon, and fail. This will be shown via Penrose criteria triggers for instability at the formation stage as well as particle orbit statistics in fully formed KEEN waves and KEEN-KEEN and KEEN-EPW interacting states. We will argue that PASTEL is a viable alternative to traditional methods with reasonable chances of success in higher dimensions. Work supported by a Grant from AFOSR PEEP.

The Department of Defense Effort to Countering the Cyberterrorism Threat: Is the Threat Real or Hyperbole

DTIC Science & Technology

2017-04-21

focusses on the policy shortfalls, organizational structure vulnerabilities, and challenges that exist in DOD. It highlights areas where...relationships within DOD, in line with traditional organizational structures adeptly addresses the current seams between kinetic and non- kinetic...Figure 2 DOD Organizational Structure http://dcmo.defense.gov/Portals/47/Documents/PDSD/201509_DoD_Organizational_Structure.pdf The majority of

Development of Novel Warfarin-Silica Composite for Controlled Drug Release.

PubMed

Parfenyuk, Elena V; Dolinina, Ekaterina S

2017-04-01

The work is devoted to synthesis and study of warfarin composites with unmodified, methyl and phenyl modified silica in order to develop controlled release formulation of the anticoagulant. The composites were prepared by two routes, adsorption and sol-gel, and characterized with FTIR spectroscopy, dynamic light scattering and DSC methods. The drug release behavior from the composites in media with pH 1.6, 6.8 and 7.4 was analyzed in vitro. The release kinetics of the warfarin - silica composites prepared by the two routes was compared among each other and with analogous silica composites with water soluble drug molsidomine. The comparative analysis showed that in general the kinetic regularities and mechanisms of release for both drugs are similar and determined by nonuniform distribution of the drugs over the silica matrixes and stability of the matrixes in the studied media for the adsorbed composites and uniformly distributed drug and more brittle structure for the sol-gel composites. The sol-gel composite of warfarin - phenyl modified silica is perspective for further development of novel warfarin formulation with controlled release because it releases warfarin according to zero-order kinetic law with approximately equal rate in the media imitating different segments of gastrointestinal tract.

Effect of the porous structure of activated carbon on the adsorption kinetics of gold(I) cyanide complex

NASA Astrophysics Data System (ADS)

Ibragimova, P. I.; Grebennikov, S. F.; Gur'yanov, V. V.; Fedyukevich, V. A.; Vorob'ev-Desyatovskii, N. V.

2014-06-01

The effect the porous structure of activated carbons obtained from furfural and coconut shells has on the kinetics of [Au(CN)2]- ion adsorption is studied. Effective diffusion coefficients for [Au(CN)2]- anions in transport and adsorbing pores and mass transfer coefficients in a transport system of the pores and in microporous zones are calculated using the statistical moments of the kinetic curve.

Oxygen reduction kinetics on Pt monolayer shell highly affected by the structure of bimetallic AuNi cores

DOE PAGES

Chen, Guangyu; Kuttiyiel, Kurian A.; Su, Dong; ...

2016-07-12

Here, we describe pronounced effects of structural changes of the AuNi cores on the oxygen reduction reaction (ORR) activity of a Pt monolayer shell. The study of alloyed AuNi nanoparticles compared with AuNi core–shell structured nanoparticles revealed configurations having different electronic and electrochemical properties. Controlled alloying of Au with Ni was essential to tune the electronic properties of Au interacting with the Pt monolayer shell to achieve suitable adsorption of O 2 on Pt for expediting the ORR. The alloyed AuNi nanoparticles made the Pt shell more catalytically active for the ORR than the core–shell structured AuNi nanoparticles. The Ptmore » monolayer supported on the alloyed AuNi nanoparticles showed the Pt mass and specific activities as high as 1.52 A mg –1 and 1.18 mA cm –2, respectively, with almost no loss over 5 000 cycles of stability test. This high ORR activity is ascribed to the role of nonspecific steric configuration of Ni atoms changing the electronic properties of the alloy that affect the oxygen and water interaction with the Pt shell and facilitate increased ORR kinetics.« less

Simulation of metal additive manufacturing microstructures using kinetic Monte Carlo

DOE PAGES

Rodgers, Theron M.; Madison, Jonathan D.; Tikare, Veena

2017-04-19

Additive manufacturing (AM) is of tremendous interest given its ability to realize complex, non-traditional geometries in engineered structural materials. But, microstructures generated from AM processes can be equally, if not more, complex than their conventionally processed counterparts. While some microstructural features observed in AM may also occur in more traditional solidification processes, the introduction of spatially and temporally mobile heat sources can result in significant microstructural heterogeneity. While grain size and shape in metal AM structures are understood to be highly dependent on both local and global temperature profiles, the exact form of this relation is not well understood. Wemore » implement an idealized molten zone and temperature-dependent grain boundary mobility in a kinetic Monte Carlo model to predict three-dimensional grain structure in additively manufactured metals. In order to demonstrate the flexibility of the model, synthetic microstructures are generated under conditions mimicking relatively diverse experimental results present in the literature. Simulated microstructures are then qualitatively and quantitatively compared to their experimental complements and are shown to be in good agreement.« less

Communication: Relationship between local structure and the stability of water in hydrophobic confinement

NASA Astrophysics Data System (ADS)

Altabet, Y. Elia; Debenedetti, Pablo G.

2017-12-01

Liquid water confined between nanoscale hydrophobic objects can become metastable with respect to its vapor at nanoscale separations. While the separations are only several molecular diameters, macroscopic theories are often invoked to interpret the thermodynamics and kinetics of water under confinement. We perform detailed rate and free energy calculations via molecular simulations in order to assess the dependence of the rate of evaporation, free energy barriers, and free energy differences between confined liquid and vapor upon object separation and compare them to the relevant macroscopic theories. At small enough separations, the rate of evaporation appears to deviate significantly from the predictions of classical nucleation theory, and we attribute such deviations to changes in the structure of the confined liquid film. However, the free energy difference between the confined liquid and vapor phases agrees quantitatively with macroscopic theory, and the free energy barrier to condensation displays qualitative agreement. Overall, the present work suggests that theories attempting to capture the kinetic behavior of nanoscale systems should incorporate structural details rather than treating it as a continuum.

Sacrificial bonds and hidden length in biomaterials -- a kinetic description of strength and toughness in bone

NASA Astrophysics Data System (ADS)

Lieou, Charles K. C.; Elbanna, Ahmed E.; Carlson, Jean M.

2013-03-01

Sacrificial bonds and hidden length in structural molecules account for the greatly increased fracture toughness of biological materials compared to synthetic materials without such structural features, by providing a molecular-scale mechanism of energy dissipation. One example of occurrence of sacrificial bonds and hidden length is in the polymeric glue connection between collagen fibrils in animal bone. In this talk, we propose a simple kinetic model that describes the breakage of sacrificial bonds and the revelation of hidden length, based on Bell's theory. We postulate a master equation governing the rates of bond breakage and formation, at the mean-field level, allowing for the number of bonds and hidden lengths to take up non-integer values between successive, discrete bond-breakage events. This enables us to predict the mechanical behavior of a quasi-one-dimensional ensemble of polymers at different stretching rates. We find that both the rupture peak heights and maximum stretching distance increase with the stretching rate. In addition, our theory naturally permits the possibility of self-healing in such biological structures.

Antioxidant capacity of flavanols and gallate esters: pulse radiolysis studies.

PubMed

Bors, W; Michel, C

1999-12-01

Reactivities of several proanthocyanidins (monomers of condensed tannins) and gallate esters (representing hydrolyzable tannins) with hydroxyl radicals, azide radicals, and superoxide anions were investigated using pulse radiolysis combined with kinetic spectroscopy. We determined the scavenging rate constants and the decay kinetics of the aroxyl radicals both at the wavelength of the semiquinone absorption (275 nm) and the absorption band of the gallate ester ketyl radical (400-420 nm). For most compounds second-order decay kinetics were observed, which reflect disproportionation of the semiquinones. In the case of the oligomeric hydrolysable tannins, pentagalloyl glucose and tannic acid, the decay kinetics were more complex involving sequential first-order and second-order reactions, which could only be resolved by kinetic modeling. A correlation of the reaction rates with hydroxyl radicals (k*OH) with the number of adjacent aromatic hydroxyl groups (i.e., representing catechol and/or pyrogallol structures) was obtained for both condensed and hydrolyzable tannins. Similar correlation for the reactions with azide radicals and superoxide anions are less obvious, but exist as well. We consider proanthocyanidins superior radical scavenging agents as compared with the monomeric flavonols and flavones and propose that these substances rather than the flavonoids proper represent the antioxidative principle in red wine and green tea.

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

Li, Jincheng; Kim, Tong-Ho; Jiao, Wenyuan

Recent work has shown that Bi incorporation increases during molecular beam epitaxy (MBE) when surface processes are kinetically limited through increased growth rate. Herein we explore how the structural and optical properties of GaAs{sub 1−x}Bi{sub x} films are modified when grown under conditions with varying degrees of kinetic limitations realized through growth temperature and growth rate changes. Within the typical window of MBE growth conditions for GaAs{sub 1−x}Bi{sub x}, we compare films with similar (∼3%) compositions grown under conditions of reduced kinetic limitations, i.e., relatively low gallium supersaturation achieved at higher temperatures (∼350 °C) and lower growth rates (∼0.5 μm/h), tomore » those grown farther from equilibrium, specifically, higher supersaturation achieved at lower growth temperatures (∼290 °C) and higher growth rates (∼1.4 μm/h). Both the x-ray diffraction full width at half maximum of the omega-2theta scan and the 300 K photoluminescence intensity increase when samples are grown under less kinetically limited conditions. We interpret these findings in relation to the incorporation of Bi-related microstructural defects that are more readily formed during less kinetically limited growth. These defects lead to enhanced luminescence efficiency due to the spatial localization of carriers.« less

Applying Simulated In Vivo Motions to Measure Human Knee and ACL Kinetics

PubMed Central

Herfat, Safa T.; Boguszewski, Daniel V.; Shearn, Jason T.

2013-01-01

Patients frequently experience anterior cruciate ligament (ACL) injuries but current ACL reconstruction strategies do not restore the native biomechanics of the knee, which can contribute to the early onset of osteoarthritis in the long term. To design more effective treatments, investigators must first understand normal in vivo knee function for multiple activities of daily living (ADLs). While the 3D kinematics of the human knee have been measured for various ADLs, the 3D kinetics cannot be directly measured in vivo. Alternatively, the 3D kinetics of the knee and its structures can be measured in an animal model by simulating and applying subject-specific in vivo joint motions to a joint using robotics. However, a suitable biomechanical surrogate should first be established. This study was designed to apply a simulated human in vivo motion to human knees to measure the kinetics of the human knee and ACL. In pursuit of establishing a viable biomechanical surrogate, a simulated in vivo ovine motion was also applied to human knees to compare the loads produced by the human and ovine motions. The motions from the two species produced similar kinetics in the human knee and ACL. The only significant difference was the intact knee compression force produced by the two input motions. PMID:22227973

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.

Ring structure modifications of phenylalanine 19 increase fibrillation kinetics and reduce toxicity of amyloid β (1-40).

PubMed

Korn, Alexander; Surendran, Dayana; Krueger, Martin; Maiti, Sudipta; Huster, Daniel

2018-05-24

We investigated the influence of the chemical structure of the phenylalanine side chain in position 19 of the 40 residue amyloid β peptide. Side chain modifications in this position yielded fibrils of essentially unaltered morphology, structure, and dynamics, but significantly increased fibrillation kinetics and diminished the toxicity of the peptides.

Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5’-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway

PubMed Central

Torini, Juliana Roberta; Brandão-Neto, José; DeMarco, Ricardo; Pereira, Humberto D'Muniz

2016-01-01

Schistosoma mansoni do not have de novo purine pathways and rely on purine salvage for their purine supply. It has been demonstrated that, unlike humans, the S. mansoni is able to produce adenine directly from adenosine, although the enzyme responsible for this activity was unknown. In the present work we show that S. mansoni 5´-deoxy-5´-methylthioadenosine phosphorylase (MTAP, E.C. 2.4.2.28) is capable of use adenosine as a substrate to the production of adenine. Through kinetics assays, we show that the Schistosoma mansoni MTAP (SmMTAP), unlike the mammalian MTAP, uses adenosine substrate with the same efficiency as MTA phosphorolysis, which suggests that this enzyme is part of the purine pathway salvage in S. mansoni and could be a promising target for anti-schistosoma therapies. Here, we present 13 SmMTAP structures from the wild type (WT), including three single and one double mutant, and generate a solid structural framework for structure description. These crystal structures of SmMTAP reveal that the active site contains three substitutions within and near the active site when compared to it mammalian counterpart, thus opening up the possibility of developing specific inhibitors to the parasite MTAP. The structural and kinetic data for 5 substrates reveal the structural basis for this interaction, providing substract for inteligent design of new compounds for block this enzyme activity. PMID:27935959

Synthetic polyester-hydrolyzing enzymes from thermophilic actinomycetes.

PubMed

Wei, Ren; Oeser, Thorsten; Zimmermann, Wolfgang

2014-01-01

Thermophilic actinomycetes produce enzymes capable of hydrolyzing synthetic polyesters such as polyethylene terephthalate (PET). In addition to carboxylesterases, which have hydrolytic activity predominantly against PET oligomers, esterases related to cutinases also hydrolyze synthetic polymers. The production of these enzymes by actinomycetes as well as their recombinant expression in heterologous hosts is described and their catalytic activity against polyester substrates is compared. Assays to analyze the enzymatic hydrolysis of synthetic polyesters are evaluated, and a kinetic model describing the enzymatic heterogeneous hydrolysis process is discussed. Structure-function and structure-stability relationships of actinomycete polyester hydrolases are compared based on molecular dynamics simulations and recently solved protein structures. In addition, recent progress in enhancing their activity and thermal stability by random or site-directed mutagenesis is presented. © 2014 Elsevier Inc. All rights reserved.

Effect of heating rate and kinetic model selection on activation energy of nonisothermal crystallization of amorphous felodipine.

PubMed

Chattoraj, Sayantan; Bhugra, Chandan; Li, Zheng Jane; Sun, Changquan Calvin

2014-12-01

The nonisothermal crystallization kinetics of amorphous materials is routinely analyzed by statistically fitting the crystallization data to kinetic models. In this work, we systematically evaluate how the model-dependent crystallization kinetics is impacted by variations in the heating rate and the selection of the kinetic model, two key factors that can lead to significant differences in the crystallization activation energy (Ea ) of an amorphous material. Using amorphous felodipine, we show that the Ea decreases with increase in the heating rate, irrespective of the kinetic model evaluated in this work. The model that best describes the crystallization phenomenon cannot be identified readily through the statistical fitting approach because several kinetic models yield comparable R(2) . Here, we propose an alternate paired model-fitting model-free (PMFMF) approach for identifying the most suitable kinetic model, where Ea obtained from model-dependent kinetics is compared with those obtained from model-free kinetics. The most suitable kinetic model is identified as the one that yields Ea values comparable with the model-free kinetics. Through this PMFMF approach, nucleation and growth is identified as the main mechanism that controls the crystallization kinetics of felodipine. Using this PMFMF approach, we further demonstrate that crystallization mechanism from amorphous phase varies with heating rate. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Drug-Target Kinetics in Drug Discovery.

PubMed

Tonge, Peter J

2018-01-17

The development of therapies for the treatment of neurological cancer faces a number of major challenges including the synthesis of small molecule agents that can penetrate the blood-brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concentration. Time dependent target occupancy is a function of both the drug and target concentration as well as the thermodynamic and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissociation. The discovery and deployment of compounds with optimized kinetic effects requires information on the structure-kinetic relationships that modulate the kinetics of binding, and the molecular factors that control the translation of drug-target kinetics to time-dependent drug activity in the disease state. This Review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodynamic and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The Review concludes with a description of a mechanistic PK/PD model that integrates drug-target kinetics into predictions of drug activity.

Origami Arrays as Substrates for the Determination of Reaction Kinetics Using High-Speed Atomic Force Microscopy.

PubMed

Rahman, Masudur; Day, B Scott; Neff, David; Norton, Michael L

2017-08-01

DNA nanostructures (DN) are powerful platforms for the programmable assembly of nanomaterials. As applications for DN both as a structural material and as a support for functional biomolecular sensing systems develop, methods enabling the determination of reaction kinetics in real time become increasingly important. In this report, we present a study of the kinetics of streptavidin binding onto biotinylated DN constructs enabled by these planar structures. High-speed AFM was employed at a 2.5 frame/s rate to evaluate the kinetics and indicates that the binding fully saturates in less than 60 s. When the the data was fitted with an adsorption-limited kinetic model, a forward rate constant of 5.03 × 10 5 s -1 was found.

How Kinetics within the Unfolded State Affects Protein Folding: an Analysis Based on Markov State Models and an Ultra-Long MD Trajectory

PubMed Central

Deng, Nan-jie; Dai, Wei

2013-01-01

Understanding how kinetics in the unfolded state affects protein folding is a fundamentally important yet less well-understood issue. Here we employ three different models to analyze the unfolded landscape and folding kinetics of the miniprotein Trp-cage. The first is a 208 μs explicit solvent molecular dynamics (MD) simulation from D. E. Shaw Research containing tens of folding events. The second is a Markov state model (MSM-MD) constructed from the same ultra-long MD simulation; MSM-MD can be used to generate thousands of folding events. The third is a Markov state model built from temperature replica exchange MD simulations in implicit solvent (MSM-REMD). All the models exhibit multiple folding pathways, and there is a good correspondence between the folding pathways from direct MD and those computed from the MSMs. The unfolded populations interconvert rapidly between extended and collapsed conformations on time scales ≤ 40 ns, compared with the folding time of ≈ 5 μs. The folding rates are independent of where the folding is initiated from within the unfolded ensemble. About 90 % of the unfolded states are sampled within the first 40 μs of the ultra-long MD trajectory, which on average explores ~27 % of the unfolded state ensemble between consecutive folding events. We clustered the folding pathways according to structural similarity into “tubes”, and kinetically partitioned the unfolded state into populations that fold along different tubes. From our analysis of the simulations and a simple kinetic model, we find that when the mixing within the unfolded state is comparable to or faster than folding, the folding waiting times for all the folding tubes are similar and the folding kinetics is essentially single exponential despite the presence of heterogeneous folding paths with non-uniform barriers. When the mixing is much slower than folding, different unfolded populations fold independently leading to non-exponential kinetics. A kinetic partition of the Trp-cage unfolded state is constructed which reveals that different unfolded populations have almost the same probability to fold along any of the multiple folding paths. We are investigating whether the results for the kinetics in the unfolded state of the twenty-residue Trp-cage is representative of larger single domain proteins. PMID:23705683

Fourier transform infrared microspectroscopic analysis of the effects of cereal type and variety within a type of grain on structural makeup in relation to rumen degradation kinetics.

PubMed

Walker, Amanda M; Yu, Peiqiang; Christensen, Colleen R; Christensen, David A; McKinnon, John J

2009-08-12

The objectives of this study were to use Fourier transform infrared microspectroscopy (FTIRM) to determine structural makeup (features) of cereal grain endosperm tissue and to reveal and identify differences in protein and carbohydrate structural makeup between different cereal types (corn vs barley) and between different varieties within a grain (barley CDC Bold, CDC Dolly, Harrington, and Valier). Another objective was to investigate how these structural features relate to rumen degradation kinetics. The items assessed included (1) structural differences in protein amide I to nonstructural carbohydrate (NSC, starch) intensity and ratio within cellular dimensions; (2) molecular structural differences in the secondary structure profile of protein, alpha-helix, beta-sheet, and their ratio; (3) structural differences in NSC to amide I ratio profile. From the results, it was observed that (1) comparison between grain types [corn (cv. Pioneer 39P78) vs barley (cv. Harrington)] showed significant differences in structural makeup in terms of NSC, amide I to NSC ratio, and rumen degradation kinetics (degradation ratio, effective degradability of dry matter, protein and NSC) (P < 0.05); (2) comparison between varieties within a grain (barley varieties) also showed significant differences in structural makeup in terms of amide I, NSC, amide I to NSC ratio, alpha-helix and beta-sheet protein structures, and rumen degradation kinetics (effective degradability of dry matter, protein, and NSC) (P < 0.05); (3) correlation analysis showed that the amide I to NSC ratio was strongly correlated with rumen degradation kinetics in terms of the degradation rate (R = 0.91, P = 0.086) and effective degradability of dry matter (R = 0.93, P = 0.071). The results suggest that with the FTIRM technique, the structural makeup differences between cereal types and between different varieties within a type of grain could be revealed. These structural makeup differences were related to the rate and extent of rumen degradation.

Formation of polymeric toroidal-spiral particles.

PubMed

Sharma, Vishal; Szymusiak, Magdalena; Shen, Hao; Nitsche, Ludwig C; Liu, Ying

2012-01-10

Compared to spherical matrices, particles with well-defined internal structure provide large surface to volume ratio and predictable release kinetics for the encapsulated payloads. We describe self-assembly of polymeric particles, whereby competitive kinetics of viscous sedimentation, diffusion, and cross-linking yield a controllable toroidal-spiral (T-S) structure. Precursor polymeric droplets are splashed through the surface of a less dense, miscible solution, after which viscous forces entrain the surrounding bulk solution into the sedimenting polymer drop to form T-S channels. The intricate structure forms because low interfacial tension between the two miscible solutions is dominated by viscous forces. The biocompatible polymer, poly(ethylene glycol) diacrylate (PEG-DA), is used to demonstrate the solidification of the T-S shapes at various configurational stages by UV-triggered cross-linking. The dimensions of the channels are controlled by Weber number during impact on the surface, and Reynolds number and viscosity ratio during subsequent sedimentation. We anticipate applications of the T-S particle in drug delivery, wherein diffusion through these T-S channels and the polymer matrix would offer parallel release pathways for molecules of different sizes. Polyphosphate, as a model macromolecule, is entrained in T-S particles during their formation. The in vitro release kinetics of polyphosphate from the T-S particles with various channel length and width is reported. In addition, self-assembly of T-S particles occurs in a single step under benign conditions for delicate macromolecules, and appears conducive to scaleup.

Human Growth Hormone Adsorption Kinetics and Conformation on Self-Assembled Monolayers

PubMed Central

Buijs, Jos; Britt, David W.; Hlady, Vladimir

2012-01-01

The adsorption process of the recombinant human growth hormone on organic films, created by self-assembly of octadecyltrichlorosilane, arachidic acid, and dipalmitoylphosphatidylcholine, is investigated and compared to adsorption on silica and methylated silica substrates. Information on the adsorption process of human growth hormone (hGH) is obtained by using total internal reflection fluorescence (TIRF). The intensity, spectra, and quenching of the intrinsic fluorescence emitted by the growth hormone’s single tryptophan are monitored and related to adsorption kinetics and protein conformation. For the various alkylated hydrophobic surfaces with differences in surface density and conformational freedom it is observed that the adsorbed amount of growth hormone is relatively large if the alkyl chains are in an ordered structure while the amounts adsorbed are considerably lower for adsorption onto less ordered alkyl chains of fatty acid and phospholipid layers. Adsorption on methylated surfaces results in a relatively large conformational change in the growth hormone’s structure, as displayed by a 7 nm blue shift in emission wavelength and a large increase in the effectiveness of fluorescence quenching. Conformational changes are less evident for hGH adsorption onto the fatty acid and phospholipid alkyl chains. Adsorption kinetics on the hydrophilic head groups of the self-assembled monolayers are similar to those on solid hydrophilic surfaces. The relatively small conformational changes in the hGH structure observed for adsorption on silica are even further reduced for adsorption on fatty acid head groups. PMID:25125795

Dynamics of barite growth in porous media quantified by in situ synchrotron X-ray tomography

NASA Astrophysics Data System (ADS)

Godinho, jose; Gerke, kirill

2016-04-01

Current models used to formulate mineral sequestration strategies of dissolved contaminants in the bedrock often neglect the effect of confinement and the variation of reactive surface area with time. In this work, in situ synchrotron X-ray micro-tomography is used to quantify barite growth rates in a micro-porous structure as a function of time during 13.5 hours with a resolution of 1 μm. Additionally, the 3D porous network at different time frames are used to simulate the flow velocities and calculate the permeability evolution during the experiment. The kinetics of barite growth under porous confinement is compared with the kinetics of barite growth on free surfaces in the same fluid composition. Results are discussed in terms of surface area normalization and the evolution of flow velocities as crystals fill the porous structure. During the initial hours the growth rate measured in porous media is similar to the growth rate on free surfaces. However, as the thinner flow paths clog the growth rate progressively decreases, which is correlated to a decrease of local flow velocity. The largest pores remain open, enabling growth to continue throughout the structure. Quantifying the dynamics of mineral precipitation kinetics in situ in 4D, has revealed the importance of using a time dependent reactive surface area and accounting for the local properties of the porous network, when formulating predictive models of mineral precipitation in porous media.

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

NASA Astrophysics Data System (ADS)

Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; van Houten, Bennett; He, Chuan; Ansari, Anjum; Min, Jung-Hyun

2015-01-01

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

DOE PAGES

Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; ...

2015-01-06

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivitymore » arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Lastly, kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.« less

Kinetic mechanism for reversible structural transition in MoTe2 induced by excess charge carriers

NASA Astrophysics Data System (ADS)

Rubel, O.

2018-06-01

Kinetic of a reversible structural transition between insulating (2H) and metallic (1T ') phases in a monolayer MoTe2 due to an electrostatic doping is studied using first-principle calculations. The driving force for the structural transition is the energy gained by transferring excess electrons from the bottom of the conduction band to lower energy gapless states in the metallic phase as have been noticed in earlier studies. The corresponding structural transformation involves dissociation of Mo-Te bonds (one per formula unit), which results in a kinetic energy barrier of 0.83 eV. The transformation involves a consecutive movement of atoms similar to a domain wall motion. The presence of excess charge carriers modifies not only the total energy of the initial and final states, but also lowers an energy of the transition state. An experimentally observed hysteresis in the switching process can be attributed to changes in the kinetic energy barrier due to its dependence on the excess carrier density.

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.

The Role of Knowledge Structures in the Ability of Preservice Elementary Teachers to Diagnose a Child's Understanding of Molecular Kinetics

ERIC Educational Resources Information Center

Bischoff, Paul J.

2006-01-01

This study explored preservice teachers' (n = 25) knowledge structures and their mastery of content knowledge in relation to their ability to diagnose the strengths and weaknesses of a fourth grader's videotaped explanations of a scientific phenomenon, i.e., molecular kinetic properties of air. Participants' knowledge structures were analyzed…

Study of Barley Grain Molecular Structure for Ruminants Using DRIFT, FTIR-ATR and Synchrotron Radiation Infrared Microspectroscopy (SR-IMS): A Review

NASA Astrophysics Data System (ADS)

Yu, Peiqiang

2012-05-01

Barley inherent structures are highly associated with nutrient utilization and availability in both humans and animals. Barley has different degradation kinetics compared with other cereal grains. It has a relatively higher degradation rate and extent, which often cause digestive disorder in the rumen. Therefore understanding barley inherent structure at cellular and molecular levels and processing-induced structure changes is important, because we can manipulate barley inherent structures and digestive behaviors. Several molecular spectroscopy techniques can be used to detect barley inherent structures at cellular and molecular levels. This article reviews several applications of the IR molecular spectral bioanalytical techniques - DRIFT, FT/IR-ATR and SR-IMS for barley chemistry, molecular structure and molecular nutrition research

A Census of Plasma Waves and Structures Associated With an Injection Front in the Inner Magnetosphere

NASA Astrophysics Data System (ADS)

Malaspina, David M.; Ukhorskiy, Aleksandr; Chu, Xiangning; Wygant, John

2018-04-01

Now that observations have conclusively established that the inner magnetosphere is abundantly populated with kinetic electric field structures and nonlinear waves, attention has turned to quantifying the ability of these structures and waves to scatter and accelerate inner magnetospheric plasma populations. A necessary step in that quantification is determining the distribution of observed structure and wave properties (e.g., occurrence rates, amplitudes, and spatial scales). Kinetic structures and nonlinear waves have broadband signatures in frequency space, and consequently, high-resolution time domain electric and magnetic field data are required to uniquely identify such structures and waves as well as determine their properties. However, most high-resolution fields data are collected with a strong bias toward high-amplitude signals in a preselected frequency range, strongly biasing observations of structure and wave properties. In this study, an ˜45 min unbroken interval of 16,384 samples/s field burst data, encompassing an electron injection event, is examined. This data set enables an unbiased census of the kinetic structures and nonlinear waves driven by this electron injection, as well as determination of their "typical" properties. It is found that the properties determined using this unbiased burst data are considerably different than those inferred from amplitude-biased burst data, with significant implications for wave-particle interactions due to kinetic structures and nonlinear waves in the inner magnetosphere.

[The accuracy of rapid equilibrium assumption in steady-state enzyme kinetics is the function of equilibrium segment structure and properties].

PubMed

Vrzheshch, P V

2015-01-01

Quantitative evaluation of the accuracy of the rapid equilibrium assumption in the steady-state enzyme kinetics was obtained for an arbitrary mechanism of an enzyme-catalyzed reaction. This evaluation depends only on the structure and properties of the equilibrium segment, but doesn't depend on the structure and properties of the rest (stationary part) of the kinetic scheme. The smaller the values of the edges leaving equilibrium segment in relation to values of the edges within the equilibrium segment, the higher the accuracy of determination of intermediate concentrations and reaction velocity in a case of the rapid equilibrium assumption.

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Kinetic parameters and structural variations in Cu-Al-Mn and Cu-Al-Mn-Mg shape memory alloys

NASA Astrophysics Data System (ADS)

Canbay, Canan Aksu

2017-02-01

In this work polycrystalline Cu-Al-Mn and Cu-Al-Mn-Mg SMAs were fabricated by arc melting. The thermal analysis was made to determine the characteristic transformation temperatures of the samples and kinetic parameters. Also the effect of Mg on transformation temperatures and kinetic parameters detected. The structural analysis was made to designate the diffraction planes of martensite phase at room temperature and this was supported by optical measurement observations.

Kinetic models in industrial biotechnology - Improving cell factory performance.

PubMed

Almquist, Joachim; Cvijovic, Marija; Hatzimanikatis, Vassily; Nielsen, Jens; Jirstrand, Mats

2014-07-01

An increasing number of industrial bioprocesses capitalize on living cells by using them as cell factories that convert sugars into chemicals. These processes range from the production of bulk chemicals in yeasts and bacteria to the synthesis of therapeutic proteins in mammalian cell lines. One of the tools in the continuous search for improved performance of such production systems is the development and application of mathematical models. To be of value for industrial biotechnology, mathematical models should be able to assist in the rational design of cell factory properties or in the production processes in which they are utilized. Kinetic models are particularly suitable towards this end because they are capable of representing the complex biochemistry of cells in a more complete way compared to most other types of models. They can, at least in principle, be used to in detail understand, predict, and evaluate the effects of adding, removing, or modifying molecular components of a cell factory and for supporting the design of the bioreactor or fermentation process. However, several challenges still remain before kinetic modeling will reach the degree of maturity required for routine application in industry. Here we review the current status of kinetic cell factory modeling. Emphasis is on modeling methodology concepts, including model network structure, kinetic rate expressions, parameter estimation, optimization methods, identifiability analysis, model reduction, and model validation, but several applications of kinetic models for the improvement of cell factories are also discussed. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Oxygen surface exchange kinetics and stability of (La,Sr) 2 CoO 4±δ/La 1-xSr xMO 3-δ (M = Co and Fe) hetero-interfaces at intermediate temperatures

DOE PAGES

Lee, Dongkyu; Lee, Yueh-Lin; Hong, Wesley T.; ...

2014-11-13

Heterostructured oxide interfaces created by decorating Ruddlesden-Popper phases (A2BO4) or perovskites on perovskites have shown not only pronounced cation segregation at the interface and in the A2BO4 structure but also much enhanced kinetics for oxygen electrocatalysis at elevated temperatures. In this study, we report and compare the time-dependent surface exchange kinetics and stability of (La 0.5Sr 0.5) 2CoO 4 -decorated (LSC 214) La 0.6Sr 0.4Co 0.2Fe 0.8O 3-δ (LSCF 113) and La 0.8Sr 0.2CoO 3-δ (LSC 113) thin films. While LSC 214 decoration on LSC 113 greatly reduced the degradation in the surface exchange kinetics as a function of timemore » relative to LSC 113, LSCF 113 with LSC 214 coverage showed comparable surface exchange kinetics and stability to LSCF 113. This difference can be explained by greater surface stability of LSCF 113 than LSC 113 under testing conditions, and that LSC 214 decoration on LSC 113 reduced the decomposition of LSC 113 to form secondary phases that impedes oxygen exchange kinetics, and thus resulted in enhanced stability. This hypothesis is supported by the observations that annealing at 550 °C led to the formation of Sr-rich secondary particles on LSC 113 while no such particles were observed on LSCF 113. Density functional theory (DFT) computation provides further support, which revealed greater capacity of surface Sr segregation for LSCF 113 having SrO termination than LSC 113 having (La 0.25Sr 0.75)O termination for the experimental conditions, and lower energy gain to move Sr from LSCF 113 into LSC 214 relative to the LSC 214-LSC 113 system.« less

Development of a structural concept to resist impacts from multiyear ice floes, ridges, and icebergs

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

Gerwick, B.C.; Potter, R.E.; Rojansky, M.

1984-05-01

Large multi-year ice features and icebergs may have masses ranging up to 20 million tons or more and may move in the open water at speeds up to 1 knot, thus developing tremendous kinetic energy. A stepped structure concept has been developed to resist these impacts and to transfer the resultant forces and moments into the foundation thus developing a relatively high concentrated reaction force against the ice tending to spall and split it, thus causing a multi-modal failure of the ice, as well as using up kinetic energy at a relatively controlled rate. Calculated ice forces and ice failuremore » modes will be presented. The stepped structure concept is primarily applicable to production platforms in water depths of 50 to 200 meters, which are subject to impact of large ice features such as multi-year ridges, floes, and icebergs The resulting global ice loads are reduced by 50 percent or more as compared to those developed by a vertical or a steep sided structure. Overturning moments are reduced, thus reducing maxima soil bearing values. The structure itself is efficient in its use of structural materials, and is practicable for construction in prestressed reinforced concrete or steel/ concrete hybrid construction. It has acceptable draft during tow and can carry a fully outfitted deck. It is stable during all stages of installation.« less

Rapid incorporation kinetics and improved fidelity of a novel class of 3'-OH unblocked reversible terminators.

PubMed

Gardner, Andrew F; Wang, Jinchun; Wu, Weidong; Karouby, Jennifer; Li, Hong; Stupi, Brian P; Jack, William E; Hersh, Megan N; Metzker, Michael L

2012-08-01

Recent developments of unique nucleotide probes have expanded our understanding of DNA polymerase function, providing many benefits to techniques involving next-generation sequencing (NGS) technologies. The cyclic reversible termination (CRT) method depends on efficient base-selective incorporation of reversible terminators by DNA polymerases. Most terminators are designed with 3'-O-blocking groups but are incorporated with low efficiency and fidelity. We have developed a novel class of 3'-OH unblocked nucleotides, called Lightning Terminators™, which have a terminating 2-nitrobenzyl moiety attached to hydroxymethylated nucleobases. A key structural feature of this photocleavable group displays a 'molecular tuning' effect with respect to single-base termination and improved nucleotide fidelity. Using Therminator DNA polymerase, we demonstrate that these 3'-OH unblocked terminators exhibit superior enzymatic performance compared to two other reversible terminators, 3'-O-amino-TTP and 3'-O-azidomethyl-TTP. Lightning Terminators show maximum incorporation rates (k(pol)) that range from 35 to 45 nt/s, comparable to the fastest NGS chemistries, yet with catalytic efficiencies (k(pol)/K(D)) comparable to natural nucleotides. Pre-steady-state kinetic studies of thymidine analogs revealed that the major determinant for improved nucleotide selectivity is a significant reduction in k(pol) by >1000-fold over TTP misincorporation. These studies highlight the importance of structure-function relationships of modified nucleotides in dictating polymerase performance.

The two-dimensional kinetic ballooning theory for ion temperature gradient mode in tokamak

NASA Astrophysics Data System (ADS)

Xie, T.; Zhang, Y. Z.; Mahajan, S. M.; Hu, S. L.; He, Hongda; Liu, Z. Y.

2017-10-01

The two-dimensional (2D) kinetic ballooning theory is developed for the ion temperature gradient mode in an up-down symmetric equilibrium (illustrated via concentric circular magnetic surfaces). The ballooning transform converts the basic 2D linear gyro-kinetic equation into two equations: (1) the lowest order equation (ballooning equation) is an integral equation essentially the same as that reported by Dong et al., [Phys. Fluids B 4, 1867 (1992)] but has an undetermined Floquet phase variable, (2) the higher order equation for the rapid phase envelope is an ordinary differential equation in the same form as the 2D ballooning theory in a fluid model [Xie et al., Phys. Plasmas 23, 042514 (2016)]. The system is numerically solved by an iterative approach to obtain the (phase independent) eigen-value. The new results are compared to the two earlier theories. We find a strongly modified up-down asymmetric mode structure, and non-trivial modifications to the eigen-value.

Plasma kinetic effects on atomistic mix in one dimension and at structured interfaces (II)

NASA Astrophysics Data System (ADS)

Albright, Brian; Yin, Lin; Cooley, James; Haack, Jeffrey; Douglas, Melissa

2017-10-01

The Marble campaign seeks to develop a platform for studying mix evolution in turbulent, inhomogeneous, high-energy-density plasmas at the NIF. Marble capsules contain engineered CD foams, the pores of which are filled with hydrogen and tritium. During implosion, hydrodynamic stirring and plasma diffusivity mix tritium fuel into the surrounding CD plasma, leading to both DD and DT fusion neutron production. In this presentation, building upon prior work, kinetic particle-in-cell simulations using the VPIC code are used to examine kinetic effects on thermonuclear burn in Marble-like settings. Departures from Maxwellian distributions are observed near the interface and TN burn rates and inferred temperatures from synthetic neutron time of flight diagnostics are compared with those from treating the background species as Maxwellian. Work performed under the auspices of the U.S. DOE by the Los Alamos National Security, LLC Los Alamos National Laboratory and supported by the ASC and Science programs.

Structure, growth kinetics, and ledge flow during vapor-solid-solid growth of copper-catalyzed silicon nanowires.

PubMed

Wen, C-Y; Reuter, M C; Tersoff, J; Stach, E A; Ross, F M

2010-02-10

We use real-time observations of the growth of copper-catalyzed silicon nanowires to determine the nanowire growth mechanism directly and to quantify the growth kinetics of individual wires. Nanowires were grown in a transmission electron microscope using chemical vapor deposition on a copper-coated Si substrate. We show that the initial reaction is the formation of a silicide, eta'-Cu(3)Si, and that this solid silicide remains on the wire tips during growth so that growth is by the vapor-solid-solid mechanism. Individual wire directions and growth rates are related to the details of orientation relation and catalyst shape, leading to a rich morphology compared to vapor-liquid-solid grown nanowires. Furthermore, growth occurs by ledge propagation at the silicide/silicon interface, and the ledge propagation kinetics suggest that the solubility of precursor atoms in the catalyst is small, which is relevant to the fabrication of abrupt heterojunctions in nanowires.

Experimental effect of shots caused by projectiles fired from air guns with kinetic energy below 17 J.

PubMed

Smędra-Kaźmirska, Anna; Barzdo, Maciej; Kędzierski, Maciej; Antoszczyk, Łukasz; Szram, Stefan; Berent, Jarosław

2013-09-01

Pursuant to the Polish Weapons and Ammunitions Law (Legal Gazette No 53/1999 item 549 with subsequent amendments), air guns with kinetic energy of the fired projectiles below 17 J are not regarded as weapons. The aim of the study was to assess the potential effect of shots caused by projectiles of various mass and structure fired from air guns with kinetic energy below 17 J on human soft tissues. As a model of soft tissue, we used 20% gelatin blocks. After shooting, we measured the depth of gelatin block penetration by pellets fired from various distances and compared these results with autopsy findings. The results demonstrated that examined pneumatic guns may cause serious injuries, including damage to the pleura, pericardium, liver, spleen, kidneys, femoral artery, and thoracic and abdominal aorta. Experiment shown that gelatin blocks do not reflect fully the properties of the human body. © 2013 American Academy of Forensic Sciences.

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

Harding, A.W.; Foley, N.J.; Thomas, K.M.

The adsorption of water vapor on a highly microporous coconut-shell-derived carbon and a mesoporous wood-derived carbon was studied. These carbons were chosen as they had markedly different porous structures. The adsorption and desorption characteristics of water vapor on the activated carbons were investigated over the relative pressure range p/p{degree} = 0--0.9 for temperatures in the range 285--313 K in a static water vapor system. The adsorption isotherms were analyzed using the Dubinin-Serpinski equation, and this provided an assessment of the polarity of the carbons. The kinetics of water vapor adsorption and desorption were studied with different amounts of preadsorbed watermore » for set changes in pressure relative to the saturated vapor pressure (p/p{degree}). The adsorption kinetics for each relative pressure step were compared and used to calculate the activation energies for the vapor pressure increments. The kinetic results are discussed in relation to their relative position on the equilibrium isotherm and the adsorption mechanism of water vapor on activated carbons.« less

Silk Self-Assembly Mechanisms and Control-From Thermodynamics to Kinetics

PubMed Central

Lu, Qiang; Zhu, Hesun; Zhang, Cencen; Zhang, Feng; Zhang, Bing; Kaplan, David L.

2012-01-01

Silkworms and spiders generate fibres that exhibit high strength and extensibility. The underlying mechanisms involved in processing silk proteins into fiber form remain incompletely understood, resulting in the failure to fully recapitulate the remarkable properties of native fibers in vitro from regenerated silk solutions. In the present study, the extensibility and high strength of regenerated silks were achieved by mimicking the natural spinning process. Conformational transitions inside micelles, followed by aggregation of micelles and their stabilization as they relate to the metastable structure of silk are described. Subsequently, the mechanisms to control the formation of nanofibrous structures were elucidated. The results clarify that the self-assembly of silk in aqueous solution is a thermodynamically driven process where kinetics also play a key role. Four key factors, molecular mobility, charge, hydrophilic interactions and concentration underlie the process. Adjusting these factors can balance nanostructure and conformational composition, and be used to achieve silk-based materials with properties comparable to native fibers. These mechanisms suggest new directions to design silk-based multifunctional materials. PMID:22320432

Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.

PubMed

Guthke, Reinhard; Möller, Ulrich; Hoffmann, Martin; Thies, Frank; Töpfer, Susanne

2005-04-15

The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions. We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks. The proposed approach is based on both microarray data and available biological knowledge. The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series). The number of clusters was optimized using various evaluation criteria. For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge. Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes. For the construction of hypothetical network structures singular value decomposition (SVD) based methods and a newly introduced heuristic Network Generation Method here were compared. It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. Reinhard.Guthke@hki-jena.de.

Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Nakaura, Miho; Nishimura, Shigenori; Karita, Shuichi; Miyake, Hideo; Tanaka, Akiyoshi

2009-08-01

Refolding of a thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and (1)H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half-lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with beta-cyclodextrin as the native state, suggesting that the intermediate is highly-ordered and native-like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far-UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off-pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.

Brownian dynamics simulation of sickle hemoglobin bundle formation

NASA Astrophysics Data System (ADS)

Liu, Ya; Gunton, James; Chakrabarti, Amit

2010-03-01

The physical properties of biopolymer fibers, such as their stability and degree of aggregation, are implicated in many diseases, including sickle cell anemia. The natural chirality of protofilaments plays a crucial role in the formation of sickle hemoglobin fiber which leads to the permanent blockage of microvessels. We use Brownian dynamics to investigate the kinetics of fiber aggregation. The geometrical helical structure and chirality of the filaments are modeled by anisotropic patch-like interactions. We present the kinetics of fiber formation and study the possibility of a finite critical fiber bundle size. We compare our results with various experimental and theoretical results. This work is supported by grants from the NSF and the G. Harold and Leila Y. Mathers Foundation.

Mound-Interface Kinetics in Dictyostelium Aggregation

NASA Astrophysics Data System (ADS)

Tutu, Hiroki

2002-09-01

The mound development of the cellular slime mold amoebae Dictyostelium discoideum is studied with an interface kinetic model for the height of cell layers. As a competitive role for the chemotaxis, we compare two types of curvature relaxations; the surface relaxation induced by cell-substrate affinity (model A), and that comes from a cell-cell adhesive effect (model B). It is found that both models are characterized by the growth law for the maximum mound height. Based on a self-similarity scaling hypothesis for the spatial structure of streaming pattern, we suggest a scaling law for the growth of mound-height hmax ˜ t1-1/α+β/α with α = 2 (4) for the model A (B) and a number 0 ≤ β < 1.

The chemistry of peroxovanadium compounds relevant to insulin mimesis.

PubMed

Shaver, A; Ng, J B; Hall, D A; Posner, B I

The inorganic coordination chemistry of peroxovanadium compounds relevant to insulin mimesis is reviewed. The structure and kinetic reactivity of solutions of vanadate anion, vanadyl complexes and peroxovanadate complexes are briefly compared. Peroxovanadium compounds contain an oxo group, one or two peroxo ligands (O2(2-)) and an ancillary ligand which is usually bidentate. These compounds approximate a trigonal bipyramidal structure which can be divided conceptually into a polar 'oxo' half and a relatively non-polar organic half. This presents a number of interesting design variations which are discussed with respect to the development of a rudimentary structure-activity correlation of insulin mimetic ability.

Assembly kinetics determine the architecture of α-actinin crosslinked F-actin networks.

PubMed

Falzone, Tobias T; Lenz, Martin; Kovar, David R; Gardel, Margaret L

2012-05-29

The actin cytoskeleton is organized into diverse meshworks and bundles that support many aspects of cell physiology. Understanding the self-assembly of these actin-based structures is essential for developing predictive models of cytoskeletal organization. Here we show that the competing kinetics of bundle formation with the onset of dynamic arrest arising from filament entanglements and crosslinking determine the architecture of reconstituted actin networks formed with α-actinin crosslinks. Crosslink-mediated bundle formation only occurs in dilute solutions of highly mobile actin filaments. As actin polymerization proceeds, filament mobility and bundle formation are arrested concomitantly. By controlling the onset of dynamic arrest, perturbations to actin assembly kinetics dramatically alter the architecture of biochemically identical samples. Thus, the morphology of reconstituted F-actin networks is a kinetically determined structure similar to those formed by physical gels and glasses. These results establish mechanisms controlling the structure and mechanics in diverse semiflexible biopolymer networks.

VAMPnets for deep learning of molecular kinetics.

PubMed

Mardt, Andreas; Pasquali, Luca; Wu, Hao; Noé, Frank

2018-01-02

There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transformation of simulated coordinates into structural features, dimension reduction, clustering the dimension-reduced data, and estimation of a Markov state model or related model of the interconversion rates between molecular structures. This handcrafted approach demands a substantial amount of modeling expertise, as poor decisions at any step will lead to large modeling errors. Here we employ the variational approach for Markov processes (VAMP) to develop a deep learning framework for molecular kinetics using neural networks, dubbed VAMPnets. A VAMPnet encodes the entire mapping from molecular coordinates to Markov states, thus combining the whole data processing pipeline in a single end-to-end framework. Our method performs equally or better than state-of-the-art Markov modeling methods and provides easily interpretable few-state kinetic models.

On-rate based optimization of structure-kinetic relationship--surfing the kinetic map.

PubMed

Schoop, Andreas; Dey, Fabian

2015-10-01

In the lead discovery process residence time has become an important parameter for the identification and characterization of the most efficacious compounds in vivo. To enable the success of compound optimization by medicinal chemistry toward a desired residence time the understanding of structure-kinetic relationship (SKR) is essential. This article reviews various approaches to monitor SKR and suggests using the on-rate as the key monitoring parameter. The literature is reviewed and examples of compound series with low variability as well as with significant changes in on-rates are highlighted. Furthermore, findings of kinetic on-rate changes are presented and potential underlying rationales are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

Diaz, A.; Valdez, V; Rudino-Pinera, E

Neurospora crassa has two large-subunit catalases, CAT-1 and CAT-3. CAT-1 is associated with non-growing cells and accumulates particularly in asexual spores; CAT-3 is associated with growing cells and is induced under different stress conditions. It is our interest to elucidate the structure-function relationships in large-subunit catalases. Here we have determined the CAT-3 crystal structure and compared it with the previously determined CAT-1 structure. Similar to CAT-1, CAT-3 hydrogen peroxide (H{sub 2}O{sub 2}) saturation kinetics exhibited two components, consistent with the existence of two active sites: one saturated in the millimolar range and the other in the molar range. In themore » CAT-1 structure, we found three interesting features related to its unusual kinetics: (a) a constriction in the channel that conveys H{sub 2}O{sub 2} to the active site; (b) a covalent bond between the tyrosine, which forms the fifth coordination bound to the iron of the heme, and a vicinal cysteine; (c) oxidation of the pyrrole ring III to form a cis-hydroxyl group in C5 and a cis-{gamma}-spirolactone in C6. The site of heme oxidation marks the starts of the central channel that communicates to the central cavity and the shortest way products can exit the active site. CAT-3 has a similar constriction in its major channel, which could function as a gating system regulated by the H{sub 2}O{sub 2} concentration before the gate. CAT-3 functional tyrosine is not covalently bonded, but has instead the electron relay mechanism described for the human catalase to divert electrons from it. Pyrrole ring III in CAT-3 is not oxidized as it is in other large-subunit catalases whose structure has been determined. Different in CAT-3 from these enzymes is an occupied central cavity. Results presented here indicate that CAT-3 and CAT-1 enzymes represent a functional group of catalases with distinctive structural characteristics that determine similar kinetics.« less

From screen to structure with a harvestable microfluidic device.

PubMed

Stojanoff, Vivian; Jakoncic, Jean; Oren, Deena A; Nagarajan, V; Poulsen, Jens-Christian Navarro; Adams-Cioaba, Melanie A; Bergfors, Terese; Sommer, Morten O A

2011-08-01

Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.

Kinetics of methane-ethane gas replacement in clathrate-hydrates studied by time-resolved neutron diffraction and Raman spectroscopy.

PubMed

Murshed, M Mangir; Schmidt, Burkhard C; Kuhs, Werner F

2010-01-14

The kinetics of CH(4)-C(2)H(6) replacement in gas hydrates has been studied by in situ neutron diffraction and Raman spectroscopy. Deuterated ethane structure type I (C(2)H(6) sI) hydrates were transformed in a closed volume into methane-ethane mixed structure type II (CH(4)-C(2)H(6) sII) hydrates at 5 MPa and various temperatures in the vicinity of 0 degrees C while followed by time-resolved neutron powder diffraction on D20 at ILL, Grenoble. The role of available surface area of the sI starting material on the formation kinetics of sII hydrates was studied. Ex situ Raman spectroscopic investigations were carried out to crosscheck the gas composition and the distribution of the gas species over the cages as a function of structure type and compared to the in situ neutron results. Raman micromapping on single hydrate grains showed compositional and structural gradients between the surface and core of the transformed hydrates. Moreover, the observed methane-ethane ratio is very far from the one expected for a formation from a constantly equilibrated gas phase. The results also prove that gas replacement in CH(4)-C(2)H(6) hydrates is a regrowth process involving the nucleation of new crystallites commencing at the surface of the parent C(2)H(6) sI hydrate with a progressively shrinking core of unreacted material. The time-resolved neutron diffraction results clearly indicate an increasing diffusion limitation of the exchange process. This diffusion limitation leads to a progressive slowing down of the exchange reaction and is likely to be responsible for the incomplete exchange of the gases.

Identification of kinetically hot residues in proteins.

PubMed Central

Demirel, M. C.; Atilgan, A. R.; Jernigan, R. L.; Erman, B.; Bahar, I.

1998-01-01

A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in proteins, and to the possible existence of a correlation between conserved residues and those participating in the folding nuclei. Here, we use the Gaussian network model (GNM), which recently proved useful in describing the dynamic characteristics of proteins for identifying the kinetically hot residues in folded structures. These are the residues involved in the highest frequency fluctuations near the native state coordinates. Their high frequency is a manifestation of the steepness of the energy landscape near their native state positions. The theory is applied to a series of proteins whose kinetically important residues have been extensively explored: chymotrypsin inhibitor 2, cytochrome c, and related C2 proteins. Most of the residues previously pointed out to underlie the folding process of these proteins, and to be critically important for the stabilization of the tertiary fold, are correctly identified, indicating a correlation between the kinetic hot spots and the early forming structural elements in proteins. Additionally, a strong correlation between kinetically hot residues and loci of conserved residues is observed. Finally, residues that may be important for the stability of the tertiary structure of CheY are proposed. PMID:9865946

Application of the dual-kinetic-balance sets in the relativistic many-body problem of atomic structure

NASA Astrophysics Data System (ADS)

Beloy, Kyle; Derevianko, Andrei

2008-05-01

The dual-kinetic-balance (DKB) finite basis set method for solving the Dirac equation for hydrogen-like ions [V. M. Shabaev et al., Phys. Rev. Lett. 93, 130405 (2004)] is extended to problems with a non-local spherically-symmetric Dirac-Hartree-Fock potential. We implement the DKB method using B-spline basis sets and compare its performance with the widely- employed approach of Notre Dame (ND) group [W.R. Johnson, S.A. Blundell, J. Sapirstein, Phys. Rev. A 37, 307-15 (1988)]. We compare the performance of the ND and DKB methods by computing various properties of Cs atom: energies, hyperfine integrals, the parity-non-conserving amplitude of the 6s1/2-7s1/2 transition, and the second-order many-body correction to the removal energy of the valence electrons. We find that for a comparable size of the basis set the accuracy of both methods is similar for matrix elements accumulated far from the nuclear region. However, for atomic properties determined by small distances, the DKB method outperforms the ND approach.

Kinetically governed polymorphism of d(G₄T₄G₃) quadruplexes in K+ solutions.

PubMed

Prislan, Iztok; Lah, Jurij; Milanic, Matija; Vesnaver, Gorazd

2011-03-01

It has been generally recognized that understanding the molecular basis of some important cellular processes is hampered by the lack of knowledge of forces that drive spontaneous formation/disruption of G-quadruplex structures in guanine-rich DNA sequences. According to numerous biophysical and structural studies G-quadruplexes may occur in the presence of K(+) and Na(+) ions as polymorphic structures formed in kinetically governed processes. The reported kinetic models suggested to describe this polymorphism should be considered inappropriate since, as a rule, they include bimolecular single-step associations characterized by negative activation energies. In contrast, our approach in studying polymorphic behavior of G-quadruplexes is based on model mechanisms that involve only elementary folding/unfolding transitions and structural conversion steps that are characterized by positive activation energies. Here, we are investigating a complex polymorphism of d(G(4)T(4)G(3)) quadruplexes in K(+) solutions. On the basis of DSC, circular dichroism and UV spectroscopy and polyacrylamide gel electrophoresis experiments we propose a kinetic model that successfully describes the observed thermally induced conformational transitions of d(G(4)T(4)G(3)) quadruplexes in terms of single-step reactions that involve besides single strands also one tetramolecular and three bimolecular quadruplex structures.

Large eddy simulation study of the kinetic energy entrainment by energetic turbulent flow structures in large wind farms

NASA Astrophysics Data System (ADS)

VerHulst, Claire; Meneveau, Charles

2014-02-01

In this study, we address the question of how kinetic energy is entrained into large wind turbine arrays and, in particular, how large-scale flow structures contribute to such entrainment. Previous research has shown this entrainment to be an important limiting factor in the performance of very large arrays where the flow becomes fully developed and there is a balance between the forcing of the atmospheric boundary layer and the resistance of the wind turbines. Given the high Reynolds numbers and domain sizes on the order of kilometers, we rely on wall-modeled large eddy simulation (LES) to simulate turbulent flow within the wind farm. Three-dimensional proper orthogonal decomposition (POD) analysis is then used to identify the most energetic flow structures present in the LES data. We quantify the contribution of each POD mode to the kinetic energy entrainment and its dependence on the layout of the wind turbine array. The primary large-scale structures are found to be streamwise, counter-rotating vortices located above the height of the wind turbines. While the flow is periodic, the geometry is not invariant to all horizontal translations due to the presence of the wind turbines and thus POD modes need not be Fourier modes. Differences of the obtained modes with Fourier modes are documented. Some of the modes are responsible for a large fraction of the kinetic energy flux to the wind turbine region. Surprisingly, more flow structures (POD modes) are needed to capture at least 40% of the turbulent kinetic energy, for which the POD analysis is optimal, than are needed to capture at least 40% of the kinetic energy flux to the turbines. For comparison, we consider the cases of aligned and staggered wind turbine arrays in a neutral atmospheric boundary layer as well as a reference case without wind turbines. While the general characteristics of the flow structures are robust, the net kinetic energy entrainment to the turbines depends on the presence and relative arrangement of the wind turbines in the domain.

Structural effects in the interstitial solid solution system (La,Ce)(Fe,Si)13Cx-H: Correlation with hydrogenation kinetics

NASA Astrophysics Data System (ADS)

Hai, X.; Porcher, F.; Mayer, C.; Miraglia, S.

2018-02-01

Steady state and in-situ neutron powder diffraction on selected compositions of the magneto-caloric (La,Ce)(Fe,Si)13CxHy compounds has been used to locate the sites accommodated by the interstitial species and to reveal the structural modifications (breathing) that occur upon metal substitution and/or interstitial insertion. The latter type of measurement in which the sequential filling of interstitial sites is followed allows one to extract some useful hydrogenation kinetics data. This structural investigation has allowed to precise the deformations undergone by the complex metallic alloys La(Fe,Si)13 when subjected to light interstitial insertion or rare earth substitution at the cation site of the NaZn13-structure type. We attempt to correlate hydrogenation kinetics variations (depression or enhancement of the hydrogen absorption rate) with a particular inhomogeneous cell variation (breathing) and bonding of the NaZn13 structure-type.

Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition.

PubMed

Atkinson, Sarah C; Dogovski, Con; Downton, Matthew T; Czabotar, Peter E; Dobson, Renwick C J; Gerrard, Juliet A; Wagner, John; Perugini, Matthew A

2013-03-01

Lysine is one of the most limiting amino acids in plants and its biosynthesis is carefully regulated through inhibition of the first committed step in the pathway catalyzed by dihydrodipicolinate synthase (DHDPS). This is mediated via a feedback mechanism involving the binding of lysine to the allosteric cleft of DHDPS. However, the precise allosteric mechanism is yet to be defined. We present a thorough enzyme kinetic and thermodynamic analysis of lysine inhibition of DHDPS from the common grapevine, Vitis vinifera (Vv). Our studies demonstrate that lysine binding is both tight (relative to bacterial DHDPS orthologs) and cooperative. The crystal structure of the enzyme bound to lysine (2.4 Å) identifies the allosteric binding site and clearly shows a conformational change of several residues within the allosteric and active sites. Molecular dynamics simulations comparing the lysine-bound (PDB ID 4HNN) and lysine free (PDB ID 3TUU) structures show that Tyr132, a key catalytic site residue, undergoes significant rotational motion upon lysine binding. This suggests proton relay through the catalytic triad is attenuated in the presence of lysine. Our study reveals for the first time the structural mechanism for allosteric inhibition of DHDPS from the common grapevine.

Structural diversity in the dandelion (Taraxacum officinale) polyphenol oxidase family results in different responses to model substrates.

PubMed

Dirks-Hofmeister, Mareike E; Singh, Ratna; Leufken, Christine M; Inlow, Jennifer K; Moerschbacher, Bruno M

2014-01-01

Polyphenol oxidases (PPOs) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure-function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1) potentially acts as a "selector" for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates.

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

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

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

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

The protonation state around TyrD/TyrD• in photosystem II is reflected in its biphasic oxidation kinetics.

PubMed

Sjöholm, Johannes; Ho, Felix; Ahmadova, Nigar; Brinkert, Katharina; Hammarström, Leif; Mamedov, Fikret; Styring, Stenbjörn

2017-02-01

The tyrosine residue D2-Tyr160 (Tyr D ) in photosystem II (PSII) can be oxidized through charge equilibrium with the oxygen evolving complex in PSII. The kinetics of the electron transfer from Tyr D has been followed using time-resolved EPR spectroscopy after triggering the oxidation of pre-reduced Tyr D by a short laser flash. After its oxidation Tyr D is observed as a neutral radical (Tyr D • ) indicating that the oxidation is coupled to a deprotonation event. The redox state of Tyr D was reported to be determined by the two water positions identified in the crystal structure of PSII [Saito et al. (2013) Proc. Natl. Acad. Sci. USA 110, 7690]. To assess the mechanism of the proton coupled electron transfer of Tyr D the oxidation kinetics has been followed in the presence of deuterated buffers, thereby resolving the kinetic isotope effect (KIE) of Tyr D oxidation at different H/D concentrations. Two kinetic phases of Tyr D oxidation - the fast phase (msec-sec time range) and the slow phase (tens of seconds time range) were resolved as was previously reported [Vass and Styring (1991) Biochemistry 30, 830]. In the presence of deuterated buffers the kinetics was significantly slower compared to normal buffers. Furthermore, although the kinetics were faster at both high pH and pD values the observed KIE was found to be similar (~2.4) over the whole pL range investigated. We assign the fast and slow oxidation phases to two populations of PSII centers with different water positions, proximal and distal respectively, and discuss possible deprotonation events in the vicinity of Tyr D . Copyright © 2016 Elsevier B.V. All rights reserved.

The Effect on Student Achievement of Increasing Kinetic Structure of Teachers' Lectures.

ERIC Educational Resources Information Center

Lamb, William G.; And Others

1979-01-01

Tests O. R. Anderson's theory of kinetic structure of verbal communications by administering lectures on swine flu to high school biology students and then reteaching the lectures with increased commonality. Results weakly support Anderson's theory. Implications are made for training teachers to increase the commonality of their lectures. (CS)

A comprehensive investigation of structural, morphological, hydrogen absorption and magnetic properties of MmNi4.22Co0.48Mn0.15Al0.15 alloy

NASA Astrophysics Data System (ADS)

Zareii, Seyyed Mojtaba; Arabi, Hadi; Pourarian, Faiz

2014-05-01

A comprehensive study of structural, morphological, hydrogen absorption and magnetic properties of MmNi4.22 Co0.48Mn0.15Al0.15 alloy as a promising hydrogen storage media was investigated. The X-ray diffraction (XRD) profiles show that the alloy maintains its crystal structure (hexagonal LaNi5-type) even after 30 hydrogenation/dehydrogenation (H/D) cycles. However, the XRD peaks are found to be slightly broadened after cycling. SEM images reveal that particles size of the cycled sample decreases, with more uniform particle size distribution compared to noncycled ones. The pressure-composition (PC) isotherms and kinetics curves of hydrogen absorption reaction were obtained at different working temperatures by using a homemade Sievert apparatus. The enthalpy and entropy of hydride formation of the alloy were evaluated. Furthermore, the Jander diffusion and Johnson-Mehl-Avrami models as the fitting models were employed to study the kinetic mechanism of hydriding reaction and its activation energy. The room temperature magnetic measurements indicate that the milling and H/D cycling change the magnetic properties of the as-annealed alloy.

Steering Charge Kinetics of Tin Niobate Photocatalysts: Key Roles of Phase Structure and Electronic Structure

NASA Astrophysics Data System (ADS)

Huang, Shushu; Wang, Chunyan; Sun, Hao; Wang, Xiaojing; Su, Yiguo

2018-05-01

Tin niobate photocatalysts with the phase structures of froodite (SnNb2O6) and pyrochlore (Sn2Nb2O7) were obtained by a facile solvothermal method in order to explore the impact of phase structure and electronic structure on the charge kinetics and photocatalytic performance. By employing tin niobate as a model compound, the effects of phase structure over electronic structure, photocatalytic activity toward methyl orange solution and hydrogen evolution were systematically investigated. It is found that the variation of phase structure from SnNb2O6 to Sn2Nb2O7 accompanied with modulation of particle size and band edge potentials that has great consequences on photocatalytic performance. In combination with the electrochemical impedance spectroscopy (EIS), transient photocurrent responses, transient absorption spectroscopy (TAS), and the analysis of the charge-carrier dynamics suggested that variation of electronic structure has great impacts on the charge separation and transfer rate of tin niobate photocatalysts and the subsequent photocatalytic performance. Moreover, the results of the X-ray photoelectron spectroscopy (XPS) indicated that the existent of Sn4+ species in Sn2Nb2O7 could result in a decrease in photocatalytic activity. Photocatalytic test demonstrated that the SnNb2O6 (froodite) catalyst possesses a higher photocatalytic activity toward MO degradation and H2 evolution compared with the sample of Sn2Nb2O7 (pyrochlore). On the basis of spin resonance measurement and trapping experiment, it is expected that photogenerated holes, O2 -•, and OH• active species dominate the photodegradation of methyl orange.

Steering Charge Kinetics of Tin Niobate Photocatalysts: Key Roles of Phase Structure and Electronic Structure.

PubMed

Huang, Shushu; Wang, Chunyan; Sun, Hao; Wang, Xiaojing; Su, Yiguo

2018-05-23

Tin niobate photocatalysts with the phase structures of froodite (SnNb 2 O 6 ) and pyrochlore (Sn 2 Nb 2 O 7 ) were obtained by a facile solvothermal method in order to explore the impact of phase structure and electronic structure on the charge kinetics and photocatalytic performance. By employing tin niobate as a model compound, the effects of phase structure over electronic structure, photocatalytic activity toward methyl orange solution and hydrogen evolution were systematically investigated. It is found that the variation of phase structure from SnNb 2 O 6 to Sn 2 Nb 2 O 7 accompanied with modulation of particle size and band edge potentials that has great consequences on photocatalytic performance. In combination with the electrochemical impedance spectroscopy (EIS), transient photocurrent responses, transient absorption spectroscopy (TAS), and the analysis of the charge-carrier dynamics suggested that variation of electronic structure has great impacts on the charge separation and transfer rate of tin niobate photocatalysts and the subsequent photocatalytic performance. Moreover, the results of the X-ray photoelectron spectroscopy (XPS) indicated that the existent of Sn 4+ species in Sn 2 Nb 2 O 7 could result in a decrease in photocatalytic activity. Photocatalytic test demonstrated that the SnNb 2 O 6 (froodite) catalyst possesses a higher photocatalytic activity toward MO degradation and H 2 evolution compared with the sample of Sn 2 Nb 2 O 7 (pyrochlore). On the basis of spin resonance measurement and trapping experiment, it is expected that photogenerated holes, O 2 -• , and OH • active species dominate the photodegradation of methyl orange.

Head losses prediction and analysis in a bulb turbine draft tube under different operating conditions using unsteady simulations

NASA Astrophysics Data System (ADS)

Wilhelm, S.; Balarac, G.; Métais, O.; Ségoufin, C.

2016-11-01

Flow prediction in a bulb turbine draft tube is conducted for two operating points using Unsteady RANS (URANS) simulations and Large Eddy Simulations (LES). The inlet boundary condition of the draft tube calculation is a rotating two dimensional velocity profile exported from a RANS guide vane- runner calculation. Numerical results are compared with experimental data in order to validate the flow field and head losses prediction. Velocity profiles prediction is improved with LES in the center of the draft tube compared to URANS results. Moreover, more complex flow structures are obtained with LES. A local analysis of the predicted flow field using the energy balance in the draft tube is then introduced in order to detect the hydrodynamic instabilities responsible for head losses in the draft tube. In particular, the production of turbulent kinetic energy next to the draft tube wall and in the central vortex structure is found to be responsible for a large part of the mean kinetic energy dissipation in the draft tube and thus for head losses. This analysis is used in order to understand the differences in head losses for different operating points. The numerical methodology could then be improved thanks to an in-depth understanding of the local flow topology.

Chemical structure influence on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux.

PubMed

Padgett, Mark C; Tick, Geoffrey R; Carroll, Kenneth C; Burke, William R

2017-03-01

The influence of chemical structure on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux was examined. The variability of measured and UNIFAC modeled NAPL activity coefficients as a function of mole fraction was compared for two NAPL mixtures containing structurally-different contaminants of concern including toluene (TOL) or trichloroethene (TCE) within a hexadecane (HEXDEC) matrix. The results showed that dissolution from the NAPL mixtures transitioned from ideality for mole fractions >0.05 to nonideality as mole fractions decreased. In particular, the TCE generally exhibited more ideal dissolution behavior except at lower mole fractions, and may indicate greater structural/polarity similarity between the two compounds. Raoult's Law and UNIFAC generally under-predicted the batch experiment results for TOL:HEXDEC mixtures especially for mole fractions ≤0.05. The dissolution rate coefficients were similar for both TOL and TCE over all mole fractions tested. Mass flux reduction (MFR) analysis showed that more efficient removal behavior occurred for TOL and TCE with larger mole fractions compared to the lower initial mole fraction mixtures (i.e. <0.2). However, compared to TOL, TCE generally exhibited more efficient removal behavior over all mole fractions tested and may have been the result of structural and molecular property differences between the compounds. Activity coefficient variability as a function of mole fraction was quantified through regression analysis and incorporated into dissolution modeling analyses for the dynamic flushing experiments. TOL elution concentrations were modeled (predicted) reasonable well using ideal and equilibrium assumptions, but the TCE elution concentrations could not be predicted using the ideal model. Rather, the dissolution modeling demonstrated that TCE elution was better described by the nonideal model whereby NAPL-phase activity coefficient varied as a function of COC mole fraction. For dynamic column flushing experiments, dissolution rate kinetics can vary significantly with changes in NAPL volume and surface area. However, under conditions whereby NAPL volume and area are not significantly altered during dissolution, mixture nonideality effects may have a greater relative control on dissolution (elution) and MFR behavior compared to kinetic rate limitations. Copyright © 2017 Elsevier B.V. All rights reserved.

Chemical structure influence on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux

NASA Astrophysics Data System (ADS)

Padgett, Mark C.; Tick, Geoffrey R.; Carroll, Kenneth C.; Burke, William R.

2017-03-01

The influence of chemical structure on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux was examined. The variability of measured and UNIFAC modeled NAPL activity coefficients as a function of mole fraction was compared for two NAPL mixtures containing structurally-different contaminants of concern including toluene (TOL) or trichloroethene (TCE) within a hexadecane (HEXDEC) matrix. The results showed that dissolution from the NAPL mixtures transitioned from ideality for mole fractions > 0.05 to nonideality as mole fractions decreased. In particular, the TCE generally exhibited more ideal dissolution behavior except at lower mole fractions, and may indicate greater structural/polarity similarity between the two compounds. Raoult's Law and UNIFAC generally under-predicted the batch experiment results for TOL:HEXDEC mixtures especially for mole fractions ≤ 0.05. The dissolution rate coefficients were similar for both TOL and TCE over all mole fractions tested. Mass flux reduction (MFR) analysis showed that more efficient removal behavior occurred for TOL and TCE with larger mole fractions compared to the lower initial mole fraction mixtures (i.e. < 0.2). However, compared to TOL, TCE generally exhibited more efficient removal behavior over all mole fractions tested and may have been the result of structural and molecular property differences between the compounds. Activity coefficient variability as a function of mole fraction was quantified through regression analysis and incorporated into dissolution modeling analyses for the dynamic flushing experiments. TOL elution concentrations were modeled (predicted) reasonable well using ideal and equilibrium assumptions, but the TCE elution concentrations could not be predicted using the ideal model. Rather, the dissolution modeling demonstrated that TCE elution was better described by the nonideal model whereby NAPL-phase activity coefficient varied as a function of COC mole fraction. For dynamic column flushing experiments, dissolution rate kinetics can vary significantly with changes in NAPL volume and surface area. However, under conditions whereby NAPL volume and area are not significantly altered during dissolution, mixture nonideality effects may have a greater relative control on dissolution (elution) and MFR behavior compared to kinetic rate limitations.

Dye removal from textile industrial effluents by adsorption on exfoliated graphite nanoplatelets: kinetic and equilibrium studies.

PubMed

Carvallho, Marilda N; da Silva, Karolyne S; Sales, Deivson C S; Freire, Eleonora M P L; Sobrinho, Maurício A M; Ghislandi, Marcos G

2016-01-01

The concept of physical adsorption was applied for the removal of direct and reactive blue textile dyes from industrial effluents. Commercial graphite nanoplatelets were used as substrate, and the quality of the material was characterized by atomic force and transmission electron microscopies. Dye/graphite nanoplatelets water solutions were prepared varying their pH and initial dye concentration. Exceptionally high values (beyond 100 mg/L) for adsorptive capacity of graphite nanoplatelets could be achieved without complicated chemical modifications, and equilibrium and kinetic experiments were performed. Our findings were compared with the state of the art, and compared with theoretical models. Agreement between them was satisfactory, and allowed us to propose novel considerations describing the interactions of the dyes and the graphene planar structure. The work highlights the important role of these interactions, which can govern the mobility of the dye molecules and the amount of layers that can be stacked on the graphite nanoplatelets surface.

Kinetic consequences of introducing a proximal selenocysteine ligand into cytochrome P450cam.

PubMed

Vandemeulebroucke, An; Aldag, Caroline; Stiebritz, Martin T; Reiher, Markus; Hilvert, Donald

2015-11-10

The structural, electronic, and catalytic properties of cytochrome P450cam are subtly altered when the cysteine that coordinates to the heme iron is replaced with a selenocysteine. To map the effects of the sulfur-to-selenium substitution on the individual steps of the catalytic cycle, we conducted a comparative kinetic analysis of the selenoenzyme and its cysteine counterpart. Our results show that the more electron-donating selenolate ligand has only negligible effects on substrate, product, and oxygen binding, electron transfer, catalytic turnover, and coupling efficiency. Off-pathway reduction of oxygen to give superoxide is the only step significantly affected by the mutation. Incorporation of selenium accelerates this uncoupling reaction approximately 50-fold compared to sulfur, but because the second electron transfer step is much faster, the impact on overall catalytic turnover is minimal. Density functional theory calculations with pure and hybrid functionals suggest that superoxide formation is governed by a delicate interplay of spin distribution, spin state, and structural effects. In light of the remarkably similar electronic structures and energies calculated for the sulfur- and selenium-containing enzymes, the ability of the heavier atom to enhance the rate of spin crossover may account for the experimental observations. Because the selenoenzyme closely mimics wild-type P450cam, even at the level of individual steps in the reaction cycle, selenium represents a unique mechanistic probe for analyzing the role of the proximal ligand and spin crossovers in P450 chemistry.

Factor analysis for delineation of organ structures, creation of in- and output functions, and standardization of multicenter kinetic modeling

NASA Astrophysics Data System (ADS)

Schiepers, Christiaan; Hoh, Carl K.; Dahlbom, Magnus; Wu, Hsiao-Ming; Phelps, Michael E.

1999-05-01

PET imaging can quantify metabolic processes in-vivo; this requires the measurement of an input function which is invasive and labor intensive. A non-invasive, semi-automated, image based method of input function generation would be efficient, patient friendly, and allow quantitative PET to be applied routinely. A fully automated procedure would be ideal for studies across institutions. Factor analysis (FA) was applied as processing tool for definition of temporally changing structures in the field of view. FA has been proposed earlier, but the perceived mathematical difficulty has prevented widespread use. FA was utilized to delineate structures and extract blood and tissue time-activity-curves (TACs). These TACs were used as input and output functions for tracer kinetic modeling, the results of which were compared with those from an input function obtained with serial blood sampling. Dynamic image data of myocardial perfusion studies with N-13 ammonia, O-15 water, or Rb-82, cancer studies with F-18 FDG, and skeletal studies with F-18 fluoride were evaluated. Correlation coefficients of kinetic parameters obtained with factor and plasma input functions were high. Linear regression usually furnished a slope near unity. Processing time was 7 min/patient on an UltraSPARC. Conclusion: FA can non-invasively generate input functions from image data eliminating the need for blood sampling. Output (tissue) functions can be simultaneously generated. The method is simple, requires no sophisticated operator interaction and has little inter-operator variability. FA is well suited for studies across institutions and standardized evaluations.

Self-consistent multidimensional electron kinetic model for inductively coupled plasma sources

NASA Astrophysics Data System (ADS)

Dai, Fa Foster

Inductively coupled plasma (ICP) sources have received increasing interest in microelectronics fabrication and lighting industry. In 2-D configuration space (r, z) and 2-D velocity domain (νθ,νz), a self- consistent electron kinetic analytic model is developed for various ICP sources. The electromagnetic (EM) model is established based on modal analysis, while the kinetic analysis gives the perturbed Maxwellian distribution of electrons by solving Boltzmann-Vlasov equation. The self- consistent algorithm combines the EM model and the kinetic analysis by updating their results consistently until the solution converges. The closed-form solutions in the analytical model provide rigorous and fast computing for the EM fields and the electron kinetic behavior. The kinetic analysis shows that the RF energy in an ICP source is extracted by a collisionless dissipation mechanism, if the electron thermovelocity is close to the RF phase velocities. A criterion for collisionless damping is thus given based on the analytic solutions. To achieve uniformly distributed plasma for plasma processing, we propose a novel discharge structure with both planar and vertical coil excitations. The theoretical results demonstrate improved uniformity for the excited azimuthal E-field in the chamber. Non-monotonic spatial decay in electric field and space current distributions was recently observed in weakly- collisional plasmas. The anomalous skin effect is found to be responsible for this phenomenon. The proposed model successfully models the non-monotonic spatial decay effect and achieves good agreements with the measurements for different applied RF powers. The proposed analytical model is compared with other theoretical models and different experimental measurements. The developed model is also applied to two kinds of ICP discharges used for electrodeless light sources. One structure uses a vertical internal coil antenna to excite plasmas and another has a metal shield to prevent the electromagnetic radiation. The theoretical results delivered by the proposed model agree quite well with the experimental measurements in many aspects. Therefore, the proposed self-consistent model provides an efficient and reliable means for designing ICP sources in various applications such as VLSI fabrication and electrodeless light sources.

Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues.

PubMed

Perišić, Ognjen

2018-03-16

Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM. The algorithm adjusts the number of fast modes in the GNM's weighted sum calculation using the ratio of predicted and expected numbers of target residues (contact and the neighboring first-layer residues). This approach produces very good results when applied to dimers with high protein sequence length ratios. The protocol's ability to recognize near native decoys was compared to the ability of the residue-level statistical potential of Lu and Skolnick using the Sternberg and Vakser decoy dimers sets. The statistical potential produced better overall results, but in a number of cases its predicting ability was comparable, or even inferior, to the prediction ability of the adjustable GNM approach. The results presented in this paper suggest that in heterodimers at least one protein has interacting scaffold determined by the immovable, kinetically hot residues. In many cases, interacting proteins (especially if being of noticeably different sizes) either behave as a rigid lock and key or, presumably, exhibit the opposite dynamic behavior. While the binding surface of one protein is rigid and stable, its partner's interacting scaffold is more flexible and adaptable.

Ion distribution effects of turbulence on a kinetic auroral arc model

NASA Technical Reports Server (NTRS)

Cornwall, J. M.; Chiu, Y. T.

1982-01-01

An inverted-V auroral arc structure plasma-kinetic model is extended to phenomenologically include the effects of electrostatic turbulence, with k-parallel/k-perpendicular being much less than unity. It is shown that, unless plasma sheet ions are very much more energetic than the electrons, anomalous resistivity is not a large contributor to parallel electrostatic potential drops, since the support of the observed potential drop requires a greater dissipation of energy than can be provided by the plasma sheet. Wave turbulence can, however, be present, with the ion cyclotron turbulence levels suggested by the ion resonance broadening saturation mechanism of Dum and Dupree (1970) being comparable to those observed on auroral field lines. The diffusion coefficient and net growth rate are much smaller than estimates based solely on local plasma properties.

Reactivity of vinyl ethers and vinyl ribosides in UV-initiated free radical copolymerization with acceptor monomers.

PubMed

Pichavant, Loic; Guillermain, Céline; Coqueret, Xavier

2010-09-13

The reactivity of various vinyl ethers and vinyloxy derivatives of ribose in the presence of diethyl fumarate or diethyl maleate was investigated for evaluating the potential of donor-acceptor-type copolymerization applied to unsaturated monomers derived from renewable feedstock. The photochemically induced polymerization of model monomer blends in the bulk state was monitored by infrared spectroscopy. The method allowed us to examine the influence of monomer pair structure on the kinetic profiles. The simultaneous consumption of both monomers was observed, supporting an alternating copolymerization mechanism. A lower reactivity of the blends containing maleates compared with fumarates was confirmed. The obtained kinetic data revealed a general correlation between the initial polymerization rate and the Hansen parameter δ(H) associated with the H-bonding aptitude of the donor monomer.

Conserved nucleation sites reinforce the significance of Phi value analysis in protein-folding studies.

PubMed

Gianni, Stefano; Jemth, Per

2014-07-01

The only experimental strategy to address the structure of folding transition states, the so-called Φ value analysis, relies on the synergy between site directed mutagenesis and the measurement of reaction kinetics. Despite its importance, the Φ value analysis has been often criticized and its power to pinpoint structural information has been questioned. In this hypothesis, we demonstrate that comparing the Φ values between proteins not only allows highlighting the robustness of folding pathways but also provides per se a strong validation of the method. © 2014 International Union of Biochemistry and Molecular Biology.

Cholinesterase structure: Identification of residues and domains affecting organophosphate inhibition and catalysis. Annual report, 6 March 1995-5 March 1996

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

Taylor, P.W.

1996-04-01

In the initial year of the grant, we have made excellent progress in several arenas: (1) A crystal structure of a mouse acetylcholinesterase-fasciculin 2 complex has been solved. (2) Studies with enantiomeric organophosphates have yielded vital information on their binding orientation in the ground and transition states. (3) Studies in oxime reactivation of inhibited cholinesterase have uncovered the basis for enhanced reactivity of HI-6 compared to 2-PAM. (4) The interactions of fasciculin 2 with acetylcholinesterase have been studied by kinetic and site-specific mutagenesis methods.

Small Changes in the Primary Structure of Transportan 10 Alter the Thermodynamics and Kinetics of its Interaction with Phospholipid Vesicles

PubMed Central

2008-01-01

The kinetics and thermodynamics of binding of transportan 10 (tp10) and four of its variants to phospholipid vesicles, and the kinetics of peptide-induced dye efflux, were compared. Tp10 is a 21-residue, amphipathic, cationic, cell-penetrating peptide similar to helical antimicrobial peptides. The tp10 variants examined include amidated and free peptides, and replacements of tyrosine by tryptophan. Carboxy-terminal amidation or substitution of tryptophan for tyrosine enhance binding and activity. The Gibbs energies of peptide binding to membranes determined experimentally and calculated from the interfacial hydrophobicity scale are in good agreement. The Gibbs energy for insertion into the bilayer core was calculated using hydrophobicity scales of residue transfer from water to octanol and to the membrane/water interface. Peptide-induced efflux becomes faster as the Gibbs energies for binding and insertion of the tp10 variants decrease. If anionic lipids are included, binding and efflux rate increase, as expected because all tp10 variants are cationic and an electrostatic component is added. Whether the most important effect of peptide amidation is the change in charge or an enhancement of helical structure, however, still needs to be established. Nevertheless, it is clear that the changes in efflux rate reflect the differences in the thermodynamics of binding and insertion of the free and amidated peptide groups. PMID:18260641

Studies on silicon NMR characterization and kinetic modeling of the structural evolution of siloxane-based materials and their applications in drug delivery and adsorption

NASA Astrophysics Data System (ADS)

Ambati, Jyothirmai

This dissertation presents studies of the synthetic processes and applications of siloxane-based materials. Kinetic investigations of bridged organoalkoxysilanes that are precursors to organic-inorganic hybrid polysilsesquioxanes are a primary focus. Quick gelation despite extensive cyclization is found during the polymerization of bridged silane precursors except for silanes with certain short bridges. This work is an attempt to characterize and understand some of the distinct features of bridged silanes using experimental characterization, kinetic modeling and simulation. In addition to this, the dissertation shows how the properties of siloxane-materials can be engineered for drug delivery and adsorption. The phase behavior of polymerizing mixtures is first investigated to identify the solutions that favor kinetic characterization. Microphase separation is found to cause gradual loss of NMR signal for certain initial compositions. Distortionless Enhancement by Polarization Transfer 29Si NMR is employed to identify the products of polymerization of some short-bridged silanes under no signal loss conditions. This technique requires knowing indirect 29Si-1H scalar coupling constants which sometimes cannot be measured due to second-order effects. However, the B3LYP density functional method with 6-31G basis set is found to predict accurate 29Si- 1H coupling constants of organoalkoxysilanes and siloxanes. The scalar coupling constants thus estimated are employed to resolve non-trivial coupled NMR spectra and quantitative kinetic modeling is performed using the DEPT Si NMR transients. In order to investigate the role of the organic bridging group, the structural evolution of bridged and non-bridged silanes are compared using Monte Carlo simulations. Kinetic and simulation models suggest that cyclization plays a key role right from the onset of polymerization for bridged silanes even more than in non-bridged silanes. The simulations indicate that the carbosiloxane rings formed from short-bridged precursors slow down but do not prevent gelation. The tuning of siloxane-based materials for adsorption technologies are also discussed here. In the first example, antioxidant enzyme loading is investigated as a means to reduce oxidative stress generated by silica nanoparticle drug carriers. Materials are engineered for promising enzyme loading and protection from proteolysis. Second, the potential of copper sulfate impregnation to enhance adsorption of ammonia by silica is explored by molecular simulation. KEYWORDS: Sol-gel Polymerization, Kinetic Investigation, Si NMR, Bridged Silanes, DFT Calculations.

Vinyl Sulfones as Antiparasitic Agents and a Structural Basis for Drug Design*

PubMed Central

Kerr, Iain D.; Lee, Ji H.; Farady, Christopher J.; Marion, Rachael; Rickert, Mathias; Sajid, Mohammed; Pandey, Kailash C.; Caffrey, Conor R.; Legac, Jennifer; Hansell, Elizabeth; McKerrow, James H.; Craik, Charles S.; Rosenthal, Philip J.; Brinen, Linda S.

2009-01-01

Cysteine proteases of the papain superfamily are implicated in a number of cellular processes and are important virulence factors in the pathogenesis of parasitic disease. These enzymes have therefore emerged as promising targets for antiparasitic drugs. We report the crystal structures of three major parasite cysteine proteases, cruzain, falcipain-3, and the first reported structure of rhodesain, in complex with a class of potent, small molecule, cysteine protease inhibitors, the vinyl sulfones. These data, in conjunction with comparative inhibition kinetics, provide insight into the molecular mechanisms that drive cysteine protease inhibition by vinyl sulfones, the binding specificity of these important proteases and the potential of vinyl sulfones as antiparasitic drugs. PMID:19620707

Theoretical studies of Pt-Ti nanoparticles for potential use as PEMFC electrocatalysts.

PubMed

Jennings, Paul C; Pollet, Bruno G; Johnston, Roy L

2012-03-07

A theoretical investigation is presented of alloying platinum with titanium to form binary Pt-Ti nanoalloys as an alternative to the expensive pure platinum catalysts commonly used for Proton Exchange Membrane Fuel Cell cathode electrocatalysts. Density Functional Theory calculations are performed to investigate compositional effects on structural properties as well as Oxygen Reduction Reaction kinetics and poisoning effects. High symmetry A(32)-B(6) clusters are studied to investigate structural properties. From these structures binding energies of hydroxyl and carbon monoxide are studied on a range of sites on the surface of the clusters. Promising results are obtained suggesting that the bimetallic Pt-Ti nanoalloys may exhibit enhanced properties compared to pure platinum catalysts.

Dynamic analysis of the deployment for mesh reflector deployable antennas with the cable-net structure

NASA Astrophysics Data System (ADS)

Zhang, Yiqun; Li, Na; Yang, Guigeng; Ru, Wenrui

2017-02-01

This paper presents a dynamic analysis approach for the composite structure of a deployable truss and cable-net system. An Elastic Catenary Element is adopted to model the slack/tensioned cables. Then, from the energy standpoint, the kinetic energy, elasticity-potential energy and geopotential energy of the cable-net structure and deployable truss are derived. Thus, the flexible multi-body dynamic model of the deployable antenna is built based on the Lagrange equation. The effect of the cable-net tension on the antenna truss is discussed and compared with previous publications and a dynamic deployment analysis is performed. Both the simulation and experimental results verify the validity of the method presented.

Kinetic-Dominated Charging Mechanism within Representative Aqueous Electrolyte-based Electric Double-Layer Capacitors.

PubMed

Yang, Huachao; Yang, Jinyuan; Bo, Zheng; Chen, Xia; Shuai, Xiaorui; Kong, Jing; Yan, Jianhua; Cen, Kefa

2017-08-03

The chemical nature of electrolytes has been demonstrated to play a pivotal role in the charge storage of electric double-layer capacitors (EDLCs), whereas primary mechanisms are still partially resolved but controversial. In this work, a systematic exploration into EDL structures and kinetics of representative aqueous electrolytes is performed with numerical simulation and experimental research. Unusually, a novel charging mechanism exclusively predominated by kinetics is recognized, going beyond traditional views of manipulating capacitances preferentially via interfacial structural variations. Specifically, strikingly distinctive EDL structures stimulated by diverse ion sizes, valences, and mixtures manifest a virtually identical EDL capacitance, where the dielectric nature of solvents attenuates ionic effects on electrolyte redistributions, in stark contradiction with solvent-free counterpart and traditional Helmholtz theory. Meanwhile, corresponding kinetics evolve conspicuously with ionic species, intimately correlated with ion-solvent interactions. The achieved mechanisms are subsequently illuminated by electrochemical measurements, highlighting the crucial interplay between ions and solvents in regulating EDLC performances.

Assembly Kinetics Determine the Architecture of α-actinin Crosslinked F-actin Networks

PubMed Central

Falzone, Tobias T.; Lenz, Martin; Kovar, David R.; Gardel, Margaret L.

2013-01-01

The actin cytoskeleton is organized into diverse meshworks and bundles that support many aspects of cell physiology. Understanding the self-assembly of these actin-based structures is essential for developing predictive models of cytoskeletal organization. Here we show that the competing kinetics of bundle formation with the onset of dynamic arrest arising from filament entanglements and cross-linking determine the architecture of reconstituted actin networks formed with α-actinin cross-links. Cross-link mediated bundle formation only occurs in dilute solutions of highly mobile actin filaments. As actin polymerization proceeds, filament mobility and bundle formation are arrested concomitantly. By controlling the onset of dynamic arrest, perturbations to actin assembly kinetics dramatically alter the architecture of biochemically identical samples. Thus, the morphology of reconstituted F-actin networks is a kinetically determined structure similar to those formed by physical gels and glasses. These results establish mechanisms controlling the structure and mechanics in diverse semi-flexible biopolymer networks. PMID:22643888

The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

DOE PAGES

Baggetto, Loic; Bridges, Craig A.; Jumas, Dr. Jean-Claude; ...

2014-09-25

To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na 7Sn 3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Namore » 9Sn 4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na 14.78Sn 4 (Pnma), better described as Na 16-xSn 4, is Na-richer than cubic Na 15Sn 4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na 7Sn 3 and Na 15Sn 4, different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.« less

A Century of Enzyme Kinetic Analysis, 1913 to 2013

PubMed Central

Johnson, Kenneth A.

2013-01-01

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. PMID:23850893

Non-Isothermal Kinetics.

ERIC Educational Resources Information Center

Brown, M. E.; Phillpotts, C. A. R.

1978-01-01

Discusses the principle of nonisothermal kinetics and some of the factors involved in such reactions, especially when considering the reliability of the kinetic parameters, compared to those of isothermal conditions. (GA)

Comparison of petroleum generation kinetics by isothermal hydrous and nonisothermal open-system pyrolysis

USGS Publications Warehouse

Lewan, M.D.; Ruble, T.E.

2002-01-01

This study compares kinetic parameters determined by open-system pyrolysis and hydrous pyrolysis using aliquots of source rocks containing different kerogen types. Kinetic parameters derived from these two pyrolysis methods not only differ in the conditions employed and products generated, but also in the derivation of the kinetic parameters (i.e., isothermal linear regression and non-isothermal nonlinear regression). Results of this comparative study show that there is no correlation between kinetic parameters derived from hydrous pyrolysis and open-system pyrolysis. Hydrous-pyrolysis kinetic parameters determine narrow oil windows that occur over a wide range of temperatures and depths depending in part on the organic-sulfur content of the original kerogen. Conversely, open-system kinetic parameters determine broad oil windows that show no significant differences with kerogen types or their organic-sulfur contents. Comparisons of the kinetic parameters in a hypothetical thermal-burial history (2.5 ??C/my) show open-system kinetic parameters significantly underestimate the extent and timing of oil generation for Type-US kerogen and significantly overestimate the extent and timing of petroleum formation for Type-I kerogen compared to hydrous pyrolysis kinetic parameters. These hypothetical differences determined by the kinetic parameters are supported by natural thermal-burial histories for the Naokelekan source rock (Type-IIS kerogen) in the Zagros basin of Iraq and for the Green River Formation (Type-I kerogen) in the Uinta basin of Utah. Differences in extent and timing of oil generation determined by open-system pyrolysis and hydrous pyrolysis can be attributed to the former not adequately simulating natural oil generation conditions, products, and mechanisms.

Voltage gating by molecular subunits of Na+ and K+ ion channels: higher-dimensional cubic kinetics, rate constants, and temperature

PubMed Central

2015-01-01

The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m3 → m4). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. PMID:25867741

Structural and Kinetic Basis for Substrate Selectivity in Populus tremuloides Sinapyl Alcohol Dehydrogenase

PubMed Central

Bomati, Erin K.; Noel, Joseph P.

2005-01-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities. PMID:15829607

Structural and kinetic basis for substrate selectivity in Populus tremuloides sinapyl alcohol dehydrogenase.

PubMed

Bomati, Erin K; Noel, Joseph P

2005-05-01

We describe the three-dimensional structure of sinapyl alcohol dehydrogenase (SAD) from Populus tremuloides (aspen), a member of the NADP(H)-dependent dehydrogenase family that catalyzes the last reductive step in the formation of monolignols. The active site topology revealed by the crystal structure substantiates kinetic results indicating that SAD maintains highest specificity for the substrate sinapaldehyde. We also report substantial substrate inhibition kinetics for the SAD-catalyzed reduction of hydroxycinnamaldehydes. Although SAD and classical cinnamyl alcohol dehydrogenases (CADs) catalyze the same reaction and share some sequence identity, the active site topology of SAD is strikingly different from that predicted for classical CADs. Kinetic analyses of wild-type SAD and several active site mutants demonstrate the complexity of defining determinants of substrate specificity in these enzymes. These results, along with a phylogenetic analysis, support the inclusion of SAD in a plant alcohol dehydrogenase subfamily that includes cinnamaldehyde and benzaldehyde dehydrogenases. We used the SAD three-dimensional structure to model several of these SAD-like enzymes, and although their active site topologies largely mirror that of SAD, we describe a correlation between substrate specificity and amino acid substitution patterns in their active sites. The SAD structure thus provides a framework for understanding substrate specificity in this family of enzymes and for engineering new enzyme specificities.

Rate-determining Step of Flap Endonuclease 1 (FEN1) Reflects a Kinetic Bias against Long Flaps and Trinucleotide Repeat Sequences.

PubMed

Tarantino, Mary E; Bilotti, Katharina; Huang, Ji; Delaney, Sarah

2015-08-21

Flap endonuclease 1 (FEN1) is a structure-specific nuclease responsible for removing 5'-flaps formed during Okazaki fragment maturation and long patch base excision repair. In this work, we use rapid quench flow techniques to examine the rates of 5'-flap removal on DNA substrates of varying length and sequence. Of particular interest are flaps containing trinucleotide repeats (TNR), which have been proposed to affect FEN1 activity and cause genetic instability. We report that FEN1 processes substrates containing flaps of 30 nucleotides or fewer at comparable single-turnover rates. However, for flaps longer than 30 nucleotides, FEN1 kinetically discriminates substrates based on flap length and flap sequence. In particular, FEN1 removes flaps containing TNR sequences at a rate slower than mixed sequence flaps of the same length. Furthermore, multiple-turnover kinetic analysis reveals that the rate-determining step of FEN1 switches as a function of flap length from product release to chemistry (or a step prior to chemistry). These results provide a kinetic perspective on the role of FEN1 in DNA replication and repair and contribute to our understanding of FEN1 in mediating genetic instability of TNR sequences. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Pectin as an Extraordinary Natural Kinetic Hydrate Inhibitor

PubMed Central

Xu, Shurui; Fan, Shuanshi; Fang, Songtian; Lang, Xuemei; Wang, Yanhong; Chen, Jun

2016-01-01

Pectin as a novel natural kinetic hydrate inhibitor, expected to be eco-friendly and sufficiently biodegradable, was studied in this paper. The novel crystal growth inhibition (CGI) and standard induction time methods were used to evaluate its effect as hydrate inhibitor. It could successfully inhibit methane hydrate formation at subcooling temperature up to 12.5 °C and dramatically slowed the hydrate crystal growth. The dosage of pectin decreased by 66% and effective time extended 10 times than typical kinetic inhibitor. Besides, its maximum growth rate was no more than 2.0%/h, which was far less than 5.5%/h of growth rate for PVCap at the same dosage. The most prominent feature was that it totally inhibited methane hydrate crystal rapid growth when hydrate crystalline occurred. Moreover, in terms of typical natural inhibitors, the inhibition activity of pectin increased 10.0-fold in induction time and 2.5-fold in subcooling temperature. The extraordinary inhibition activity is closely related to its hydrogen bonding interaction with water molecules and the hydrophilic structure. Finally, the biodegradability and economical efficiency of pectin were also taken into consideration. The results showed the biodegradability improved 75.0% and the cost reduced by more than 73.3% compared to typical commercial kinetic inhibitors. PMID:26996773

Chain Dynamics and Structure Property Relation in High Impact Strength Polycarbonate Plastic.

DTIC Science & Technology

1985-01-04

computerized for cases involving more than one kinetic process simultaneously contributing to line narrowing. The model introduces a distributional character...F. O’Gara (Research Assistant) Department of Chemitry , Graduate Student Clark University PhD Clark University June, 1984. 4. The following...on a tetrahedral lattice is compared with a a v ,del by Weber and Hel- fand (8), based on computer simulaticns cct pOlVethvlece type chafins. These two

Multi-Scale Fusion of Information for Uncertainty Quantification and Management in Large-Scale Simulations

DTIC Science & Technology

2015-12-02

simplification of the equations but at the expense of introducing modeling errors. We have shown that the Wick solutions have accuracy comparable to...the system of equations for the coefficients of formal power series solutions . Moreover, the structure of this propagator is seemingly universal, i.e...the problem of computing the numerical solution to kinetic partial differential equa- tions involving many phase variables. These types of equations

Real-time photoelectron spectroscopy study of the oxidation reaction kinetics on p-type and n-type Si (001) surfaces

NASA Astrophysics Data System (ADS)

Yu, Zhou

Silicon oxides thermally grown on Si surface are the core gate materials of metal-oxide-semiconductor field effect transistor (MOSFET). This thin oxide layer insulates the gate terminals and the transistors substrate which make MOSFET has certain advantages over those conventional junctions, such as field-effect transistor (FET) and junction field effect transistor (JFET). With an oxide insulating layer, MOSFET is able to sustain higher input impedance and the corresponding gate leakage current can be minimized. Today, though the oxidation process on Si substrate is popular in industry, there are still some uncertainties about its oxidation kinetics. On a path to clarify and modeling the oxidation kinetics, a study of initial oxidation kinetics on Si (001) surface has attracted attentions due to having a relatively low surface electron density and few adsorption channels compared with other Si surface direction. Based on previous studies, there are two oxidation models of Si (001) that extensively accepted, which are dual oxide species mode and autocatalytic reaction model. These models suggest the oxidation kinetics on Si (001) mainly relies on the metastable oxygen atom on the surface and the kinetic is temperature dependent. Professor Yuji Takakuwa's group, Surface Physics laboratory, Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, observed surface strain existed during the oxidation kinetics on Si (001) and this is the first time that strain was discovered during Si oxidation. Therefore, it is necessary to explain where the strain comes from since none of previous model research included the surface strain (defects generation) into considerations. Moreover, recent developing of complementary metal-oxide-semiconductor (CMOS) requires a simultaneous oxidation process on p- and n-type Si substrate. However, none of those previous models included the dopant factor into the oxidation kinetic modeling. All of these points that further work is necessary to update and modify the traditional Si (001) oxidation models that had been accepted for several decades. To update and complement the Si (001) oxidation kinetics, an understanding of the temperature and dopant factor during initial oxidation kinetics on Si (001) is our first step. In this study, real-time photoelectron spectroscopy is applied to characterize the oxidized (001) surface and surface information was collected by ultraviolet photoelectron spectroscopy technique. By analyzing parameters such as O 2p spectra uptake, change of work function and the surface state in respect of p- and n- type Si (001) substrate under different temperature, the oxygen adsorption structure and the dopant factor can be determined. In this study, experiments with temperature gradients on p-type Si (001) were conducted and this aims to clarify the temperature dependent characteristic of Si (001) surface oxidation. A comparison of the O 2p uptake, change of work function and surface state between p-and n-type Si (001) is made under a normal temperature and these provides with the data to explain how the dopant factor impacts the oxygen adsorption structure on the surface. In the future, the study of the oxygen adsorption structure will lead to an explanation of the surface strain that discovered; therefore, fundamental of the initial oxidation on Si (001) would be updated and complemented, which would contribute to the future gate technology in MOSFET and CMOS.

Investigating High-School Chemical Kinetics: The Greek Chemistry Textbook and Students' Difficulties

ERIC Educational Resources Information Center

Gegios, Theodoros; Salta, Katerina; Koinis, Spyros

2017-01-01

In this study we present an analysis of how the structure and content of the Greek school textbook approaches the concepts of chemical kinetics, and an investigation of the difficulties that 11th grade Greek students face regarding these concepts. Based on the structure and content of the Greek textbook, a tool was developed and applied to…

NMR structural and kinetic assignment of fluoro-3H-naphthopyran photomerocyanines.

PubMed

Delbaere, S; Micheau, J C; Teral, Y; Bochu, C; Campredon, M; Vermeersch, G

2001-11-01

The kinetic and structural behavior of a photochromic compound, 3-(2-fluorophenyl)-3-phenyl-3H-naphtho[2,1-b]pyran (F-Py), was investigated using 1H and 19F nuclear magnetic resonance (NMR) spectroscopy. Upon irradiation, the four theoretically predicted photomerocyanines appear along with a fifth form X, whose final structure has not been elucidated. This last form and two of the photomerocyanines are thermally labile, whereas the other two do not show any signs of decay. The system has been analyzed by NMR spectroscopy. This led to the structural assignment of each photomerocyanine. The kinetics of the thermal bleaching were monitored by directly and separately measuring the concentrations of each species at regular time intervals using 19F NMR spectroscopy. We therefore propose a plausible reaction mechanism. On the basis of this mechanism, the mathematical treatment and the study of the effects of temperature led to the determination of the kinetic and thermodynamic parameters (rate coefficients, enthalpy and entropy of activation) of this photochromic system. The leading role of the labile intermediate X on the formation of trans-transoid-cis (TTC) and cis-transoid-cis (CTC) photomerocyanines is pointed out.

Nonequilibrium self-organization of colloidal particles on substrates: adsorption, relaxation, and annealing.

PubMed

Araújo, Nuno A M; Dias, Cristóvão S; Telo da Gama, Margarida M

2017-01-11

Colloidal particles are considered ideal building blocks to produce materials with enhanced physical properties. The state-of-the-art techniques for synthesizing these particles provide control over shape, size, and directionality of the interactions. In spite of these advances, there is still a huge gap between the synthesis of individual components and the management of their spontaneous organization towards the desired structures. The main challenge is the control over the dynamics of self-organization. In their kinetic route towards thermodynamically stable structures, colloidal particles self-organize into intermediate (mesoscopic) structures that are much larger than the individual particles and become the relevant units for the dynamics. To follow the dynamics and identify kinetically trapped structures, one needs to develop new theoretical and numerical tools. Here we discuss the self-organization of functionalized colloids (also known as patchy colloids) on attractive substrates. We review our recent results on the adsorption and relaxation and explore the use of annealing cycles to overcome kinetic barriers and drive the relaxation towards the targeted structures.

A physiologically based model of chromium kinetics in the rat.

PubMed

O'Flaherty, E J

1996-05-01

A physiologically based model of chromium kinetics in rats has been developed. The general structure of the model is similar to that of a model of lead kinetics in rats. Like lead chromium exchanges between plasma and the bone surfaces in contact with plasma, and also like lead, although with much lower efficiency, it can become incorporated into actively mineralizing bone. Both processes are included in the model. Parallel absorption and disposition schemes for chromium(VI) and chromium(III) are linked in the model by reduction processes occurring throughout the body, including the lung and gastrointestinal tract. Examination of a number of data sets from studies in which chromium salts were administered to rats intravenously, orally, or by intratracheal instillation established that intravenous administration, on the one hand, and oral or pulmonary administration, on the other hand, result in different disposition patterns. The model was calibrated based on published oral and intratracheal kinetic studies in rats given soluble chromium(III) and chromium(VI) salts. In the most complete of these studies, chromium concentrations were monitored in individual tissues for 42 days following intratracheal administration of a soluble chromium(VI) salt. Inclusion in the model of a urinary excretion delay was necessary in order to fit excretion data from two other intratracheal studies. Model predictions of blood chromium concentrations are compared with the results of a published kinetic study in which rats were administered a soluble chromium(VI) salt by inhalation.

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.

Correlation of conformational heterogeneity of the tryptophyl side chain and time-resolved fluorescence intensity decay kinetics

NASA Astrophysics Data System (ADS)

Laws, William R.; Ross, J. B. Alexander

1992-04-01

The time-resolved fluorescence properties of a tryptophan residue should be useful for probing protein structure, function, and dynamics. To date, however, the non-single exponential fluorescence intensity decay kinetics for numerous peptides and proteins having a single tryptophan residue have not been adequately explained. Many possibilities have been considered and include: (1) contributions from the 1La and 1Lb states of indole; (2) excited-state hydrogen exchange; and (3) environmental heterogeneity from (chi) 1 and (chi) 2 rotamers. In addition, it has been suggested that generally many factors contribute to the decay and a distribution of probabilities may be more appropriate. Two recent results support multiple species due to conformational heterogeneity as the major contributor to complex kinetics. First, a rotationally constrained tryptophan analogue has fluorescence intensity decay kinetics that can be described by the sum of two exponentials with amplitudes comparable to the relative populations of the two rotational isomers. Second, the multiple exponentials observed for tyrosine-containing model compounds and peptides correlate with the (chi) 1 rotamer populations independently determined by 1H NMR. We now report similar correlations between rotamer populations and fluorescence intensity decay kinetics for a tryptophan analogue of oxytocin. It appears for this compound that either (chi) 2 rotations do not appreciably alter the indole environment, (chi) 2 rotations are rapid enough to average the observed dependence, or only one of two possible (chi) 2 populations is associated with each (chi) 1 rotamer.

Heat-Induced Structural Changes Affect OVA-Antigen Processing and Reduce Allergic Response in Mouse Model of Food Allergy

PubMed Central

Wallner, Michael; Kverka, Miloslav; Kozakova, Hana; Srutkova, Dagmar; Klimesova, Klara; Sotkovsky, Petr; Palova-Jelinkova, Lenka; Ferreira, Fatima; Tuckova, Ludmila

2012-01-01

Background and Aims The egg protein ovalbumin (OVA) belongs to six most frequent food allergens. We investigated how thermal processing influences its ability to induce allergic symptoms and immune responses in mouse model of food allergy. Methodology/Principal Findings Effect of increased temperature (70°C and 95°C) on OVA secondary structure was characterized by circular dichroism and by the kinetics of pepsin digestion with subsequent HPLC. BALB/c mice were sensitized intraperitoneally and challenged with repeated gavages of OVA or OVA heated to 70°C (h-OVA). Levels of allergen-specific serum antibodies were determined by ELISA (IgA and IgGs) or by β-hexosaminidase release test (IgE). Specific activities of digestive enzymes were determined in brush border membrane vesicles of jejunal enterocytes. Cytokine production and changes in regulatory T cells in mesenteric lymph nodes and spleen were assessed by ELISA and FACS. Heating of OVA to 70°C caused mild irreversible changes in secondary structure compared to boiling to 95°C (b-OVA), but both OVA treatments led to markedly different digestion kinetics and Tregs induction ability in vitro, compared to native OVA. Heating of OVA significantly decreased clinical symptoms (allergic diarrhea) and immune allergic response on the level of IgE, IL-4, IL-5, IL-13. Furthermore, h-OVA induced lower activities of serum mast cell protease-1 and enterocyte brush border membrane alkaline phosphatase as compared to native OVA. On the other hand h-OVA stimulated higher IgG2a in sera and IFN-γ secretion by splenocytes. Conclusions Minor irreversible changes in OVA secondary structure caused by thermal processing changes both its digestion and antigenic epitopes formation, which leads to activation of different T cell subpopulations, induces shift towards Th1 response and ultimately reduces its allergenicity. PMID:22629361

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

Samsel, R.W.; Perelson, A.S.

Red blood cells aggregate face-to-face to form long, cylindrical, straight chains and sometimes branched structures called rouleaux. Here the authors extend a kinetic model developed by R.W. Samsel and A.S. Perelson to include both the formation and dissociation of rouleaux. Thermodynamic constraints on the rate constants of the model imposed by the principle of detailed balance were examined. Incorporation of reverse reactions allows computation of mean sizes of rouleaux and straight chain segments within rouleaux, as functions of time and at equilibrium. Using the Flory-Stockmayer method from polymer chemistry, a closed-form solution was obtained for the size distribution of straightmore » chain segments within rouleaux at any point in the evolution of the reaction. The predictions of the theory compare favorably with data collected by D. Kernick, A.W.L. Jay, S. Rowlands, and L. Skibo on the kinetics of rouleaux formation. When rouleaux grow large, they may contain rings or loops and take on the appearance of a network. The importance of including the kinetics of ring closure in the development of realistic models of rouleaux formation was demonstrated.« less

On the applicability of the standard kinetic theory to the study of nanoplasmas

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

D'Angola, A., E-mail: antonio.dangola@unibas.it; Boella, E.; GoLP/Instituto de Plasmas e Fusão Nuclear-Laboratório Associado, Instituto Superior Técnico, Avenida Rovisco Pais 1-1049-001 Lisboa

Kinetic theory applies to systems with a large number of particles, while nanoplasma generated by the interaction of ultra–short laser pulses with atomic clusters are systems composed by a relatively small number (10{sup 2} ÷ 10{sup 4}) of electrons and ions. In the paper, the applicability of the kinetic theory for studying nanoplasmas is discussed. In particular, two typical phenomena are investigated: the collisionless expansion of electrons in a spherical nanoplasma with immobile ions and the formation of shock shells during Coulomb explosions. The analysis, which is carried out comparing ensemble averages obtained by solving the exact equations of motionmore » with reference solutions of the Vlasov-Poisson model, shows that for the dynamics of the electrons the error of the usually employed models is of the order of few percents (but the standard deviation in a single experiment can be of the order of 10%). Instead, special care must be taken in the study of shock formation, as the discrete structure of the electric charge can destroy or strongly modify the phenomenon.« less

A Rationale for System-Dependent Advantages and Disadvantages of Solution Crystal Growth at Low Gravity

NASA Technical Reports Server (NTRS)

Rosenberger, Franz; Vekilov, Peter G.; Lin, Hong; Alexander, J. Iwan D.

1997-01-01

Protein crystallization experiments at reduced gravity have yielded crystals that, depending on the specific material, are either superior or inferior in their structural perfection compared to counterparts grown at normal gravity. A reduction of the crystals' quality due to their growth at low gravity cannot be understood from existing models. Our experimental investigations of the ground-based crystallization of the protein lysozyme have revealed pronounced unsteady growth layer dynamics and associated defect formation under steady external conditions. Through scaling analysis and numerical simulations we show that the observed fluctuations originate from the coupling of bulk transport with non-linear interface kinetics under mixed kinetics-transport control of the growth rate. The amplitude of the fluctuations is smallest when either transport or interfacial kinetics dominate the control of the crystallization process. Thus, depending on the specific system, crystal quality may be improved by either enhancing or suppressing the transport in the solution. These considerations provide, for the first time, a material-dependent rationale for the advantages, as well as the disadvantages, of reduced gravity for (protein) crystallization.

Improvement of Student Understanding of How Kinetic Data Facilitates the Determination of Amino Acid Catalytic Function through an Alkaline Phosphatase Structure/Mechanism Bioinformatics Exercise

ERIC Educational Resources Information Center

Grunwald, Sandra K.; Krueger, Katherine J.

2008-01-01

Laboratory exercises, which utilize alkaline phosphatase as a model enzyme, have been developed and used extensively in undergraduate biochemistry courses to illustrate enzyme steady-state kinetics. A bioinformatics laboratory exercise for the biochemistry laboratory, which complements the traditional alkaline phosphatase kinetics exercise, was…

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

On kinetic modelling for solar redox thermochemical H2O and CO2 splitting over NiFe2O4 for H2, CO and syngas production.

PubMed

Dimitrakis, Dimitrios A; Syrigou, Maria; Lorentzou, Souzana; Kostoglou, Margaritis; Konstandopoulos, Athanasios G

2017-10-11

This study aims at developing a kinetic model that can adequately describe solar thermochemical water and carbon dioxide splitting with nickel ferrite powder as the active redox material. The kinetic parameters of water splitting of a previous study are revised to include transition times and new kinetic parameters for carbon dioxide splitting are developed. The computational results show a satisfactory agreement with experimental data and continuous multicycle operation under varying operating conditions is simulated. Different test cases are explored in order to improve the product yield. At first a parametric analysis is conducted, investigating the appropriate duration of the oxidation and the thermal reduction step that maximizes the hydrogen yield. Subsequently, a non-isothermal oxidation step is simulated and proven as an interesting option for increasing the hydrogen production. The kinetic model is adapted to simulate the production yields in structured solar reactor components, i.e. extruded monolithic structures, as well.

Bovine leukemia virus nucleocapsid protein is an efficient nucleic acid chaperone

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

Qualley, Dominic F., E-mail: dqualley@berry.edu; Sokolove, Victoria L.; Ross, James L.

2015-03-13

Nucleocapsid proteins (NCs) direct the rearrangement of nucleic acids to form the most thermodynamically stable structure, and facilitate many steps throughout the life cycle of retroviruses. NCs bind strongly to nucleic acids (NAs) and promote NA aggregation by virtue of their cationic nature; they also destabilize the NA duplex via highly structured zinc-binding motifs. Thus, they are considered to be NA chaperones. While most retroviral NCs are structurally similar, differences are observed both within and between retroviral genera. In this work, we compare the NA binding and chaperone activity of bovine leukemia virus (BLV) NC to that of two othermore » retroviral NCs: human immunodeficiency virus type 1 (HIV-1) NC, which is structurally similar to BLV NC but from a different retrovirus genus, and human T-cell leukemia virus type 1 (HTLV-1) NC, which possesses several key structural differences from BLV NC but is from the same genus. Our data show that BLV and HIV-1 NCs bind to NAs with stronger affinity in relation to HTLV-1 NC, and that they also accelerate the annealing of complementary stem-loop structures to a greater extent. Analysis of kinetic parameters derived from the annealing data suggests that while all three NCs stimulate annealing by a two-step mechanism as previously reported, the relative contributions of each step to the overall annealing equilibrium are conserved between BLV and HIV-1 NCs but are different for HTLV-1 NC. It is concluded that while BLV and HTLV-1 belong to the same genus of retroviruses, processes that rely on NC may not be directly comparable. - Highlights: • BLV NC binds strongly to DNA and RNA. • BLV NC promotes mini-TAR annealing as well as HIV-1 NC. • Annealing kinetics suggest a low degree of similarity between BLV NC and HTLV-1 NC.« less

Enantioselectively controlled release of chiral drug (metoprolol) using chiral mesoporous silica materials

NASA Astrophysics Data System (ADS)

Guo, Zhen; Du, Yu; Liu, Xianbin; Ng, Siu-Choon; Chen, Yuan; Yang, Yanhui

2010-04-01

Chiral porous materials have attracted burgeoning attention on account of their potential applications in many areas, such as enantioseparation, chiral catalysis, chemical sensors and drug delivery. In this report, chiral mesoporous silica (CMS) materials with various pore sizes and structures were prepared using conventional achiral templates (other than chiral surfactant) and a chiral cobalt complex as co-template. The synthesized CMS materials were characterized by x-ray diffraction, nitrogen physisorption, scanning electron microscope and transmission electron microscope. These CMS materials, as carriers, were demonstrated to be able to control the enantioselective release of a representative chiral drug (metoprolol). The release kinetics, as modeled by the power law equation, suggested that the release profiles of metoprolol were remarkably dependent on the pore diameter and pore structure of CMS materials. More importantly, R- and S-enantiomers of metoprolol exhibited different release kinetics on CMS compared to the corresponding achiral mesoporous silica (ACMS), attributable to the existence of local chirality on the pore wall surface of CMS materials. The chirality of CMS materials on a molecular level was further substantiated by vibrational circular dichroism measurements.

Structure of kinetic Alfvén waves with small transverse scale length

NASA Astrophysics Data System (ADS)

Morales, G. J.; Maggs, J. E.

1997-11-01

This analytical study illustrates the spatial pattern of kinetic Alfvén waves excited by a current-modulating disk whose dimension a, transverse to the confining magnetic field, is comparable to the ion sound gyroradius cs/Ωi, where cs is the sound speed and Ωi the ion cyclotron frequency. The radial structure of the wave azimuthal magnetic field is found to consist of four regions: a Bessel function behavior for r

[Adsorption of perfluorooctanesulfonate (PFOS) onto modified activated carbons].

PubMed

Tong, Xi-Zhen; Shi, Bao-You; Xie, Yue; Wang, Dong-Sheng

2012-09-01

Modified coal and coconut shell based powdered activated carbons (PACs) were prepared by FeCl3 and medium power microwave treatment, respectively. Batch experiments were carried out to evaluate the characteristics of adsorption equilibrium and kinetics of perfluorooctanesulfonate (PFOS) onto original and modified PACs. Based on pore structure and surface functional groups characterization, the adsorption behaviors of modified and original PACs were compared. The competitive adsorption of humic acid (HA) and PFOS on original and modified coconut shell PACs were also investigated. Results showed that both Fe3+ and medium power microwave treatments changed the pore structure and surface functional groups of coal and coconut shell PACs, but the changing effects were different. The adsorption of PFOS on two modified coconut shell-based PACs was significantly improved. While the adsorption of modified coal-based activated carbons declined. The adsorption kinetics of PFOS onto original and modified coconut shell-based activated carbons were the same, and the time of reaching adsorption equilibrium was about 6 hours. In the presence of HA, the adsorption of PFOS by modified PAC was reduced but still higher than that of the original.

Controlling the Sn-C bonds content in SnO2@CNTs composite to form in situ pulverized structure for enhanced electrochemical kinetics.

PubMed

Cheng, Yayi; Huang, Jianfeng; Qi, Hui; Cao, Liyun; Luo, Xiaomin; Li, Jiayin; Xu, Zhanwei; Yang, Jun

2017-12-07

The Sn-C bonding content between the SnO 2 and CNTs interface was controlled by the hydrothermal method and subsequent heat treatment. Electrochemical analysis found that the SnO 2 @CNTs with high Sn-C bonding content exhibited much higher capacity contribution from alloying and conversion reaction compared with the low content of Sn-C bonding even after 200 cycles. The high Sn-C bonding content enabled the SnO 2 nanoparticles to stabilize on the CNTs surface, realizing an in situ pulverization process of SnO 2 . The in situ pulverized structure was beneficial to maintain the close electrochemical contact of the working electrode during the long-term cycling and provide ultrafast transfer paths for lithium ions and electrons, which promoted the alloying and conversion reaction kinetics greatly. Therefore, the SnO 2 @CNTs composite with high Sn-C bonding content displayed highly reversible alloying and conversion reaction. It is believed that the composite could be used as a reference for design chemically bonded metal oxide/carbon composite anode materials in lithium-ion batteries.

Macroporous Silica with Thick Framework for Steam-Stable and High-Performance Poly(ethyleneimine)/Silica CO2 Adsorbent.

PubMed

Min, Kyungmin; Choi, Woosung; Choi, Minkee

2017-06-09

Poly(ethyleneimine) (PEI)/silica has been widely studied as a solid adsorbent for post-combustion CO 2 capture. In this work, a highly macroporous silica (MacS), synthesized by secondary sintering of fumed silica, is compared with various mesoporous silicas with different pore structures as a support for PEI. The silicas with large pore diameter and volume enabled high CO 2 adsorption kinetics and capacity, because pore occlusion by the supported PEI was minimized. The steam stability of the silica structures increased with the silica wall thickness owing to suppressed framework ripening. The silicas with low steam stability showed rapid leaching of PEI, which indicated that the PEI squeezed out of the collapsed silica pores leached more readily. Consequently, MacS that had an extra-large pore volume (1.80 cm 3  g -1 ) and pore diameter (56.0 nm), and a thick wall (>10 nm), showed the most promising CO 2 adsorption kinetics and capacity as well as steam stability. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Group precipitation and age hardening of nanostructured Fe-based alloys with ultra-high strengths

DOE PAGES

Jiao, Z. B.; Luan, J. H.; Miller, M. K.; ...

2016-02-19

The precipitation of nanoparticles plays a key role in determining the properties of many structural materials, and the understanding of their formation and stabilization mechanisms has been a long standing interest in the material field. However, the critical issues involving the group precipitation of various nanoparticles and their cooperative hardening mechanism remain elusive in the newly discovered Fe-based alloys with nanostructures. Here we quantitatively elucidate the nucleation mechanism, evolution kinetics and hardening effects of the group-precipitated nanoparticles in the Fe-Cu-Ni-Al-based alloys by atom probe tomography together with both first-principles and thermodynamic calculations. Our results provide the compelling evidence for twomore » interesting but complex group precipitation pathways of nanoparticles, i.e., the Cu-rich and NiAl-based precipitations. Lastly, the co-existence of the two precipitation pathways plays a key role in age hardening kinetics and ultimately enhances the hardening response, as compared to the single particle type of strengthening, therefore providing an effective new approach for strengthening materials for structural applications.« less

Group precipitation and age hardening of nanostructured Fe-based alloys with ultra-high strengths

PubMed Central

Jiao, Z. B.; Luan, J. H.; Miller, M. K.; Yu, C. Y.; Liu, C. T.

2016-01-01

The precipitation of nanoparticles plays a key role in determining the properties of many structural materials, and the understanding of their formation and stabilization mechanisms has been a long standing interest in the material field. However, the critical issues involving the group precipitation of various nanoparticles and their cooperative hardening mechanism remain elusive in the newly discovered Fe-based alloys with nanostructures. Here we quantitatively elucidate the nucleation mechanism, evolution kinetics and hardening effects of the group-precipitated nanoparticles in the Fe-Cu-Ni-Al-based alloys by atom probe tomography together with both first-principles and thermodynamic calculations. Our results provide the compelling evidence for two interesting but complex group precipitation pathways of nanoparticles, i.e., the Cu-rich and NiAl-based precipitations. The co-existence of the two precipitation pathways plays a key role in age hardening kinetics and ultimately enhances the hardening response, as compared to the single particle type of strengthening, therefore providing an effective new approach for strengthening materials for structural applications. PMID:26892834

Mechanistic investigations of the hydrolysis of amides, oxoesters and thioesters via kinetic isotope effects and positional isotope exchange.

PubMed

Robins, Lori I; Fogle, Emily J; Marlier, John F

2015-11-01

The hydrolysis of amides, oxoesters and thioesters is an important reaction in both organic chemistry and biochemistry. Kinetic isotope effects (KIEs) are one of the most important physical organic methods for determining the most likely transition state structure and rate-determining step of these reaction mechanisms. This method induces a very small change in reaction rates, which, in turn, results in a minimum disturbance of the natural mechanism. KIE studies were carried out on both the non-enzymatic and the enzyme-catalyzed reactions in an effort to compare both types of mechanisms. In these studies the amides and esters of formic acid were chosen because this molecular structure allowed development of methodology to determine heavy-atom solvent (nucleophile) KIEs. This type of isotope effect is difficult to measure, but is rich in mechanistic information. Results of these investigations point to transition states with varying degrees of tetrahedral character that fit a classical stepwise mechanism. This article is part of a special issue entitled: Enzyme Transition States from Theory and Experiment. Copyright © 2014 Elsevier B.V. All rights reserved.

Fundamental properties of Fanaroff-Riley type II radio galaxies investigated via Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Kapińska, A. D.; Uttley, P.; Kaiser, C. R.

2012-08-01

Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large-scale structure. We explore the intrinsic and extrinsic properties of the population of Fanaroff-Riley type II (FR II) objects, i.e. their kinetic luminosities, lifetimes and the central densities of their environments. In particular, the radio and kinetic luminosity functions of these powerful radio sources are investigated using the complete, flux-limited radio catalogues of the Third Cambridge Revised Revised Catalogue (3CRR) and Best et al. We construct multidimensional Monte Carlo simulations using semi-analytical models of FR II source time evolution to create artificial samples of radio galaxies. Unlike previous studies, we compare radio luminosity functions found with both the observed and simulated data to explore the best-fitting fundamental source parameters. The new Monte Carlo method we present here allows us to (i) set better limits on the predicted fundamental parameters of which confidence intervals estimated over broad ranges are presented and (ii) generate the most plausible underlying parent populations of these radio sources. Moreover, as has not been done before, we allow the source physical properties (kinetic luminosities, lifetimes and central densities) to co-evolve with redshift, and we find that all the investigated parameters most likely undergo cosmological evolution. Strikingly, we find that the break in the kinetic luminosity function must undergo redshift evolution of at least (1 + z)3. The fundamental parameters are strongly degenerate, and independent constraints are necessary to draw more precise conclusions. We use the estimated kinetic luminosity functions to set constraints on the duty cycles of these powerful radio sources. A comparison of the duty cycles of powerful FR IIs with those determined from radiative luminosities of active galactic nuclei of comparable black hole mass suggests a transition in behaviour from high to low redshifts, corresponding to either a drop in the typical black hole mass of powerful FR IIs at low redshifts, or a transition to a kinetically dominated, radiatively inefficient FR II population.

Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

Homodimeric archaeal histones and heterodimeric eukaryotic histones share a conserved structure but fold through different kinetic mechanisms, with a correlation between faster folding/association rates and the population of kinetic intermediates. Wild-type hMfB (from Methanothermus fervidus) has no intrinsic fluorophores; Met35, which is Tyr in hyperthermophilic archaeal histones such as hPyA1 (from Pyrococcus strain GB-3A), was mutated to Tyr and Trp. Two Tyr-to-Trp mutants of hPyA1 were also characterized. All fluorophores were introduced into the long, central α-helix of the histone fold. Far-UV circular dichroism (CD) indicated that the fluorophores did not significantly alter the helical content of the histones. The equilibrium unfolding transitions of the histone variants were two-state, reversible processes, with ΔG°(H2O) values within 1 kcal/mol of the wild-type dimers. The hPyA1 Trp variants fold by two-state kinetic mechanisms like wild-type hPyA1, but with increased folding and unfolding rates, suggesting that the mutated residues (Tyr-32 and Tyr-36) contribute to transition state structure. Like wild-type hMfB, M35Y and M35W hMfB fold by a three-state mechanism, with a stopped-flow CD burst-phase monomeric intermediate. The M35 mutants populate monomeric intermediates with increased secondary structure and stability but exhibit decreased folding rates; this suggests that nonnative interactions occur from burial of the hydrophobic Tyr and Trp residues in this kinetic intermediate. These results implicate the long central helix as a key component of the structure in the kinetic monomeric intermediates of hMfB as well as the dimerization transition state in the folding of hPyA1. PMID:18096639

Similarities in Photodegradation of Cyanobacteria-Derived and Marine Fluorescent Dissolved Organic Matter

NASA Astrophysics Data System (ADS)

Ianiri, H. L.; Timko, S.; Gonsior, M.

2016-02-01

Marine dissolved organic matter (DOM) is one of the largest reduced carbon reservoirs on Earth, yet we only have a limited understanding of its production, cycling, degradation, and overall structure. It was previously believed that a significant portion of refractory dissolved organic carbon (RDOC) in the ocean was derived from terrestrial sources, however recent studies indicated that the majority of marine DOM might be produced in situ by marine biota. Previous research has found that terrestrial and microbial DOM fluorescent signatures are similar, complicating the identification of the origins of marine fluorescent DOM (FDOM). However, photodegradation kinetics of terrestrial and microbial-derived DOM are expected to be different due to their assumed different chemical compositions. In this study we analyzed for the first time the photodegradation kinetics of microbial-derived DOM originating from different cyanobacteria strains. Cyanobacterial-derived DOM were exposed to simulated sunlight for a total of 20 hours while recording excitation emission matrix (EEM) fluorescence every twenty minutes to observe the photodegradation of this specific FDOM. Parallel Factor Analysis (PARAFAC) was applied to deconvolute the EEM matrices into six separate components. The photodegradation kinetics was then calculated for each component and compared with previously obtained photodegradation data of marine and terrestrial FDOM. This six component PARAFAC model was similar to those generated from open ocean data and global DOM data sets. The "humic-like" FDOM was also found in cyanobacteria FDOM and showed similar fluorescence intensities and percent fluorescence loss when compared to marine DOM. The degradation kinetics of the "humic-like" component of microbial-derived DOM was faster than that of terrestrial-derived DOM, and marine FDOM samples showed degradation kinetics more similar to microbial-derived FDOM. This indicates marine FDOM is more similar in chemical composition to microbial-derived FDOM than terrestrial-derived FDOM, supporting the hypothesis that the majority of marine FDOM is produced in situ.

Influence of the partial volume correction method on 18F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM

PubMed Central

Bowen, Spencer L.; Byars, Larry G.; Michel, Christian J.; Chonde, Daniel B.; Catana, Ciprian

2014-01-01

Kinetic parameters estimated from dynamic 18F-fluorodeoxyglucose PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For OSEM, image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting 18F-fluorodeoxyglucose dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation GTM PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in CMRGlc estimates, although by less than 5% in most cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters. PMID:24052021

Toxicokinetics of perfluorooctane sulfonate in rabbits under environmentally realistic exposure conditions and comparative assessment between mammals and birds.

PubMed

Tarazona, J V; Rodríguez, C; Alonso, E; Sáez, M; González, F; San Andrés, M D; Jiménez, B; San Andrés, M I

2016-01-22

This article describes the toxicokinetics of perfluorooctane sulfonate (PFOS) in rabbits under low repeated dosing, equivalent to 0.085μg/kg per day, and the observed differences between rabbits and chickens. The best fitting for both species was provided by a simple pseudo monocompartmental first-order kinetics model, regulated by two rates, and accounting for real elimination as well as binding of PFOS to non-exchangeable structures. Elimination was more rapid in rabbits, with a pseudo first-order dissipation half-life of 88 days compared to the 230 days observed for chickens. By contrast, the calculated assimilation efficiency for rabbits was almost 1, very close to full absorption, significantly higher than the 0.66 with confidence intervals of 0.64 and 0.68 observed for chickens. The results confirm a very different kinetics than that observed in single-dose experiments confirming clear dose-related differences in apparent elimination rates in rabbits, as previously described for humans and other mammals; suggesting the role of a capacity-limited saturable process resulting in different kinetic behaviours for PFOS in high dose versus environmentally relevant low dose exposure conditions. The model calculations confirmed that the measured maximum concentrations were still far from the steady state situation, and that the different kinetics between birds and mammals should may play a significant role in the biomagnifications assessment and potential exposure for humans and predators. For the same dose regime, the steady state concentration was estimated at about 36μg PFOS/L serum for rabbits, slightly above one-half of the 65μg PFOS/L serum estimated for chickens. The toxicokinetic parameters presented here can be used for higher-tier bioaccumulation estimations of PFOS in rabbits and chickens as starting point for human health exposure assessments and as surrogate values for modeling PFOS kinetics in wild mammals and bird in exposure assessment of predatory species. Published by Elsevier Ireland Ltd.

Flocculation kinetics and aggregate structure of kaolinite mixtures in laminar tube flow.

PubMed

Vaezi G, Farid; Sanders, R Sean; Masliyah, Jacob H

2011-03-01

Flocculation is commonly used in various solid-liquid separation processes in chemical and mineral industries to separate desired products or to treat waste streams. This paper presents an experimental technique to study flocculation processes in laminar tube flow. This approach allows for more realistic estimation of the shear rate to which an aggregate is exposed, as compared to more complicated shear fields (e.g. stirred tanks). A direct sampling method is used to minimize the effect of sampling on the aggregate structure. A combination of aggregate settling velocity and image analysis was used to quantify the structure of the aggregate. Aggregate size, density, and fractal dimension were found to be the most important aggregate structural parameters. The two methods used to determine aggregate fractal dimension were in good agreement. The effects of advective flow through an aggregate's porous structure and transition-regime drag coefficient on the evaluation of aggregate density were considered. The technique was applied to investigate the flocculation kinetics and the evolution of the aggregate structure of kaolin particles with an anionic flocculant under conditions similar to those of oil sands fine tailings. Aggregates were formed using a well controlled two-stage aggregation process. Detailed statistical analysis was performed to investigate the establishment of dynamic equilibrium condition in terms of aggregate size and density evolution. An equilibrium steady state condition was obtained within 90 s of the start of flocculation; after which no further change in aggregate structure was observed. Although longer flocculation times inside the shear field could conceivably cause aggregate structure conformation, statistical analysis indicated that this did not occur for the studied conditions. The results show that the technique and experimental conditions employed here produce aggregates having a well-defined, reproducible structure. Copyright © 2011. Published by Elsevier Inc.

Effect of Homogenizing Heat Treatment of Liquid Aluminum-Copper Alloys on the Structure of Rapidly Crystallized Specimens

NASA Astrophysics Data System (ADS)

Astaf'ev, V. V.; Kurochkin, A. R.; Yablonskikh, T. I.; Brodova, I. G.; Popel', P. S.

2017-11-01

Centrifugal casting into a massive slot chill mold was used to prepare two series of specimens of alloys of the Al - Cu system, containing from 10 to 32.2 at.% Cu. The first series was fabricated without a homogenizing heat treatment of the melt, while the second series was fabricated with heating of the melt to 1400°C. Both kinds of specimens were cast at the same temperature in order to provide for the same cooling rate of about 104 K/sec. The structures, phase compositions and microhardnesses of the structural components are compared. It is established that the homogenizing heat treatment changes the kinetics of crystallization and, hence, the proportion of phases in the alloy structure and the copper content in them.

Theoretical and Experimental Approaches towards study of Methane Occupation Dynamics within Gas Hydrates

NASA Astrophysics Data System (ADS)

Mendonca, P.; Shemella, P.; Nayak, S.; Sharma, A.

2006-12-01

Hydrate structures of hydrocarbon (commonly methane hydrates) within the continental shelf regions are considered a huge energy resource since they are a significant reservoir for terrestrial carbon. Any changes, abrupt or continual, will have an impact on the carbon (as well as water) cycle. However, tapping into this reservoir for energy resource has been challenging from both technical and scientific fronts primarily because any rapid release of methane (CH4) will likely have serious impact on the global climate of Earth as well as the stability of the continental shelf. While fossil fuel combustion derived CO2 in the atmosphere is considered a major contributor to global warming, the massive amounts of methane release from the gas hydrates has been a point of debate for its impact on the global climate. Due to the lack of a clear physical mechanism for such structural destabilization, environmental changes within the ocean setting (viz. temperature, salinity or biology) are typically assigned as possible causes. A good kinetic model that ties into structural instability of these essentially non-stoichiometric compounds at both the macromolecular (thermodynamic) and nanometric scale is essential. Preliminary experiments on single crystal methane hydrate high pressure phase (~1.0GPa) indicate a measurable kinetics of methane diffusion upon bringing structural disorder to the single crystal. Although there have been several kinetic studies of gas-hydrate nucleation and dissociation, systematic study of kinetics (and dynamics) of diffusion based changes within the gas hydrates has been lacking. In addition to experimental data on single crystal methane hydrates, we will present a first principle study on the structure, energetic, and dynamics of sI phase methane hydrate. We use density functional theory to study the energetic effect of the occupancy of neighboring cages in a cluster model system consisting of two sI gas hydrates. In this situation there can be two, one, or no methane, and we find that the binding for the first methane is exothermic. The second methane binding is endothermic, suggesting that the stability of a methane molecule is determined by the occupancy of adjacent cages. Using these results, we will present the calculated binding energies of a periodic system based on crystal structure data and compare them to the cluster method. This combined experimental and theoretical investigation is aimed at generating fundamental dataset that can be tested for the broader impact of such processes on the global carbon cycle.

Design, synthesis, kinetic mechanism and molecular docking studies of novel 1-pentanoyl-3-arylthioureas as inhibitors of mushroom tyrosinase and free radical scavengers.

PubMed

Larik, Fayaz Ali; Saeed, Aamer; Channar, Pervaiz Ali; Muqadar, Urooj; Abbas, Qamar; Hassan, Mubashir; Seo, Sung-Yum; Bolte, Michael

2017-12-01

A series of novel 1-pentanoyl-3-arylthioureas was designed as new mushroom tyrosinase inhibitors and free radical scavengers. The title compounds were obtained in excellent yield and characterized by FTIR, 1 H NMR, 13 C NMR and X-ray crystallography in case of compound (4a). The inhibitory effects on mushroom tyrosinase and DPPH were evaluated and it was observed that 1-Pentanoyl-3-(4-methoxyphenyl) thiourea (4f) showed tyrosinase inhibitory activity (IC 50 1.568 ± 0.01 mM) comparable to Kojic acid (IC 50 16.051 ± 1.27 mM). Interestingly compound 4f exhibited higher antioxidant potential compared to other derivatives. The docking studies of synthesized 1-Pentanoyl-3-arylthioureas analogues were also carried out against tyrosinase protein (PDBID 2ZMX) to compare the binding affinities with IC 50 values. The predicted binding affinities are in good agreement with the IC 50 values as compound (4f) showed highest binding affinity (-7.50 kcal/mol) compared to others derivatives. The kinetic mechanism analyzed by Line-weavere Burk plots exhibited that compound (4f) inhibit the enzyme inhibits the tyrosinase non-competitively to form an enzyme inhibitor complex. The inhibition constants Ki calculated from Dixon plots for compound (4f) is 1.10 μM. It was also found from kinetic analysis that derivative 4f irreversible enzyme inhibitor complex. It is proposed on the basis of our investigation that title compound (4f) may serve as lead structure for the design of more potent tyrosinase inhibitors. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): Spectral tuning and light-activated kinetics.

PubMed

van Hazel, Ilke; Dungan, Sarah Z; Hauser, Frances E; Morrow, James M; Endler, John A; Chang, Belinda S W

2016-07-01

Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates. © 2016 The Protein Society.

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

NASA Astrophysics Data System (ADS)

Lockard, Tom E.

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

Pressure-induced kinetics of the α to ω transition in zirconium

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

Jacobsen, M. K.; Velisavljevic, N., E-mail: nenad@lanl.gov; Sinogeikin, S. V.

Diamond anvil cells (DAC) coupled with x-ray diffraction (XRD) measurements are one of the primary techniques for investigating structural stability of materials at high pressure-temperature (P-T) conditions. DAC-XRD has been predominantly used to resolve structural information at set P-T conditions and, consequently, provides P-T phase diagram information on a broad range of materials. With advances in large scale synchrotron x-ray facilities and corresponding x-ray diagnostic capabilities, it is now becoming possible to perform sub-second time resolved measurements on micron sized DAC samples. As a result, there is an opportunity to gain valuable information about the kinetics of structural phase transformationsmore » and extend our understanding of material behavior at high P-T conditions. Using DAC-XRD time resolved measurements, we have investigated the kinetics of the α to ω transformation in zirconium. We observe a clear time and pressure dependence in the martensitic α-ω transition as a function of pressure-jump, i.e., drive pressure. The resulting data are fit using available kinetics models, which can provide further insight into transformation mechanism that influence transformation kinetics. Our results help shed light on the discrepancies observed in previous measurements of the α-ω transition pressure in zirconium.« less

Fully kinetic simulations of collisionless, mesothermal plasma emission: Macroscopic plume structure and microscopic electron characteristics

NASA Astrophysics Data System (ADS)

Hu, Yuan; Wang, Joseph

2017-03-01

This paper presents a fully kinetic particle particle-in-cell simulation study on the emission of a collisionless plasma plume consisting of cold beam ions and thermal electrons. Results are presented for both the two-dimensional macroscopic plume structure and the microscopic electron kinetic characteristics. We find that the macroscopic plume structure exhibits several distinctive regions, including an undisturbed core region, an electron cooling expansion region, and an electron isothermal expansion region. The properties of each region are determined by microscopic electron kinetic characteristics. The division between the undisturbed region and the cooling expansion region approximately matches the Mach line generated at the edge of the emission surface, and that between the cooling expansion region and the isothermal expansion region approximately matches the potential well established in the beam. The interactions between electrons and the potential well lead to a new, near-equilibrium state different from the initial distribution for the electrons in the isothermal expansion region. The electron kinetic characteristics in the plume are also very anisotropic. As the electron expansion process is mostly non-equilibrium and anisotropic, the commonly used assumption that the electrons in a collisionless, mesothermal plasma plume may be treated as a single equilibrium fluid in general is not valid.

Pressure-induced kinetics of the α to ω transition in zirconium

DOE PAGES

Jacobsen, M. K.; Velisavljevic, N.; Sinogeikin, S. V.

2015-07-13

Diamond anvil cells (DAC) coupled with x-ray diffraction (XRD) measurements are one of the primary techniques for investigating structural stability of materials at high pressure-temperature (P-T) conditions. DAC-XRD has been predominantly used to resolve structural information at set P-T conditions and, consequently, provides P-T phase diagram information on a broad range of materials. With advances in large scale synchrotron x-ray facilities and corresponding x-ray diagnostic capabilities, it is now becoming possible to perform sub-second time resolved measurements on micron sized DAC samples. As a result, there is an opportunity to gain valuable information about the kinetics of structural phase transformationsmore » and extend our understanding of material behavior at high P-T conditions. Using DAC-XRD time resolved measurements, we have investigated the kinetics of the α to ω transformation in zirconium. We observe a clear time and pressure dependence in the martensitic α-ω transition as a function of pressure-jump, i.e., drive pressure. The resulting data are fit using available kinetics models, which can provide further insight into transformation mechanism that influence transformation kinetics. Our results help shed light on the discrepancies observed in previous measurements of the α-ω transition pressure in zirconium.« less

Guanidine hydrochloride-induced alkali molten globule model of horse ferrocytochrome c.

PubMed

Jain, Rishu; Kaur, Sandeep; Kumar, Rajesh

2013-02-01

This article compares structural, kinetic and thermodynamic properties of previously unknown guanidine hydrochloride (GdnHCl)-induced alkali molten globule (MG) state of horse 'ferrocytochrome c' (ferrocyt c) with the known NaCl-induced alkali-MG state of ferrocyt c. It is well known that Cl(-) arising from GdnHCl refolds and stabilizes the acid-denatured protein to MG state. We demonstrate that the GdnH(+) arising from GdnHCl (≤0.2 M) also transforms the base-denatured CO-liganded ferrocyt c (carbonmonoxycyt c) to MG state by making the electrostatic interactions to the negative charges of the protein. Structural and molecular properties extracted from the basic spectroscopic (circular dichroism (CD), fluorescence, FTIR and NMR) experiments suggest that the GdnH(+)- and Na(+)-induced MG states of base-denatured carbonmonoxycyt c are molecular compact states containing native-like secondary structures and disordered tertiary structures. Kinetic experiments involving the measurement of the CO association to the alkaline ferrocyt c in the presence of different GdnHCl and NaCl concentrations indicate that the Na(+)-induced MG state is more constrained relative to that of GdnH(+)-induced MG state. Analyses of thermal (near UV-CD) denaturation curves of the base-denatured protein in the presence of different GdnHCl and NaCl concentration also indicate that the Na(+)-induced MG state is thermally more stable than the GdnH(+)-induced MG state.

Approximate models for the ion-kinetic regime in inertial-confinement-fusion capsule implosions

DOE PAGES

Hoffman, Nelson M.; Zimmerman, George B.; Molvig, Kim; ...

2015-05-19

“Reduced” (i.e., simplified or approximate) ion-kinetic (RIK) models in radiation-hydrodynamic simulations permit a useful description of inertial-confinement-fusion (ICF) implosions where kinetic deviations from hydrodynamic behavior are important. For implosions in or near the kinetic regime (i.e., when ion mean free paths are comparable to the capsule size), simulations using a RIK model give a detailed picture of the time- and space-dependent structure of imploding capsules, allow an assessment of the relative importance of various kinetic processes during the implosion, enable explanations of past and current observations, and permit predictions of the results of future experiments. The RIK simulation method describedmore » here uses moment-based reduced kinetic models for transport of mass, momentum, and energy by long-mean-free-path ions, a model for the decrease of fusion reactivity owing to the associated modification of the ion distribution function, and a model of hydrodynamic turbulent mixing. Transport models are based on local gradient-diffusion approximations for the transport of moments of the ion distribution functions, with coefficients to impose flux limiting or account for transport modification. After calibration against a reference set of ICF implosions spanning the hydrodynamic-to-kinetic transition, the method has useful, quantifiable predictive ability over a broad range of capsule parameter space. Calibrated RIK simulations show that an important contributor to ion species separation in ICF capsule implosions is the preferential flux of longer-mean-free-path species out of the fuel and into the shell, leaving the fuel relatively enriched in species with shorter mean free paths. Also, the transport of ion thermal energy is enhanced in the kinetic regime, causing the fuel region to have a more uniform, lower ion temperature, extending over a larger volume, than implied by clean simulations. Furthermore, we expect that the success of our simple approach will motivate continued theoretical research into the development of first-principles-based, comprehensive, self-consistent, yet useable models of kinetic multispecies ion behavior in ICF plasmas.« less

Kinetics of corrosion inhibition of aluminum in acidic media by water-soluble natural polymeric chondroitin-4-sulfate as anionic polyelectrolyte inhibitor.

PubMed

Hassan, Refat M; Ibrahim, Samia M; Takagi, Hideo D; Sayed, Suzan A

2018-07-15

Corrosion inhibition of aluminum (Al) in hydrochloric acid by anionic polyelectrolyte chondroitin-4-sulfate (CS) polysaccharide has been studied using both gasometrical and weight-loss techniques. The results drawn from these two techniques are comparable and exhibit negligible differences. The inhibition efficiency was found to increase with increasing the inhibitor concentration and decreased with increasing temperature. The inhibition action of CS on Al metal surface was found to obey both of Langmuir and Freundlich isotherms. The factors affecting the corrosion rates such as the concentration and geometrical structure of the inhibitor, concentration of the corrosive medium, and the temperature were examined. The kinetic parameters were evaluated and a suitable corrosion mechanism consistent with the results obtained is discussed. Copyright © 2018. Published by Elsevier Ltd.

Predicting mesoscale microstructural evolution in electron beam welding

DOE PAGES

Rodgers, Theron M.; Madison, Jonathan D.; Tikare, Veena; ...

2016-03-16

Using the kinetic Monte Carlo simulator, Stochastic Parallel PARticle Kinetic Simulator, from Sandia National Laboratories, a user routine has been developed to simulate mesoscale predictions of a grain structure near a moving heat source. Here, we demonstrate the use of this user routine to produce voxelized, synthetic, three-dimensional microstructures for electron-beam welding by comparing them with experimentally produced microstructures. When simulation input parameters are matched to experimental process parameters, qualitative and quantitative agreement for both grain size and grain morphology are achieved. The method is capable of simulating both single- and multipass welds. As a result, the simulations provide anmore » opportunity for not only accelerated design but also the integration of simulation and experiments in design such that simulations can receive parameter bounds from experiments and, in turn, provide predictions of a resultant microstructure.« less

Coherent Rayleigh-Brillouin scattering measurements of bulk viscosity of polar and nonpolar gases, and kinetic theory.

PubMed

Meijer, A S; de Wijn, A S; Peters, M F E; Dam, N J; van de Water, W

2010-10-28

We investigate coherent Rayleigh-Brillouin spectroscopy as an efficient process to measure the bulk viscosity of gases at gigahertz frequencies. Scattered spectral distributions are measured using a Fizeau spectrometer. We discuss the statistical error due to the fluctuating mode structure of the used pump laser. Experiments were done for both polar and nonpolar gases and the bulk viscosity was obtained from the spectra using the Tenti S6 model. Results are compared to simple classical kinetic models of molecules with internal degrees of freedom. At the extremely high (gigahertz) frequencies of our experiment, most internal vibrational modes remain frozen and the bulk viscosity is dominated by the rotational degrees of freedom. Our measurements show that the molecular dipole moments have unexpectedly little influence on the bulk viscosity at room temperature and moderate pressure.

Shock wave structure in rarefied polyatomic gases with large relaxation time for the dynamic pressure

NASA Astrophysics Data System (ADS)

Taniguchi, Shigeru; Arima, Takashi; Ruggeri, Tommaso; Sugiyama, Masaru

2018-05-01

The shock wave structure in rarefied polyatomic gases is analyzed based on extended thermodynamics (ET). In particular, the case with large relaxation time for the dynamic pressure, which corresponds to large bulk viscosity, is considered by adopting the simplest version of extended thermodynamics with only 6 independent fields (ET6); the mass density, the velocity, the temperature and the dynamic pressure. Recently, the validity of the theoretical predictions by ET was confirmed by the numerical analysis based on the kinetic theory in [S Kosuge and K Aoki: Phys. Rev. Fluids, Vol. 3, 023401 (2018)]. It was shown that numerical results using the polyatomic version of ellipsoidal statistical model agree with the theoretical predictions by ET for small or moderately large Mach numbers. In the present paper, first, we compare the theoretical predictions by ET6 with the ones by kinetic theory for large Mach number under the same assumptions, that is, the gas is polytropic and the bulk viscosity is proportional to the temperature. Second, the shock wave structure for large Mach number in a non-polytropic gas is analyzed with the particular interest in the effect of the temperature dependence of specific heat and the bulk viscosity on the shock wave structure. Through the analysis of the case of a rarefied carbon dioxide (CO2) gas, it is shown that these temperature dependences play important roles in the precise analysis of the structure for strong shock waves.

Voltage gating by molecular subunits of Na+ and K+ ion channels: higher-dimensional cubic kinetics, rate constants, and temperature.

PubMed

Fohlmeister, Jürgen F

2015-06-01

The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m(3) → m(4)). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. Copyright © 2015 the American Physiological Society.

Generalized hydrodynamic reductions of the kinetic equation for a soliton gas

NASA Astrophysics Data System (ADS)

Pavlov, M. V.; Taranov, V. B.; El, G. A.

2012-05-01

We derive generalized multiflow hydrodynamic reductions of the nonlocal kinetic equation for a soliton gas and investigate their structure. These reductions not only provide further insight into the properties of the new kinetic equation but also could prove to be representatives of a novel class of integrable systems of hydrodynamic type beyond the conventional semi-Hamiltonian framework.

Kinetic Control of Aqueous Hydrolysis: Modulating Structure/Property Relationships in Inorganic Crystals

NASA Astrophysics Data System (ADS)

Neilson, James R.

2011-12-01

A grand challenge in materials science and chemistry revolves around the preparation of materials with desired properties by controlling structure on multiple length scales. Biology approaches this challenge by evolving tactics to transform soluble precursors into materials and composites with macro-scale and atomic precision. Studies of biomineralization in siliceous sponges led to the discovery of slow, catalytic hydrolysis of molecular precursors in the biogenesis of silica skeletal elements with well defined micro- and nano-scale architectures. However, the role of aqueous hydrolysis in the limit of kinetic control is not well understood; this allows us to form a central hypothesis: that the kinetics of hydrolysis modulate the structures of materials and their properties. As a model system, the diffusion of a simple hydrolytic catalyst (such as ammonia) across an air-water interface into a metal salt solution reproduces some aspects of the chemistry found in biomineralization, namely kinetic and vectorial control. Variation of the catalyst concentration modulates the hydrolysis rate, and thus alters the resulting structure of the inorganic crystals. Using aqueous solutions of cobalt(II) chloride, each product (cobalt hydroxide chloride) forms with a unique composition, despite being prepared from identical mother liquors. Synchrotron X-ray total scattering methods are needed to locate the atomic positions in the material, which are not aptly described by a traditional crystallographic unit cell due to structural disorder. Detailed definition of the structure confirms that the hydrolysis conditions systematically modulate the arrangement of atoms in the lattice. This tightly coupled control of crystal formation and knowledge of local and average structures of these materials provides insight into the unusual magnetic properties of these cobalt hydroxides. The compounds studied show significant and open magnetization loops with little variation with composition or structure, yet subtle and systematic changes in the mean-field spin interaction strength and spin entropy loss. Meanwhile, neutron powder diffraction reveals a fully compensated Ńeel state; a detailed analysis of the local structure defines the aperiodic clusters of polyhedra responsible for magnetic order. The rate of hydrolysis of metal precursors modulates the disposition of these polyhedral clusters. The strategy of kinetically controlling aqueous hydrolysis also extends to the formation of stoichiometrically ordered bimetallic crystals [MSn(OH)6], where the hydrolysis behavior for dissimilar metal cations must be controlled via counteranions or precursor selection. In the formation of these ordered double perovskite hydroxides, the rate of hydrolysis is held constant in the limit of kinetic control. Instead, the propensities of different cations to undergo controlled hydrolysis are probed by their ability to form ordered crystals. Collectively, these studies demonstrate how systematic variation in the kinetic conditions of materials preparation and the character of each solute control the structure and properties of materials, with a precision not attainable through traditional or near-equilibrium approaches.

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

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

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

Time-resolved spectroscopy of dye-labeled photoactive yellow protein suggests a pathway of light-induced structural changes in the N-terminal cap.

PubMed

Hoersch, Daniel; Otto, Harald; Cusanovich, Michael A; Heyn, Maarten P

2009-07-14

The photoreceptor PYP responds to light activation with global conformational changes. These changes are mainly located in the N-terminal cap of the protein, which is approximately 20 A away from the chromophore binding pocket and separated from it by the central beta-sheet. The question of the propagation of the structural change across the central beta-sheet is of general interest for the superfamily of PAS domain proteins, for which PYP is the structural prototype. Here we measured the kinetics of the structural changes in the N-terminal cap by transient absorption spectroscopy on the ns to second timescale. For this purpose the cysteine mutants A5C and N13C were prepared and labeled with thiol reactive 5-iodoacetamidofluorescein (IAF). A5 is located close to the N-terminus, while N13 is part of helix alpha1 near the functionally important salt bridge E12-K110 between the N-terminal cap and the central anti-parallel beta-sheet. The absorption spectrum of the dye is sensitive to its environment, and serves as a sensor for conformational changes near the labeling site. In both labeled mutants light activation results in a transient red-shift of the fluorescein absorption spectrum. To correlate the conformational changes with the photocycle intermediates of the protein, we compared the kinetics of the transient absorption signal of the dye with that of the p-hydroxycinnamoyl chromophore. While the structural change near A5 is synchronized with the rise of the I(2) intermediate, which is formed in approximately 200 mus, the change near N13 is delayed and rises with the next intermediate I(2)', which forms in approximately 2 ms. This indicates that different parts of the N-terminal cap respond to light activation with different kinetics. For the signaling pathway of photoactive yellow protein we propose a model in which the structural signal propagates from the chromophore binding pocket across the central beta-sheet via the N-terminal region to helix alpha1, resulting in a large change in the protein conformation.

Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues

PubMed Central

Perišić, Ognjen

2018-01-01

Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM. The algorithm adjusts the number of fast modes in the GNM’s weighted sum calculation using the ratio of predicted and expected numbers of target residues (contact and the neighboring first-layer residues). This approach produces very good results when applied to dimers with high protein sequence length ratios. The protocol’s ability to recognize near native decoys was compared to the ability of the residue-level statistical potential of Lu and Skolnick using the Sternberg and Vakser decoy dimers sets. The statistical potential produced better overall results, but in a number of cases its predicting ability was comparable, or even inferior, to the prediction ability of the adjustable GNM approach. The results presented in this paper suggest that in heterodimers at least one protein has interacting scaffold determined by the immovable, kinetically hot residues. In many cases, interacting proteins (especially if being of noticeably different sizes) either behave as a rigid lock and key or, presumably, exhibit the opposite dynamic behavior. While the binding surface of one protein is rigid and stable, its partner’s interacting scaffold is more flexible and adaptable. PMID:29547506

Comparative analysis of human gait while wearing thong-style flip-flops versus sneakers.

PubMed

Shroyer, Justin F; Weimar, Wendi H

2010-01-01

Flip-flops are becoming a common footwear option. Casual observation has indicated that individuals wear flip-flops beyond their structural limit and have a different gait while wearing flip-flops versus shoes. This alteration in gait may cause the anecdotal foot and lower-limb discomfort associated with wearing flip-flops. To investigate the effect of sneakers versus thong-style flip-flops on gait kinematics and kinetics, 56 individuals (37 women and 19 men) were randomly assigned to a footwear order (flip-flops or sneakers first) and were asked to wear the assigned footwear on the day before and the day of testing. On each testing day, participants were videotaped as they walked at a self-selected pace across a force platform. A 2 (sex) x 2 (footwear) repeated-measures analysis of variance (P = .05) was used for statistical analysis. Significant interaction effects of footwear and sex were found for maximal anterior force, attack angle, and ankle angle during the swing phase. Footwear significantly affected stride length, ankle angle at the beginning of double support and during the swing phase, maximal braking impulse, and stance time. Flip-flops resulted in a shorter stride, a larger ankle angle at the beginning of double support and during the swing phase, a smaller braking impulse, and a shorter stance time compared with sneakers. The effects of footwear on gait kinetics and kinematics is extensive, but there is limited research on the effect of thong-style flip-flops on gait. These results suggest that flip-flops have an effect on several kinetic and kinematic variables compared with sneakers.

Rippled Quasiperpendicular Shock Observed by the Magnetospheric Multiscale Spacecraft.

PubMed

Johlander, A; Schwartz, S J; Vaivads, A; Khotyaintsev, Yu V; Gingell, I; Peng, I B; Markidis, S; Lindqvist, P-A; Ergun, R E; Marklund, G T; Plaschke, F; Magnes, W; Strangeway, R J; Russell, C T; Wei, H; Torbert, R B; Paterson, W R; Gershman, D J; Dorelli, J C; Avanov, L A; Lavraud, B; Saito, Y; Giles, B L; Pollock, C J; Burch, J L

2016-10-14

Collisionless shock nonstationarity arising from microscale physics influences shock structure and particle acceleration mechanisms. Nonstationarity has been difficult to quantify due to the small spatial and temporal scales. We use the closely spaced (subgyroscale), high-time-resolution measurements from one rapid crossing of Earth's quasiperpendicular bow shock by the Magnetospheric Multiscale (MMS) spacecraft to compare competing nonstationarity processes. Using MMS's high-cadence kinetic plasma measurements, we show that the shock exhibits nonstationarity in the form of ripples.

Rippled Quasiperpendicular Shock Observed by the Magnetospheric Multiscale Spacecraft

NASA Technical Reports Server (NTRS)

Johlander, A.; Schwartz, S. J.; Vaivads, A.; Khotyaintsev, Yu. V.; Gingell, I.; Peng, I. B.; Markidis, S.; Lindqvist, P.-A.; Ergun, R. E.; Marklund, G. T.;

Macroscopic aspects of interfacial reactions

NASA Technical Reports Server (NTRS)

Heckel, R. W.

1976-01-01

The extent of interdiffusion and formation of new phases is determined by the constitution diagram of the alloy system, the interdiffusion coefficients of the phases present, and the thermal conditions (temperature and time) associated with the bonding process and/or subsequent use of the bonded structure. In many instance, the kinetics of interdiffusion and phase formation can be predicted from known parameters using numerical methods and computer techniques. Predictions are compared with experimentally determined parameters for a variety of metallurgical alloy systems.

Structural Diversity in the Dandelion (Taraxacum officinale) Polyphenol Oxidase Family Results in Different Responses to Model Substrates

PubMed Central

Dirks-Hofmeister, Mareike E.; Singh, Ratna; Leufken, Christine M.; Inlow, Jennifer K.; Moerschbacher, Bruno M.

2014-01-01

Polyphenol oxidases (PPOs) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure–function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1) potentially acts as a “selector” for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates. PMID:24918587

Crustacean derived calcium phosphate systems: Application in defluoridation of drinking water in East African rift valley.

PubMed

Wagutu, Agatha W; Machunda, Revocatus; Jande, Yusufu Abeid Chande

2018-04-05

Calcium phosphate adsorbents, derived from prawns and crabs shell biomass wastes have been developed using wet chemistry and low temperature treatment. The adsorbents were characterized by X-ray diffractometry and Fourier transform infrared spectroscopy. Batch adsorption test were carried out to investigate their effectiveness in adsorption of fluoride from ground and surface waters. Adsorption capacities were compared with bone char and synthetic hydroxyapatite (CCHA). Results indicate that prawns derived adsorbent (PHA) formed hexagonal structure with phases identifiable with hydroxyapatite while crabs based adsorbent (CHA) formed predominantly monoclinic structure with crystalline phase characteristic of brushite. Vibrational analysis and kinetic studies predicted defluoridation occurred mainly by ion exchange and ion adsorption mechanisms. Defluoridation capacity of the adsorbents was found to be superior compared to bone char and CCHA. CHA was the most effective with efficiencies above 92% and highest capacity of 13.6 mg/g in field water with fluoride concentration of 5-70 mg/L. PHA had highest capacity of 8.5 mg/g which was still better than 2.6 mg/g recorded by CCHA and bone char. Adsorption was best described by pseudo 2nd order kinetics. The findings indicate that crustacean derived calcium phosphate systems have better potential for defluoridation than traditional bone char and synthetic systems. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Small Angle Neutron Scattering Study in Multi-Component Polymer Systems: Spinodal Decomposition and Beyond

NASA Astrophysics Data System (ADS)

Han, Charles

Institute for Advanced Study, Shenzhen University, Shenzhen, China In memory of Professor John Kohn at this symposium, a time resolved SANS study for the early stage of spinodal decomposition kinetics of deuterated polycarbonate/poly(methylmethacrylate) blend will be reviewed which gives a clear proof of the Cahn-Hillard-Cook theory. This early stage of spinodal decomposition kinetics has been observed starting from the dimension (q-l) comparable to the single chain radius of gyration, Rg\\ , for a binary polymer mixture. The results provide an unequivocal quantitative measure of the virtual structure factor, S (q, ∞); the relationship of qm and qc through rate of growth, Cahn-plot analysis, and singularity in S (q, ∞); the growth of fluctuation of qRg <1 and intra-chain relaxation of qRg >1. More recent study of using mixed suspensions of polystyrene microspheres and poly(N-isopropylacrylamide) microgels as a molecular model system which has a long range repulsive interaction potential and a short range attractive potential, will also be discussed. In this model system, dynamic gelation, transition to soft glass state and cross-over to hard glass state will be demonstrated and compared with available theories for glass transition in structural materials. Acknowledgements go to: Polymers Division, and NCNR of NIST, and to ICCAS, Beijing, China. Also to my colleagues: M. Motowoka, H. Jinnai, T. Hashimoto, G.C. Yuan and H. Cheng.

Phase Transition in Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under Static Compression: An Application of the First-Principles Method Specialized for CHNO Solid Explosives.

PubMed

Zhang, Lei; Jiang, Sheng-Li; Yu, Yi; Long, Yao; Zhao, Han-Yue; Peng, Li-Juan; Chen, Jun

2016-11-10

The first-principles method is challenged by accurate prediction of van der Waals interactions, which are ubiquitous in nature and crucial for determining the structure of molecules and condensed matter. We have contributed to this by constructing a set of pseudopotentials and pseudoatomic orbital basis specialized for molecular systems consisting of C/H/N/O elements. The reliability of the present method is verified from the interaction energies of 45 kinds of complexes (comparing with CCSD(T)) and the crystalline structures of 23 kinds of typical explosive solids (comparing with experiments). Using this method, we have studied the phase transition of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under static compression up to 50 GPa. Kinetically, intramolecular deformation has priority in the competition with intermolecular packing deformation by ∼87%. A possible γ → β phase transition is found at around 2.10 GPa, and the migration of H 2 O has an effect of kinetically pushing this process. We make it clear that no β → δ/ε → δ phase transition occurs at 27 GPa, which has long been a hot debate in experiments. In addition, the P-V relation, bulk modulus, and acoustic velocity are also predicted for α-, δ-, and γ-HMX, which are experimentally unavailable.

Functional modulation of a protein folding landscape via side-chain distortion

PubMed Central

Kelch, Brian A.; Salimi, Neema L.; Agard, David A.

2012-01-01

Ultrahigh-resolution (< 1.0 Å) structures have revealed unprecedented and unexpected details of molecular geometry, such as the deformation of aromatic rings from planarity. However, the functional utility of such energetically costly strain is unknown. The 0.83 Å structure of α-lytic protease (αLP) indicated that residues surrounding a conserved Phe side-chain dictate a rotamer which results in a ∼6° distortion along the side-chain, estimated to cost 4 kcal/mol. By contrast, in the closely related protease Streptomyces griseus Protease B (SGPB), the equivalent Phe adopts a different rotamer and is undistorted. Here, we report that the αLP Phe side-chain distortion is both functional and conserved in proteases with large pro regions. Sequence analysis of the αLP serine protease family reveals a bifurcation separating those sequences expected to induce distortion and those that would not, which correlates with the extent of kinetic stability. Structural and folding kinetics analyses of family members suggest that distortion of this side-chain plays a role in increasing kinetic stability within the αLP family members that use a large Pro region. Additionally, structural and kinetic folding studies of mutants demonstrate that strain alters the folding free energy landscape by destabilizing the transition state (TS) relative to the native state (N). Although side-chain distortion comes at a cost of foldability, it suppresses the rate of unfolding, thereby enhancing kinetic stability and increasing protein longevity under harsh extracellular conditions. This ability of a structural distortion to enhance function is unlikely to be unique to αLP family members and may be relevant in other proteins exhibiting side-chain distortions. PMID:22635267

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.

PubMed

Chen, Xiang; He, Si-Min; Bu, Dongbo; Zhang, Fa; Wang, Zhiyong; Chen, Runsheng; Gao, Wen

2008-09-15

RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is proved to be NP-hard. Due to kinetic reasons the real RNA secondary structure often has local instead of global minimum free energy. This implies that we may improve the performance of RNA secondary structure prediction by taking kinetics into account and minimize free energy in a local area. we propose a novel algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Still based on MFE criterion, FlexStem adopts comprehensive energy models that allow complex pseudoknots. Unlike classical thermodynamic methods, our approach aims to simulate the RNA folding process by successive addition of maximal stems, reducing the search space while maintaining or even improving the prediction accuracy. This reduced space is constructed by our maximal stem strategy and stem-adding rule induced from elaborate statistical experiments on real RNA secondary structures. The strategy and the rule also reflect the folding characteristic of RNA from a new angle and help compensate for the deficiency of merely relying on MFE in RNA structure prediction. We validate FlexStem by applying it to tRNAs, 5SrRNAs and a large number of pseudoknotted structures and compare it with the well-known algorithms such as RNAfold, PKNOTS, PknotsRG, HotKnots and ILM according to their overall sensitivities and specificities, as well as positive and negative controls on pseudoknots. The results show that FlexStem significantly increases the prediction accuracy through its local search strategy. Software is available at http://pfind.ict.ac.cn/FlexStem/. Supplementary data are available at Bioinformatics online.

Broad-Bandwidth Chiral Sum Frequency Generation Spectroscopy for Probing the Kinetics of Proteins at Interfaces

PubMed Central

2016-01-01

The kinetics of proteins at interfaces plays an important role in biological functions and inspires solutions to fundamental problems in biomedical sciences and engineering. Nonetheless, due to the lack of surface-specific and structural-sensitive biophysical techniques, it still remains challenging to probe protein kinetics in situ and in real time without the use of spectroscopic labels at interfaces. Broad-bandwidth chiral sum frequency generation (SFG) spectroscopy has been recently developed for protein kinetic studies at interfaces by tracking the chiral vibrational signals of proteins. In this article, we review our recent progress in kinetic studies of proteins at interfaces using broad-bandwidth chiral SFG spectroscopy. We illustrate the use of chiral SFG signals of protein side chains in the C–H stretch region to monitor self-assembly processes of proteins at interfaces. We also present the use of chiral SFG signals from the protein backbone in the N–H stretch region to probe the real-time kinetics of proton exchange between protein and water at interfaces. In addition, we demonstrate the applications of spectral features of chiral SFG that are typical of protein secondary structures in both the amide I and the N–H stretch regions for monitoring the kinetics of aggregation of amyloid proteins at membrane surfaces. These studies exhibit the power of broad-bandwidth chiral SFG to study protein kinetics at interfaces and the promise of this technique in research areas of surface science to address fundamental problems in biomedical and material sciences. PMID:26196215

Dielectric aggregation kinetics of cells in a uniform AC electric field.

PubMed

Tada, Shigeru; Natsuya, Tomoyuki; Tsukamoto, Akira

2014-01-01

Cell manipulation and separation technologies have potential biological and medical applications, including advanced clinical protocols such as tissue engineering. An aggregation model was developed for a human carcinoma (HeLa) cell suspension exposed to a uniform AC electric field, in order to explore the field-induced structure formation and kinetics of cell aggregates. The momentum equations of cells under the action of the dipole-dipole interaction were solved theoretically and the total time required to form linear string-like cluster was derived. The results were compared with those of a numerical simulation. Experiments using HeLa cells were also performed for comparison. The total time required to form linear string-like clusters was derived from a simple theoretical model of the cell cluster kinetics. The growth rates of the average string length of cell aggregates showed good agreement with those of the numerical simulation. In the experiment, cells were found to form massive clusters on the bottom of a chamber. The results imply that the string-like cluster grows rapidly by longitudinal attraction when the electric field is first applied and that this process slows at later times and is replaced by lateral coagulation of short strings. The findings presented here are expected to enable design of methods for the organization of three-dimensional (3D) cellular structures without the use of micro-fabricated substrates, such as 3D biopolymer scaffolds, to manipulate cells into spatial arrangement.

Three-dimensional quantitative structure-activity relationship studies on UGT1A9-mediated 3-O-glucuronidation of natural flavonols using a pharmacophore-based comparative molecular field analysis model.

PubMed

Wu, Baojian; Morrow, John Kenneth; Singh, Rashim; Zhang, Shuxing; Hu, Ming

2011-02-01

Glucuronidation is often recognized as one of the rate-determining factors that limit the bioavailability of flavonols. Hence, design and synthesis of more bioavailable flavonols would benefit from the establishment of predictive models of glucuronidation using kinetic parameters [e.g., K(m), V(max), intrinsic clearance (CL(int)) = V(max)/K(m)] derived for flavonols. This article aims to construct position (3-OH)-specific comparative molecular field analysis (CoMFA) models to describe UDP-glucuronosyltransferase (UGT) 1A9-mediated glucuronidation of flavonols, which can be used to design poor UGT1A9 substrates. The kinetics of recombinant UGT1A9-mediated 3-O-glucuronidation of 30 flavonols was characterized, and kinetic parameters (K(m), V(max), CL(int)) were obtained. The observed K(m), V(max), and CL(int) values of 3-O-glucuronidation ranged from 0.04 to 0.68 μM, 0.04 to 12.95 nmol/mg/min, and 0.06 to 109.60 ml/mg/min, respectively. To model UGT1A9-mediated glucuronidation, 30 flavonols were split into the training (23 compounds) and test (7 compounds) sets. These flavonols were then aligned by mapping the flavonols to specific common feature pharmacophores, which were used to construct CoMFA models of V(max) and CL(int), respectively. The derived CoMFA models possessed good internal and external consistency and showed statistical significance and substantive predictive abilities (V(max) model: q(2) = 0.738, r(2) = 0.976, r(pred)(2) = 0.735; CL(int) model: q(2) = 0.561, r(2) = 0.938, r(pred)(2) = 0.630). The contour maps derived from CoMFA modeling clearly indicate structural characteristics associated with rapid or slow 3-O-glucuronidation. In conclusion, the approach of coupling CoMFA analysis with a pharmacophore-based structural alignment is viable for constructing a predictive model for regiospecific glucuronidation rates of flavonols by UGT1A9.

Use of ferrous iron by metallo-β-lactamases.

PubMed

Cahill, Samuel T; Tarhonskaya, Hanna; Rydzik, Anna M; Flashman, Emily; McDonough, Michael A; Schofield, Christopher J; Brem, Jürgen

2016-10-01

Metallo-β-lactamases (MBLs) catalyse the hydrolysis of almost all β-lactam antibacterials including the latest generation carbapenems and are a growing worldwide clinical problem. It is proposed that MBLs employ one or two zinc ion cofactors in vivo. Isolated MBLs are reported to use transition metal ions other than zinc, including copper, cadmium and manganese, with iron ions being a notable exception. We report kinetic and biophysical studies with the di-iron(II)-substituted metallo-β-lactamase II from Bacillus cereus (di-Fe(II) BcII) and the clinically relevant B1 subclass Verona integron-encoded metallo-β-lactamase 2 (di-Fe(II) VIM-2). The results reveal that MBLs can employ ferrous iron in catalysis, but with altered kinetic and inhibition profiles compared to the zinc enzymes. A crystal structure of di-Fe(II) BcII reveals only small overall changes in the active site compared to the di-Zn(II) enzyme including retention of the di-metal bridging water; however, the positions of the metal ions are altered in the di-Fe(II) compared to the di-Zn(II) structure. Stopped-flow analyses reveal that the mechanism of nitrocefin hydrolysis by both di-Fe(II) BcII and di-Fe(II) VIM-2 is altered compared to the di-Zn(II) enzymes. Notably, given that the MBLs are the subject of current medicinal chemistry efforts, the results raise the possibility the Fe(II)-substituted MBLs may be of clinical relevance under conditions of low zinc availability, and reveal potential variation in inhibitor activity against the differently metallated MBLs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

A century of enzyme kinetic analysis, 1913 to 2013.

PubMed

Johnson, Kenneth A

2013-09-02

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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.

A cuboctahedral platinum (Pt79) nanocluster enclosed by well defined facets favours di-sigma adsorption and improves the reaction kinetics for methanol fuel cells.

PubMed

Mahata, Arup; Choudhuri, Indrani; Pathak, Biswarup

2015-08-28

The methanol dehydrogenation steps are studied very systematically on the (111) facet of a cuboctahedral platinum (Pt79) nanocluster enclosed by well-defined facets. The various intermediates formed during the methanol decompositions are adsorbed at the edge and bridge site of the facet either vertically (through C- and O-centres) or in parallel. The di-sigma adsorption (in parallel) on the (111) facet of the nanocluster is the most stable structure for most of the intermediates and such binding improves the interaction between the substrate and the nanocluster and thus the catalytic activity. The reaction thermodynamics, activation barrier, and temperature dependent reaction rates are calculated for all the successive methanol dehydrogenation steps to understand the methanol decomposition mechanism, and these values are compared with previous studies to understand the catalytic activity of the nanocluster. We find the catalytic activity of the nanocluster is excellent while comparing with any previous reports and the methanol dehydrogenation thermodynamics and kinetics are best when the intermediates are adsorbed in a di-sigma manner.

Focused-based multifractal analysis of the wake in a wind turbine array utilizing proper orthogonal decomposition

NASA Astrophysics Data System (ADS)

Kadum, Hawwa; Ali, Naseem; Cal, Raúl

2016-11-01

Hot-wire anemometry measurements have been performed on a 3 x 3 wind turbine array to study the multifractality of the turbulent kinetic energy dissipations. A multifractal spectrum and Hurst exponents are determined at nine locations downstream of the hub height, and bottom and top tips. Higher multifractality is found at 0.5D and 1D downstream of the bottom tip and hub height. The second order of the Hurst exponent and combination factor show an ability to predict the flow state in terms of its development. Snapshot proper orthogonal decomposition is used to identify the coherent and incoherent structures and to reconstruct the stochastic velocity using a specific number of the POD eigenfunctions. The accumulation of the turbulent kinetic energy in top tip location exhibits fast convergence compared to the bottom tip and hub height locations. The dissipation of the large and small scales are determined using the reconstructed stochastic velocities. The higher multifractality is shown in the dissipation of the large scale compared to small-scale dissipation showing consistency with the behavior of the original signals.

Investigation of Electron Loss Processes in CO2/He/N2 Electric Discharges.

DTIC Science & Technology

1980-12-01

Background......................4 Structure of a Discharge. ............. 4 Electron Kinetics..................7 Plasma Chemistry .................. 14...Electron Kinetic Reactions. ............ 11 II C 2/IN 2/He Electron Kinetics ............ 15 III Plasma Chemistry Reactions. ............ 17 IV...effects (Ref 2:317- 323). Table II also lists some of the reactions they found to be possibly important. Plasma Chemistry In order to understand what is

Large scale structures in the kinetic gravity braiding model that can be unbraided

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

Kimura, Rampei; Yamamoto, Kazuhiro, E-mail: rampei@theo.phys.sci.hiroshima-u.ac.jp, E-mail: kazuhiro@hiroshima-u.ac.jp

2011-04-01

We study cosmological consequences of a kinetic gravity braiding model, which is proposed as an alternative to the dark energy model. The kinetic braiding model we study is characterized by a parameter n, which corresponds to the original galileon cosmological model for n = 1. We find that the background expansion of the universe of the kinetic braiding model is the same as the Dvali-Turner's model, which reduces to that of the standard cold dark matter model with a cosmological constant (ΛCDM model) for n equal to infinity. We also find that the evolution of the linear cosmological perturbation inmore » the kinetic braiding model reduces to that of the ΛCDM model for n = ∞. Then, we focus our study on the growth history of the linear density perturbation as well as the spherical collapse in the nonlinear regime of the density perturbations, which might be important in order to distinguish between the kinetic braiding model and the ΛCDM model when n is finite. The theoretical prediction for the large scale structure is confronted with the multipole power spectrum of the luminous red galaxy sample of the Sloan Digital Sky survey. We also discuss future prospects of constraining the kinetic braiding model using a future redshift survey like the WFMOS/SuMIRe PFS survey as well as the cluster redshift distribution in the South Pole Telescope survey.« less

Mechanistic insights into the active site and allosteric communication pathways in human nonmuscle myosin-2C

PubMed Central

Preller, Matthias

2017-01-01

Despite a generic, highly conserved motor domain, ATP turnover kinetics and their activation by F-actin vary greatly between myosin-2 isoforms. Here, we present a 2.25 Å pre-powerstroke state (ADP⋅VO4) crystal structure of the human nonmuscle myosin-2C motor domain, one of the slowest myosins characterized. In combination with integrated mutagenesis, ensemble-solution kinetics, and molecular dynamics simulation approaches, the structure reveals an allosteric communication pathway that connects the distal end of the motor domain with the active site. Disruption of this pathway by mutation of hub residue R788, which forms the center of a cluster of interactions connecting the converter, the SH1-SH2 helix, the relay helix, and the lever, abolishes nonmuscle myosin-2 specific kinetic signatures. Our results provide insights into structural changes in the myosin motor domain that are triggered upon F-actin binding and contribute critically to the mechanochemical behavior of stress fibers, actin arcs, and cortical actin-based structures. PMID:29256864

Kinetic analysis of the effects of target structure on siRNA efficiency

NASA Astrophysics Data System (ADS)

Chen, Jiawen; Zhang, Wenbing

2012-12-01

RNAi efficiency for target cleavage and protein expression is related to the target structure. Considering the RNA-induced silencing complex (RISC) as a multiple turnover enzyme, we investigated the effect of target mRNA structure on siRNA efficiency with kinetic analysis. The 4-step model was used to study the target cleavage kinetic process: hybridization nucleation at an accessible target site, RISC-mRNA hybrid elongation along with mRNA target structure melting, target cleavage, and enzyme reactivation. At this model, the terms accounting for the target accessibility, stability, and the seed and the nucleation site effects are all included. The results are in good agreement with that of experiments which show different arguments about the structure effects on siRNA efficiency. It shows that the siRNA efficiency is influenced by the integrated factors of target's accessibility, stability, and the seed effects. To study the off-target effects, a simple model of one siRNA binding to two mRNA targets was designed. By using this model, the possibility for diminishing the off-target effects by the concentration of siRNA was discussed.

Enthalpy and high temperature relaxation kinetics of stable vapor-deposited glasses of toluene

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

Bhattacharya, Deepanjan; Sadtchenko, Vlad, E-mail: vlad@gwu.edu

Stable non-crystalline toluene films of micrometer and nanometer thicknesses were grown by vapor deposition at distinct rates and probed by fast scanning calorimetry. Fast scanning calorimetry is shown to be extremely sensitive to the structure of the vapor-deposited phase and was used to characterize simultaneously its kinetic stability and its thermodynamic properties. According to our analysis, transformation of vapor-deposited samples of toluene during heating with rates in excess 10{sup 5} K s{sup −1} follows the zero-order kinetics. The transformation rate correlates strongly with the initial enthalpy of the sample, which increases with the deposition rate according to sub-linear law. Analysismore » of the transformation kinetics of vapor-deposited toluene films of various thicknesses reveal a sudden increase in the transformation rate for films thinner than 250 nm. The change in kinetics seems to correlate with the surface roughness scale of the substrate. The implications of these findings for the formation mechanism and structure of vapor-deposited stable glasses are discussed.« less

Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics

NASA Astrophysics Data System (ADS)

Polotto, Franciele; Drigo Filho, Elso; Chahine, Jorge; Oliveira, Ronaldo Junio de

2018-03-01

This work developed analytical methods to explore the kinetics of the time-dependent probability distributions over thermodynamic free energy profiles of protein folding and compared the results with simulation. The Fokker-Planck equation is mapped onto a Schrödinger-type equation due to the well-known solutions of the latter. Through a semi-analytical description, the supersymmetric quantum mechanics formalism is invoked and the time-dependent probability distributions are obtained with numerical calculations by using the variational method. A coarse-grained structure-based model of the two-state protein Tm CSP was simulated at a Cα level of resolution and the thermodynamics and kinetics were fully characterized. Analytical solutions from non-equilibrium conditions were obtained with the simulated double-well free energy potential and kinetic folding times were calculated. It was found that analytical folding time as a function of temperature agrees, quantitatively, with simulations and experiments from the literature of Tm CSP having the well-known 'U' shape of the Chevron Plots. The simple analytical model developed in this study has a potential to be used by theoreticians and experimentalists willing to explore, quantitatively, rates and the kinetic behavior of their system by informing the thermally activated barrier. The theory developed describes a stochastic process and, therefore, can be applied to a variety of biological as well as condensed-phase two-state systems.

The mechanism of interactions between tea polyphenols and porcine pancreatic alpha‐amylase: Analysis by inhibition kinetics, fluorescence quenching, differential scanning calorimetry and isothermal titration calorimetry

PubMed Central

Sun, Lijun; Gidley, Michael J.

2017-01-01

Scope This study aims to use a combination of biochemical and biophysical methods to derive greater mechanistic understanding of the interactions between tea polyphenols and porcine pancreatic α‐amylase (PPA). Methods and results The interaction mechanism was studied through fluorescence quenching (FQ), differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC) and compared with inhibition kinetics. The results showed that a higher quenching effect of polyphenols corresponded to a stronger inhibitory activity against PPA. The red‐shift of maximum emission wavelength of PPA bound with some polyphenols indicated a potential structural unfolding of PPA. This was also suggested by the decreased thermostability of PPA with these polyphenols in DSC thermograms. Through thermodynamic binding analysis of ITC and inhibition kinetics, the equilibrium of competitive inhibition was shown to result from the binding of particularly galloylated polyphenols with specific sites on PPA. There were positive linear correlations between the reciprocal of competitive inhibition constant (1/K ic), quenching constant (K FQ) and binding constant (K itc). Conclusion The combination of inhibition kinetics, FQ, DSC and ITC can reasonably characterize the interactions between tea polyphenols and PPA. The galloyl moiety is an important group in catechins and theaflavins in terms of binding with and inhibiting the activity of PPA. PMID:28618113

Rapid three-dimensional microfluidic mixer for high viscosity solutions to unravel earlier folding kinetics of G-quadruplex under molecular crowding conditions.

PubMed

Liu, Chao; Li, Ying; Li, Yiwei; Chen, Peng; Feng, Xiaojun; Du, Wei; Liu, Bi-Feng

2016-01-01

Rapid mixing of highly viscous solutions is a great challenge, which helps to analyze the reaction kinetics in viscous liquid phase, particularly to discover the folding kinetics of macromolecules under molecular crowding conditions mimicking the conditions inside cells. Here, we demonstrated a novel microfluidic mixer based on Dean flows with three-dimensional (3D) microchannel configuration for fast mixing of high-viscosity fluids. The main structure contained three consecutive subunits, each consisting of a "U"-type channel followed by a chamber with different width and height. Thus, the two solutions injected from the two inlets would undergo a mixing in the first "U"-type channel due to the Dean flow effect, and simultaneous vortices expansions in both horizontal and vertical directions in the following chamber. Numerical simulations and experimental characterizations confirmed that the micromixer could achieve a mixing time of 122.4μs for solutions with viscosities about 33.6 times that of pure water. It was the fastest micromixer for high viscosity solutions compared with previous reports. With this highly efficient 3D microfluidic mixer, we further characterized the early folding kinetics of human telomere G-quadruplex under molecular crowding conditions, and unravelled a new folding process within 550μs. Copyright © 2015 Elsevier B.V. All rights reserved.

The Synergy Between Total Scattering and Advanced Simulation Techniques: Quantifying Geopolymer Gel Evolution

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

White, Claire; Bloomer, Breaunnah E.; Provis, John L.

2012-05-16

With the ever increasing demands for technologically advanced structural materials, together with emerging environmental consciousness due to climate change, geopolymer cement is fast becoming a viable alternative to traditional cements due to proven mechanical engineering characteristics and the reduction in CO2 emitted (approximately 80% less CO2 emitted compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of the molecular changes responsible for nanostructural evolution during the geopolymerization process. Here, in-situ total scattering measurements in the form of X-ray pair distribution function (PDF) analysis are used to quantify the extent of reaction of metakaolin/slag alkali-activated geopolymer binders, includingmore » the effects of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerization reaction. Restricting quantification of the kinetics to the initial ten hours of reaction does not enable elucidation of the true extent of the reaction, but using X-ray PDF data obtained after 128 days of reaction enables more accurate determination of the initial extent of reaction. The synergies between the in-situ X-ray PDF data and simulations conducted by multiscale density functional theory-based coarse-grained Monte Carlo analysis are outlined, particularly with regard to the potential for the X-ray data to provide a time scale for kinetic analysis of the extent of reaction obtained from the multiscale simulation methodology.« less

Thermal inactivation kinetics of β-galactosidase during bread baking.

PubMed

Zhang, Lu; Chen, Xiao Dong; Boom, Remko M; Schutyser, Maarten A I

2017-06-15

In this study, β-galactosidase was utilized as a model enzyme to investigate the mechanism of enzyme inactivation during bread baking. Thermal inactivation of β-galactosidase was investigated in a wheat flour/water system at varying temperature-moisture content combinations, and in bread during baking at 175 or 205°C. In the wheat flour/water system, the thermostability of β-galactosidase increased with decreased moisture content, and a kinetic model was accurately fitted to the corresponding inactivation data (R 2 =0.99). Interestingly, the residual enzyme activity in the bread crust (about 30%) was hundredfold higher than that in the crumb (about 0.3%) after baking, despite the higher temperature in the crust throughout baking. This result suggested that the reduced moisture content in the crust increased the thermostability of the enzyme. Subsequently, the kinetic model reasonably predicted the enzyme inactivation in the crumb using the same parameters derived from the wheat flour/water system. However, the model predicted a lower residual enzyme activity in the crust compared with the experimental result, which indicated that the structure of the crust may influence the enzyme inactivation mechanism during baking. The results reported can provide a quantitative understanding of the thermal inactivation kinetics of enzyme during baking, which is essential to better retain enzymatic activity in bakery products supplemented with heat-sensitive enzymes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of Oxidation Kinetics of Nitrite-Oxidizing Bacteria: Nitrite Availability as a Key Factor in Niche Differentiation

PubMed Central

Nowka, Boris; Daims, Holger

2014-01-01

Nitrification has an immense impact on nitrogen cycling in natural ecosystems and in wastewater treatment plants. Mathematical models function as tools to capture the complexity of these biological systems, but kinetic parameters especially of nitrite-oxidizing bacteria (NOB) are lacking because of a limited number of pure cultures until recently. In this study, we compared the nitrite oxidation kinetics of six pure cultures and one enrichment culture representing three genera of NOB (Nitrobacter, Nitrospira, Nitrotoga). With half-saturation constants (Km) between 9 and 27 μM nitrite, Nitrospira bacteria are adapted to live under significant substrate limitation. Nitrobacter showed a wide range of lower substrate affinities, with Km values between 49 and 544 μM nitrite. However, the advantage of Nitrobacter emerged under excess nitrite supply, sustaining high maximum specific activities (Vmax) of 64 to 164 μmol nitrite/mg protein/h, contrary to the lower activities of Nitrospira of 18 to 48 μmol nitrite/mg protein/h. The Vmax (26 μmol nitrite/mg protein/h) and Km (58 μM nitrite) of “Candidatus Nitrotoga arctica” measured at a low temperature of 17°C suggest that Nitrotoga can advantageously compete with other NOB, especially in cold habitats. The kinetic parameters determined represent improved basis values for nitrifying models and will support predictions of community structure and nitrification rates in natural and engineered ecosystems. PMID:25398863

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

NASA Technical Reports Server (NTRS)

Malkin, Alexander J.

1998-01-01

During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization".

Mutational Studies Uncover Non-Native Structure in the Dimeric Kinetic Intermediate of the H2A-H2B Heterodimer

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2010-01-01

The folding pathway of the histone H2A-H2B heterodimer minimally includes an on-pathway, dimeric, burst-phase intermediate, I2. The partially folded H2A and H2B monomers populated at equilibrium were characterized as potential monomeric kinetic intermediates. Folding kinetics were compared for initiation from isolated, folded monomers and the heterodimer unfolded in 4 M urea. The observed rates were virtually identical above 0.4 M urea, exhibiting a log-linear relationship on the final denaturant concentration. Below ~0.4 M urea (concentrations inaccessible from the 4 M urea unfolded state), a roll-over in the rates was observed; this suggests that a component of the I2 ensemble contains non-native structure that rearranges/isomerizes to a more native-like species. The contribution of helix propensity to the stability of the I2 ensemble was assessed with a set of H2A-H2B mutants containing Ala and Gly replacements at nine sites, focusing mainly on the long, central α2 helix. Equilibrium and kinetic folding/unfolding data were collected to determine the effects of the mutations on the stability of I2 and the transition state between I2 and N2. This limited mutational study indicated that residues in the α2 helices of H2A and H2B, as well as α1 of H2B and both the C-terminus of α3 and the short αC helix of H2A contribute to the stability of the I2 burst phase species. Interestingly, at least eight of the nine targeted residues stabilize I2 by interactions that are non-native to some extent. Given that destabilizing I2 and these non-native interactions does not accelerate folding, it is concluded that the native and non-native structure present in the I2 ensemble enables efficient folding of H2A-H2B. PMID:20600120

Structural and Functional Characterization of the TRI101 Trichothecene 3-O-Acetyltransferase from Fusarium sporotrichioides and Fusarium graminearum: KINETIC INSIGHTS TO COMBATING FUSARIUM HEAD BLIGHT

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

Garvey, Graeme S.; McCormick, Susan P.; Rayment, Ivan

2008-06-30

Fusarium head blight (FHB) is a plant disease with serious economic and health impacts. It is caused by fungal species belonging to the genus Fusarium and the mycotoxins they produce. Although it has proved difficult to combat this disease, one strategy that has been examined is the introduction of an indigenous fungal protective gene into cereals such as wheat barley and rice. Thus far the gene of choice has been tri101 whose gene product catalyzes the transfer of an acetyl group from acetyl coenzyme A to the C3 hydroxyl moiety of several trichothecene mycotoxins. In vitro this has been shownmore » to reduce the toxicity of the toxins by {approx}100-fold but has demonstrated limited resistance to FHB in transgenic cereal. To understand the molecular basis for the differences between in vitro and in vivo resistance the three-dimensional structures and kinetic properties of two TRI101 orthologs isolated from Fusarium sporotrichioides and Fusarium graminearum have been determined. The kinetic results reveal important differences in activity of these enzymes toward B-type trichothecenes such as deoxynivalenol. These differences in activity can be explained in part by the three-dimensional structures for the ternary complexes for both of these enzymes with coenzyme A and trichothecene mycotoxins. The structural and kinetic results together emphasize that the choice of an enzymatic resistance gene in transgenic crop protection strategies must take into account the kinetic profile of the selected protein.« less

A hybrid MD-kMC algorithm for folding proteins in explicit solvent.

PubMed

Peter, Emanuel Karl; Shea, Joan-Emma

2014-04-14

We present a novel hybrid MD-kMC algorithm that is capable of efficiently folding proteins in explicit solvent. We apply this algorithm to the folding of a small protein, Trp-Cage. Different kMC move sets that capture different possible rate limiting steps are implemented. The first uses secondary structure formation as a relevant rate event (a combination of dihedral rotations and hydrogen-bonding formation and breakage). The second uses tertiary structure formation events through formation of contacts via translational moves. Both methods fold the protein, but via different mechanisms and with different folding kinetics. The first method leads to folding via a structured helical state, with kinetics fit by a single exponential. The second method leads to folding via a collapsed loop, with kinetics poorly fit by single or double exponentials. In both cases, folding times are faster than experimentally reported values, The secondary and tertiary move sets are integrated in a third MD-kMC implementation, which now leads to folding of the protein via both pathways, with single and double-exponential fits to the rates, and to folding rates in good agreement with experimental values. The competition between secondary and tertiary structure leads to a longer search for the helix-rich intermediate in the case of the first pathway, and to the emergence of a kinetically trapped long-lived molten-globule collapsed state in the case of the second pathway. The algorithm presented not only captures experimentally observed folding intermediates and kinetics, but yields insights into the relative roles of local and global interactions in determining folding mechanisms and rates.

Importance of the structure and nanoporosity of organic matter on the desorption kinetics of benzo[a]pyrene in sediments.

PubMed

Huang, Youda; Zhang, Dainan; Duan, Dandan; Yang, Yu; Xiong, Yongqiang; Ran, Yong

2017-06-01

The desorption kinetics and mechanism were investigated using a Tenax extraction technique on different sediments spiked with radiocarbon-labeled benzo[a]pyrene (BaP). Five sedimentary fractions were sequentially fractionated, and the only nonhydrolyzable organic carbon fractions (NHC) were characterized using advanced solid-state 13 C nuclear magnetic resonance spectroscopy (NMR), improved six end-member model, and a CO 2 gas adsorption technique. The sediments contained high percentages of algaenan and/or sporopollenin but low percentages of black carbon and lignin. A first-order, two-compartment kinetics model described the desorption process very well (R 2  > 0.990). Although some of the organic carbon fractions were significantly related to the desorption kinetics parameters, the NHC fractions showed the highly significant correlation. Moreover, the nanoporosity or specific surface area (SSA) of the NHC fractions was highly related to their OC contents and aliphatic C (R 2  = 0.960, p < 0.01). The multiple regression equations among the desorption kinetics parameters, structural parameters, and nanoporosity were well established (R 2 =>0.999). Nanoporosity and aromatic C were the dominant contributors. Furthermore, the enhanced percentages of desorbed BaP at elevated temperatures significantly showed a linear regression with the structure and nanoporosity. To our knowledge, the above evidence demonstrates for the first time that the transfer (or diffusion) of BaP in the nanopores of condensed aromatic components is the dominant mechanism of the desorption kinetics of BaP at organic matter particle scale. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stress-dependence of kinetic transitions at atomistic defects

NASA Astrophysics Data System (ADS)

Ball, S. L.; Alexander, K. C.; Schuh, C. A.

2018-01-01

The full second-rank activation volume tensors associated with vacancy migration in FCC copper and HCP titanium as well as transition events in the Σ5 (2 1 0) grain boundary in copper are calculated and analyzed. The full tensorial results quantitatively illustrate how the conventional use of an activation volume scalar in atomistic studies of the kinetic processes of complex defects can miss important stress dependencies, in that neither hydrostatic pressure nor deviatoric stress dependencies can be considered alone as dominating the response. The results speak to the importance of anisotropies in the stress-dependence of atomistic kinetics, including crystal structure anisotropy, elastic anisotropy, and defect structure or migration-path anisotropies.

Studies of Methane Counterflow Flames at Low Pressures

NASA Astrophysics Data System (ADS)

Burrell, Robert Roe

Methane is the smallest hydrocarbon molecule, the fuel most widely studied in fundamental flame structure studies, and a major component of natural gas. Despite many decades of research into the fundamental chemical kinetics involved in methane oxidation, ongoing advancements in research suggest that more progress can be made. Though practical combustors of industrial and commercial significance operate at high pressures and turbulent flow conditions, fundamental understanding of combustion chemistry in flames is more readily obtained for low pressure and laminar flow conditions. Measurements were performed from 1 to 0.1 atmospheres for premixed methane/air and non-premixed methane-nitrogen/oxygen flames in a counterflow. Comparative modeling with quasi-one-dimensional strained flame codes revealed bias-induced errors in measured velocities up to 8% at 0.1 atmospheres due to tracer particle phase velocity slip in the low density gas reacting flow. To address this, a numerically-assisted correction scheme consisting of direct simulation of the particle phase dynamics in counterflow was implemented. Addition of reactions describing the prompt dissociation of formyl radicals to an otherwise unmodified USC Mech II kinetic model was found to enhance computed flame reactivity and substantially improve the predictive capability of computed results for measurements at the lowest pressures studied. Yet, the same modifications lead to overprediction of flame data at 1 atmosphere where results from the unmodified USC Mech II kinetic mechanism agreed well with ambient pressure flame data. The apparent failure of a single kinetic model to capture pressure dependence in methane flames motivates continued skepticism regarding the current understanding of pressure dependence in kinetic models, even for the simplest fuels.

PIV study of flow through porous structure using refractive index matching

NASA Astrophysics Data System (ADS)

Häfeli, Richard; Altheimer, Marco; Butscher, Denis; Rudolf von Rohr, Philipp

2014-05-01

An aqueous solution of sodium iodide and zinc iodide is proposed as a fluid that matches the refractive index of a solid manufactured by rapid prototyping. This enabled optical measurements in single-phase flow through porous structures. Experiments were also done with an organic index-matching fluid (anisole) in porous structures of different dimensions. To compare experiments with different viscosities and dimensions, we employed Reynolds similarity to deduce the scaling laws. One of the target quantities of our investigation was the dissipation rate of turbulent kinetic energy. Different models for the dissipation rate estimation were evaluated by comparing isotropy ratios. As in many other studies also, our experiments were not capable of resolving the velocity field down to the Kolmogorov length scale, and therefore, the dissipation rate has to be considered as underestimated. This is visible in experiments of different relative resolutions. However, being near the Kolmogorov scale allows estimating a reproducible, yet underestimated spatial distribution of dissipation rate inside the porous structure. Based on these results, the model was used to estimate the turbulent diffusivity. Comparing it to the dispersion coefficient obtained in the same porous structure, we conclude that even at the turbulent diffusivity makes up only a small part of mass transfer in axial direction. The main part is therefore attributed to Taylor dispersion.

Elucidating dominant pathways of the nano-particle self-assembly process.

PubMed

Zeng, Xiangze; Li, Bin; Qiao, Qin; Zhu, Lizhe; Lu, Zhong-Yuan; Huang, Xuhui

2016-09-14

Self-assembly processes play a key role in the fabrication of functional nano-structures with widespread application in drug delivery and micro-reactors. In addition to the thermodynamics, the kinetics of the self-assembled nano-structures also play an important role in determining the formed structures. However, as the self-assembly process is often highly heterogeneous, systematic elucidation of the dominant kinetic pathways of self-assembly is challenging. Here, based on mass flow, we developed a new method for the construction of kinetic network models and applied it to identify the dominant kinetic pathways for the self-assembly of star-like block copolymers. We found that the dominant pathways are controlled by two competing kinetic parameters: the encounter time Te, characterizing the frequency of collision and the transition time Tt for the aggregate morphology change from rod to sphere. Interestingly, two distinct self-assembly mechanisms, diffusion of an individual copolymer into the aggregate core and membrane closure, both appear at different stages (with different values of Tt) of a single self-assembly process. In particular, the diffusion mechanism dominates the middle-sized semi-vesicle formation stage (with large Tt), while the membrane closure mechanism dominates the large-sized vesicle formation stage (with small Tt). Through the rational design of the hydrophibicity of the copolymer, we successfully tuned the transition time Tt and altered the dominant self-assembly pathways.

Morphology and kinetics of the formation of polyamide benzimidazole in N-methylpyrrolidone

NASA Astrophysics Data System (ADS)

Khanchich, O. A.; Larionov, V. B.; Biryukov, A. L.

2018-02-01

Polymerization-optical methods were used to study the supermolecular structure in the gelation of systems based on polyamidobenzimidazole (PABI) in N-methylpyrrolidone (N-MP) and the kinetics of phase transformations during polymer coagulation from a the solution. It was found that the use of N-MP leads to the appearance in the PABI-N-MP-H2O system of spherulites having a structure characteristic of LC structures. It is shown that the alternation of metastable structures upon gelation of the PABY - N-MP-H2O system is consistent with the appearance of the LC phase of the cholesteric type.

Chemical bonding in hydrogen and lithium under pressure

DOE PAGES

Naumov, Ivan I.; Hemley, Russell J.; Hoffmann, Roald; ...

2015-08-12

Though hydrogen and lithium have been assigned a common column of the periodic table, their crystalline states under common conditions are drastically different: the former at temperatures where it is crystalline is a molecular insulator whereas the latter is a metal that takes on simple structures. On compression, however, the two come to share some structural and other similarities associated with the insulator-to-metal and metal-to-insulator transitions, respectively. To gain a deeper understanding of differences and parallels in the behaviors of compressed hydrogen and lithium, we performed an ab-initio comparative study of these systems in selected identical structures. Both elements undergomore » a continuous pressure-induced s-p electronic transition, though this is at a much earlier stage of development for H. The valence charge density accumulates in interstitial regions in Li but not in H in structures examined over the same range of compression. Moreover, the valence charge density distributions or electron localization functions for the same arrangement of atoms mirror each other as one proceeds from one element to the other. Application of the viral theorem shows that the kinetic and potential energies jump across the first-order phase transitions in H and Li are opposite in sign because of non-local effects in the Li pseudopotential. Finally, the common tendency of compressed H and Li to adopt three-fold coordinated structures as found is explained by the fact that such structures are capable of yielding a profound pseudogap in the electronic densities of states at the Fermi level, thereby reducing the kinetic energy. Lastly, these results have implications for the phase diagrams of these elements and also for the search for new structures with novel properties.« less

Habit modification of potassium acid phthalate (KAP) single crystals by impurities

NASA Astrophysics Data System (ADS)

Murugakoothan, P.; Mohan Kumar, R.; Ushasree, P. M.; Jayavel, R.; Dhanasekaran, R.; Ramasamy, P.

1999-12-01

Nonlinear optical materials potassium dihydrogen phosphate (KDP), urea and L-arginine phosphate (LAP)-doped KAP crystals were grown by the slow cooling method. The LAP-doped crystals show pronounced habit modification compared to KDP and urea doping. The effect of these impurities on growth kinetics, surface morphology, habit modification, structure, optical and mechanical properties have been studied. Among the three impurities, urea doping yields high mechanical stability and optical transmission and for KDP and LAP doping there is a decrease in optical transmission.

Magnesium Nanoparticles for Hydrogen Storage: Structure, Kinetics and Thermodynamics

NASA Astrophysics Data System (ADS)

Pasquini, L.; Brighi, M.; Montone, A.; Vittori Antisari, M.; Dam, B.; Palmisano, V.; Bonetti, E.

2012-08-01

Magnesium nanoparticles coated by a native oxide shell and decorated by palladium clusters were synthesized by the inert gas condensation technique. The kinetics and thermodynamics of hydrogen sorption were investigated by Sieverts measurements at high temperature and by optical hydrogenography close to ambient temperature. The structure and morphology of the nanoparticles were studied by electron microscopy and X-ray diffraction both in the as-prepared state and after hydrogen sorption cycles.

Visible-Light Initiated Free-Radical/Cationic Ring-Opening Hybrid Photopolymerization of Methacrylate/Epoxy: Polymerization Kinetics, Crosslinking Structure, and Dynamic Mechanical Properties.

PubMed

Ge, Xueping; Ye, Qiang; Song, Linyong; Misra, Anil; Spencer, Paulette

2015-04-01

The effects of polymerization kinetics and chemical miscibility on the crosslinking structure and mechanical properties of polymers cured by visible-light initiated free-radical/cationic ring-opening hybrid photopolymerization are determined. A three-component initiator system is used and the monomer system contains methacrylates and epoxides. The photopolymerization kinetics is monitored in situ by Fourier transform infrared-attenuated total reflectance. The crosslinking structure is studied by modulated differential scanning calorimetry and dynamic mechanical analysis. X-ray microcomputed tomography is used to evaluate microphase separation. The mechanical properties of polymers formed by hybrid formed by free-radical polymerization. These investigations mark the first time that the benefits of the chain transfer reaction between epoxy and hydroxyl groups of methacrylate, on the crosslinking network and microphase separation during hybrid visible-light initiated photopolymerization, have been determined.

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

AFOSR/ONR Contractors Meeting - Combustion, Rocket Propulsion, Diagnostics of Reacting Flow

DTIC Science & Technology

1990-06-15

GASIFICATION KINETICS OF SOLID BORON AND PYROLITIC GRAPHrrE Because of the energetic potential of boron as a solid fuel (or fuel additive) and the likely...87 Kinetic Studies of Metal Combustion in Propulsion, A. Fontijn, P. M. Futerko and A. G. Slavejkov .............................. 90...Measurements and Chemical Kinetic Simulation of the Structure of Model Propellant Flames, M. C. Branch and H. Dindi .......... 94 High-Rate Thermal

Effects of Soot Structure on Soot Oxidation Kinetics

DTIC Science & Technology

2011-06-01

information from PSDs, temperature, gas -phase composition was used to develop an oxidation kinetic expression that accounts for the effects of...from PSDs, temperature, gas -phase composition was used to develop an oxidation kinetic expression that accounts for the effects of temperature, O2, and...systematic studies of these effects under the temperatures and times of interest to soot oxidation in gas turbine engines. Studies have shown that soot

Variations in protein/flavin hydrogen bonding in a LOV domain produce non-Arrhenius kinetics of adduct decay†

PubMed Central

Zoltowski, Brian D.; Nash, Abigail I.; Gardner, Kevin H.

2011-01-01

Light Oxygen Voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue-light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark state cleavage of the photochemically-generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2 and ribityl hydroxyls with the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. PMID:21923139

Variations in protein-flavin hydrogen bonding in a light, oxygen, voltage domain produce non-Arrhenius kinetics of adduct decay.

PubMed

Zoltowski, Brian D; Nash, Abigail I; Gardner, Kevin H

2011-10-18

Light, oxygen, voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine-tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark-state cleavage of the photochemically generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2, and ribityl hydroxyls and the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility, and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. © 2011 American Chemical Society

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure

PubMed Central

Filippova, Ekaterina V.; Kuhn, Misty L.; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Ballicora, Miguel A.

2015-01-01

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase (GNAT) superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key towards understanding the regulation of polyamine levels in bacteria during pathogenesis. PMID:25623305

Energy Dissipation and Phase-Space Dynamics in Eulerian Vlasov-Maxwell Turbulence

NASA Astrophysics Data System (ADS)

Tenbarge, Jason; Juno, James; Hakim, Ammar

2017-10-01

Turbulence in a magnetized plasma is a primary mechanism responsible for transforming energy at large injection scales into small-scale motions, which are ultimately dissipated as heat in systems such as the solar corona, wind, and other astrophysical objects. At large scales, the turbulence is well described by fluid models of the plasma; however, understanding the processes responsible for heating a weakly collisional plasma such as the solar wind requires a kinetic description. We present a fully kinetic Eulerian Vlasov-Maxwell study of turbulence using the Gkeyll simulation framework, including studies of the cascade of energy in phase space and formation and dissipation of coherent structures. We also leverage the recently developed field-particle correlations to diagnose the dominant sources of dissipation and compare the results of the field-particle correlation to other dissipation measures. NSF SHINE AGS-1622306 and DOE DE-AC02-09CH11466.

Layer-by-Layer Assembly of Glucose Oxidase on Carbon Nanotube Modified Electrodes.

PubMed

Suroviec, Alice H

2017-01-01

The use of enzymatically modified electrodes for the detection of glucose or other non-electrochemically active analytes is becoming increasingly common. Direct heterogeneous electron transfer to glucose oxidase has been shown to be kinetically difficult, which is why electron transfer mediators or indirect detection is usually used for monitoring glucose with electrochemical sensors. It has been found, however, that electrodes modified with single or multi-walled carbon nanotubes (CNTs) demonstrate fast heterogeneous electron transfer kinetics as compared to that found for traditional electrodes. Incorporating CNTs into the assembly of electrochemical glucose sensors, therefore, affords the possibility of facile electron transfer to glucose oxidase, and a more direct determination of glucose. This chapter describes the methods used to use CNTs in a layer-by-layer structure along with glucose oxidase to produce an enzymatically modified electrode with high turnover rates, increased stability and shelf-life.

Proton deflectometry of laser-driven relativistic electron jet from thin foil target

NASA Astrophysics Data System (ADS)

Huang, Chengkun; Palaniyappan, S.; Gautier, D. C.; Johnson, R. P.; Shimada, T.; Fernandez, J. C.; Tsung, F. S.; Mori, W. B.

2017-10-01

Near critical density relativistic electron jets from laser solid interaction carry currents approaching the Alfvén-limit and tens of kilo-Tesla magnetic fields. Such jets are often found in kinetic simulations with low areal density targets, but have not been confirmed experimentally. They may be used for X/gamma-ray generation and is also important for the understanding of post-transparency plasma dynamics. With a short-pulse probe beam at the Trident laser facility, we employed proton deflectometry to infer the jet's properties, structure and the long-time dynamics. We develop corresponding GEANT4 simulation model of the proton deflectometry, with input from the kinetic PIC simulations in 2D and quasi-3D geometry, to compare with the experimental radiography images. Detail comparison of the experimental and simulation features in the deflectometry will be discussed. Work supported by the LDRD program at LANL.

Behavior of S1- and S2-ovalbumin and S-ovalbumin A1 in urea solution: kinetics and equilibria.

PubMed

McKenzie, Hugh A; Frier, Robert D

2003-04-01

The isolation of S-, S1-, and S2-ovalbumin from domestic hen egg R-ovalbumin and of two methods for S-ovalbumin A1 are described. The first is by heat treatment of R-ovalbumin A1 and the second is of R-ovalbumin followed by fractionation on Sepharose. A kinetics and equilibrium study is made of their behavior in the presence of urea and compared with that of R-ovalbumins. As anticipated, the S-ovalbumins are much more resistant to urea than R-ovalbumins. Unlike the latter, S-ovalbumins' equilibrium profiles have a simpler sigmoidal shape. The unfolding of S1- and S2-ovalbumin is an order of magnitude slower than that of R-ovalbumin. Some possible structural differences between R- and S-ovalbumin forms and their significance are discussed.

Gaining Control over Radiolytic Synthesis of Uniform Sub-3-nanometer Palladium Nanoparticles: Use of Aromatic Liquids in the Electron Microscope

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

Abellan Baeza, Patricia; Parent, Lucas R.; Al Hasan, Naila M.

2016-01-07

Synthesizing nanomaterials of uniform shape and size is of critical importance to access and manipulate the novel structure-property relationships arising at the nanoscale. In this work we synthesize Pd nanoparticles with well-controlled size using in situ liquid-stage scanning transmission electron microscopy (STEM) and demonstrate a match between the reaction kinetics and products of the radiolytic and chemical syntheses of size-stabilized Pd nanoparticles. We quantify the effect of electron dose on the nucleation kinetics, and compare these results with in situ small angle X-ray scattering (SAXS) experiments investigating the effect of temperature during chemical synthesis. This work introduces methods for precisemore » control of nanoparticle synthesis in the STEM and provides a means to uncover the fundamental processes behind the size and shape stabilization of nanoparticles.« less

Hydrogen assisted growth of high quality epitaxial graphene on the C-face of 4H-SiC

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

Cai, Tuocheng; Jia, Zhenzhao; Yan, Baoming

2015-01-05

We demonstrate hydrogen assisted growth of high quality epitaxial graphene on the C-face of 4H-SiC. Compared with the conventional thermal decomposition technique, the size of the growth domain by this method is substantially increased and the thickness variation is reduced. Based on the morphology of epitaxial graphene, the role of hydrogen is revealed. It is found that hydrogen acts as a carbon etchant. It suppresses the defect formation and nucleation of graphene. It also improves the kinetics of carbon atoms via hydrocarbon species. These effects lead to increase of the domain size and the structure quality. The consequent capping effectmore » results in smooth surface morphology and suppression of multilayer growth. Our method provides a viable route to fine tune the growth kinetics of epitaxial graphene on SiC.« less

Fixing atmospheric CO2 by environment adaptive sorbent and renewable energy

NASA Astrophysics Data System (ADS)

Wang, T.; Liu, J.; Ge, K.; Fang, M.

2014-12-01

Fixing atmospheric CO2, followed by geologic storage in remote areas is considered an environmentally secure approach to climate mitigation. A moisture swing sorbent was investigated in the laboratory for CO2 capture at a remote area with humid and windy conditions. The energy requirement of moisture swing absorption could be greatly reduced compared to that of traditional high-temperature thermal swing, by assuming that the sorbent can be naturally dried and regenerated at ambient conditions. However, for currently developed moisture swing materials, the CO2 capacity would drop significantly at high relative humidity. The CO2 capture amount can be reduced by the poor thermodynamics and kinetics at high relative humidity or low temperature. Similar challenges also exist for thermal or vacuum swing sorbents. Developing sorbent materials which adapt to specific environments, such as high humidity or low temperature, can ensure sufficient capture capacity on the one hand, and realize better economics on the other hand (Figure 1) .An environment adaptive sorbent should have the abilities of tunable capacity and fast kinetics at extreme conditions, such as high humidity or low temperature. In this presentation, the possibility of tuning CO2 absorption capacity of a polymerized ionic liquid material is discussed. The energy requirement evaluation shows that tuning the CO2 binding energy of sorbent, rather than increasing the temperature or reducing the humidity of air, could be much more economic. By determining whether the absorption process is controlled by physical diffusion controlled or chemical reaction, an effective approach to fast kinetics at extreme conditions is proposed. A shrinking core model for mass transfer kinetics is modified to cope with the relatively poor kinetics of air capture. For the studied sample which has a heterogeneous structure, the kinetic analysis indicates a preference of sorbent particle size optimization, rather than support layer optimization. Chemical reaction kinetics could be enhanced by stronger binding energy or higher temperature. However, the total kinetics can only be significantly improved by chemical reaction enhancement if the physical diffusion is fast enough.

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

PubMed

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

2017-11-22

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

Disturbed left and right ventricular kinetic energy in patients with repaired tetralogy of Fallot: pathophysiological insights using 4D-flow MRI.

PubMed

Sjöberg, Pia; Bidhult, Sebastian; Bock, Jelena; Heiberg, Einar; Arheden, Håkan; Gustafsson, Ronny; Nozohoor, Shahab; Carlsson, Marcus

2018-04-17

Indications for pulmonary valve replacement (PVR) in patients with pulmonary regurgitation (PR) after repaired tetralogy of Fallot (rToF) are debated. We aimed to compare right (RV) and left ventricular (LV) kinetic energy (KE) measured by 4D-flow magnetic resonance imaging (MRI) in patients to controls, to further understand the pathophysiological effects of PR. Fifteen patients with rToF with PR > 20% and 14 controls underwent MRI. Ventricular volumes and KE were quantified from cine MRI and 4D-flow, respectively. Lagrangian coherent structures were used to discriminate KE in the PR. Restrictive RV physiology was defined as end-diastolic forward flow. LV systolic peak KE was lower in rToF, 2.8 ± 1.1 mJ, compared to healthy volunteers, 4.8 ± 1.1 mJ, p < 0.0001. RV diastolic peak KE was higher in rToF (7.7 ± 4.3 mJ vs 3.1 ± 1.3 mJ, p = 0.0001) and the difference most pronounced in patients with non-restrictive RV physiology. KE was primarily located in the PR volume at the time of diastolic peak KE, 64 ± 17%. This is the first study showing disturbed KE in patients with rToF and PR, in both the RV and LV. The role of KE as a potential early marker of ventricular dysfunction to guide intervention needs to be addressed in future studies. • Kinetic energy (KE) reflects ventricular performance • KE is a potential marker of ventricular dysfunction in Fallot patients • KE is disturbed in both ventricles in patients with tetralogy of Fallot • KE contributes to the understanding of the pathophysiology of pulmonary regurgitation • Lagrangian coherent structures enable differentiation of ventricular inflows.

Influence of Size and Shape of Silica Supports on the Sol⁻Gel Surface Molecularly Imprinted Polymers for Selective Adsorption of Gossypol.

PubMed

Zhi, Keke; Wang, Lulu; Zhang, Yagang; Jiang, Yingfang; Zhang, Letao; Yasin, Akram

2018-05-11

The influence of various silica gel supports with different shapes and sizes on the recognition properties of surface molecular imprinted polymers (MIPs) was investigated. MIPs for selective recognition and adsorption of gossypol were synthesized via the sol⁻gel process with a surface imprinting technique on silica gel substrates. 3-aminopropyltriethoxysilane (APTES) and tetraethoxysilane (TEOS) were chosen as the functional monomer and the cross-linker. The morphology and structure of the gossypol-MIPs were characterized using Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), and a standard Brunauer⁻Emett⁻Teller (BET) analysis. Results indicated that the surface imprinted polymer layer facilitated the removal and rebinding of the template, and thus, achieved fast binding kinetics. Compared with the MIPs prepared on irregularly shaped silica with a broad particle size distribution, the MIPs using regularly-shaped silica of uniform size showed higher imprinting factor (IF), and the MIP made with a relatively larger sized (60 μm) spherical silica, demonstrated higher adsorption capacity compared to the MIPs made with smaller sized, spherical silica. The MIP prepared with 60 μm spherically shaped silica, featured a fast adsorption kinetic of 10 min, and a saturated adsorption capacity of 204 mg·g −1 . The gossypol-MIP had higher selectivity (IF = 2.20) for gossypol over its structurally-similar analogs ellagic acid (IF = 1.13) and quercetin (IF = 1.20). The adsorption data of the MIP correlated well with the pseudo-second-order kinetic model and the Freundlich isotherm model, which implied that chemical adsorption dominated, and that multilayer adsorption occurred. Furthermore, the MIP exhibited an excellent regeneration performance, and the adsorption capacity of the MIP for gossypol only decreased by 6% after six reused cycles, indicating good application potential for selective adsorption of gossypol.

Hydrolytic catalysis and structural stabilization in a designed metalloprotein

PubMed Central

Zastrow, Melissa L.; Peacock, Anna F. A.; Stuckey, Jeanne A.; Pecoraro, Vincent L.

2011-01-01

Metal ions are an important part of many natural proteins, providing structural, catalytic and electron transfer functions. Reproducing these functions in a designed protein is the ultimate challenge to our understanding of them. Here, we present an artificial metallohydrolase, which has been shown by X-ray crystallography to contain two different metal ions – a Zn(II) ion which is important for catalytic activity and a Hg(II) ion which provides structural stability. This metallohydrolase displays catalytic activity that compares well with several characteristic reactions of natural enzymes. It catalyses p-nitrophenyl acetate hydrolysis (pNPA) to within ~100-fold of the efficiency of human carbonic anhydrase (CA)II and is at least 550-fold better than comparable synthetic complexes. Similarly, CO2 hydration occurs with an efficiency within ~500-fold of CAII. While histidine residues in the absence of Zn(II) exhibit pNPA hydrolysis, miniscule apopeptide activity is observed for CO2 hydration. The kinetic and structural analysis of this first de novo designed hydrolytic metalloenzyme uncovers necessary design features for future metalloenzymes containing one or more metals. PMID:22270627

Harmonic Chain with Velocity Flips: Thermalization and Kinetic Theory

NASA Astrophysics Data System (ADS)

Lukkarinen, Jani; Marcozzi, Matteo; Nota, Alessia

2016-12-01

We consider the detailed structure of correlations in harmonic chains with pinning and a bulk velocity flip noise during the heat relaxation phase which occurs on diffusive time scales, for t=O(L^2) where L is the chain length. It has been shown earlier that for non-degenerate harmonic interactions these systems thermalize, and the dominant part of the correlations is given by local thermal equilibrium determined by a temperature profile which satisfies a linear heat equation. Here we are concerned with two new aspects about the thermalization process: the first order corrections in 1 / L to the local equilibrium correlations and the applicability of kinetic theory to study the relaxation process. Employing previously derived explicit uniform estimates for the temperature profile, we first derive an explicit form for the first order corrections to the particle position-momentum correlations. By suitably revising the definition of the Wigner transform and the kinetic scaling limit we derive a phonon Boltzmann equation whose predictions agree with the explicit computation. Comparing the two results, the corrections can be understood as arising from two different sources: a current-related term and a correction to the position-position correlations related to spatial changes in the phonon eigenbasis.

Controlled release of functional proteins through designer self-assembling peptide nanofiber hydrogel scaffold

PubMed Central

Koutsopoulos, Sotirios; Unsworth, Larry D.; Nagai, Yusuke; Zhang, Shuguang

2009-01-01

The release kinetics for a variety of proteins of a wide range of molecular mass, hydrodynamic radii, and isoelectric points through a nanofiber hydrogel scaffold consisting of designer self-assembling peptides were studied by using single-molecule fluorescence correlation spectroscopy (FCS). In contrast to classical diffusion experiments, the single-molecule approach allowed for the direct determination of diffusion coefficients for lysozyme, trypsin inhibitor, BSA, and IgG both inside the hydrogel and after being released into the solution. The results of the FCS analyses and the calculated pristine in-gel diffusion coefficients were compared with the values obtained from the Stokes–Einstein equation, Fickian diffusion models, and the literature. The release kinetics suggested that protein diffusion through nanofiber hydrogels depended primarily on the size of the protein. Protein diffusivities decreased, with increasing hydrogel nanofiber density providing a means of controlling the release kinetics. Secondary and tertiary structure analyses and biological assays of the released proteins showed that encapsulation and release did not affect the protein conformation and functionality. Our results show that this biocompatible and injectable designer self-assembling peptide hydrogel system may be useful as a carrier for therapeutic proteins for sustained release applications. PMID:19273853

Spatiotemporal dynamics of DNA repair proteins following laser microbeam induced DNA damage – When is a DSB not a DSB?☆

PubMed Central

Reynolds, Pamela; Botchway, Stanley W.; Parker, Anthony W.; O’Neill, Peter

2013-01-01

The formation of DNA lesions poses a constant threat to cellular stability. Repair of endogenously and exogenously produced lesions has therefore been extensively studied, although the spatiotemporal dynamics of the repair processes has yet to be fully understood. One of the most recent advances to study the kinetics of DNA repair has been the development of laser microbeams to induce and visualize recruitment and loss of repair proteins to base damage in live mammalian cells. However, a number of studies have produced contradictory results that are likely caused by the different laser systems used reflecting in part the wavelength dependence of the damage induced. Additionally, the repair kinetics of laser microbeam induced DNA lesions have generally lacked consideration of the structural and chemical complexity of the DNA damage sites, which are known to greatly influence their reparability. In this review, we highlight the key considerations when embarking on laser microbeam experiments and interpreting the real time data from laser microbeam irradiations. We compare the repair kinetics from live cell imaging with biochemical and direct quantitative cellular measurements for DNA repair. PMID:23688615

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

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

Li, Minjing; Qian, Wei-jun; Gao, Yuqian

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes asmore » time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates« less

Kinetics of Cyclic Oxidation and Cracking and Finite Element Analysis of MA956 and Sapphire/MA956 Composite System

NASA Technical Reports Server (NTRS)

Lee, Kang N.; Arya, Vinod K.; Halford, Gary R.; Barrett, Charles A.

1996-01-01

Sapphire fiber-reinforced MA956 composites hold promise for significant weight savings and increased high-temperature structural capability, as compared to unreinforced MA956. As part of an overall assessment of the high-temperature characteristics of this material system, cyclic oxidation behavior was studied at 1093 C and 1204 C. Initially, both sets of coupons exhibited parabolic oxidation kinetics. Later, monolithic MA956 exhibited spallation and a linear weight loss, whereas the composite showed a linear weight gain without spallation. Weight loss of the monolithic MA956 resulted from the linking of a multiplicity of randomly oriented and closely spaced surface cracks that facilitated ready spallation. By contrast, cracking of the composite's oxide layer was nonintersecting and aligned nominally parallel with the orientation of the subsurface reinforcing fibers. Oxidative lifetime of monolithic MA956 was projected from the observed oxidation kinetics. Linear elastic, finite element continuum, and micromechanics analyses were performed on coupons of the monolithic and composite materials. Results of the analyses qualitatively agreed well with the observed oxide cracking and spallation behavior of both the MA956 and the Sapphire/MA956 composite coupons.

Titania-Coated Silica Alone and Modified by Sodium Alginate as Sorbents for Heavy Metal Ions

NASA Astrophysics Data System (ADS)

Kołodyńska, D.; Gęca, M.; Skwarek, E.; Goncharuk, O.

2018-04-01

The novel organic-inorganic biohybrid composite adsorbent was synthesized based on nanosized silica-titania modified with alginate within the development of effective adsorbent for heavy metal ions. Effects of metal species Cu(II), Zn(II), Cd(II), and Pb(II); concentrations; pH; temperature; and adsorption onto titania-coated silica (ST20) initial or modified by sodium alginate (ST20-ALG) were studied. The equilibrium and kinetic data of metal ions adsorption were analyzed using Langmuir and Freundlich adsorption models and kinetic models: pseudo first order, pseudo second order, intraparticle kinetic model, and Elovich. The maximum sorption capacities observed were higher for the ST20-ALG composite compared to the initial ST20 oxide for all studied metal ions, namely their values for ST20-ALG were 22.44 mg g- 1 for Cu(II) adsorption, 19.95 mg g- 1 for Zn(II), 18.85 mg g- 1 for Cd(II), and 32.49 mg g- 1 for Pb(II). Structure and properties of initial silica-titania ST20 and modified by sodium alginate ST20-ALG adsorbents were analyzed using nitrogen adsorption/desorption isotherms, ATR-FTIR, SEM-EDS, and pHpzc techniques.

Kinetic transition in the order-disorder transformation at a solid/liquid interface

NASA Astrophysics Data System (ADS)

Galenko, P. K.; Nizovtseva, I. G.; Reuther, K.; Rettenmayr, M.

2018-01-01

Phase-field analysis for the kinetic transition in an ordered crystal structure growing from an undercooled liquid is carried out. The results are interpreted on the basis of analytical and numerical solutions of equations describing the dynamics of the phase field, the long-range order parameter as well as the atomic diffusion within the crystal/liquid interface and in the bulk crystal. As an example, the growth of a binary A50B50 crystal is described, and critical undercoolings at characteristic changes of growth velocity and the long-range order parameter are defined. For rapidly growing crystals, analogies and qualitative differences are found in comparison with known non-equilibrium effects, particularly solute trapping and disorder trapping. The results and model predictions are compared qualitatively with results of the theory of kinetic phase transitions (Chernov 1968 Sov. Phys. JETP 26, 1182-1190) and with experimental data obtained for rapid dendritic solidification of congruently melting alloy with order-disorder transition (Hartmann et al. 2009 Europhys. Lett. 87, 40007 (doi:10.1209/0295-5075/87/40007)). This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

Nanometer-scale hydrogen 'portals' for the control of magnesium hydride formation.

PubMed

Chung, Chia-Jung; Nivargi, Chinmay; Clemens, Bruce

2015-11-21

Magnesium and Mg-based material systems are attractive candidates for hydrogen storage but limited by unsuitable thermodynamic and kinetic properties. In particular, the kinetics are too slow at room temperature and atmospheric pressure. To study the hydride formation kinetics in a controlled way, we have designed a unique 'nanoportal' structure of Pd nanoparticles deposited on epitaxial Mg thin films, through which the hydride will nucleate only under Pd nanoparticles. We propose a growth mechanism for the hydrogenation reaction in the nanoportal structure, which is supported by scanning electron microscopy (SEM) images of hydrogenated samples exhibiting consistent results. Interestingly, the grain boundaries of Mg films play an important role in hydride nucleation and growth processes. Kinetic modeling based on the Johnson-Mehl-Avrami-Kolmogorov (JMAK) formalism seems to agree with the two-dimensional nucleation and growth mechanism hypothesized and the overall reaction rate is limited by hydrogen flux through the interface between the Pd nanoparticle and the underlying Mg film. The fact that in our structure Mg can be transformed completely into MgH2 with only a small percentage of Pd nanoparticles offers possibilities for future on-board storage applications.

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.

Comparative assessment of in vitro release kinetics of calcitonin polypeptide from biodegradable microspheres.

PubMed

Prabhu, Sunil; Sullivan, Jennifer L; Betageri, Guru V

2002-01-01

The objective of our study was to compare the in vitro release kinetics of a sustained-release injectable microsphere formulation of the polypeptide drug, calcitonin (CT), to optimize the characteristics of drug release from poly-(lactide-co-glycolide) (PLGA) copolymer biodegradable microspheres. A modified solvent evaporation and double emulsion technique was used to prepare the microspheres. Release kinetic studies were carried out in silanized tubes and dialysis bags, whereby microspheres were suspended and incubated in phosphate buffered saline, sampled at fixed intervals, and analyzed for drug content using a modified Lowry protein assay procedure. An initial burst was observed whereby about 50% of the total dose of the drug was released from the microspheres within 24 hr and 75% within 3 days. This was followed by a period of slow release over a period of 3 weeks in which another 10-15% of drug was released. Drug release from the dialysis bags was more gradual, and 50% CT was released only after 4 days and 75% after 12 days of release. Scanning electron micrographs revealed spherical particles with channel-like structures and a porous surface after being suspended in an aqueous solution for 5 days. Differential scanning calorimetric studies revealed that CT was present as a mix of amorphous and crystalline forms within the microspheres. Overall, these studies demonstrated that sustained release of CT from PLGA microspheres over a 3-week period is feasible and that release of drug from dialysis bags was more predictable than from tubes.

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

Houtz, Robert, L.

This project focused on a molecular and biochemical characterization of the protein methyltransferases responsible for methylation of the LS and SS in Rubisco, and the associated functional consequences accompanying these modifications. Our results provided some of the most informative structural and mechanistic understandings of SET domain protein methyltransferases. These results also positioned us to provide the first unambiguous assignment of the kinetic reaction mechanism for SET-domain protein methyltransferases, and to design and engineer an alternative substrate for Rubisco LSMT, enabling substrate specificity and functional significance studies. We demonstrated that the minimal substrate recognized by Rubisco LSMT is free lysine asmore » well as monomethyllysine, an observation corroborated both by structural analyses as well as enzymatic activity and subsequent product distribution analyses. Ternary complexes between Rubisco LSMT and free lysine compared to complexes with monomethyllysine demonstrated that the structural basis for multiple methyl group additions is a consequence of hydrogen-bond driven spatial shifts in the amino group of Lys-14, which maintains the direct in-line geometry necessary for SN2 nucleophilic attack. The structural observations are also consistent with the previous proposal that the multiplicity of methyl group additions takes place through a processive mechanism, with successive methyl group additions to an enzyme protein complex which does not disassociate prior to the formation of trimethyllysine. This mechanism has important implications, since the regulation of gene expression by SET domain histone methyltransferases is not only dependent on site-specific lysine methylation, but also the degree of methylation. We examined the kinetic reaction mechanism for three different types of SET domain protein methyltransferases, each under conditions supporting mono-, di-, or trimethyllysine formation corroborated by product analyses. Additionally, the tight initial binding of Rubisco LSMT to Rubisco also allowed us to design a novel immobilized complex between Rubisco and Rubisco LSMT, which allowed for an unambiguous demonstration of the requirement for trimethyllysine formation prior to disassociation of the Rubisco LSMT:Rubisco complex, and therefore proof of the processive mechanism for methyl group transfer. These kinetic studies also demonstrated that an important factor has been overlooked in all kinetic analyses of SET domain protein methyltransferases reported to date. This factor is the influence of the low turnover number for SET domain protein methyltransferases and how, relative to the time-frame of kinetic enzyme assays, this can generate changes in kinetic profiles shifting reciprocal plot patterns from random/ordered bi-bi to the real kinetic reaction mechanism plots of ping-pong. Although the ternary complexes of Rubisco LSMT with S-Adenosylhomocysteine and lysine and monomethyllysine were informative in regard to reaction mechanism, they were not helpful in identifying the mechanism used by Rubisco LSMT for determining substrate specificity. We were unsuccessful at obtaining ternary complexes of Rubisco LSMT with bound synthetic polypeptide substrates, as has been reported for several histone methyltransferases. However, we were able to model a polypeptide sequence corresponding to the N-terminal region of the LS of Rubisco into the apparent substrate binding cleft in Rubisco LSMT. Knowledge of the determinants of polypeptide substrate specificity are important for identifying possible alternate substrates, as well as the possibility of generating more desirable substrates amenable to site-directed mutagenesis experiments unlike Rubisco. We determined that Rubisco LSMT is capable of methylating synthetic polypeptide mimics of the N-terminal region of the LS, both free as well as conjugated to keyhole limpet hemacyanin, but with considerable less efficiency than intact holoenzyme.« less

Reynolds stress structures in a self-similar adverse pressure gradient turbulent boundary layer at the verge of separation.

NASA Astrophysics Data System (ADS)

Atkinson, C.; Sekimoto, A.; Jiménez, J.; Soria, J.

2018-04-01

Mean Reynolds stress profiles and instantaneous Reynolds stress structures are investigated in a self-similar adverse pressure gradient turbulent boundary layer (APG-TBL) at the verge of separation using data from direct numerical simulations. The use of a self-similar APG-TBL provides a flow domain in which the flow gradually approaches a constant non-dimensional pressure gradient, resulting in a flow in which the relative contribution of each term in the governing equations is independent of streamwise position over a domain larger than two boundary layer thickness. This allows the flow structures to undergo a development that is less dependent on the upstream flow history when compared to more rapidly decelerated boundary layers. This APG-TBL maintains an almost constant shape factor of H = 2.3 to 2.35 over a momentum thickness based Reynolds number range of Re δ 2 = 8420 to 12400. In the APG-TBL the production of turbulent kinetic energy is still mostly due to the correlation of streamwise and wall-normal fluctuations, 〈uv〉, however the contribution form the other components of the Reynolds stress tensor are no longer negligible. Statistical properties associated with the scale and location of sweeps and ejections in this APG-TBL are compared with those of a zero pressure gradient turbulent boundary layer developing from the same inlet profile, resulting in momentum thickness based range of Re δ 2 = 3400 to 3770. In the APG-TBL the peak in both the mean Reynolds stress and the production of turbulent kinetic energy move from the near wall region out to a point consistent with the displacement thickness height. This is associated with a narrower distribution of the Reynolds stress and a 1.6 times higher relative number of wall-detached negative uv structures. These structures occupy 5 times less of the boundary layer volume and show a similar reduction in their streamwise extent with respect to the boundary layer thickness. A significantly lower percentage of wall-attached structures is observed in the present case when compared with a similar investigation of a rapidly decelerating APG-TBL, suggesting that these wall-attached features could be the remanent from the lower pressure gradient domain upstream.

Characterization of the Microchemical Structure of Seed Endosperm within a Cellular Dimension among Six Barley Varieties with Distinct Degradation Kinetics, Using Ultraspatially Resolved Synchrotron-Based Infrared Synchrotron-Based Infrared

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

Liu, N.; Yu, P

2010-01-01

Barley varieties have similar chemical composition but exhibit different rumen degradation kinetics and nutrient availability. These biological differences may be related to molecular, structural, and chemical makeup among the seed endosperm tissue. No detailed study was carried out. The objectives of this study were: (1) to use a molecular spectroscopy technique, synchrotron-based Fourier transform infrared microspectroscopy (SFTIRM), to determine the microchemical-structural features in seed endosperm tissue of six developed barley varieties; (2) to study the relationship among molecular-structural characteristics, degradation kinetics, and nutrient availability in six genotypes of barley. The results showed that inherent microchemical-structural differences in the endosperm amongmore » the six barley varieties were detected by the synchrotron-based analytical technique, SFTIRM, with the univariate molecular spectral analysis. The SFTIRM spectral profiles differed (P < 0.05) among the barley samples in terms of the peak ratio and peak area and height intensities of amides I (ca. 1650 cm{sup -1}) and II (ca. 1550 cm{sup -1}), cellulosic compounds (ca. 1240 cm{sup -1}), CHO component peaks (the first peak at the region ca. 1184-1132 cm{sup -1}, the second peak at ca. 1132-1066 cm{sup -1}, and the third peak at ca. 1066-950 cm{sup -1}). With the SFTIRM technique, the structural characteristics of the cereal seeds were illuminated among different cultivars at an ultraspatial resolution. The structural differences of barley seeds may be one reason for the various digestive behaviors and nutritive values in ruminants. The results show weak correlations between the functional groups spectral data (peak area, height intensities, and ratios) and rumen biodegradation kinetics (rate and extent of nutrient degradation). Weak correlations may indicate that limited variations of these six barley varieties might not be sufficient to interpret the relationship between spectroscopic information and the nutrient value of barley grain, although significant differences in biodegradation kinetics were observed. In conclusion, the studies demonstrated the potential of ultraspatially resolved synchrotron based technology (SFTIRM) to reveal the structural and chemical makeup within cellular and subcellular dimensions without destruction of the inherent structure of cereal grain tissue.« less

Effects of Phenylalanine Substitutions in Gramicidin A on the Kinetics of Channel Formation in Vesicles and Channel Structure in SDS Micelles

PubMed Central

Jordan, J. B.; Easton, P. L.; Hinton, J. F.

2005-01-01

The common occurrence of Trp residues at the aqueous-lipid interface region of transmembrane channels is thought to be indicative of its importance for insertion and stabilization of the channel in membranes. To further investigate the effects of Trp→Phe substitution on the structure and function of the gramicidin channel, four analogs of gramicidin A have been synthesized in which the tryptophan residues at positions 9, 11, 13, and 15 are sequentially replaced with phenylalanine. The three-dimensional structure of each viable analog has been determined using a combination of two-dimensional NMR techniques and distance geometry-simulated annealing structure calculations. These phenylalanine analogs adopt a homodimer motif, consisting of two β6.3 helices joined by six hydrogen bonds at their NH2-termini. The replacement of the tryptophan residues does not have a significant effect on the backbone structure of the channels when compared to native gramicidin A, and only small effects are seen on side-chain conformations. Single-channel conductance measurements have shown that the conductance and lifetime of the channels are significantly affected by the replacement of the tryptophan residues (Wallace, 2000; Becker et al., 1991). The variation in conductance appears to be caused by the sequential removal of a tryptophan dipole, thereby removing the ion-dipole interaction at the channel entrance and at the ion binding site. Channel lifetime variations appear to be related to changing side chain-lipid interactions. This is supported by data relating to transport and incorporation kinetics. PMID:15501932

Effects of phenylalanine substitutions in gramicidin A on the kinetics of channel formation in vesicles and channel structure in SDS micelles.

PubMed

Jordan, J B; Easton, P L; Hinton, J F

2005-01-01

The common occurrence of Trp residues at the aqueous-lipid interface region of transmembrane channels is thought to be indicative of its importance for insertion and stabilization of the channel in membranes. To further investigate the effects of Trp-->Phe substitution on the structure and function of the gramicidin channel, four analogs of gramicidin A have been synthesized in which the tryptophan residues at positions 9, 11, 13, and 15 are sequentially replaced with phenylalanine. The three-dimensional structure of each viable analog has been determined using a combination of two-dimensional NMR techniques and distance geometry-simulated annealing structure calculations. These phenylalanine analogs adopt a homodimer motif, consisting of two beta6.3 helices joined by six hydrogen bonds at their NH2-termini. The replacement of the tryptophan residues does not have a significant effect on the backbone structure of the channels when compared to native gramicidin A, and only small effects are seen on side-chain conformations. Single-channel conductance measurements have shown that the conductance and lifetime of the channels are significantly affected by the replacement of the tryptophan residues (Wallace, 2000; Becker et al., 1991). The variation in conductance appears to be caused by the sequential removal of a tryptophan dipole, thereby removing the ion-dipole interaction at the channel entrance and at the ion binding site. Channel lifetime variations appear to be related to changing side chain-lipid interactions. This is supported by data relating to transport and incorporation kinetics.

Kinetic parameters of cholinesterase interactions with organophosphates: retrieval and comparison tools available through ESTHER database: ESTerases, alpha/beta Hydrolase Enzymes and Relatives.

PubMed

Chatonnet, A; Hotelier, T; Cousin, X

1999-05-14

Cholinesterases are targets for organophosphorus compounds which are used as insecticides, chemical warfare agents and drugs for the treatment of disease such as glaucoma, or parasitic infections. The widespread use of these chemicals explains the growing of this area of research and the ever increasing number of sequences, structures, or biochemical data available. Future advances will depend upon effective management of existing information as well as upon creation of new knowledge. The ESTHER database goal is to facilitate retrieval and comparison of data about structure and function of proteins presenting the alpha/beta hydrolase fold. Protein engineering and in vitro production of enzymes allow direct comparison of biochemical parameters. Kinetic parameters of enzymatic reactions are now included in the database. These parameters can be searched and compared with a table construction tool. ESTHER can be reached through internet (http://www.ensam.inra.fr/cholinesterase). The full database or the specialised X-window Client-server system can be downloaded from our ftp server (ftp://ftp.toulouse.inra.fr./pub/esther). Forms can be used to send updates or corrections directly from the web.

Kinetics of the formation of a protein corona around nanoparticles.

PubMed

Zhdanov, Vladimir P; Cho, Nam-Joon

2016-12-01

Interaction of metal or oxide nanoparticles (NPs) with biological soft matter is one of the central phenomena in basic and applied biology-oriented nanoscience. Often, this interaction includes adsorption of suspended proteins on the NP surface, resulting in the formation of the protein corona around NPs. Structurally, the corona contains a "hard" monolayer shell directly contacting a NP and a more distant weakly associated "soft" shell. Chemically, the corona is typically composed of a mixture of distinct proteins. The corresponding experimental and theoretical studies have already clarified many aspects of the corona formation. The process is, however, complex, and its understanding is still incomplete. Herein, we present a kinetic mean-field model of the formation of the "hard" corona with emphasis on the role of (i) protein-diffusion limitations and (ii) interplay between competitive adsorption of distinct proteins and irreversible reconfiguration of their native structure. The former factor is demonstrated to be significant only in the very beginning of the corona formation. The latter factor is predicted to be more important. It may determine the composition of the corona on the time scales comparable or longer than a few hours. Copyright © 2016 Elsevier Inc. All rights reserved.

Pemetrexed degradation by photocatalytic process: Kinetics, identification of transformation products and estimation of toxicity.

PubMed

Secrétan, Philippe-Henri; Karoui, Maher; Levi, Yves; Sadou-Yayé, Hassane; Tortolano, Lionel; Solgadi, Audrey; Yagoubi, Najet; Do, Bernard

2018-05-15

This study employed a UV-A/visible/TiO 2 system to investigate the degradation of pemetrexed, an antifolate agent used in chemotherapy. The laboratory-scale method employed a photostability chamber that could be used to study multiple samples. Reversed-phase HPLC coupled with high-resolution ESI-LTQ-Orbitrap mass spectrometry was used to determine the transformation products (TPs) of PEME. Based on the identified TPs and existing chemical knowledge, the mechanism of degradation of the target compound was proposed. Concentrations were monitored as a function of time, and the degradation kinetics were compared. The structures of seven TPs, four of which have not been described to date, were proposed. Most of the TPs stemmed from OH radical additions to the dihydropyrrole moiety and oxidative decarboxylation of the glutamate residue. Based on the elucidated structures, a computational toxicity assessment was performed, showing that the TPs with higher log D values than the parent compound are more toxic than the PEME itself. To support these findings, the toxicities of irradiated samples on Vibrio fischeri were monitored over time. The experimental results corresponded well with the results of previous computational studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Integrated and spectral energetics of the GLAS general circulation model

NASA Technical Reports Server (NTRS)

Tenenbaum, J.

1981-01-01

Integrated and spectral error energetics of the Goddard Laboratory for Atmospheric Sciences (GLAS) general circulation model are compared with observations for periods in January 1975, 1976, and 1977. For two cases the model shows significant skill in predicting integrated energetics quantities out to two weeks, and for all three cases, the integrated monthly mean energetics show qualitative improvements over previous versions of the model in eddy kinetic energy and barotropic conversions. Fundamental difficulties remain with leakage of energy to the stratospheric level. General circulation model spectral energetics predictions are compared with the corresponding observational spectra on a day by day basis. Eddy kinetic energy can be correct while significant errors occur in the kinetic energy of wavenumber three. Single wavenumber dominance in eddy kinetic energy and the correlation of spectral kinetic and potential energy are demonstrated.

Structural metatransition of energetically tangled crystalline phases.

PubMed

Zhou, Dan; Li, Quan; Zheng, Weitao; Ma, Yanming; Chen, Changfeng

2017-02-08

We solve the longstanding puzzle of pressure induced structural evolution of SnSe using a swarm structure search method combined with first-principles phonon and kinetic barrier calculations. Our results identify a dynamic set of nearly degenerate crystalline SnSe phases that are separated by low kinetic barriers and undergo an unusual type of structural transitions characterized by a dynamically changing mix of the constituent phases. We introduce a new concept of structural metatransition to highlight the transitional nature of such phase transitions. Our theoretical prediction is corroborated by X-ray diffraction measurements, and this intriguing phenomenon offers insights into the enigmatic property variations of SnSe under pressure. This work raises prospects of considerably improving characterization and understanding of intrinsic multiphase crystals and their dynamic evolution.

Comparative evaluation of adsorption kinetics of diclofenac and isoproturon by activated carbon.

PubMed

Torrellas, Silvia A; Rodriguez, Araceli R; Escudero, Gabriel O; Martín, José María G; Rodriguez, Juan G

2015-01-01

Adsorption mechanism of diclofenac and isoproturon onto activated carbon has been proposed using Langmuir and Freundlich isotherms. Adsorption capacity and optimum adsorption isotherms were predicted by nonlinear regression method. Different kinetic equations, pseudo-first-order, pseudo-second-order, intraparticle diffusion model and Bangham kinetic model, were applied to study the adsorption kinetics of emerging contaminants on activated carbon in two aqueous matrices.

KINETIC MODELING OF COUNTERFLOW DIFFUSION FLAMES OF BUTADIENE. (R828193)

EPA Science Inventory

A comprehensive, semi-detailed kinetic scheme was used to simulate the chemical structures of counterflow diffusion and fuel-rich premixed 1,3-butadiene flames, to better understand the formation of polycyclic aromatic hydrocarbons (PAH). The results showed that model predicti...

The initial value problem in Lagrangian drift kinetic theory

NASA Astrophysics Data System (ADS)

Burby, J. W.

2016-06-01

> Existing high-order variational drift kinetic theories contain unphysical rapidly varying modes that are not seen at low orders. These unphysical modes, which may be rapidly oscillating, damped or growing, are ushered in by a failure of conventional high-order drift kinetic theory to preserve the structure of its parent model's initial value problem. In short, the (infinite dimensional) system phase space is unphysically enlarged in conventional high-order variational drift kinetic theory. I present an alternative, `renormalized' variational approach to drift kinetic theory that manifestly respects the parent model's initial value problem. The basic philosophy underlying this alternate approach is that high-order drift kinetic theory ought to be derived by truncating the all-orders system phase-space Lagrangian instead of the usual `field particle' Lagrangian. For the sake of clarity, this story is told first through the lens of a finite-dimensional toy model of high-order variational drift kinetics; the analogous full-on drift kinetic story is discussed subsequently. The renormalized drift kinetic system, while variational and just as formally accurate as conventional formulations, does not support the troublesome rapidly varying modes.

Competition between crystallization and vitrification of the rigid amorphous fraction in poly(3-hydroxybutyrate)

NASA Astrophysics Data System (ADS)

Di Lorenzo, Maria Laura; Righetti, Maria Cristina; Gazzano, Massimo

2012-07-01

Semicrystalline polymers have a metastable nanophase structure, where the various nanophases can be crystal, liquid, glass, or mesophase. This multi-level structure is determined by a competition among self-organization, crystallization, and vitrification of the amorphous segments and is established during material processing. The kinetics of such competition is here determined for poly(3-hydroxybutyrate) (PHB), as vitrification/devitrification of the rigid amorphous fraction strongly affects crystallization kinetics of PHB.

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

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

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

Steady state plasma [3H]-noradrenaline kinetics in quadriplegic chronic spinal cord injury patients.

PubMed

Krum, H; Brown, D J; Rowe, P R; Louis, W J; Howes, L G

1990-08-01

1. Steady state plasma noradrenaline kinetics were measured in eight male quadriplegic patients and in eight age and sex matched controls. 2. Plasma noradrenaline levels were significantly lower in quadriplegic patients compared to controls. Noradrenaline spillover rate was markedly reduced in quadriplegics compared to controls while noradrenaline clearance was similar in both groups. 3. Noradrenaline kinetics in quadriplegic patients differ from peripheral autonomic neuropathy patients where reductions in both the spillover and clearance of noradrenaline are present.

Small amplitude Kinetic Alfven waves in a superthermal electron-positron-ion plasma

NASA Astrophysics Data System (ADS)

Adnan, Muhammad; Mahmood, Sahahzad; Qamar, Anisa; Tribeche, Mouloud

2016-11-01

We are investigating the propagating properties of coupled Kinetic Alfven-acoustic waves in a low beta plasma having superthermal electrons and positrons. Using the standard reductive perturbation method, a nonlinear Korteweg-de Vries (KdV) type equation is derived which describes the evolution of Kinetic Alfven waves. It is found that nonlinearity and Larmor radius effects can compromise and give rise to solitary structures. The parametric role of superthermality and positron content on the characteristics of solitary wave structures is also investigated. It is found that only sub-Alfvenic and compressive solitons are supported in the present model. The present study may find applications in a low β electron-positron-ion plasma having superthermal electrons and positrons.

Note: Setup for chemical atmospheric control during in situ grazing incidence X-ray scattering of printed thin films

DOE PAGES

Pröller, Stephan; Moseguí González, Daniel; Zhu, Chenhuii; ...

2017-06-01

In order to tailor the assembling of polymers and organic molecules, a deeper understanding of the kinetics involved in thin film production is necessary. While post-production characterization only provides insight on the final film structure, more sophisticated experimental setups are needed to probe the structure formation processes in situ during deposition. The drying kinetics of a deposited organic thin film strongly influences the assembling process on the nanometer scale. Lastly, this work presents an experimental setup that enables fine control of the atmosphere composition surrounding the sample during slot die coating, while simultaneously probing the film formation kinetics using inmore » situ grazing incidence X-ray scattering and spectroscopy.« less

Zero kinetic energy photoelectron spectroscopy of tryptamine and the dissociation pathway of the singly hydrated cation cluster.

PubMed

Gu, Quanli; Knee, J L

2012-09-14

The relative ionization energies of tryptamine conformations are determined by zero kinetic energy photoelectron spectroscopy and photoionization efficiency measurements. The relative cationic conformational stabilities are compared to the published results for the neutral molecule. In the cation, the interaction strength changes significantly between amino group and either the phenyl or the pyrrole moiety of the indole chromophore where most of the positive charge is located, leading to different conformational structures and relative conformer energies in the cation. In particular, the measured adiabatic ionization potential of isomer B is 60,928 ± 5 cm(-1), at least 400 cm(-1) higher than any of the 6 other tryptamine isomers which all have ionization potentials within 200 cm(-1) of each other. In addition to the monomer, measurements were made on the A conformer of the tryptamine(+)-H(2)O complex including the ionization threshold and cation dissociation energy measured using a threshold photoionization fragmentation method. The water cluster exhibits an unexpectedly high ionization potential of 60,307 ± 100 cm(-1), close to the conformer A monomer of 60 320 ± 100 cm(-1). It also exhibits surprisingly low dissociation energy of 1750 ± 150 cm(-1) compared to other H-bonding involved cation-H(2)O complexes which are typically several thousands of wavenumbers higher. Quantum chemical calculations indicate that upon ionization the structure of the parent molecule in the water complex remains mostly unchanged due to the rigid intermolecular double hydrogen bonded water molecule bridging the monomer backbone and its side chain thus leading to the high ionization potential in the water cluster. The surprisingly low dissociation energy measured in the cationic water complex is attributed to the formation of a much more stable structural isomer H(+) in the exit channel.

Molecular basis of thermostability enhancement of Renilla luciferase at higher temperatures by insertion of a disulfide bridge into the structure.

PubMed

Fanaei Kahrani, Zahra; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

2017-02-01

Renilla luciferase (RLuc), also known as Renilla-luciferin 2-monooxygenase, is a light producing enzyme used in many biotechnological applications such as bioreporters. However, its kinetics stability -especially at higher temperatures- is a limiting factor for developing thermostable bioreporters. The aim of this study was to improve the stability of super Renilla luciferase 8 (SRLuc 8) which is a red-emitter variety of RLuc at higher temperatures, by introduction of a disulfide bridge into its structure. In this study, the choice of the proper disulfide bond formation was based on computational methods and enzyme functionality (active site position) which is called geometric-functional method. N45 and A71 at the N-terminal of the enzyme were selected for directed evolution. The engineered luciferase was called C-SRLuc 8 and its activity and stability were assayed. The results indicated that the kinetic stability of C-SRLuc 8 increased significantly at 60°C to 70°C as compared to SRLuc 8; the residual activity of C-SRLuc 8 was approximately 20% after incubation at 65°C for 5min. Moreover, the enzyme activity decreased compared with SRLuc 8. The molecular basis of the structural changes was considered using molecular dynamics simulations and the results indicated that the N45C/A71C crosslink was involved in a hotspot foldon which seemed to be the rate-limiting step of conformational collapse at higher temperatures. The present study may provide an opportunity for the development of the next-generation of thermostable RLuc-based biosensors. Copyright © 2016. Published by Elsevier B.V.

A Histidine Aspartate Ionic Lock Gates the Iron Passage in Miniferritins from Mycobacterium smegmatis*

PubMed Central

Williams, Sunanda Margrett; Chandran, Anu V.; Vijayabaskar, Mahalingam S.; Roy, Sourav; Balaram, Hemalatha; Vishveshwara, Saraswathi; Vijayan, Mamannamana; Chatterji, Dipankar

2014-01-01

Dps (DNA-binding protein from starved cells) are dodecameric assemblies belonging to the ferritin family that can bind DNA, carry out ferroxidation, and store iron in their shells. The ferritin-like trimeric pore harbors the channel for the entry and exit of iron. By representing the structure of Dps as a network we have identified a charge-driven interface formed by a histidine aspartate cluster at the pore interface unique to Mycobacterium smegmatis Dps protein, MsDps2. Site-directed mutagenesis was employed to generate mutants to disrupt the charged interactions. Kinetics of iron uptake/release of the wild type and mutants were compared. Crystal structures were solved at a resolution of 1.8–2.2 Å for the various mutants to compare structural alterations vis à vis the wild type protein. The substitutions at the pore interface resulted in alterations in the side chain conformations leading to an overall weakening of the interface network, especially in cases of substitutions that alter the charge at the pore interface. Contrary to earlier findings where conserved aspartate residues were found crucial for iron release, we propose here that in the case of MsDps2, it is the interplay of negative-positive potentials at the pore that enables proper functioning of the protein. In similar studies in ferritins, negative and positive patches near the iron exit pore were found to be important in iron uptake/release kinetics. The unique ionic cluster in MsDps2 makes it a suitable candidate to act as nano-delivery vehicle, as these gated pores can be manipulated to exhibit conformations allowing for slow or fast rates of iron release. PMID:24573673

Administration of structured lipid composed of MCT and fish oil reduces net protein catabolism in enterally fed burned rats.

PubMed Central

Teo, T C; DeMichele, S J; Selleck, K M; Babayan, V K; Blackburn, G L; Bistrian, B R

1989-01-01

The effects of enteral feeding with safflower oil or a structured lipid (SL) derived from 60% medium-chain triglyceride (MCT) and 40% fish oil (MCT/fish oil) on protein and energy metabolism were compared in gastrostomy-fed burned rats (30% body surface area) by measuring oxygen consumption, carbon dioxide production, nitrogen balance, total liver protein, whole-body leucine kinetics, and rectus muscle and liver protein fractional synthetic rates (FSR, %/day). Male Sprague-Dawley rats (195 +/- 5g) received 50 ml/day of an enteral regimen containing 50 kcal, 2 g amino acids, and 40% nonprotein calories as lipid for three days. Protein kinetics were estimated by using a continuous L-[1-14C] leucine infusion technique on day 2. Thermally injured rats enterally fed MCT/fish oil yielded significantly higher daily and cumulative nitrogen balances (p less than or equal to 0.025) and rectus muscle (39%) FSR (p less than or equal to 0.05) when compared with safflower oil. MCT/fish oil showed a 22% decrease (p less than or equal to 0.005) in per cent flux oxidized and a 7% (p less than or equal to 0.05) decrease in total energy expenditure (TEE) versus safflower oil. A 15% increase in liver FSR was accompanied by a significant elevation (p less than or equal to 0.025) in total liver protein with MCT/fish oil. This novel SL shares the properties of other structured lipids in that it reduces the net protein catabolic effects of burn injury, in part, by influencing tissue protein synthetic rates. The reduction in TEE is unique to MCT/fish oil and may relate to the ability of fish oil to diminish the injury response. PMID:2500898

Center for Extended Magnetohydrodynamics Modeling - Final Technical Report

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

Parker, Scott

This project funding supported approximately 74 percent of a Ph.D. graduate student, not including costs of travel and supplies. We had a highly successful research project including the development of a second-order implicit electromagnetic kinetic ion hybrid model [Cheng 2013, Sturdevant 2016], direct comparisons with the extended MHD NIMROD code and kinetic simulation [Schnack 2013], modeling of slab tearing modes using the fully kinetic ion hybrid model and finally, modeling global tearing modes in cylindrical geometry using gyrokinetic simulation [Chen 2015, Chen 2016]. We developed an electromagnetic second-order implicit kinetic ion fluid electron hybrid model [Cheng 2013]. As a firstmore » step, we assumed isothermal electrons, but have included drift-kinetic electrons in similar models [Chen 2011]. We used this simulation to study the nonlinear evolution of the tearing mode in slab geometry, including nonlinear evolution and saturation [Cheng 2013]. Later, we compared this model directly to extended MHD calculations using the NIMROD code [Schnack 2013]. In this study, we investigated the ion-temperature-gradient instability with an extended MHD code for the first time and got reasonable agreement with the kinetic calculation in terms of linear frequency, growth rate and mode structure. We then extended this model to include orbit averaging and sub-cycling of the ions and compared directly to gyrokinetic theory [Sturdevant 2016]. This work was highlighted in an Invited Talk at the International Conference on the Numerical Simulation of Plasmas in 2015. The orbit averaging sub-cycling multi-scale algorithm is amenable to hybrid architectures with GPUS or math co-processors. Additionally, our participation in the Center for Extend Magnetohydrodynamics motivated our research on developing the capability for gyrokinetic simulation to model a global tearing mode. We did this in cylindrical geometry where the results could be benchmarked with existing eigenmode calculations. First, we developed a gyrokinetic code capable of simulating long wavelengths using a fluid electron model [Chen 2015]. We benchmarked this code with an eigenmode calculation. Besides having to rewrite the field solver due to the breakdown in the gyrokinetic ordering for long wavelengths, very high radial resolution was required. We developed a technique where we used the solution from the eigenmode solver to specify radial boundary conditions allowing for a very high radial resolution of the inner solution. Using this technique enabled us to use our direct algorithm with gyrokinetic ions and drift kinetic electrons [Chen 2016]. This work was highlighted in an Invited Talk at the American Physical Society - Division of Plasma Physics in 2015.« less

Application of the dual-kinetic-balance sets in the relativistic many-body problem of atomic structure

NASA Astrophysics Data System (ADS)

Beloy, Kyle; Derevianko, Andrei

2008-09-01

The dual-kinetic-balance (DKB) finite basis set method for solving the Dirac equation for hydrogen-like ions [V.M. Shabaev et al., Phys. Rev. Lett. 93 (2004) 130405] is extended to problems with a non-local spherically-symmetric Dirac-Hartree-Fock potential. We implement the DKB method using B-spline basis sets and compare its performance with the widely-employed approach of Notre Dame (ND) group [W.R. Johnson, S.A. Blundell, J. Sapirstein, Phys. Rev. A 37 (1988) 307-315]. We compare the performance of the ND and DKB methods by computing various properties of Cs atom: energies, hyperfine integrals, the parity-non-conserving amplitude of the 6s-7s transition, and the second-order many-body correction to the removal energy of the valence electrons. We find that for a comparable size of the basis set the accuracy of both methods is similar for matrix elements accumulated far from the nuclear region. However, for atomic properties determined by small distances, the DKB method outperforms the ND approach. In addition, we present a strategy for optimizing the size of the basis sets by choosing progressively smaller number of basis functions for increasingly higher partial waves. This strategy exploits suppression of contributions of high partial waves to typical many-body correlation corrections.

Chromophoric spin-labeled β-lactam antibiotics for ENDOR structural characterization of reaction intermediates of class A and class C β-lactamases

NASA Astrophysics Data System (ADS)

Mustafi, Devkumar; Hofer, Jennifer E.; Huang, Wanzhi; Palzkill, Timothy; Makinen, Marvin W.

2004-05-01

The chromophoric spin-label substrate 6- N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M -1 cm -1 at 275 nm compared to 670 M -1 cm -1 at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/ KM, determined under initial velocity conditions, were 637±36 s -1 and 13.8±1.4×10 6 M -1 s -1, respectively, for hydrolysis catalyzed by TEM-1 β-lactamase of E. coli, and 0.5±0.04 s -1 and 3.9±0.4×10 4 M -1 s -1 for hydrolysis catalyzed by the β-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 β-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H 2O (30:70, v:v) cryosolvent mixtures buffered to pH ∗ 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 °C was ≥3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 β-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme.

A study on the non Maxwellian nature of ion velocity distribution functions using Magnetospheric Multiscale (MMS) data

NASA Astrophysics Data System (ADS)

Valentini, F.; Perri, S.; Yordanova, E.; Paterson, W. R.; Gershman, D. J.; Giles, B. L.; Pollock, C. J.; Dorelli, J.; Avanov, L. A.; Lavraud, B.; Saito, Y.; Nakamura, R.; Fischer, D.; Baumjohann, W.; Plaschke, F.; Narita, Y.; Magnes, W.; Russell, C. T.; Strangeway, R. J.; Le Contel, O.

2017-12-01

The interplanetary space is permeated by a plasma where effects of collisions among particles can be considered negligible. In such a weekly collisional medium, in the range of scales where kinetic effects dominate the plasma dynamics, the particle velocity distribution functions (VDF) are observed to be far from the thermodynamic equilibrium. Moreover, recent numerical self-consistent and nonlinear models of plasma turbulence dynamics have shown the presence of significant non-Maxwellian features in the particle VDFs, caused by kinetic effects, which become dominant in the turbulent cascade at ion scales. In particular, a kinetic hybrid Vlasov-Maxwell (HVM) numerical code, which reproduces the turbulent energy cascade down to ion scales, has highlighted significant departures of the ion VDFs from Maxwellian and a local temperature anisotropy close to current sheets structures generated by the turbulent cascade and close to regions of high ion vorticity.In this work, we make use of the high resolution (150 ms) ion and electron VDFs from Fast Plasma Investigation (FPI) instrument on board MMS and the about 1kHz resolution magnetic field data to investigate the possible presence of non-Maxwellian features in the ion VDFs close to intermittent magnetic structures and regions of high current density and vorticity. The data are relevant to a period where the MMS spacecraft was immersed in the turbulent magnetosheath (see Yordanova et al., 2016). The aim is to compare the analysis made by Valentini et al., 2016 on proton and alpha particles in the HVM simulations with the analysis made on the MMS data, and to deeply characterize the ion dynamics in the near Earth plasma. It is worth mentioning that thanks to its very high resolution plasma data, MMS has given the opportunity to study in details kinetic effects in plasma turbulence, down to electron scales.

Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.

1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

Structural and Biochemical Studies on the Regulation of Biotin Carboxylase by Substrate Inhibition and Dimerization

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

C Chou; L Tong

2011-12-31

Biotin carboxylase (BC) activity is shared among biotin-dependent carboxylases and catalyzes the Mg-ATP-dependent carboxylation of biotin using bicarbonate as the CO{sub 2} donor. BC has been studied extensively over the years by structural, kinetic, and mutagenesis analyses. Here we report three new crystal structures of Escherichia coli BC at up to 1.9 {angstrom} resolution, complexed with different ligands. Two structures are wild-type BC in complex with two ADP molecules and two Ca{sup 2+} ions or two ADP molecules and one Mg{sup 2+} ion. One ADP molecule is in the position normally taken by the ATP substrate, whereas the other ADPmore » molecule occupies the binding sites of bicarbonate and biotin. One Ca{sup 2+} ion and the Mg{sup 2+} ion are associated with the ADP molecule in the active site, and the other Ca{sup 2+} ion is coordinated by Glu-87, Glu-288, and Asn-290. Our kinetic studies confirm that ATP shows substrate inhibition and that this inhibition is competitive against bicarbonate. The third structure is on the R16E mutant in complex with bicarbonate and Mg-ADP. Arg-16 is located near the dimer interface. The R16E mutant has only a 2-fold loss in catalytic activity compared with the wild-type enzyme. Analytical ultracentrifugation experiments showed that the mutation significantly destabilized the dimer, although the presence of substrates can induce dimer formation. The binding modes of bicarbonate and Mg-ADP are essentially the same as those to the wild-type enzyme. However, the mutation greatly disrupted the dimer interface and caused a large re-organization of the dimer. The structures of these new complexes have implications for the catalysis by BC.« less

Structural and Biochemical Studies on the Regulation of Biotin Carboxylase by Substrate Inhibition and Dimerization

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

Chou, Chi-Yuan; Tong, Liang

2012-06-19

Biotin carboxylase (BC) activity is shared among biotin-dependent carboxylases and catalyzes the Mg-ATP-dependent carboxylation of biotin using bicarbonate as the CO{sub 2} donor. BC has been studied extensively over the years by structural, kinetic, and mutagenesis analyses. Here we report three new crystal structures of Escherichia coli BC at up to 1.9 {angstrom} resolution, complexed with different ligands. Two structures are wild-type BC in complex with two ADP molecules and two Ca{sup 2+} ions or two ADP molecules and one Mg{sup 2+} ion. One ADP molecule is in the position normally taken by the ATP substrate, whereas the other ADPmore » molecule occupies the binding sites of bicarbonate and biotin. One Ca{sup 2+} ion and the Mg{sup 2+} ion are associated with the ADP molecule in the active site, and the other Ca{sup 2+} ion is coordinated by Glu-87, Glu-288, and Asn-290. Our kinetic studies confirm that ATP shows substrate inhibition and that this inhibition is competitive against bicarbonate. The third structure is on the R16E mutant in complex with bicarbonate and Mg-ADP. Arg-16 is located near the dimer interface. The R16E mutant has only a 2-fold loss in catalytic activity compared with the wild-type enzyme. Analytical ultracentrifugation experiments showed that the mutation significantly destabilized the dimer, although the presence of substrates can induce dimer formation. The binding modes of bicarbonate and Mg-ADP are essentially the same as those to the wild-type enzyme. However, the mutation greatly disrupted the dimer interface and caused a large re-organization of the dimer. The structures of these new complexes have implications for the catalysis by BC.« less

pH driven fibrillar aggregation of the super-sweet protein Y65R-MNEI: A step-by-step structural analysis.

PubMed

Pica, Andrea; Leone, Serena; Di Girolamo, Rocco; Donnarumma, Federica; Emendato, Alessandro; Rega, Michele Fortunato; Merlino, Antonello; Picone, Delia

2018-04-01

MNEI and its variant Y65R-MNEI are sweet proteins with potential applications as sweeteners in food industry. Also, they are often used as model systems for folding and aggregation studies. X-ray crystallography was used to structurally characterize Y65R-MNEI at five different pHs, while circular dichroism and fluorescence spectroscopy were used to study their thermal and chemical stability. ThT assay and AFM were used for studying the kinetics of aggregation and morphology of the aggregates. Crystal structures of Y65R-MNEI revealed the existence of a dimer in the asymmetric unit, which, depending on the pH, assumes either an open or a closed conformation. The pH dramatically affects kinetics of formation and morphology of the aggregates: both MNEI and Y65R-MNEI form fibrils at acidic pH while amorphous aggregates are observed at neutral pH. The mutation Y65R induces structural modifications at the C-terminal region of the protein, which account for the decreased stability of the mutant when compared to MNEI. Furthermore, the pH-dependent conformation of the Y65R-MNEI dimer may explain the different type of aggregates formed as a function of pH. The investigation of the structural bases of aggregation gets us closer to the possibility of controlling such process, either by tuning the physicochemical environmental parameters or by site directed mutagenesis. This knowledge is helpful to expand the range of stability of proteins with potential industrial applications, such as MNEI and its mutant Y65R-MNEI, which should ideally preserve their structure and soluble state through a wide array of conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Cardiorespiratory Kinetics Determined by Pseudo-Random Binary Sequences - Comparisons between Walking and Cycling.

PubMed

Koschate, J; Drescher, U; Thieschäfer, L; Heine, O; Baum, K; Hoffmann, U

2016-12-01

This study aims to compare cardiorespiratory kinetics as a response to a standardised work rate protocol with pseudo-random binary sequences between cycling and walking in young healthy subjects. Muscular and pulmonary oxygen uptake (V̇O 2 ) kinetics as well as heart rate kinetics were expected to be similar for walking and cycling. Cardiac data and V̇O 2 of 23 healthy young subjects were measured in response to pseudo-random binary sequences. Kinetics were assessed applying time series analysis. Higher maxima of cross-correlation functions between work rate and the respective parameter indicate faster kinetics responses. Muscular V̇O 2 kinetics were estimated from heart rate and pulmonary V̇O 2 using a circulatory model. Muscular (walking vs. cycling [mean±SD in arbitrary units]: 0.40±0.08 vs. 0.41±0.08) and pulmonary V̇O 2 kinetics (0.35±0.06 vs. 0.35±0.06) were not different, although the time courses of the cross-correlation functions of pulmonary V̇O 2 showed unexpected biphasic responses. Heart rate kinetics (0.50±0.14 vs. 0.40±0.14; P=0.017) was faster for walking. Regarding the biphasic cross-correlation functions of pulmonary V̇O 2 during walking, the assessment of muscular V̇O 2 kinetics via pseudo-random binary sequences requires a circulatory model to account for cardio-dynamic distortions. Faster heart rate kinetics for walking should be considered by comparing results from cycle and treadmill ergometry. © Georg Thieme Verlag KG Stuttgart · New York.

Mechanism of drug release from silica-gelatin aerogel-Relationship between matrix structure and release kinetics.

PubMed

Veres, Péter; Kéri, Mónika; Bányai, István; Lázár, István; Fábián, István; Domingo, Concepción; Kalmár, József

2017-04-01

Specific features of a silica-gelatin aerogel (3 wt.% gelatin content) in relation to drug delivery has been studied. It was confirmed that the release of both ibuprofen (IBU) and ketoprofen (KET) is about tenfold faster from loaded silica-gelatin aerogel than from pure silica aerogel, although the two matrices are structurally very similar. The main goal of the study was to understand the mechanistic background of the striking difference between the delivery properties of these closely related porous materials. Hydrated and dispersed silica-gelatin aerogel has been characterized by NMR cryoporometry, diffusiometry and relaxometry. The pore structure of the silica aerogel remains intact when it disintegrates in water. In contrast, dispersed silica-gelatin aerogel develops a strong hydration sphere, which reshapes the pore walls and deforms the pore structure. The drug release kinetics was studied on a few minutes time scale with 1s time resolution. Simultaneous evaluation of all relevant kinetic and structural information confirmed that strong hydration of the silica-gelatin skeleton facilitates the rapid desorption and dissolution of the drugs from the loaded aerogel. Such a driving force is not operative in pure silica aerogels. Copyright © 2017 Elsevier B.V. All rights reserved.

Carbon monoxide recombination dynamics in truncated hemoglobins studied with visible-pump midIR-probe spectroscopy.

PubMed

Lapini, Andrea; Di Donato, Mariangela; Patrizi, Barbara; Marcelli, Agnese; Lima, Manuela; Righini, Roberto; Foggi, Paolo; Sciamanna, Natascia; Boffi, Alberto

2012-08-02

Carbon monoxide recombination dynamics upon photodissociation with visible light has been characterized by means of ultrafast visible-pump/MidIR probe spectroscopy for the truncated hemoglobins from Thermobifida fusca and Bacillus subtilis. Photodissociation has been induced by exciting the sample at two different wavelengths: 400 nm, corresponding to the heme absorption in the B-band, and 550 nm, in the Q-bands. The bleached iron-CO coordination band located at 1850-1950 cm(-1) and the free CO absorption band in the region 2050-2200 cm(-1) have been observed by probe pulses tuned in the appropriate infrared region. The kinetic traces measured at 1850-1950 cm(-1) reveal multiexponential subnanosecond dynamics that have been interpreted as arising from fast geminate recombination of the photolyzed CO. A compared analysis of the crystal structure of the two proteins reveals a similar structure of their distal heme pocket, which contains conserved polar and aromatic amino acid residues closely interacting with the iron ligand. Although fast geminate recombination is observed in both proteins, several kinetic differences can be evidenced, which can be interpreted in terms of a different structural flexibility of the corresponding heme distal pockets. The analysis of the free CO band-shape and of its dynamic evolution brings out novel features about the nature of the docking site inside the protein cavity.

Elastase kinetics and structural features of colorimetric and fluorescent peptides on cellulose nanocrystals

USDA-ARS?s Scientific Manuscript database

Human neutrophil elastase (HNE) and porcine pancreatic elastase (PPE) are serine proteases with destructive proteolytic activity. Because of this activity, there is considerable interest in elastase sensors. Herein we report the synthesis, characterization, and kinetic profiles of tri- and tetrapept...

Shock tube study of the fuel structure effects on the chemical kinetic mechanisms responsible for soot formation, part 2

NASA Technical Reports Server (NTRS)

Frenklach, M.; Clary, D. W.; Ramachandra, M. K.

1985-01-01

Soot formation in oxidation of allene, 1,3-butadiene, vinylacetylene and chlorobenzene and in pyrolysis of ethylene, vinylacetylene, 1-butene, chlorobenzene, acetylen-hydrogen, benzene-acetylene, benzene-butadiene and chlorobenzene-acetylene argon-diluted mixtures was studied behind reflected shock waves. The results are rationalized within the framework of the conceptual models. It is shown that vinylacetylene is much less sooty than allene, which indicates that conjugation by itself is not a sufficient factor for determining the sooting tendency of a molecule. Structural reactivity in the context of the chemical kinetics is the dominant factor in soot formation. Detailed chemical kinetic modeling of soot formation in pyrolysis of acetylene is reported. The main mass growth was found to proceed through a single dominant route composed of conventional radical reactions. The practically irreversible formation reactions of the fused polycyclic aromatics and the overshoot by hydrogen atom over its equilibrium concentration are the g-driving kinetic forces for soot formation.

Substrate specificity and kinetic properties of enzymes belonging to the hormone-sensitive lipase family: comparison with non-lipolytic and lipolytic carboxylesterases.

PubMed

Chahinian, Henri; Ali, Yassine Ben; Abousalham, Abdelkarim; Petry, Stefan; Mandrich, Luigi; Manco, Guiseppe; Canaan, Stephane; Sarda, Louis

2005-12-30

We have studied the kinetics of hydrolysis of triacylglycerols, vinyl esters and p-nitrophenyl butyrate by four carboxylesterases of the HSL family, namely recombinant human hormone-sensitive lipase (HSL), EST2 from Alicyclobacillus acidocaldarius, AFEST from Archeoglobus fulgidus, and protein RV1399C from Mycobacterium tuberculosis. The kinetic properties of enzymes of the HSL family have been compared to those of a series of lipolytic and non-lipolytic carboxylesterases including human pancreatic lipase, guinea pig pancreatic lipase related protein 2, lipases from Mucor miehei and Thermomyces lanuginosus, cutinase from Fusarium solani, LipA from Bacillus subtilis, porcine liver esterase and Esterase A from Aspergilus niger. Results indicate that human HSL, together with other lipolytic carboxylesterases, are active on short chain esters and hydrolyze water insoluble trioctanoin, vinyl laurate and olive oil, whereas the action of EST2, AFEST, protein RV1399C and non-lipolytic carboxylesterases is restricted to solutions of short chain substrates. Lipolytic and non-lipolytic carboxylesterases can be differentiated by their respective value of K(0.5) (apparent K(m)) for the hydrolysis of short chain esters. Among lipolytic enzymes, those possessing a lid domain display higher activity on tributyrin, trioctanoin and olive oil suggesting, then, that the lid structure contributes to enzyme binding to triacylglycerols. Progress reaction curves of the hydrolysis of p-nitrophenyl butyrate by lipolytic carboxylesterases with lid domain show a latency phase which is not observed with human HSL, non-lipolytic carboxylesterases, and lipolytic enzymes devoid of a lid structure as cutinase.

Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.

PubMed

Bandyopadhyay, Pradipta; Kuntz, Irwin D

2009-01-01

The determination of protein structure using distance constraints is a new and promising field of study. One implementation involves attaching residues of a protein using a cross-linking agent, followed by protease digestion, analysis of the resulting peptides by mass spectroscopy, and finally sequence threading to detect the protein folds. In the present work, we carry out computational modeling of the kinetics of cross-linking reactions in proteins using the master equation approach. The rate constants of the cross-linking reactions are estimated using the pKas and the solvent-accessible surface areas of the residues involved. This model is tested with fibroblast growth factor (FGF) and cytochrome C. It is consistent with the initial experimental rate data for individual lysine residues for cytochrome C. Our model captures all observed cross-links for FGF and almost 90% of the observed cross-links for cytochrome C, although it also predicts cross-links that were not observed experimentally (false positives). However, the analysis of the false positive results is complicated by the fact that experimental detection of cross-links can be difficult and may depend on specific experimental conditions such as pH, ionic strength. Receiver operator characteristic plots showed that our model does a good job in predicting the observed cross-links. Molecular dynamics simulations showed that for cytochrome C, in general, the two lysines come closer for the observed cross-links as compared to the false positive ones. For FGF, no such clear pattern exists. The kinetic model and MD simulation can be used to study proposed cross-linking protocols.

Non-isothermal crystallization kinetics and characterization of biodegradable poly(butylene succinate-co-neopentyl glycol succinate) copolyesters.

PubMed

Xie, Wen-Jie; Zhou, Xiao-Ming

2015-01-01

Both biodegradable aliphatic neat poly(butylene succinate) (PBS) and poly(butylene succinate-co-neopentyl glycol succinate) (P(BS-co-NPGS)) copolyesters with different 1,4-butanediol/neopentyl glycol ratios were synthesized through a two-step process of transesterification and polycondensation using stannous chloride and 4-Methylbenzenesulfonic acid as the co-catalysts. The structure, non-isothermal crystallization behavior, crystalline morphology and crystal structure of neat PBS and P(BS-co-NPGS) copolyesters were characterized by (1)H NMR, differential scanning calorimetry (DSC), polarized optical microscope (POM) and wide angle X-ray diffraction (WAXD), respectively. The Avrami equation modified by Jeziorny and Mo's method was employed to describe the non-isothermal crystallization kinetics of the neat PBS and its copolyesters. The modified Avrami equation could adequately describe the primary stage of non-isothermal crystallization kinetics of the neat PBS and its copolyesters. Mo's method provided a fairly satisfactory description of the non-isothermal crystallization of neat PBS and its copolyesters. Interestingly, the values of 1/t1/2, Zc and F(T) obtained by the modified Avrami equation and Mo's method analysis indicated that the crystallization rate increased first and then decreased with an increase of NPGS content compared that of neat PBS, whereas the crystallization mechanism almost kept unchanged. The results of tensile testing showed that the ductility of PBS was largely improved by incorporating NPGS units. The elongation at break increased remarkably with increasing NPGS content. In particular, the sample with 20% NPGS content showed around 548% elongation at break. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Kinetic, Thermodynamic, and Structural Insight into the Mechanism of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis

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

Wubben, Thomas J.; Mesecar, Andrew D.; UIC)

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine (PhP) to form dephosphocoenzyme A. This reaction sits at the branch point between the de novo pathway and the salvage pathway, and has been shown to be a rate-limiting step in the biosynthesis of CoA. Importantly, bacterial and mammalian PPATs share little sequence homology, making the enzyme a potential target for antibiotic development. A series of steady-state kinetic, product inhibition, and direct binding studies with Mycobacterium tuberculosis PPAT (MtPPAT) was conducted and suggests that the enzyme utilizesmore » a nonrapid-equilibrium random bi-bi mechanism. The kinetic response of MtPPAT to the binding of ATP was observed to be sigmoidal under fixed PhP concentrations, but substrate inhibition was observed at high PhP concentrations under subsaturating ATP concentrations, suggesting a preferred pathway to ternary complex formation. Negative cooperativity in the kinetic response of MtPPAT to PhP binding was observed under certain conditions and confirmed thermodynamically by isothermal titration calorimetry, suggesting the formation of an asymmetric quaternary structure during sequential ligation of substrates. Asymmetry in binding was also observed in isothermal titration calorimetry experiments with dephosphocoenzyme A and CoA. X-ray structures of MtPPAT in complex with PhP and the nonhydrolyzable ATP analogue adenosine-5'-[({alpha},{beta})-methyleno]triphosphate were solved to 1.57 {angstrom} and 2.68 {angstrom}, respectively. These crystal structures reveal small conformational changes in enzyme structure upon ligand binding, which may play a role in the nonrapid-equilibrium mechanism. We suggest that the proposed kinetic mechanism and asymmetric character in MtPPAT ligand binding may provide a means of reaction and pathway regulation in addition to that of the previously determined CoA feedback.« less

A kinetic theory for age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Chou, Tom; Greenman, Chris

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but they are structurally unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Conversely, current theories that include size-dependent population dynamics (e.g., carrying capacity) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a BBGKY-like hierarchy. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution. NSF.

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

French, Jarrod B.; Ealick, Steven E., E-mail: see3@cornell.edu

The crystal structure of 5-hydroxyisourate hydrolase from K. pneumoniae and the steady-state kinetic parameters of the native enzyme as well as several mutants provide insights into the catalytic mechanism of this enzyme and the possible roles of the active-site residues. The stereospecific oxidative degradation of uric acid to (S)-allantoin has recently been demonstrated to proceed via two unstable intermediates and requires three separate enzymatic reactions. The second step of this reaction, the conversion of 5-hydroxyisourate (HIU) to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, is catalyzed by HIU hydrolase (HIUH). The high-resolution crystal structure of HIUH from the opportunistic pathogen Klebsiella pneumoniae (KpHIUH) has been determined.more » KpHIUH is a homotetrameric protein that, based on sequence and structural similarity, belongs to the transthyretin-related protein family. In addition, the steady-state kinetic parameters for this enzyme and four active-site mutants have been measured. These data provide valuable insight into the functional roles of the active-site residues. Based upon the structural and kinetic data, a mechanism is proposed for the KpHIUH-catalyzed reaction.« less

Microstructure and hydrogenation properties of a melt-spun non-stoichiometric Zr-based Laves phase alloy

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

Zhang, Tiebang, E-mail: tiebangzhang@nwpu.edu.cn; Zhang, Yunlong; Li, Jinshan

2016-01-15

Alloy with composition of Zr{sub 0.9}Ti{sub 0.1}V{sub 1.7} off normal stoichiometric proportion is selected to investigate the effect of defects introduced by non-stoichiometry on hydrogenation kinetics of Zr–Ti–V Laves phase alloys. Microstructure and phase constituent of melt-spun ribbons have been investigated in this work. The activation process, hydrogenation kinetics, thermodynamics characteristics and hydride phase constituent of as-cast alloy and melt-spun ribbons are also compared. Comparing with the as-cast alloy, the dominant Laves phase ZrV{sub 2} is preserved, V-BCC phase is reduced and α-Zr phase is replaced by a small amount of Zr{sub 3}V{sub 3}O phase in melt-spun ribbons. Melt-spun ribbonsmore » exhibit easy activation and fast initial hydrogen absorption on account of the increased specific surface area. However, the decrease in unit cell volume of the dominant phase leads to the decrease in hydrogen absorption capacity. Melt-spinning technique raises the equilibrium pressure and decreases the stability of hydride due to the decrease of unit cell volume and the elimination of α-Zr phase, respectively. Melt-spun ribbons with fine grains show improved hydrogen absorption kinetics comparing with that of the as-cast alloy. Meanwhile, the prevalent micro twins observed within melt-spun ribbons are believed to account for the improved hydrogen absorption kinetics. - Highlights: • Role of defects on hydrogenation kinetics of Zr-based alloys is proposed. • Microstructure and hydrogenation properties of as-cast/melt-spun alloy are compared. • Melt-spinning technique improves the hydrogenation kinetics of Zr{sub 0.9}Ti{sub 0.1}V{sub 1.7} alloy. • Refined grains and twin defects account for improved hydrogen absorption kinetics.« less

Influence of the partial volume correction method on 18F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM

NASA Astrophysics Data System (ADS)

Bowen, Spencer L.; Byars, Larry G.; Michel, Christian J.; Chonde, Daniel B.; Catana, Ciprian

2013-10-01

Kinetic parameters estimated from dynamic 18F-fluorodeoxyglucose (18F-FDG) PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For ordered subsets expectation maximization (OSEM), image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting 18F-FDG dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation geometric transfer matrix PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in cerebral metabolic rate of glucose estimates, although by less than 5% in most cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters.

Influence of the partial volume correction method on (18)F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM.

PubMed

Bowen, Spencer L; Byars, Larry G; Michel, Christian J; Chonde, Daniel B; Catana, Ciprian

2013-10-21

Kinetic parameters estimated from dynamic (18)F-fluorodeoxyglucose ((18)F-FDG) PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For ordered subsets expectation maximization (OSEM), image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting (18)F-FDG dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation geometric transfer matrix PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in cerebral metabolic rate of glucose estimates, although by less than 5% in most cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters.

Atomistic Simulations of Graphene Growth: From Kinetics to Mechanism.

PubMed

Qiu, Zongyang; Li, Pai; Li, Zhenyu; Yang, Jinlong

2018-03-20

Epitaxial growth is a promising strategy to produce high-quality graphene samples. At the same time, this method has great flexibility for industrial scale-up. To optimize growth protocols, it is essential to understand the underlying growth mechanisms. This is, however, very challenging, as the growth process is complicated and involves many elementary steps. Experimentally, atomic-scale in situ characterization methods are generally not feasible at the high temperature of graphene growth. Therefore, kinetics is the main experimental information to study growth mechanisms. Theoretically, first-principles calculations routinely provide atomic structures and energetics but have a stringent limit on the accessible spatial and time scales. Such gap between experiment and theory can be bridged by atomistic simulations using first-principles atomic details as input and providing the overall growth kinetics, which can be directly compared with experiment, as output. Typically, system-specific approximations should be applied to make such simulations computationally feasible. By feeding kinetic Monte Carlo (kMC) simulations with first-principles parameters, we can directly simulate the graphene growth process and thus understand the growth mechanisms. Our simulations suggest that the carbon dimer is the dominant feeding species in the epitaxial growth of graphene on both Cu(111) and Cu(100) surfaces, which enables us to understand why the reaction is diffusion limited on Cu(111) but attachment limited on Cu(100). When hydrogen is explicitly considered in the simulation, the central role hydrogen plays in graphene growth is revealed, which solves the long-standing puzzle into why H 2 should be fed in the chemical vapor deposition of graphene. The simulation results can be directly compared with the experimental kinetic data, if available. Our kMC simulations reproduce the experimentally observed quintic-like behavior of graphene growth on Ir(111). By checking the simulation results, we find that such nonlinearity is caused by lattice mismatch, and the induced growth front inhomogeneity can be universally used to predict growth behaviors in other heteroepitaxial systems. Notably, although experimental kinetics usually gives useful insight into atomic mechanisms, it can sometimes be misleading. Such pitfalls can be avoided via atomistic simulations, as demonstrated in our study of the graphene etching process. Growth protocols can be designed theoretically with computational kinetic and mechanistic information. By contrasting the different activation energies involved in an atom-exchange-based carbon penetration process for monolayer and bilayer graphene, we propose a three-step strategy to grow high-quality bilayer graphene. Based on first-principles parameters, a kinetic pathway toward the high-density, ordered N doping of epitaxial graphene on Cu(111) using a C 5 NCl 5 precursor is also identified. These studies demonstrate that atomistic simulations can unambiguously produce or reproduce the kinetic information on graphene growth, which is pivotal to understanding the growth mechanism and designing better growth protocols. A similar strategy can be used in growth mechanism studies of other two-dimensional atomic crystals.

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by Its dodecameric structure

DOE PAGES

Filippova, Ekaterina V.; Kuhn, Misty L.; Osipiuk, Jerzy; ...

2015-01-23

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence ofmore » a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis.« less

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure.

PubMed

Filippova, Ekaterina V; Kuhn, Misty L; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Ballicora, Miguel A; Anderson, Wayne F

2015-03-27

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis. Copyright © 2015. Published by Elsevier Ltd.

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by Its dodecameric structure

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

Filippova, Ekaterina V.; Kuhn, Misty L.; Osipiuk, Jerzy

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence ofmore » a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis.« less

Kinetic Damage from Meteorites

NASA Technical Reports Server (NTRS)

Cooke, William; Brown, Peter; Matney, Mark

2017-01-01

A Near Earth object impacting into Earth's atmosphere may produce damaging effects at the surface due to airblast, thermal pulse, or kinetic impact in the form of meteorites. At large sizes (>many tens of meters), the damage is amplified by the hypersonic impact of these large projectiles moving with cosmic velocity, leaving explosively produced craters. However, much more common is simple "kinetic" damage caused by the impact of smaller meteorites moving at terminal speeds. As of this date a handful of instances are definitively known of people or structures being directly hit and/or damaged by the kinetic impact of meteorites. Meteorites known to have struck humans include the Sylacauga, Alabama fall (1954) and the Mbale meteorite fall (1992). Much more common is kinetic meteorite damage to cars, buildings, and even a post box (Claxton, Georgia - 1984). Historical accounts indicate that direct kinetic damage by meteorites may be more common than recent accounts suggest (Yau et al., 1994). In this talk we will examine the contemporary meteorite flux and estimate the frequency of kinetic damage to various structures, as well as how the meteorite flux might affect the rate of human casualties. This will update an earlier study by Halliday et al (1985), adding variations expected in meteorite flux with latitude (Le Feuvre and Wieczorek, 2008) and validating these model predictions of speed and entry angle with observations from the NASA and SOMN fireball networks. In particular, we explore the physical characteristics of bright meteors which may be used as a diagnostic for estimating which fireballs produce meteorites and hence how early warning of such kinetic damage may be estimated in advance through observations and modelling.

Kinetic Damage from Meteorites

NASA Technical Reports Server (NTRS)

Cooke, William; Brown, Peter; Matney, Mark

2017-01-01

A Near Earth object impacting into Earth's atmosphere may produce damaging effects at the surface due to airblast, thermal pulse, or kinetic impact in the form of meteorites. At large sizes (greater than many tens of meters), the damage is amplified by the hypersonic impact of these large projectiles moving with cosmic velocity, leaving explosively produced craters. However, much more common is simple "kinetic" damage caused by the impact of smaller meteorites moving at terminal speeds. As of this date a handful of instances are definitively known of people or structures being directly hit and/or damaged by the kinetic impact of meteorites. Meteorites known to have struck humans include the Sylacauga, Alabama fall (1954) and the Mbale meteorite fall (1992). Much more common is kinetic meteorite damage to cars, buildings, and even a post box (Claxton, Georgia - 1984). Historical accounts indicate that direct kinetic damage by meteorites may be more common than recent accounts suggest (Yau et al., 1994). In this talk we will examine the contemporary meteorite flux and estimate the frequency of kinetic damage to various structures, as well as how the meteorite flux might affect the rate of human casualties. This will update an earlier study by Halliday et al (1985), adding variations expected in meteorite flux with latitude (Le Feuvre and Wieczorek, 2008) and validating these model predictions of speed and entry angle with observations from the NASA and SOMN fireball networks. In particular, we explore the physical characteristics of bright meteors which may be used as a diagnostic for estimating which fireballs produce meteorites and hence how early warning of such kinetic damage may be estimated in advance through observations and modeling.

Kinetics on cocondensation of phenol and urea

Treesearch

Bunichiro Tomita; Yasunori Yoshida; Chung-Yun. Hse

1993-01-01

The chemical kinetics on cocondensation between methylolphenols and urea under acidic condition were investigated using 2- and 4-hydroxybenzyl alcohols as well as 2,4,6-trimethylolphenol as model compounds. The reactivity of the cocondensation were compared between o- and p-methylol groups. Moreover, the kinetics on self-condensations of monomethylolphenols and...

Kinetics of Acid Reactions: Making Sense of Associated Concepts

ERIC Educational Resources Information Center

Tan, Kim Chwee Daniel; Treagust, David F.; Chandrasegaran, A. L.; Mocerino, Mauro

2010-01-01

In chemical kinetics, in addition to the concepts related to kinetics, stoichiometry, chemical equilibrium and the characteristics of the reactants are often involved when comparing the rates of different reactions, making such comparisons very challenging for students at all levels, as well as for pre-service science teachers. Consequently, four…

Is case-based learning an effective teaching strategy to challenge students' alternative conceptions regarding chemical kinetics?

NASA Astrophysics Data System (ADS)

Yalçınkaya, Eylem; Taştan-Kırık, Özgecan; Boz, Yezdan; Yıldıran, Demet

2012-07-01

Background: Case-based learning (CBL) is simply teaching the concept to the students based on the cases. CBL involves a case, which is a scenario based on daily life, and study questions related to the case, which allows students to discuss their ideas. Chemical kinetics is one of the most difficult concepts for students in chemistry. Students have generally low levels of conceptual understanding and many alternative conceptions regarding it. Purpose: This study aimed to explore the effect of CBL on dealing with students' alternative conceptions about chemical kinetics. Sample: The sample consists of 53 high school students from one public high school in Turkey. Design and methods : Nonequivalent pre-test and post-test control group design was used. Reaction Rate Concept Test and semi-structured interviews were used for data collection. Convenience sampling technique was followed. For data analysis, the independent samples t-test and ANOVA was performed. Results : Both concept test and interview results showed that students instructed with cases had better understanding of core concepts of chemical kinetics and had less alternative conceptions related to the subject matter compared to the control group students, despite the fact that it was impossible to challenge all the alternative conceptions in the experimental group. Conclusions: CBL is an effective teaching method for challenging students' alternative conceptions in the context of chemical kinetics. Since using cases in small groups and whole class discussions has been found to be an effective way to cope with the alternative conceptions, it can be applied to other subjects and grade levels in high schools with a higher sample size. Furthermore, the effect of this method on academic achievement, motivation and critical thinking skills are other variables that can be investigated for future studies in the subject area of chemistry.

Anthocyanin kinetics are dependent on anthocyanin structure

USDA-ARS?s Scientific Manuscript database

The kinetics of anthocyanin metabolism was investigated in a human feeding trial. Volunteers (n=12) consumed purple carrots containing five different anthocyanin forms: cyanidin-3-(2”-xylose-6”-glucose-galactoside), cyanidin-3-(2”-xylose-galactoside), cyanidin-3-(2”-xylose-6”-sinapoyl-glucose-galac...

An Analysis Technique/Automated Tool for Comparing and Tracking Analysis Modes of Different Finite Element Models

NASA Technical Reports Server (NTRS)

Towner, Robert L.; Band, Jonathan L.

2012-01-01

An analysis technique was developed to compare and track mode shapes for different Finite Element Models. The technique may be applied to a variety of structural dynamics analyses, including model reduction validation (comparing unreduced and reduced models), mode tracking for various parametric analyses (e.g., launch vehicle model dispersion analysis to identify sensitivities to modal gain for Guidance, Navigation, and Control), comparing models of different mesh fidelity (e.g., a coarse model for a preliminary analysis compared to a higher-fidelity model for a detailed analysis) and mode tracking for a structure with properties that change over time (e.g., a launch vehicle from liftoff through end-of-burn, with propellant being expended during the flight). Mode shapes for different models are compared and tracked using several numerical indicators, including traditional Cross-Orthogonality and Modal Assurance Criteria approaches, as well as numerical indicators obtained by comparing modal strain energy and kinetic energy distributions. This analysis technique has been used to reliably identify correlated mode shapes for complex Finite Element Models that would otherwise be difficult to compare using traditional techniques. This improved approach also utilizes an adaptive mode tracking algorithm that allows for automated tracking when working with complex models and/or comparing a large group of models.

Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

PubMed

Rajabi, Khadijeh

2015-01-01

A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

Structural and Thermodynamic Factors of Suppressed Interdiffusion Kinetics in Multi-component High-entropy Materials

PubMed Central

Chang, Shou-Yi; Li, Chen-En; Huang, Yi-Chung; Hsu, Hsun-Feng; Yeh, Jien-Wei; Lin, Su-Jien

2014-01-01

We report multi-component high-entropy materials as extraordinarily robust diffusion barriers and clarify the highly suppressed interdiffusion kinetics in the multi-component materials from structural and thermodynamic perspectives. The failures of six alloy barriers with different numbers of elements, from unitary Ti to senary TiTaCrZrAlRu, against the interdiffusion of Cu and Si were characterized, and experimental results indicated that, with more elements incorporated, the failure temperature of the barriers increased from 550 to 900°C. The activation energy of Cu diffusion through the alloy barriers was determined to increase from 110 to 163 kJ/mole. Mechanistic analyses suggest that, structurally, severe lattice distortion strains and a high packing density caused by different atom sizes, and, thermodynamically, a strengthened cohesion provide a total increase of 55 kJ/mole in the activation energy of substitutional Cu diffusion, and are believed to be the dominant factors of suppressed interdiffusion kinetics through the multi-component barrier materials. PMID:24561911

Crystal Structure of an LSD-Bound Human Serotonin Receptor

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

Wacker, Daniel; Wang, Sheng; McCorvy, John D.

The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatlymore » accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.« less

Crystal Structure of an LSD-Bound Human Serotonin Receptor.

PubMed

Wacker, Daniel; Wang, Sheng; McCorvy, John D; Betz, Robin M; Venkatakrishnan, A J; Levit, Anat; Lansu, Katherine; Schools, Zachary L; Che, Tao; Nichols, David E; Shoichet, Brian K; Dror, Ron O; Roth, Bryan L

2017-01-26

The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT 2B . The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT 2B R and 5-HT 2A R-a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

Controlling enzymatic activity by immobilization on graphene oxide

NASA Astrophysics Data System (ADS)

Bolibok, Paulina; Wiśniewski, Marek; Roszek, Katarzyna; Terzyk, Artur P.

2017-04-01

In this study, graphene oxide (GO) has been applied as a matrix for enzyme immobilization. The protein adsorption capacity of GO is much higher than of other large surface area carbonaceous materials. Its structure and physicochemical properties are reported beneficial also for enzymatic activity modifications. The experimental proof was done here that GO-based biocatalytic systems with immobilized catalase are modifiable in terms of catalyzed reaction kinetic constants. It was found that activity and stability of catalase, considered here as model enzyme, closely depend on enzyme/GO ratio. The changes in kinetic parameters can be related to secondary structure alterations. The correlation between enzyme/GO ratio and kinetic and structure parameters is reported for the first time and enables the conscious control of biocatalytic processes and their extended applications. The biological activity of obtained biocatalytic systems was confirmed in vitro by the use of functional test. The addition of immobilized catalase improved the cells' viability after they were exposed to hydrogen peroxide and tert-butyl-hydroperoxide used as source of reactive oxygen species.

Computational modelling of mesoscale dislocation patterning and plastic deformation of single crystals

NASA Astrophysics Data System (ADS)

Xia, Shengxu; El-Azab, Anter

2015-07-01

We present a continuum dislocation dynamics model that predicts the formation of dislocation cell structure in single crystals at low strains. The model features a set of kinetic equations of the curl type that govern the space and time evolution of the dislocation density in the crystal. These kinetic equations are coupled to stress equilibrium and deformation kinematics using the eigenstrain approach. A custom finite element method has been developed to solve the coupled system of equations of dislocation kinetics and crystal mechanics. The results show that, in general, dislocations self-organize in patterns under their mutual interactions. However, the famous dislocation cell structure has been found to form only when cross slip is implemented in the model. Cross slip is also found to lower the yield point, increase the hardening rate, and sustain an increase in the dislocation density over the hardening regime. Analysis of the cell structure evolution reveals that the average cell size decreases with the applied stress, which is consistent with the similitude principle.

Multi-scale kinetics of a field-directed colloidal phase transition.

PubMed

Swan, James W; Vasquez, Paula A; Whitson, Peggy A; Fincke, E Michael; Wakata, Koichi; Magnus, Sandra H; De Winne, Frank; Barratt, Michael R; Agui, Juan H; Green, Robert D; Hall, Nancy R; Bohman, Donna Y; Bunnell, Charles T; Gast, Alice P; Furst, Eric M

2012-10-02

Polarizable colloids are expected to form crystalline equilibrium phases when exposed to a steady, uniform field. However, when colloids become localized this field-induced phase transition arrests and the suspension persists indefinitely as a kinetically trapped, percolated structure. We anneal such gels formed from magneto-rheological fluids by toggling the field strength at varied frequencies. This processing allows the arrested structure to relax periodically to equilibrium--colloid-rich, cylindrical columns. Two distinct growth regimes are observed: one in which particle domains ripen through diffusive relaxation of the gel, and the other where the system-spanning structure collapses and columnar domains coalesce apparently through field-driven interactions. There is a stark boundary as a function of magnetic field strength and toggle frequency distinguishing the two regimes. These results demonstrate how kinetic barriers to a colloidal phase transition are subverted through measured, periodic variation of driving forces. Such directed assembly may be harnessed to create unique materials from dispersions of colloids.

Transition Behaviors of Configurations of Colloidal Particles at a Curved Oil-Water Interface

PubMed Central

Lee, Mina; Xia, Ming; Park, Bum Jun

2016-01-01

We studied the transition behaviors of colloidal arrangements confined at a centro-symmetrically curved oil-water interface. We found that assemblies composed of several colloidal particles at the curved interface exhibit at least two unique patterns that can be attributed to two factors: heterogeneity of single-colloid self-potential and assembly kinetics. The presence of the two assembly structures indicates that an essential energy barrier between the two structures exists and that one of the structures is kinetically stable. This energy barrier can be overcome via external stimuli (e.g., convection and an optical force), leading to dynamic transitions of the assembly patterns. PMID:28773263

A triplex ribozyme expression system based on a single hairpin ribozyme.

PubMed

Aquino-Jarquin, Guillermo; Benítez-Hess, María Luisa; DiPaolo, Joseph A; Alvarez-Salas, Luis M

2008-09-01

Triplex ribozyme (RZ) configurations allow for the individual activity of trans-acting RZs in multiple expression cassettes (multiplex), thereby increasing target cleavage relative to conventionally expressed RZs. Although hairpin RZs have been advantageously compared to hammerhead RZs, their longer size and structural features complicated triplex design. We present a triplex expression system based on a single hairpin RZ with transcleavage capability and simple engineering. The system was tested in vitro using cis- and trans-cleavage kinetic assays against a known target RNA from HPV-16 E6/E7 mRNA. Single and multiplex triplex RZ constructs were more efficient in cleaving the target than tandem-cloned hairpin RZs, suggesting that the release of individual RZs enhanced trans-cleavage kinetics. Multiplex systems constructed with two different hairpin RZs resulted in better trans-cleavage compared to standard double-RZ constructs. In addition, the triplex RZ performed cis- and trans-cleavage in cervical cancer cells. The use of triplex configurations with multiplex RZs permit differential targeting of the same or different RNA, thus improving potential use against unstable targets. This prototype will provide the basis for the development of future RZ-based therapies and technologies.

Impacts of the Mesoscale Ocean-Atmosphere Coupling on the Peru-Chile Ocean Dynamics: The Current-Induced Wind Stress Modulation

NASA Astrophysics Data System (ADS)

Oerder, V.; Colas, F.; Echevin, V.; Masson, S.; Lemarié, F.

2018-02-01

The ocean dynamical responses to the surface current-wind stress interaction at the oceanic mesoscale are investigated in the South-East Pacific using a high-resolution regional ocean-atmosphere coupled model. Two simulations are compared: one includes the surface current in the wind stress computation while the other does not. In the coastal region, absolute wind velocities are different between the two simulations but the wind stress remains very similar. As a consequence, the mean regional oceanic circulation is almost unchanged. On the contrary, the mesoscale activity is strongly reduced when taking into account the effect of the surface current on the wind stress. This is caused by a weakening of the eddy kinetic energy generation near the coast by the wind work and to intensified offshore eddy damping. We show that, above coherent eddies, the current-stress interaction generates eddy damping through Ekman pumping and eddy kinetic energy dissipation through wind work. This alters significantly the coherent eddy vertical structures compared with the control simulation, weakening the temperature and vorticity anomalies and increasing strongly the vertical velocity anomalies associated to eddies.

3,4-Ethylenedioxythiophene functionalized graphene with palladium nanoparticles for enhanced electrocatalytic oxygen reduction reaction

NASA Astrophysics Data System (ADS)

Choe, Ju Eun; Ahmed, Mohammad Shamsuddin; Jeon, Seungwon

2015-05-01

Poly(3,4-ethylenedioxythiophene) functionalized graphene with palladium nanoparticles (denoted as Pd/PEDOT/rGO) has been synthesized for electrochemical oxygen reduction reaction (ORR) in alkaline solution. The structural features of catalyst are characterized by scanning electron microscopy, transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy. The TEM images suggest a well dispersed PdNPs onto PEDOT/rGO film. The ORR activity of Pd/PEDOT/rGO has been investigated via cyclic voltammetry (CV), rotating disk electrode (RDE) and rotating ring disk electrode (RRDE) techniques in 0.1 M KOH aqueous solution. Comparative CV analysis suggests a general approach of intermolecular charge-transfer in between graphene sheet and PdNPs via PEDOT which leads to the better PdNPs dispersion and subsequently superior ORR kinetics. The results from ORR measurements show that Pd/PEDOT/rGO has remarkable electrocatalytic activity and stability compared to Pd/rGO and state-of-the-art Pt/C. The Koutecky-Levich and Tafel analysis suggest that the proposed main path in the ORR mechanism has direct four-electron transfer process with faster transfer kinetic rate on the Pd/PEDOT/rGO.

Do orthotic walkers affect knee and hip function during gait?

PubMed

Richards, Jim; Payne, Katherine; Myatt, Darren; Chohan, Ambreen

2016-02-01

Much previous research on orthotic walkers has focussed on their ability to offload structures in the foot and ankle; however, little is known about their effects on lower limb mechanics. This study aimed to determine effects of two orthotic walkers on the biomechanics of the knee and hip joints compared to standardised footwear. A total of 10 healthy participants walked under three conditions: Walker A (Össur, Iceland), Walker B (DJO Global, USA) and standardised footwear (Hotter, UK). Kinematic and kinetic data were collected using a Qualisys motion analysis system (Qualisys Medical AB, Sweden) and force plates (AMTI, Boston, MA, USA). Significant differences were seen in hip kinematics and knee moments between walkers and standardised footwear and in knee kinematics between Walker A and standardised footwear. Both walkers show significant kinematic and kinetic differences compared with standardised footwear; however, Walker A appeared to produce greater deviation, including potentially damaging greater hyperextension moments at the knee. Further research is needed into the effects of orthotic walkers on knee and hip joint mechanics, which should help to inform future designs of walker, with greater focus on obtaining a more normal gait pattern. © The International Society for Prosthetics and Orthotics 2014.

Comparative analysis of thermal behavior, isothermal crystallization kinetics and polymorphism of palm oil fractions.

PubMed

Zhang, Xia; Li, Lin; Xie, He; Liang, Zhili; Su, Jianyu; Liu, Guoqin; Li, Bing

2013-01-15

Thermal behavior of palm stearin (PS) and palm olein (PO) was explored by monitoring peak temperature transitions by differential scanning calorimetry (DSC). The fatty acid composition (FAC), isothermal crystallization kinetics studied by pulsed Nuclear Magnetic Resonance (pNMR) and isothermal microstructure were also compared. The results indicated that the fatty acid composition had an important influence on the crystallization process. PS and PO both exhibited more multiple endotherms than exotherms which showed irregular peak shapes. An increasing in cooling rate, generally, was associated with an increase in peak size. Application of the Avaimi equation to isothermal crystallization of PS and PO revealed different nucleation and growth mechanisms based on the Avrami exponents. PS quickly reached the end of crystallization because of more saturated triacylglycerol (TAG). The Avrami index of PS were the same as PO under the same isothermal condition at lower temperatrue, indicating that the crystallization mechanism of the two samples based on super-cooling state were the same. According to the polarized light microscope (PLM) images, crystal morphology of PS and PO was different. With the temperature increased, the structure of crystal network of both PS and PO gradually loosened.

Enhanced picture of protein-folding intermediates using organic solvents in H/D exchange and quench-flow experiments

PubMed Central

Nishimura, Chiaki; Dyson, H. Jane; Wright, Peter E.

2005-01-01

Hydrogen/deuterium exchange followed by trapping of the labeled species in the aprotic solvent DMSO has been used to elucidate structure in both the burst-phase molten globule-folding intermediate of apomyoglobin and in an equilibrium intermediate that models the kinetic intermediate. Precise estimates can be made of exchange times in an interrupted exchange-out experiment at pH 4 followed by analysis in DMSO solution, giving extensive sequence-specific information about the structure of the equilibrium intermediate. In addition, the use of DMSO as a solvent for NMR measurements after quench-flow pH-pulse labeling experiments gives a greatly increased data set for the elucidation of the kinetic folding pathway. Interestingly, differences are observed in some regions of apomyoglobin between the equilibrium and kinetic intermediates. These differences are quantitative rather than qualitative; that is, the overall patterns of labeling and secondary structure formation remain similar between the two species. However, local differences are observed, which probably reflect the difference in the solution conditions for the equilibrium experiment (pH 4) vs. the kinetic experiment (pH 6) and the change in the status of the stabilizing hydrogen bond between the side chains of His-24 and His-119. PMID:15769860

Small-Molecule Effectors of Hepatitis B Virus Capsid Assembly Give Insight into Virus Life Cycle▿

PubMed Central

Bourne, Christina; Lee, Sejin; Venkataiah, Bollu; Lee, Angela; Korba, Brent; Finn, M. G.; Zlotnick, Adam

2008-01-01

The relationship between the physical chemistry and biology of self-assembly is poorly understood, but it will be critical to quantitatively understand infection and for the design of antivirals that target virus genesis. Here we take advantage of heteroaryldihydropyrimidines (HAPs), which affect hepatitis B virus (HBV) assembly, to gain insight and correlate in vitro assembly with HBV replication in culture. Based on a low-resolution crystal structure of a capsid-HAP complex, a closely related series of HAPs were designed and synthesized. These differentially strengthen the association between neighboring capsid proteins, alter the kinetics of assembly, and give rise to aberrant structures incompatible with a functional capsid. The chemical nature of the HAP variants correlated well with the structure of the HAP binding pocket. The thermodynamics and kinetics of in vitro assembly had strong and predictable effects on product morphology. However, only the kinetics of in vitro assembly had a strong correlation with inhibition of HBV replication in HepG2.2.15 cells; there was at best a weak correlation between assembly thermodynamics and replication. The correlation between assembly kinetics and virus suppression implies a competition between successful assembly and misassembly, small molecule induced or otherwise. This is a predictive and testable model for the mechanism of action of assembly effectors. PMID:18684823

Kinetics and Products of Chromium(VI) Reduction by Iron(II/III)-Bearing Clay Minerals.

PubMed

Joe-Wong, Claresta; Brown, Gordon E; Maher, Kate

2017-09-05

Hexavalent chromium is a water-soluble pollutant, the mobility of which can be controlled by reduction of Cr(VI) to less soluble, environmentally benign Cr(III). Iron(II/III)-bearing clay minerals are widespread potential reductants of Cr(VI), but the kinetics and pathways of Cr(VI) reduction by such clay minerals are poorly understood. We reacted aqueous Cr(VI) with two abiotically reduced clay minerals: an Fe-poor montmorillonite and an Fe-rich nontronite. The effects of ionic strength, pH, total Fe content, and the fraction of reduced structural Fe(II) [Fe(II)/Fe(total)] were examined. The last variable had the largest effect on Cr(VI) reduction kinetics: for both clay minerals, the rate constant of Cr(VI) reduction varies by more than 3 orders of magnitude with Fe(II)/Fe(total) and is described by a linear free energy relationship. Under all conditions examined, Cr and Fe K-edge X-ray absorption near-edge structure spectra show that the main Cr-bearing product is a Cr(III)-hydroxide and that Fe remains in the clay structure after reacting with Cr(VI). This study helps to quantify our understanding of the kinetics of Cr(VI) reduction by Fe(II/III)-bearing clay minerals and may improve predictions of Cr(VI) behavior in subsurface environments.

Virtual screening of cocrystal formers for CL-20

NASA Astrophysics Data System (ADS)

Zhou, Jun-Hong; Chen, Min-Bo; Chen, Wei-Ming; Shi, Liang-Wei; Zhang, Chao-Yang; Li, Hong-Zhen

2014-08-01

According to the structure characteristics of 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (CL-20) and the kinetic mechanism of the cocrystal formation, the method of virtual screening CL-20 cocrystal formers by the criterion of the strongest intermolecular site pairing energy (ISPE) was proposed. In this method the strongest ISPE was thought to determine the first step of the cocrystal formation. The prediction results for four sets of common drug molecule cocrystals by this method were compared with those by the total ISPE method from the reference (Musumeci et al., 2011), and the experimental results. This method was then applied to virtually screen the CL-20 cocrystal formers, and the prediction results were compared with the experimental results.

Use of Hilbert Curves in Parallelized CUDA code: Interaction of Interstellar Atoms with the Heliosphere

NASA Astrophysics Data System (ADS)

Destefano, Anthony; Heerikhuisen, Jacob

2015-04-01

Fully 3D particle simulations can be a computationally and memory expensive task, especially when high resolution grid cells are required. The problem becomes further complicated when parallelization is needed. In this work we focus on computational methods to solve these difficulties. Hilbert curves are used to map the 3D particle space to the 1D contiguous memory space. This method of organization allows for minimized cache misses on the GPU as well as a sorted structure that is equivalent to an octal tree data structure. This type of sorted structure is attractive for uses in adaptive mesh implementations due to the logarithm search time. Implementations using the Message Passing Interface (MPI) library and NVIDIA's parallel computing platform CUDA will be compared, as MPI is commonly used on server nodes with many CPU's. We will also compare static grid structures with those of adaptive mesh structures. The physical test bed will be simulating heavy interstellar atoms interacting with a background plasma, the heliosphere, simulated from fully consistent coupled MHD/kinetic particle code. It is known that charge exchange is an important factor in space plasmas, specifically it modifies the structure of the heliosphere itself. We would like to thank the Alabama Supercomputer Authority for the use of their computational resources.

Understanding the Formation of Kinetically Stable Compounds and the Development of Thin Film Pair Distribution Function Analysis

NASA Astrophysics Data System (ADS)

Wood, Suzannah Rebecca

Navigating the synthesis landscape poses many challenges when developing novel solid state materials. Advancements in both synthesis and characterization are necessary to facilitate the targeting of specific materials. This dissertation discusses the formation of chalcogenide heterostructures and their properties in the first part and the development of thin film pair distribution function analysis (tfPDF) in the second part. The heterostructures were formed by the self-assembly of designed precursors deposited by physical vapor deposition in a modulated elemental reactants approach, which provides the control and predictability to synthesis. Specifically, a series of (BiSe)1+delta(TiSe2) n, where n = 2,3,&4, were synthesized to explore the extent of charge transfer from the BiSe to TiSe2 layers. To further explore the role Bi plays in charge donation, a family of structurally similar compounds, (Bix Sn1-xSe)1+deltaTiSe2, where 0≥x≥1, were synthesized and characterized. Electrical measurements show doping efficiency decreases as x increases, correlated with the structural distortion and the formation of periodic antiphase boundaries containing Bi-Bi pairs. The first heterostructures composed of three unique structural types were synthesized and Bi2Se3 layer thickness was used to tune electrical properties and further explore charge transfer. To better understand the potential energy landscape on which these kinetically stable compounds exist, two investigations were undertaken. The first was a study of the formation and subsequent decomposition of [(BiSe)1+delta]n(TiSe2)n compounds, where n= 2&3, the second an investigation of precursor structure for thermodynamically stable FeSb2 and kinetically stable FeSb3. The second section describes the development of thin film pair distribution function analysis, a technique in which total scattering data for pair distribution function (PDF) analysis is obtained from thin films, suitable for local structure analysis. This study illustrates how analysis of the local structure in amorphous precursor films can help to understand the crystallization processes of metastable phases and enables a range of new local structure studies of thin films. tfPDF was then demonstrated on In-Ga-O film materials and compared to traditional powder PDF analysis. This highlights differences between the products, and the utility of tfPDF to determined structural features of amorphous materials. This dissertation includes previously published and unpublished co-authored materials.

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.

Arsenate Adsorption On Ruthenium Oxides: A Spectroscopic And Kinetic Investigation

EPA Science Inventory

Arsenate adsorption on amorphous (RuO₂•1.1H₂O) and crystalline (RuO₂) ruthenium oxides was evaluated using spectroscopic and kinetic methods to elucidate the adsorption mechanism. Extended X-ray absorption fine structure spectroscopy (EXAFS) was ...

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

NASA Technical Reports Server (NTRS)

Kaplan, G.

1983-01-01

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

Linear prediction and single-channel recording.

PubMed

Carter, A A; Oswald, R E

1995-08-01

The measurement of individual single-channel events arising from the gating of ion channels provides a detailed data set from which the kinetic mechanism of a channel can be deduced. In many cases, the pattern of dwells in the open and closed states is very complex, and the kinetic mechanism and parameters are not easily determined. Assuming a Markov model for channel kinetics, the probability density function for open and closed time dwells should consist of a sum of decaying exponentials. One method of approaching the kinetic analysis of such a system is to determine the number of exponentials and the corresponding parameters which comprise the open and closed dwell time distributions. These can then be compared to the relaxations predicted from the kinetic model to determine, where possible, the kinetic constants. We report here the use of a linear technique, linear prediction/singular value decomposition, to determine the number of exponentials and the exponential parameters. Using simulated distributions and comparing with standard maximum-likelihood analysis, the singular value decomposition techniques provide advantages in some situations and are a useful adjunct to other single-channel analysis techniques.

In vitro evaluation of flow patterns and turbulent kinetic energy in trans-catheter aortic valve prostheses.

PubMed

Giese, Daniel; Weiss, Kilian; Baeßler, Bettina; Madershahian, Navid; Choi, Yeong-Hoon; Maintz, David; Bunck, Alexander C

2018-02-01

The objective of the current work was to evaluate flow and turbulent kinetic energy in different transcatheter aortic valve implants using highly undersampled time-resolved multi-point 3-directional phase-contrast measurements (4D Flow MRI) in an in vitro setup. A pulsatile flow setup was used with a compliant tubing mimicking a stiff left ventricular outflow tract and ascending aorta. Five different implants were measured using a highly undersampled multi-point 4D Flow MRI sequence. Velocities and turbulent kinetic energy values were analysed and compared. Strong variations of turbulent kinetic energy distributions between the valves were observed. Maximum turbulent kinetic energy values ranged from 100 to over 500 J/m 3 while through-plane velocities were similar between all valves. Highly accelerated 4D Flow MRI for the measurement of velocities and turbulent kinetic energy values allowed for the assessment of hemodynamic parameters in five different implant models. The presented setup, measurement protocol and analysis methods provides an efficient approach to compare different valve implants and could aid future novel valve designs.

LIGKA: A linear gyrokinetic code for the description of background kinetic and fast particle effects on the MHD stability in tokamaks

NASA Astrophysics Data System (ADS)

Lauber, Ph.; Günter, S.; Könies, A.; Pinches, S. D.

2007-09-01

In a plasma with a population of super-thermal particles generated by heating or fusion processes, kinetic effects can lead to the additional destabilisation of MHD modes or even to additional energetic particle modes. In order to describe these modes, a new linear gyrokinetic MHD code has been developed and tested, LIGKA (linear gyrokinetic shear Alfvén physics) [Ph. Lauber, Linear gyrokinetic description of fast particle effects on the MHD stability in tokamaks, Ph.D. Thesis, TU München, 2003; Ph. Lauber, S. Günter, S.D. Pinches, Phys. Plasmas 12 (2005) 122501], based on a gyrokinetic model [H. Qin, Gyrokinetic theory and computational methods for electromagnetic perturbations in tokamaks, Ph.D. Thesis, Princeton University, 1998]. A finite Larmor radius expansion together with the construction of some fluid moments and specification to the shear Alfvén regime results in a self-consistent, electromagnetic, non-perturbative model, that allows not only for growing or damped eigenvalues but also for a change in mode-structure of the magnetic perturbation due to the energetic particles and background kinetic effects. Compared to previous implementations [H. Qin, mentioned above], this model is coded in a more general and comprehensive way. LIGKA uses a Fourier decomposition in the poloidal coordinate and a finite element discretisation in the radial direction. Both analytical and numerical equilibria can be treated. Integration over the unperturbed particle orbits is performed with the drift-kinetic HAGIS code [S.D. Pinches, Ph.D. Thesis, The University of Nottingham, 1996; S.D. Pinches et al., CPC 111 (1998) 131] which accurately describes the particles' trajectories. This allows finite-banana-width effects to be implemented in a rigorous way since the linear formulation of the model allows the exchange of the unperturbed orbit integration and the discretisation of the perturbed potentials in the radial direction. Successful benchmarks for toroidal Alfvén eigenmodes (TAEs) and kinetic Alfvén waves (KAWs) with analytical results, ideal MHD codes, drift-kinetic codes and other codes based on kinetic models are reported.

Electrochemical and kinetic studies of ultrafast laser structured LiFePO4 electrodes

NASA Astrophysics Data System (ADS)

Mangang, M.; Gotcu-Freis, P.; Seifert, H. J.; Pfleging, W.

2015-03-01

Due to a growing demand of cost-efficient lithium-ion batteries with an increased energy and power density as well as an increased life-time, the focus is set on intercalation cathode materials like LiFePO4. It has a high practical capacity, is environmentally friendly and has low material costs. However, its low electrical conductivity and low ionic diffusivity are major drawbacks for its use in electrochemical storage devices or electric vehicles. By adding conductive agents, the electrical conductivity can be enhanced. By increasing the surface of the cathode material which is in direct contact with the liquid electrolyte the lithium-ion diffusion kinetics can be improved. A new approach to increase the surface of the active material without changing the active particle packing density or the weight proportion of carbon black is the laser-assisted generation of 3D surface structures in electrode materials. In this work, ultrafast laser radiation was used to create a defined surface structure in LiFePO4 electrodes. It was shown that by using ultrashort laser pulses instead of nanosecond laser pulses, the ablation efficiency could be significantly increased. Furthermore, melting and debris formation were reduced. To investigate the diffusion kinetics, electrochemical methods such as cyclic voltammetry and galvanostatic intermittent titration technique were applied. It could be shown that due to a laser generated 3D structure, the lithium-ion diffusion kinetic, the capacity retention and cell life-time can be significantly improved.

Numerical impact simulation of gradually increased kinetic energy transfer has the potential to break up folded protein structures resulting in cytotoxic brain tissue edema.

PubMed

von Holst, Hans; Li, Xiaogai

2013-07-01

Although the consequences of traumatic brain injury (TBI) and its treatment have been improved, there is still a substantial lack of understanding the mechanisms. Numerical simulation of the impact can throw further lights on site and mechanism of action. A finite element model of the human head and brain tissue was used to simulate TBI. The consequences of gradually increased kinetic energy transfer was analyzed by evaluating the impact intracranial pressure (ICP), strain level, and their potential influences on binding forces in folded protein structures. The gradually increased kinetic energy was found to have the potential to break apart bonds of Van der Waals in all impacts and hydrogen bonds at simulated impacts from 6 m/s and higher, thereby superseding the energy in folded protein structures. Further, impacts below 6 m/s showed none or very slight increase in impact ICP and strain levels, whereas impacts of 6 m/s or higher showed a gradual increase of the impact ICP and strain levels reaching over 1000 KPa and over 30%, respectively. The present simulation study shows that the free kinetic energy transfer, impact ICP, and strain levels all have the potential to initiate cytotoxic brain tissue edema by unfolding protein structures. The definition of mild, moderate, and severe TBI should thus be looked upon as the same condition and separated only by a gradual severity of impact.

Structure and Kinetic Stability of the p63 Tetramerization Domain

PubMed Central

Natan, Eviatar; Joerger, Andreas C.

2012-01-01

The p53 family of transcription factors—comprising p53, p63 and p73—plays an important role in tumor prevention and development. Essential to their function is the formation of tetramers, allowing cooperative binding to their DNA response elements. We solved crystal structures of the human p63 tetramerization domain, showing that p63 forms a dimer of dimers with D2 symmetry composed of highly intertwined monomers. The primary dimers are formed via an intramolecular β-sheet and hydrophobic helix packing (H1), a hallmark of all p53 family members. Like p73, but unlike p53, p63 requires a second helix (H2) to stabilize the architecture of the tetramer. In order to investigate the impact of structural differences on tetramer stability, we measured the subunit exchange reaction of p53 family homotetramers by nanoflow electrospray mass spectrometry. There were differences in both the kinetics and the pattern of the exchange reaction, with the p53 and p63 tetramers exhibiting much faster exchange kinetics than p73. The structural similarity between p63 and p73 rationalizes previous observations that p63 and p73 form mixed tetramers, and the kinetic data reveal the dissociation of the p73 homotetramers as the rate-limiting step for heterotetramer formation. Differential stability of the tetramers may play an important role in the cross talk between different isoforms and regulation of p53, p63 and p73 function in the cell cycle. PMID:22100306

Size effects in tin-based lead-free solder joints: Kinetics of bond formation and mechanical characteristics

NASA Astrophysics Data System (ADS)

Abdelhadi, Ousama Mohamed Omer

Continuous miniaturization of microelectronic interconnects demands smaller joints with comparable microstructural and structural sizes. As the size of joints become smaller, the volume of intermetallics (IMCs) becomes comparable with the joint size. As a result, the kinetics of bond formation changes and the types and thicknesses of IMC phases that form within the constrained region of the bond varies. This dissertation focuses on investigating combination effects of process parameters and size on kinetics of bond formation, resulting microstructure and the mechanical properties of joints that are formed under structurally constrained conditions. An experiment is designed where several process parameters such as time of bonding, temperature, and pressure, and bond thickness as structural chracteristic, are varied at multiple levels. The experiment is then implemented on the process. Scanning electron microscope (SEM) is then utilized to determine the bond thickness, IMC phases and their thicknesses, and morphology of the bonds. Electron backscatter diffraction (EBSD) is used to determine the grain size in different regions, including the bulk solder, and different IMC phases. Physics-based analytical models have been developed for growth kinetics of IMC compounds and are verified using the experimental results. Nanoindentation is used to determine the mechanical behavior of IMC phases in joints in different scales. Four-point bending notched multilayer specimen and four-point bending technique were used to determine fracture toughness of the bonds containing IMCs. Analytical modeling of peeling and shear stresses and fracture toughness in tri-layer four-point bend specimen containing intermetallic layer was developed and was verified and validated using finite element simulation and experimental results. The experiment is used in conjunction with the model to calculate and verify the fracture toughness of Cu6Sn5 IMC materials. As expected two different IMC phases, η-phase (Cu6Sn 5) and epsilon-phase (Cu3Sn), were found in almost all the cases regardless of the process parameters and size levels. The physics-based analytical model was successfully able to capture the governing mechanisms of IMC growth: chemical reaction controlled and diffusion-controlled. Examination of microstructures of solder joints of different sizes revealed the size of the solder joint has no effect on the type of IMCs formed during the process. Joint size, however, affected the thickness of IMC layers significantly. IMC layers formed in the solder joints of smaller sizes were found to be thicker than those in the solder joints of larger sizes. The growth rate constants and activation energies of Cu3Sn IMC layer were also reported and related to joint thickness. In an effort to optimize the EBSD imaging in the multi-layer configuration, an improved specimen preparation technique and optimum software parameters were determined. Nanoindentation results show that size effects play a major role on the mechanical properties of micro-scale solder joints. Smaller joints show higher Young's modulus, hardness, and yield strength and lower work hardening exponents comparing to thicker joints. To obtain the stress concentration factors in a multilayer specimen with IMC layer as bonding material, a four-point bending notched configuration was used. The analytical solutions developed for peeling and shear stresses in notched structure were used to evaluate the stresses at IMC interface layers. Results were in good agreement with the finite-element simulation. The values of interfacial stresses were utilized in obtaining fracture toughness of the IMC material. (Abstract shortened by UMI.)

Insights into the Functional Architecture of the Catalytic Center of a Maize β-Glucosidase Zm-p60.11

PubMed Central

Zouhar, Jan; Vévodová, Jitka; Marek, Jaromír; Damborský, Jir̆í; Su, Xiao-Dong; Brzobohatý, Br̆etislav

2001-01-01

The maize (Zea mays) β-glucosidase Zm-p60.1 has been implicated in regulation of plant development by the targeted release of free cytokinins from cytokinin-O-glucosides, their inactive storage forms. The crystal structure of the wild-type enzyme was solved at 2.05-Å resolution, allowing molecular docking analysis to be conducted. This indicated that the enzyme specificity toward substrates with aryl aglycones is determined by aglycone aromatic system stacking with W373, and interactions with edges of F193, F200, and F461 located opposite W373 in a slot-like aglycone-binding site. These aglycone-active site interactions recently were hypothesized to determine substrate specificity in inactive enzyme substrate complexes of ZM-Glu1, an allozyme of Zm-p60.1. Here, we test this hypothesis by kinetic analysis of F193I/Y/W mutants. The decreased Km of all mutants confirmed the involvement of F193 in determining enzyme affinity toward substrates with an aromatic aglycone. It was unexpected that a 30-fold decrease in kcat was found in F193I mutant compared with the wild type. Kinetic analysis and computer modeling demonstrated that the F193-aglycone-W373 interaction not only contributes to aglycone recognition as hypothesized previously but also codetermines catalytic rate by fixing the glucosidic bond in an orientation favorable for attack by the catalytic pair, E186 and E401. The catalytic pair, assigned initially by their location in the structure, was confirmed by kinetic analysis of E186D/Q and E401D/Q mutants. It was unexpected that the E401D as well as C205S and C211S mutations dramatically impaired the assembly of a catalysis-competent homodimer, suggesting novel links between the active site structure and dimer formation. PMID:11706179

Crystallization kinetics of Mg–Cu–Yb–Ca–Ag metallic glasses

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

Tsarkov, Andrey A., E-mail: tsarkov@misis.ru; WPI Advanced Institute for Materials Research, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 980-8577; Zanaeva, Erzhena N.

The paper presents research into a Mg–Cu–Yb system based metallic glassy alloys. Metallic glasses were prepared using induction melting and further injection on a spinning copper wheel. The effect of alloying by Ag and Ca on the glass forming ability and the kinetics of crystallization of Mg–Cu–Yb system based alloys were studied. The differential scanning calorimeter and X-ray diffractometer were used to investigate the kinetics of crystallization and the phase composition of the samples. An indicator of glass forming ability, effective activation energy of crystallization, and enthalpy of mixing were calculated. An increase of the Ca and Ag content hasmore » a positive effect on the glass forming ability, the effective activation energy of crystallization, and the enthalpy of mixing. The highest indicators of the glass forming ability and the thermal stability were found for alloys that contain both alloying elements. The Ag addition suppresses precipitation of the Mg{sub 2}Cu phase during crystallization. A dual-phase glassy-nanocrystalline Mg structure was obtained in Mg{sub 65}Cu{sub 25}Yb{sub 10} and Mg{sub 59.5}Cu{sub 22.9}Yb{sub 11}Ag{sub 6.6} alloys after annealing. Bulk samples with a composite glassy-crystalline structure were obtained in Mg{sub 59.5}Cu{sub 22.9}Yb{sub 11}Ag{sub 6.6} and Mg{sub 64}Cu{sub 21}Yb{sub 9.5}Ag{sub 5.5} alloys. A thermodynamic database for the Mg–Cu–Yb–Ca–Ag system was created to compare the process of crystallization of alloys with polythermal sections of the Mg–Cu–Yb–Ca–Ag phase diagram. - Highlights: • New alloy compositions based on Mg–Cu–Yb system were developed and investigated. • Increasing content of Ag and Ca leads to improving GFA. • Bulk samples with a composite glassy-crystalline structure were obtained. • Thermodynamic database for Mg–Cu–Yb–Ca–Ag system was created.« less

Drug–Target Kinetics in Drug Discovery

PubMed Central

2017-01-01

The development of therapies for the treatment of neurological cancer faces a number of major challenges including the synthesis of small molecule agents that can penetrate the blood-brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concentration. Time dependent target occupancy is a function of both the drug and target concentration as well as the thermodynamic and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissociation. The discovery and deployment of compounds with optimized kinetic effects requires information on the structure–kinetic relationships that modulate the kinetics of binding, and the molecular factors that control the translation of drug–target kinetics to time-dependent drug activity in the disease state. This Review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodynamic and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The Review concludes with a description of a mechanistic PK/PD model that integrates drug–target kinetics into predictions of drug activity. PMID:28640596

COMPUTER SIMULATION STUDY OF AMYLOID FIBRIL FORMATION BY PALINDROMIC SEQUENCES IN PRION PEPTIDES

PubMed Central

Wagoner, Victoria; Cheon, Mookyung; Chang, Iksoo; Hall, Carol

2011-01-01

We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113–120 (AGAAAAGA) and the mouse prion protein MoPrP 111–120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)4, A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well-ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures. PMID:21557317

Efficient Generation of Chemiluminescence during the reduction of manganese(IV) ions with lactic acid

NASA Astrophysics Data System (ADS)

Tsaplev, Yu. B.

2016-12-01

The kinetics and mechanism of chemiluminescence during the reduction of manganese(IV) ions with lactic acid in an H2SO4-AcOH medium are studied. Kinetic spectrophotometric measurements are used to determine the profiles of change in the concentrations of Mn(IV) and Mn(III) ions during the reaction. The results from kinetic spectrophotometric measurements are compared to the light yield kinetics. The quantum chemiluminescence and chemiexcitation yields reach record values.

Modeling and experimental studies on intermittent starch feeding and citrate addition in simultaneous saccharification and fermentation of starch to flavor compounds.

PubMed

Chavan, Abhijit R; Raghunathan, Anuradha; Venkatesh, K V

2009-04-01

Simultaneous saccharification and fermentation (SSF) is a combined process of saccharification of a renewable bioresource and fermentation process to produce products, such as lactic acid and ethanol. Recently, SSF has been extensively used to convert various sources of cellulose and starch into fermentative products. Here, we present a study on production of buttery flavors, namely diacetyl and acetoin, by growing Lactobacillus rhamnosus on a starch medium containing the enzyme glucoamylase. We further develop a structured kinetics for the SSF process, which includes enzyme and growth kinetics. The model was used to simulate the effect of pH and temperature on the SSF process so as to obtain optimum operating conditions. The model was experimentally verified by conducting SSF using an initial starch concentration of 100 g/L. The study demonstrated that the developed kinetic was able to suggest strategies for improved productivities. The developed model was able to accurately predict the enhanced productivity of flavors in a three stage process with intermittent addition of starch. Experimental and simulations demonstrated that citrate addition can also lead to enhanced productivity of flavors. The developed optimal model for SSF was able to capture the dynamics of SSF in batch mode as well as in a three stage process. The structured kinetics was also able to quantify the effect of multiple substrates present in the medium. The study demonstrated that structured kinetic models can be used in the future for design and optimization of SSF as a batch or a fed-batch process.

Identification and analysis of novel R308K mutation in glucokinase of type 2 diabetic patient and its kinetic correlation.

PubMed

Yellapu, Nanda Kumar; Valasani, Koteswara Rao; Pasupuleti, Santhosh Kumar; Gopal, Sowjenya; Potukuchi Venkata Gurunadha Krishna, Sarma; Matcha, Bhaskar

2014-01-01

Glucokinase (GK) plays a critical role in glucose homeostasis and the mutations in GK gene result in pathogenic complications known as Maturity Onset Diabetes of the Young 2, an autosomal dominant form of diabetic condition. In the present study, GK was purified from human liver tissue and the pure enzyme showed single band in SDS-PAGE with a molecular weight of 50 kDa. The kinetics of pure GK showed enzyme activity of 0.423±0.02 µM glucose-6-phosphate (G6P)/mL/Min and Km value of 6.66±0.02 µM. These values were compared in the liver biopsy of a clinically proven type 2 diabetic patient, where GK kinetics showed decreased enzyme activity of 0.16±0.025 µM G6P/mL/Min and increased Km of 23±0.9 µM, indicating the hyperglycemic condition in the patient. The genetic analysis of 10th exon of GK gene from this patient showed a R308K mutation. To substantiate these results, comparative molecular dynamics and docking studies were carried out where a higher docking score (-10.218 kcal/mol) was observed in the mutated GK than wild-type GK structure (-12.593 kcal/mol) indicating affinity variations for glucose. During the simulation process, glucose was expelled out from the mutant conformation but not from wild-type GK, making glucose unavailable for phosphorylation. Therefore, these results conclusively explain hyperglycemic condition in this patient. © 2014 International Union of Biochemistry and Molecular Biology, Inc.

Synthesis, kinetic mechanism and docking studies of vanillin derivatives as inhibitors of mushroom tyrosinase.

PubMed

Ashraf, Zaman; Rafiq, Muhammad; Seo, Sung-Yum; Babar, Mustafeez Mujtaba; Zaidi, Najam-us-Sahar Sadaf

2015-09-01

The purpose of the present study was to discover the extent of contribution to antityrosinase activity by adding hydroxy substituted benzoic acid, cinnamic acid and piperazine residues to vanillin. The study showed the transformation of vanillin into esters as shown in (4a-4d), (6a-6b), and (8a-8b). In addition, the relationship between structures of these esters and their mushroom tyrosinase inhibitory activity was explored. The kinetics of inhibition on mushroom tyrosinase by these esters was also investigated. It was found that hydroxyl substituted benzoic acid derivatives were weak inhibitors; however hydroxy or chloro substituted cinnamic acid and piperazine substituted derivatives were able to induce significant tyrosinase inhibition. The mushroom tyrosinase (PDBID 2ZWE) was docked with synthesized vanillin derivatives and their calculated binding energies were compared with experimental IC50 values which provided positive correlation. The most potent derivative 2-(4-formyl-2-methoxyphenoxy)-2-oxoethyl (2E)-3-(4-hydroxyphenyl)prop-2-enoate (6a) possesses hydroxy substituted cinnamic acid scaffold having IC50 value 16.13 μM with binding energy of -7.2 kcal/mol. The tyrosinase inhibitory activity of (6a) is comparable with standard kojic acid. Kinetic analysis indicated that compound 6a was mixed-type tyrosinase inhibitor with inhibition constant values Ki (13 μM) and Ki' (53 μM) and formed reversible enzyme inhibitor complex. The active vanillin analog (6a) was devoid of toxic effects as shown in cytotoxic studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

The effects of superset configuration on kinetic, kinematic, and perceived exertion in the barbell bench press.

PubMed

Weakley, Jonathon Js; Till, Kevin; Read, Dale B; Phibbs, Padraic J; Roe, Gregory; Darrall-Jones, Joshua; Jones, Ben L

2017-08-04

Training that is efficient and effective is of great importance to an athlete. One method of improving efficiency is by incorporating supersets into resistance training routines. However, the structuring of supersets is still unexplored. Therefore, the purpose of this study was to assess the effects of agonist-antagonist (A-A), alternate peripheral (A-P), and similar biomechanical (SB) superset configurations on rate of perceived exertion (RPE), kinetic and kinematic changes during the bench press. 10 subjects performed resistance training protocols in a randomized-crossover design, with magnitude-based inferences assessing changes/differences within and between protocols. Changes in RPE were very likely and almost certainly greater in the A-P and SB protocols when compared with the A-A, while all superset protocols had very likely to almost certain reductions in mean velocity and power from baseline. Reductions in mean velocity and power were almost certainly greater in the SB protocol, with differences between the A-A and A-P protocols being unclear. Decreases in peak force were likely and almost certain in the A-A and SB protocols respectively, with changes in A-P being unclear. Differences between these protocols showed likely greater decreases in SB peak forces when compared to A-A, with all other superset comparisons being unclear. This study demonstrates the importance of exercise selection when incorporating supersets into a training routine. It is suggested that the practitioner uses A-A supersets when aiming to improve training efficiency and minimize reductions in kinetic and kinematic output of the agonist musculature while completing the barbell bench press.

Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.

PubMed

Alvizo, Oscar; Mittal, Seema; Mayo, Stephen L; Schiffer, Celia A

2012-07-01

HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease. Copyright © 2012 The Protein Society.

An insight into intrinsic interfacial properties between Li metals and Li10GeP2S12 solid electrolytes.

PubMed

Chen, Bingbing; Ju, Jiangwei; Ma, Jun; Zhang, Jianjun; Xiao, Ruijuan; Cui, Guanglei; Chen, Liquan

2017-11-29

Density functional theory simulations and experimental studies were performed to investigate the interfacial properties, including lithium ion migration kinetics, between lithium metal anode and solid electrolyte Li 10 GeP 2 S 12 (LGPS). The LGPS[001] plane was chosen as the studied surface because the easiest Li + migration pathway is along this direction. The electronic structure of the surface states indicated that the electrochemical stability was reduced at both the PS 4 - and GeS 4 -teminated surfaces. For the interface cases, the equilibrium interfacial structures of lithium metal against the PS 4 -terminated LGPS[001] surface (Li/PS 4 -LGPS) and the GeS 4 -terminated LGPS[001] surface (Li/GeS 4 -LGPS) were revealed based on the structural relaxation and adhesion energy analysis. Solid electrolyte interphases were expected to be formed at both Li/PS 4 -LGPS and Li/GeS 4 -LGPS interfaces, resulting in an unstable state of interface and large interfacial resistance, which was verified by the EIS results of the Li/LGPS/Li cell. In addition, the simulations of the migration kinetics show that the energy barriers for Li + crossing the Li/GeS 4 -LGPS interface were relatively low compared with the Li/PS 4 -LGPS interface. This may contribute to the formation of Ge-rich phases at the Li/LGPS interface, which can tune the interfacial structures to improve the ionic conductivity for future all-solid-state batteries. This work will offer a thorough understanding of the Li/LGPS interface, including local structures, electronic states and Li + diffusion behaviors in all-solid-state batteries.

CFD Modeling of a CFB Riser Using Improved Inlet Boundary Conditions

NASA Astrophysics Data System (ADS)

Peng, B. T.; Zhang, C.; Zhu, J. X.; Qi, X. B.

2010-03-01

A computational fluid dynamics (CFD) model based on Eulerian-Eulerian approach coupled with granular kinetics theory was adopted to investigate the hydrodynamics and flow structures in a circulating fluidized bed (CFB) riser column. A new approach to specify the inlet boundary conditions was proposed in this study to simulate gas-solids flow in CFB risers more accurately. Simulation results were compared with the experimental data, and good agreement between the numerical results and experimental data was observed under different operating conditions, which indicates the effectiveness and accuracy of the CFD model with the proposed inlet boundary conditions. The results also illustrate a clear core annulus structure in the CFB riser under all operating conditions both experimentally and numerically.

Structural properties of a-Si films and their effect on aluminum induced crystallization

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

Tankut, Aydin; Ozkol, Engin; Karaman, Mehmet

2015-10-15

In this paper, we report the influence of the structural properties of amorphous silicon (a-Si) on its subsequent crystallization behavior via the aluminum induced crystallization (AIC) method. Two distinct a-Si deposition techniques, electron beam evaporation and plasma enhanced chemical vapor deposition (PECVD), are compared for their effect on the overall AIC kinetics as well as the properties of the final poly-crystalline (poly-Si) silicon film. Raman and FTIR spectroscopy results indicate that the PECVD grown a-Si films has higher intermediate-range order, which is enhanced for increased hydrogen dilution during deposition. With increasing intermediate-range order of the a-Si, the rate of AICmore » is diminished, leading larger poly-Si grain size.« less

Native denaturation differential scanning fluorimetry: Determining the effect of urea using a quantitative real-time thermocycler.

PubMed

Childers, Christine L; Green, Stuart R; Dawson, Neal J; Storey, Kenneth B

2016-09-01

The effect of protein stability on kinetic function is monitored with many techniques that often require large amounts of expensive substrates and specialized equipment not universally available. We present differential scanning fluorimetry (DSF), a simple high-throughput assay performed in real-time thermocyclers, as a technique for analysis of protein unfolding. Furthermore, we demonstrate a correlation between the half-maximal rate of protein unfolding (Knd), and protein unfolding by urea (I50). This demonstrates that DSF methods can determine the structural stability of an enzyme's active site and can compare the relative structural stability of homologous enzymes with a high degree of sequence similarity. Copyright © 2016 Elsevier Inc. All rights reserved.

Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme.

PubMed Central

Sigurdsson, S T; Tuschl, T; Eckstein, F

1995-01-01

Distinct structural models for the hammerhead ribozyme derived from single-crystal X-ray diffraction and fluorescence resonance energy transfer (FRET) measurements have been compared. Both models predict the same overall geometry, a wishbone shape with helices II and III nearly colinear and helix I positioned close to helix II. However, the relative orientations of helices I and II are different. To establish whether one of the models represents a kinetically active structure, a new crosslinking procedure was developed in which helices I and II of hammerhead ribozymes were disulfide-crosslinked via the 2' positions of specific sugar residues. Crosslinking residues on helices I and II that are close according to the X-ray structure did not appreciably reduce the catalytic efficiency. In contrast, crosslinking residues closely situated according to the FRET model dramatically reduced the cleavage rate by at least three orders of magnitude. These correlations between catalytic efficiencies and spatial proximities are consistent with the X-ray structure. PMID:7489517

Self-organizing Large-scale Structures in Earth's Foreshock Waves

NASA Astrophysics Data System (ADS)

Ganse, U.; Pfau-Kempf, Y.; Turc, L.; Hoilijoki, S.; von Alfthan, S.; Vainio, R. O.; Palmroth, M.

2017-12-01

Earth's foreshock is populated by plasma waves in the ULF regime, assumed to be caused by wave instabilities of shock-reflected particle beams. While in-situ observation of these waves has provided plentiful data of their amplitudes, frequencies, obliquities and relation to local plasma conditions, global-scale structures are hard to grasp from observation data alone. The hybrid-Vlasov simulation system Vlasiator, designed for kinetic modeling of the Earth's magnetosphere, has been employed to study foreshock formation under radial and near-radial IMF conditions on global scales. Structures arising in the foreshock can be comprehensively studied and directly compared to observation results. Our modeling results show that foreshock waves present emergent large-scale structures, in which regions of waves with similar phase exist. At the interfaces of these regions ("spines") we observe high wave obliquity, higher beam densities and lower beam velocities than inside them. We characterize these apparently self-organizing structures through the interplay between wave- and beam properties and present the microphysical mechanisms involved in their creation.

Structure of a Clostridium botulinum C143S thiaminase I/thiamin complex reveals active site architecture .

PubMed

Sikowitz, Megan D; Shome, Brateen; Zhang, Yang; Begley, Tadhg P; Ealick, Steven E

2013-11-05

Thiaminases are responsible for the degradation of thiamin and its metabolites. Two classes of thiaminases have been identified based on their three-dimensional structures and their requirements for a nucleophilic second substrate. Although the reactions of several thiaminases have been characterized, the physiological role of thiamin degradation is not fully understood. We have determined the three-dimensional X-ray structure of an inactive C143S mutant of Clostridium botulinum (Cb) thiaminase I with bound thiamin at 2.2 Å resolution. The C143S/thiamin complex provides atomic level details of the orientation of thiamin upon binding to Cb-thiaminase I and the identity of active site residues involved in substrate binding and catalysis. The specific roles of active site residues were probed by using site directed mutagenesis and kinetic analyses, leading to a detailed mechanism for Cb-thiaminase I. The structure of Cb-thiaminase I is also compared to the functionally similar but structurally distinct thiaminase II.

Spectral method for a kinetic swarming model

DOE PAGES

Gamba, Irene M.; Haack, Jeffrey R.; Motsch, Sebastien

2015-04-28

Here we present the first numerical method for a kinetic description of the Vicsek swarming model. The kinetic model poses a unique challenge, as there is a distribution dependent collision invariant to satisfy when computing the interaction term. We use a spectral representation linked with a discrete constrained optimization to compute these interactions. To test the numerical scheme we investigate the kinetic model at different scales and compare the solution with the microscopic and macroscopic descriptions of the Vicsek model. Lastly, we observe that the kinetic model captures key features such as vortex formation and traveling waves.

Reactivity of molecular dioxygen towards a series of isostructural dichloroiron(III) complexes with tripodal tetraamine ligands: general access to mu-oxodiiron(III) complexes and effect of alpha-fluorination on the reaction kinetics.

PubMed

Thallaj, Nasser K; Rotthaus, Olaf; Benhamou, Leila; Humbert, Nicolas; Elhabiri, Mourad; Lachkar, Mohammed; Welter, Richard; Albrecht-Gary, Anne-Marie; Mandon, Dominique

2008-01-01

We have synthesized the mono, di-, and tri-alpha-fluoro ligands in the tris(2-pyridylmethyl)amine (TPA) series, namely, FTPA, F(2)TPA and F(3)TPA, respectively. Fluorination at the alpha-position of these nitrogen-containing tripods shifts the oxidation potential of the ligand by 45-70 mV per added fluorine atom. The crystal structures of the dichloroiron(II) complexes with FTPA and F(2)TPA reveal that the iron center lies in a distorted octahedral geometry comparable to that already found in TPAFeCl(2). All spectroscopic data indicate that the geometry is retained in solution. These three isostructural complexes all react with molecular dioxygen to yield stable mu-oxodiiron(III) complexes. Crystal structure analyses are reported for each of these three mu-oxo compounds. With TPA, a symmetrical structure is obtained for a dicationic compound with the tripod coordinated in the kappa(4)N coordination mode. With FTPA, the compound is a neutral mu-oxodiiron(III) complex with a kappa(3)N coordination mode of the ligand. Oxygenation of the F(2)TPA complex gave a neutral unsymmetrical compound, the structure of which is reminiscent of that already found with the trifluorinated ligand. On reduction, all mu-oxodiiron(III) complexes revert to the starting iron(II) species. The oxygenation reaction parallels the well-known formation of mu-oxo derivatives from dioxygen in the chemistry of porphyrins reported almost three decades ago. The striking feature of the series of iron(II) precursors is the effect of the ligand on the kinetics of oxygenation of the complexes. Whereas the parent complex undergoes 90 % conversion over 40 h, the monofluorinated ligand provides a complex that has fully reacted after 30 h, whereas the reaction time for the complex with the difluorinated ligand is only 10 h. Analysis of the spectroscopic data reveals that formation of the mu-oxo complexes proceeds in two distinct reversible kinetic steps with k(1) approximately 10 k(2). For TPAFeCl(2) and FTPAFeCl(2) only small variations in the k(1) and k(2) values are observed. By contrast, F(2)TPAFeCl(2) exhibits k(1) and k(2) values that are ten times higher. These differences in kinetics are interpreted in the light of structural and electronic effects, especially the Lewis acidity at the metal center. Our results suggest coordination of dioxygen as an initial step in the process leading to formation of mu-oxodiiron(III) compounds, by contrast with an unlikely outer-sphere reduction of dioxygen, which generally occurs at negative potentials.

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

DOE PAGES

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

2017-09-25

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

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/. PMID:21297972

Statistical analysis of kinetic energy entrainment in a model wind turbine array boundary layer

NASA Astrophysics Data System (ADS)

Cal, Raul Bayoan; Hamilton, Nicholas; Kang, Hyung-Suk; Meneveau, Charles

2012-11-01

For large wind farms, kinetic energy must be entrained from the flow above the wind turbines to replenish wakes and enable power extraction in the array. Various statistical features of turbulence causing vertical entrainment of mean-flow kinetic energy are studied using hot-wire velocimetry data taken in a model wind farm in a scaled wind tunnel experiment. Conditional statistics and spectral decompositions are employed to characterize the most relevant turbulent flow structures and determine their length-scales. Sweep and ejection events are shown to be the largest contributors to the vertical kinetic energy flux, although their relative contribution depends upon the location in the wake. Sweeps are shown to be dominant in the region above the wind turbine array. A spectral analysis of the data shows that large scales of the flow, about the size of the rotor diameter in length or larger, dominate the vertical entrainment. The flow is more incoherent below the array, causing decreased vertical fluxes there. The results show that improving the rate of vertical kinetic energy entrainment into wind turbine arrays is a standing challenge and would require modifying the large-scale structures of the flow. This work was funded in part by the National Science Foundation (CBET-0730922, CBET-1133800 and CBET-0953053).

Modeling the Homogenization Kinetics of As-Cast U-10wt% Mo alloys

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

Xu, Zhijie; Joshi, Vineet; Hu, Shenyang Y.

2016-01-15

Low-enriched U-22at% Mo (U-10Mo) alloy has been considered as an alternative material to replace the highly enriched fuels in research reactors. For the U-10Mo to work effectively and replace the existing fuel material, a thorough understanding of the microstructure development from as-cast to the final formed structure is required. The as-cast microstructure typically resembles an inhomogeneous microstructure with regions containing molybdenum-rich and -lean regions, which may affect the processing and possibly the in-reactor performance. This as-cast structure must be homogenized by thermal treatment to produce a uniform Mo distribution. The development of a modeling capability will improve the understanding ofmore » the effect of initial microstructures on the Mo homogenization kinetics. In the current work, we investigated the effect of as-cast microstructure on the homogenization kinetics. The kinetics of the homogenization was modeled based on a rigorous algorithm that relates the line scan data of Mo concentration to the gray scale in energy dispersive spectroscopy images, which was used to generate a reconstructed Mo concentration map. The map was then used as realistic microstructure input for physics-based homogenization models, where the entire homogenization kinetics can be simulated and validated against the available experiment data at different homogenization times and temperatures.« less

Kinetic analyses of vasculogenesis inform mechanistic studies

PubMed Central

Winfree, Seth; Chu, Chenghao; Tu, Wanzhu; Blue, Emily K.; Gohn, Cassandra R.; Dunn, Kenneth W.

2017-01-01

Vasculogenesis is a complex process by which endothelial stem and progenitor cells undergo de novo vessel formation. Quantitative assessment of vasculogenesis is a central readout of endothelial progenitor cell functionality. However, current assays lack kinetic measurements. To address this issue, new approaches were developed to quantitatively assess in vitro endothelial colony-forming cell (ECFC) network formation in real time. Eight parameters of network structure were quantified using novel Kinetic Analysis of Vasculogenesis (KAV) software. KAV assessment of structure complexity identified two phases of network formation. This observation guided the development of additional vasculogenic readouts. A tissue cytometry approach was established to quantify the frequency and localization of dividing ECFCs. Additionally, Fiji TrackMate was used to quantify ECFC displacement and speed at the single-cell level during network formation. These novel approaches were then implemented to identify how intrauterine exposure to maternal diabetes mellitus (DM) impairs fetal ECFC vasculogenesis. Fetal ECFCs exposed to maternal DM form fewer initial network structures, which are not stable over time. Correlation analyses demonstrated that ECFC samples with greater division in branches form fewer closed network structures. Additionally, reductions in average ECFC movement over time decrease structural connectivity. Identification of these novel phenotypes utilizing the newly established methodologies provides evidence for the cellular mechanisms contributing to aberrant ECFC vasculogenesis. PMID:28100488

Kinetic control of intralayer cobalt coordination in layered hydroxides: Co(1-0.5x)(oct) Co(x)(tet) (OH)2 (Cl)x (H2O)n.

PubMed

Neilson, James R; Schwenzer, Birgit; Seshadri, Ram; Morse, Daniel E

2009-12-07

We report the synthesis and characterization of new structural variants of the isotypic compound with the generic chemical formula, Co(1-0.5x)(oct) Co(x)(tet) (OH)2 (Cl)x (H2O)n, all modifications of an alpha-Co(OH)2 lattice. We show that the occupancy of tetrahedrally coordinated cobalt sites and associated chloride ligands, x, is modulated by the rate of formation of the respective layered hydroxide salts from kinetically controlled aqueous hydrolysis at an air-water interface. This new level of structural control is uniquely enabled by the slow diffusion of a hydrolytic catalyst, a simple technique. Independent structural characterizations of the compounds separately describe various attributes of the materials on different length scales, revealing details hidden by the disordered average structures. The precise control over the population of distinct octahedrally and tetrahedrally coordinated cobalt ions in the lattice provides a gentle, generic method for modulating the coordination geometry of cobalt in the material without disturbing the lattice or using additional reagents. A mechanism is proposed to reconcile the observation of the kinetic control of the structure with competing interactions during the initial stages of hydrolysis and condensation.

Kinetics of Mismatch Formation opposite Lesions by the Replicative DNA Polymerase from Bacteriophage RB69

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

Hogg, Matthew; Rudnicki, Jean; Midkiff, John

2010-04-12

The fidelity of DNA replication is under constant threat from the formation of lesions within the genome. Oxidation of DNA bases leads to the formation of altered DNA bases such as 8-oxo-7,8-dihydroguanine, commonly called 8-oxoG, and 2-hydroxyadenenine, or 2-OHA. In this work we have examined the incorporation kinetics opposite these two oxidatively derived lesions as well as an abasic site analogue by the replicative DNA polymerase from bacteriophage RB69. We compared the kinetic parameters for both wild type and the low fidelity L561A variant. While nucleotide incorporation rates (k{sub pol}) were generally higher for the variant, the presence of amore » lesion in the templating position reduced the ability of both the wild-type and variant DNA polymerases to form ternary enzyme-DNA-dNTP complexes. Thus, the L561A substitution does not significantly affect the ability of the RB69 DNA polymerase to recognize damaged DNA; instead, the mutation increases the probability that nucleotide incorporation will occur. We have also solved the crystal structure of the L561A variant forming an 8-oxoG {center_dot} dATP mispair and show that the propensity for forming this mispair depends on an enlarged polymerase active site.« less

Ultrafine Nanocrystalline CeO2@C-Containing NaAlH4 with Fast Kinetics and Good Reversibility for Hydrogen Storage.

PubMed

Zhang, Xin; Liu, Yongfeng; Wang, Ke; Li, You; Gao, Mingxia; Pan, Hongge

2015-12-21

A nanocrystalline CeO2@C-containing NaAlH4 composite is successfully synthesized in situ by hydrogenating a NaH-Al mixture doped with CeO2@C. Compared with NaAlH4 , the as-prepared CeO2@C-containing NaAlH4 composite, with a minor amount of excess Al, exhibits significantly improved hydrogen storage properties. The dehydrogenation onset temperature of the hydrogenated [NaH-Al-7 wt % CeO2@C]-0.04Al sample is 77 °C lower than that of the pristine sample because of a reduced kinetic barrier. More importantly, the dehydrogenated sample absorbs ∼4.7 wt % hydrogen within 35 min at 100°C and 10 MPa of hydrogen. Compositional and structural analyses reveal that CeO2 is converted to CeH2 during ball milling and that the newly formed CeH2 works with the excess of Al to synergistically improve the hydrogen storage properties of NaAlH4. Our findings will aid in the rational design of novel catalyst-doped complex hydride systems with low operating temperatures, fast kinetics, and long-term cyclability. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient Ligation of the Schistosoma Hammerhead Ribozyme †

PubMed Central

Canny, Marella D.; Jucker, Fiona M.; Pardi, Arthur

2011-01-01

The hammerhead ribozyme from Schistosoma mansoni is the best characterized of the natural hammerhead ribozymes. Biophysical, biochemical, and structural studies have shown that the formation of the loop-loop tertiary interaction between stems I and II alters the global folding, cleavage kinetics, and conformation of the catalytic core of this hammerhead, leading to a ribozyme that is readily cleaved under physiological conditions. This study investigates the ligation kinetics and the internal equilibrium between cleavage and ligation for the Schistosoma hammerhead. Single turnover kinetic studies on a construct where the ribozyme cleaves and ligates substrate(s) in trans showed up to 23% ligation when starting from fully cleaved products. This was achieved by a ~2,000-fold increase in the rate of ligation compared to a minimal hammerhead without the loop-loop tertiary interaction, yielding an internal equilibrium that ranges from 2–3 at physiological Mg2+ ion concentrations (0.1 –1 mM). Thus, the natural Schistosoma hammerhead ribozyme is almost as efficient at ligation as it is at cleavage. The results here are consistent with a model where formation of the loop-loop tertiary interaction leads to a higher population of catalytically active molecules, and where formation of this tertiary interaction has a much larger effect on the ligation than the cleavage activity of the Schistosoma hammerhead ribozyme. PMID:17319693

Kinetic isotope effects and how to describe them

PubMed Central

Karandashev, Konstantin; Xu, Zhen-Hao; Meuwly, Markus; Vaníček, Jiří; Richardson, Jeremy O.

2017-01-01

We review several methods for computing kinetic isotope effects in chemical reactions including semiclassical and quantum instanton theory. These methods describe both the quantization of vibrational modes as well as tunneling and are applied to the ⋅H + H2 and ⋅H + CH4 reactions. The absolute rate constants computed with the semiclassical instanton method both using on-the-fly electronic structure calculations and fitted potential-energy surfaces are also compared directly with exact quantum dynamics results. The error inherent in the instanton approximation is found to be relatively small and similar in magnitude to that introduced by using fitted surfaces. The kinetic isotope effect computed by the quantum instanton is even more accurate, and although it is computationally more expensive, the efficiency can be improved by path-integral acceleration techniques. We also test a simple approach for designing potential-energy surfaces for the example of proton transfer in malonaldehyde. The tunneling splittings are computed, and although they are found to deviate from experimental results, the ratio of the splitting to that of an isotopically substituted form is in much better agreement. We discuss the strengths and limitations of the potential-energy surface and based on our findings suggest ways in which it can be improved. PMID:29282447

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

Saw, C K

To date a global kinetic rate law has not been written to accurately describe solid-solid phase transformations of HMX and TATB where contributions from grain size effects, binder contents, and impurity levels are explicitly defined. Our recent work presented at the 2001 SCCM topical APS meeting, Atlanta, GA, demonstrated one can not confidently use the second harmonic generation (SHG) diagnostic to study energetic material phase transitions where non-uniform grain size distributions are present. For example, in HMX, the early arrival of SHG before the XRD in the SHG/XRD simultaneous high temperature experiment clearly indicates the partial molecular conversion from centrosymmetricmore » to non-centrosymmetric without any structural changes as exhibit by the XRD pattern. This conversion is attributed to the changes of the surface molecules due to the differences in potential between the surface and the bulk. The present paper reports on accurate XRD measurements following changes of {beta}-HMX to {delta}-HMX at elevated temperature. The results are compared for sample with 2 different grain sizes for HMX. We report accurate temperature dependent lattice parameters and hence volume and linear thermal expansion coefficients along each crystallographic axis. We have also conducted kinetic studies of the behavior of 2 grain-sizes of HMX and concluded that their kinetics, are drastically different.« less

Time-resolved rhodopsin activation currents in a unicellular expression system.

PubMed Central

Sullivan, J M; Shukla, P

1999-01-01

The early receptor current (ERC) is the charge redistribution occurring in plasma membrane rhodopsin during light activation of photoreceptors. Both the molecular mechanism of the ERC and its relationship to rhodopsin conformational activation are unknown. To investigate whether the ERC could be a time-resolved assay of rhodopsin structure-function relationships, the distinct sensitivity of modern electrophysiological tools was employed to test for flash-activated ERC signals in cells stably expressing normal human rod opsin after regeneration with 11-cis-retinal. ERCs are similar in waveform and kinetics to those found in photoreceptors. The action spectrum of the major R(2) charge motion is consistent with a rhodopsin photopigment. The R(1) phase is not kinetically resolvable and the R(2) phase, which overlaps metarhodopsin-II formation, has a rapid risetime and complex multiexponential decay. These experiments demonstrate, for the first time, kinetically resolved electrical state transitions during activation of expressed visual pigment in a unicellular environment (single or fused giant cells) containing only 6 x 10(6)-8 x 10(7) molecules of rhodopsin. This method improves measurement sensitivity 7 to 8 orders of magnitude compared to other time-resolved techniques applied to rhodopsin to study the role particular amino acids play in conformational activation and the forces that govern those transitions. PMID:10465746

Determination of the DNA-binding kinetics of three related but heteroimmune bacteriophage repressors using EMSA and SPR analysis

PubMed Central

Henriksson-Peltola, Petri; Sehlén, Wilhelmina; Haggård-Ljungquist, Elisabeth

2007-01-01

Bacteriophages P2, P2 Hy dis and WΦ are very similar but heteroimmune Escherichia coli phages. The structural genes show over 96% identity, but the repressors show between 43 and 63% identities. Furthermore, the operators, which contain two directly repeated sequences, vary in sequence, length, location relative to the promoter and spacing between the direct repeats. We have compared the in vivo effects of the wild type and mutated operators on gene expression with the complexes formed between the repressors and their wild type or mutated operators using electrophoretic mobility shift assay (EMSA), and real-time kinetics of the protein–DNA interactions using surface plasmon resonance (SPR) analysis. Using EMSA, the repressors formed different protein–DNA complexes, and only WΦ was significantly affected by point mutations. However, SPR analysis showed a reduced association rate constant and an increased dissociation rate constant for P2 and WΦ operator mutants. The association rate constants of P2 Hy dis was too fast to be determined. The P2 Hy dis dissociation response curves were shown to be triphasic, while both P2 and WΦ C were biphasic. Thus, the kinetics of complex formation and the nature of the complexes formed differ extensively between these very closely related phages. PMID:17412705

Kinetic Modeling of Radiative Turbulence in Relativistic Astrophysical Plasmas: Particle Acceleration and High-Energy Flares

NASA Astrophysics Data System (ADS)

Uzdensky, Dmitri

Relativistic astrophysical plasma environments routinely produce intense high-energy emission, which is often observed to be nonthermal and rapidly flaring. The recently discovered gamma-ray (> 100 MeV) flares in Crab Pulsar Wind Nebula (PWN) provide a quintessential illustration of this, but other notable examples include relativistic active galactic nuclei (AGN) jets, including blazars, and Gamma-ray Bursts (GRBs). Understanding the processes responsible for the very efficient and rapid relativistic particle acceleration and subsequent emission that occurs in these sources poses a strong challenge to modern high-energy astrophysics, especially in light of the necessity to overcome radiation reaction during the acceleration process. Magnetic reconnection and collisionless shocks have been invoked as possible mechanisms. However, the inferred extreme particle acceleration requires the presence of coherent electric-field structures. How such large-scale accelerating structures (such as reconnecting current sheets) can spontaneously arise in turbulent astrophysical environments still remains a mystery. The proposed project will conduct a first-principles computational and theoretical study of kinetic turbulence in relativistic collisionless plasmas with a special focus on nonthermal particle acceleration and radiation emission. The main computational tool employed in this study will be the relativistic radiative particle-in-cell (PIC) code Zeltron, developed by the team members at the Univ. of Colorado. This code has a unique capability to self-consistently include the synchrotron and inverse-Compton radiation reaction force on the relativistic particles, while simultaneously computing the resulting observable radiative signatures. This proposal envisions performing massively parallel, large-scale three-dimensional simulations of driven and decaying kinetic turbulence in physical regimes relevant to real astrophysical systems (such as the Crab PWN), including the radiation reaction effects. In addition to measuring the general fluid-level statistical properties of kinetic turbulence (e.g., the turbulent spectrum in the inertial and sub-inertial range), as well as the overall energy dissipation and particle acceleration, the proposed study will also investigate their intermittency and time variability, resulting in direction- and time-resolved emitted photon spectra and direction- and energy-resolved light curves, which can then be compared with observations. To gain deeper physical insight into the intermittent particle acceleration processes in turbulent astrophysical environments, the project will also identify and analyze statistically the current sheets, shocks, and other relevant localized particle-acceleration structures found in the simulations. In particular, it will assess whether relativistic kinetic turbulence in PWN can self-consistently generate such structures that are long and strong enough to accelerate large numbers of particles to the PeV energies required to explain the Crab gamma-ray flares, and where and under what conditions such acceleration can occur. The results of this research will also advance our understanding the origin of ultra-rapid TeV flares in blazar jets and will have important implications for GRB prompt emission, as well as AGN radio-lobes and radiatively-inefficient accretion flows, such as the flow onto the supermassive black hole at our Galactic Center.

Influence of Au and TiO2 structures on hydrogen dissociation over TiO2/Au(100)

NASA Astrophysics Data System (ADS)

Nakamura, I.; Mantoku, H.; Furukawa, T.; Takahashi, A.; Fujitani, T.

2012-11-01

We performed H2-D2 exchange reactions over TiOx/Au(100) and compared the observed reaction kinetics with those reported for TiOx/Au(111) in order to clarify the influence of the Au and TiO2 structures on dissociation of H2 molecules. Low energy electron diffraction observations showed that the TiO2 produced on Au(100) was disordered, in contrast to the comparatively ordered TiO2 structure formed on Au(111). The activation energies and the turnover frequencies for HD formation over TiO2/Au(100) agreed well with those for TiO2/Au(111), clearly indicating that the hydrogen dissociation sites created over TiO2/Au(100) were the perimeter interface between stoichiometric TiO2 and Au, as was previously concluded for TiO2/Au(111). We concluded that the creation of active sites for hydrogen dissociation was independent of the Au and TiO2 structures consisting perimeter interface, and that local bonds that formed between Au and O atoms of stoichiometric TiO2 were essential for the creation of active sites.

Comparative study of particle structure evolution during water sorption: skim and whole milk powders.

PubMed

Murrieta-Pazos, I; Gaiani, C; Galet, L; Cuq, B; Desobry, S; Scher, J

2011-10-01

Surface composition of dairy powders influences significantly a quantity of functional properties such as rehydration, caking, agglomeration. Nevertheless, the kinetic of water uptake by the powders was never directly related to the structure and the composition of the surface. In this work, the effect of relative humidity on the structural reorganization of two types of dairy powder was studied. The water-powder interaction for industrial whole milk powder, and skim milk powder was studied using dynamic vapor sorption. The water sorption isotherms were fitted with a Brunner-Emmet-Teller model and each stage of the sorption curve was analyzed with a Fickian diffusion. The water content in the monolayer predicted for each powder and the moisture diffusivity calculated were discussed and compared. Concurrently, powders microstructure and powders surface under variable relative humidity were assessed by X-ray photoelectron spectroscopy, scanning electron microscopy coupled with energy dispersive X-ray and atomic force microscopy. A correlation between the data obtained from the sorption isotherms and the modifications of structure allowed us to conclude that powder microstructure and chemical state of the components could play an important role in determining the water diffusivity. Copyright © 2011 Elsevier B.V. All rights reserved.

Effect of thermal pretreatment on chemical composition, physical structure and biogas production kinetics of wheat straw.

PubMed

Rajput, Asad Ayub; Zeshan; Visvanathan, Chettiyappan

2018-05-21

Hard lignocellulosic structure of wheat straw is the main hindrance in its anaerobic digestion. Thus, a laboratory scale batch experiment was conducted to study the effect of thermal pretreatment on anaerobic digestion of wheat straw. For this purpose, different thermal pretreatment temperatures of 120, 140, 160 and 180 °C were studied and the results were compared with raw wheat straw. Significant differences in biogas production were observed at temperature higher than 160 °C. Highest biogas yield of 615 Nml/gVS and volatile solids reduction of 69% was observed from wheat straw pretreated at 180 °C. Wheat straw pretreated at 180 °C showed 53% higher biogas yield as compared to untreated. Further, FTIR analysis revealed change in chemical bonds of lignocellulosic structure of wheat straw. Modified Gompertz model was best fitted on biogas production data and predicted shorter lag phase time and higher biogas production as the pretreatment temperature increased. Overall, change in lignocellulosic structure and increase in cellulose content were the main reason in enhancing biogas production. Copyright © 2018 Elsevier Ltd. All rights reserved.

The D1 and D2 proteins of dinoflagellates: unusually accumulated mutations which influence on PSII photoreaction.

PubMed

Iida, Satoko; Kobiyama, Atsushi; Ogata, Takehiko; Murakami, Akio

2008-01-01

Plastid encoded genes of the dinoflagellates are rapidly evolving and most divergent. The importance of unusually accumulated mutations on structure of PSII core protein and photosynthetic function was examined in the dinoflagellates, Symbiodinium sp. and Alexandrium tamarense. Full-length cDNA sequences of psbA (D1 protein) and psbD (D2 protein) were obtained and compared with the other oxygen-evolving photoautotrophs. Twenty-three amino acid positions (7%) for the D1 protein and 34 positions (10%) for the D2 were mutated in the dinoflagellates, although amino acid residues at these positions were conserved in cyanobacteria, the other algae, and plant. Many mutations were likely to distribute in the N-terminus and the D-E interhelical loop of the D1 protein and helix B of D2 protein, while the remaining regions were well conserved. The different structural properties in these mutated regions were supported by hydropathy profiles. The chlorophyll fluorescence kinetics of the dinoflagellates was compared with Synechocystis sp. PCC6803 in relation to the altered protein structure.

Characterization of dipeptidylcarboxypeptidase of Leishmania donovani: a molecular model for structure based design of antileishmanials

NASA Astrophysics Data System (ADS)

Baig, Mirza Saqib; Kumar, Ashutosh; Siddiqi, Mohammad Imran; Goyal, Neena

2010-01-01

Leishmania donovani dipeptidylcarboxypeptidsae (LdDCP), an angiotensin converting enzyme (ACE) related metallopeptidase has been identified and characterized as a putative drug target for antileishmanial chemotherapy. The kinetic parameters for LdDCP with substrate, Hip-His-Leu were determined as, Km, 4 mM and Vmax, 1.173 μmole/ml/min. Inhibition studies revealed that known ACE inhibitors (captopril and bradykinin potentiating peptide; BPP1) were weak inhibitors for LdDCP as compared to human testicular ACE (htACE) with Ki values of 35.8 nM and 3.9 μM, respectively. Three dimensional model of LdDCP was generated based on crystal structure of Escherichia coli DCP (EcDCP) by means of comparative modeling and assessed using PROSAII, PROCHECK and WHATIF. Captopril docking with htACE, LdDCP and EcDCP and analysis of molecular electrostatic potentials (MEP) suggested that the active site domain of three enzymes has several minor but potentially important structural differences. These differences could be exploited for designing selective inhibitor of LdDCP thereby antileishmanial compounds either by denovo drug design or virtual screening of small molecule databases.

Dynamic Structure Factor and Transport Coefficients of a Homogeneously Driven Granular Fluid in Steady State

NASA Astrophysics Data System (ADS)

Vollmayr-Lee, Katharina; Zippelius, Annette; Aspelmeier, Timo

2011-03-01

We study the dynamic structure factor of a granular fluid of hard spheres, driven into a stationary nonequilibrium state by balancing the energy loss due to inelastic collisions with the energy input due to driving. The driving is chosen to conserve momentum, so that fluctuating hydrodynamics predicts the existence of sound modes. We present results of computer simulations which are based on an event driven algorithm. The dynamic structure factor F (q , ω) is determined for volume fractions 0.05, 0.1 and 0.2 and coefficients of normal restitution 0.8 and 0.9. We observe sound waves, and compare our results for F (q , ω) with the predictions of generalized fluctuating hydrodynamics which takes into account that temperature fluctuations decay either diffusively or with a finite relaxation rate, depending on wave number and inelasticity. We determine the speed of sound and the transport coefficients and compare them to the results of kinetic theory. K.V.L. thanks the Institute of Theoretical Physics, University of Goettingen, for financial support and hospitality.

Intramolecular structural model for photoinduced plasticity in chalcogenide glasses

NASA Astrophysics Data System (ADS)

Yannopoulos, S. N.

2003-08-01

Selected spectral features of Raman spectra of glassy As2S3 subjected to elongation stress and sub-band-gap light illumination are analyzed and compared with polarization-dependent information obtained from the bulk glass at room temperature and near the glass transition temperature. The data are suggestive of specific structural changes which involve the transformation of atomic arrangements from realgarlike As4S4 molecules, originally present in virgin (untreated) fibers, into planar orpimentlike clusters. Implications of these atomic rearrangements to the incipient photoinduced fluidity—the onset of plastic deformation—in As2S3 glass are discussed. Kinetics of photoinduced plastic changes is compared to that of Raman spectra changes, revealing a qualitative similar behavior. An approximate estimation of the relative contribution of intermolecular rearrangements and the intramolecular structural mechanism proposed in this paper has revealed that the latter is responsible for almost 30% of the photoinduced elongation of the fiber’s length at room temperature. The proposed mechanism can as well serve as rationale for understanding the photoinduced volume expansion observed in chalcogenide glasses.

Chemical kinetics as a contract sport

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

Kolb, C.E.

1990-01-01

Earlier in this century chemical kinetics was a basic physical chemistry research topic widely pursued in leading academic chemistry departments. Chemical kinetics now appears to be a discipline practiced chiefly for its applications to societal problems. The chemical kinetics activities directed by D.M. Golden at SRI International are strikingly successful in generating data for key applied problems while at the same time advancing our understanding of chemical kinetics as a scientific discipline. In this talk, the author will contrast the chemical kinetics activities in two contract R D laboratories, one on the right side of the U.S. (ARI) and themore » other on the left (SRI). Their approach to common applied problems ranging from stratospheric heterogeneous kinetics to plasma etching systems for semiconductor processing will be compared and contrasted. Empirically discovered Golden Rules for the pursuit of quality chemical kinetics research in a contract R D environment will be presented and discussed.« less

The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations1

PubMed Central

Just, Victoria J.; Burrell, Matthew R.; Bowater, Laura; McRobbie, Iain; Stevenson, Clare E. M.; Lawson, David M.; Bornemann, Stephen

2007-01-01

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural. PMID:17680775

Multiple lesion track structure model

NASA Technical Reports Server (NTRS)

Wilson, John W.; Cucinotta, Francis A.; Shinn, Judy L.

1992-01-01

A multilesion cell kinetic model is derived, and radiation kinetic coefficients are related to the Katz track structure model. The repair-related coefficients are determined from the delayed plating experiments of Yang et al. for the C3H10T1/2 cell system. The model agrees well with the x ray and heavy ion experiments of Yang et al. for the immediate plating, delaying plating, and fractionated exposure protocols employed by Yang. A study is made of the effects of target fragments in energetic proton exposures and of the repair-deficient target-fragment-induced lesions.

Magnetostructural Transition Kinetics in Shocked Iron

DOE PAGES

Surh, Michael P.; Benedict, Lorin X.; Sadigh, Babak

2016-08-15

Here, a generalized Heisenberg model is implemented to study the effect of thermal magnetic disorder on kinetics of the Fe α–ε transition. The barrier to bulk martensitic displacement remains large in α-Fe shocked well past the phase line but is much reduced in the [001] α–ε boundary. The first result is consistent with observed overdriving to metastable α, while the second suggests structural instability, as implied by observation of a [001] shock transformation front without plastic relaxation. Reconciling both behaviors may require concurrent treatment of magnetic and structural order.

Symmetrical kinematics does not imply symmetrical kinetics in people with transtibial amputation using cycling model.

PubMed

Childers, W Lee; Kogler, Géza F

2014-01-01

People with amputation move asymmetrically with regard to kinematics (joint angles) and kinetics (joint forces and moments). Clinicians have traditionally sought to minimize kinematic asymmetries, assuming kinetic asymmetries would also be minimized. A cycling model evaluated locomotor asymmetries. Eight individuals with unilateral transtibial amputation pedaled with 172 mm-length crank arms on both sides (control condition) and with the crank arm length shortened to 162 mm on the amputated side (CRANK condition). Pedaling kinetics and limb kinematics were recorded. Joint kinetics, joint angles (mean and range of motion [ROM]), and pedaling asymmetries were calculated from force pedals and with a motion capture system. A one-way analysis of variance with tukey post hoc compared kinetics and kinematics across limbs. Statistical significance was set to p

Raman studies of methane-ethane hydrate metastability.

PubMed

Ohno, Hiroshi; Strobel, Timothy A; Dec, Steven F; Sloan, E Dendy; Koh, Carolyn A

2009-03-05

The interconversion of methane-ethane hydrate from metastable to stable structures was studied using Raman spectroscopy. sI and sII hydrates were synthesized from methane-ethane gas mixtures of 65% or 93% methane in ethane and water, both with and without the kinetic hydrate inhibitor, poly(N-vinylcaprolactam). The observed faster structural conversion rate in the higher methane concentration atmosphere can be explained in terms of the differences in driving force (difference in chemical potential of water in sI and sII hydrates) and kinetics (mass transfer of gas and water rearrangement). The kinetic hydrate inhibitor increased the conversion rate at 65% methane in ethane (sI is thermodynamically stable) but retards the rate at 93% methane in ethane (sII is thermodynamically stable), implying there is a complex interaction between the polymer, water, and hydrate guests at crystal surfaces.

Block matrix based LU decomposition to analyze kinetic damping in active plasma resonance spectroscopy

NASA Astrophysics Data System (ADS)

Roehl, Jan Hendrik; Oberrath, Jens

2016-09-01

``Active plasma resonance spectroscopy'' (APRS) is a widely used diagnostic method to measure plasma parameter like electron density. Measurements with APRS probes in plasmas of a few Pa typically show a broadening of the spectrum due to kinetic effects. To analyze the broadening a general kinetic model in electrostatic approximation based on functional analytic methods has been presented [ 1 ] . One of the main results is, that the system response function Y(ω) is given in terms of the matrix elements of the resolvent of the dynamic operator evaluated for values on the imaginary axis. To determine the response function of a specific probe the resolvent has to be approximated by a huge matrix which is given by a banded block structure. Due to this structure a block based LU decomposition can be implemented. It leads to a solution of Y(ω) which is given only by products of matrices of the inner block size. This LU decomposition allows to analyze the influence of kinetic effects on the broadening and saves memory and calculation time. Gratitude is expressed to the internal funding of Leuphana University.

An experimental and kinetic modeling study on dimethyl carbonate (DMC) pyrolysis and combustion

DOE PAGES

Sun, Wenyu; Yang, Bin; Hansen, Nils; ...

2015-12-08

Because of the absence of C–C bonds and the large oxygen content in its molecular structure, dimethyl carbonate (DMC) is a promising oxygenated additive or substitute for hydrocarbon fuels. In order to understand its chemical oxidation and combustion kinetics, flow reactor pyrolysis at different pressures (40, 200 and 1040 mbar) and low-pressure laminar premixed flames with different equivalence ratios (1.0 and 1.5) were investigated. Mole fraction profiles of many reaction intermediates and products were obtained within estimated experimental uncertainties. From theoretical calculations and estimations, a detailed kinetic model for DMC pyrolysis and high-temperature combustion consisting of 257 species and 1563more » reactions was developed. The performance of the kinetic model was then analyzed using detailed chemical composition information, primarily from the present measurements. In addition, it was examined against the chemical structure of an opposed-flow diffusion flame, relying on global combustion properties such as the ignition delay times and laminar burning velocities. Furthermore, these extended comparisons yielded overall satisfactory agreement, demonstrating the applicability of the present model over a wide range of high-temperature conditions.« less

Role of filament annealing in the kinetics and thermodynamics of nucleated polymerization.

PubMed

Michaels, Thomas C T; Knowles, Tuomas P J

2014-06-07

The formation of nanoscale protein filaments from soluble precursor molecules through nucleated polymerization is a common form of supra-molecular assembly phenomenon. This process underlies the generation of a range of both functional and pathological structures in nature. Filament breakage has emerged as a key process controlling the kinetics of the growth reaction since it increases the number of filament ends in the system that can act as growth sites. In order to ensure microscopic reversibility, however, the inverse process of fragmentation, end-to-end annealing of filaments, is a necessary component of a consistent description of such systems. Here, we combine Smoluchowski kinetics with nucleated polymerization models to generate a master equation description of protein fibrillization, where filamentous structures can undergo end-to-end association, in addition to elongation, fragmentation, and nucleation processes. We obtain self-consistent closed-form expressions for the growth kinetics and discuss the key physics that emerges from considering filament fusion relative to current fragmentation only models. Furthermore, we study the key time scales that describe relaxation to equilibrium.

Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation.

PubMed

Hu, Shenshen; Sharma, Sudhir C; Scouras, Alexander D; Soudackov, Alexander V; Carr, Cody A Marcus; Hammes-Schiffer, Sharon; Alber, Tom; Klinman, Judith P

2014-06-11

The enzyme soybean lipoxygenase (SLO) has served as a prototype for hydrogen-tunneling reactions, as a result of its unusual kinetic isotope effects (KIEs) and their temperature dependencies. Using a synergy of kinetic, structural, and theoretical studies, we show how the interplay between donor-acceptor distance and active-site flexibility leads to catalytic behavior previously predicted by quantum tunneling theory. Modification of the size of two hydrophobic residues by site-specific mutagenesis in SLO reduces the reaction rate 10(4)-fold and is accompanied by an enormous and unprecedented room-temperature KIE. Fitting of the kinetic data to a non-adiabatic model implicates an expansion of the active site that cannot be compensated by donor-acceptor distance sampling. A 1.7 Å resolution X-ray structure of the double mutant further indicates an unaltered backbone conformation, almost identical side-chain conformations, and a significantly enlarged active-site cavity. These findings show the compelling property of room-temperature hydrogen tunneling within a biological context and demonstrate the very high sensitivity of such tunneling to barrier width.

Structural and catalytic roles of amino acid residues located at substrate-binding pocket in Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase.

PubMed

Chen, Je-Hsin; Tsai, Li-Chu; Huang, Hsiao-Chuan; Shyur, Lie-Fen

2010-10-01

We created 12 mutant enzymes (E11L, F40I, Y42L, N44L, N44Q, E47I, L62G, K64A, K64M, R137M, R137Q, and N139A) from the truncated Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase (TF-glucanase). The enzymes were used to investigate the structural and catalytic roles of specific amino acid residues located at the catalytic pocket and having direct interactions with glucose subsites of the product beta-1,3-1,4-cellotriose (CLTR). Fluorescence spectrometry showed no discernible changes in secondary structures among purified TF-glucanase and the mutants. Kinetic analyses showed E11L, F40I, Y42L, R137M, and R137Q with a >10-fold decrease of specific activity (11.2- to 67.4-fold), and E11L, N44Q, E47I, K64M, R137M, R137Q, and N139A with a 2.17- to 4.3-fold increase of K(m) value when compared with TF-glucanase. Notably, E11L, R137Q, R137M, F40I, and N139A showed the most significant decrease in catalytic efficiency relative to TF-glucanase, by 2155-, 84.9-, 48.5-, 41.1-, and 19.1-fold, respectively; the five mutants showed the greatest changes in comparative energy DeltaDeltaG(b), with values of 1.94 to 4.92 kcal/mol. Combined with results from kinetic and structure modeling analyses of all mutant enzymes and X-ray crystallography of F40I, we elucidate that Glu11, Phe40, Arg137, and Asn139 play a crucial role in the catalysis of TF-glucanase owing to their local and direct interaction through hydrogen bonds or van der Waals stacking interaction by aromatic rings onto the glucose subsites -3, -2, and -1 of CLTR/substrate. The overall globular structures in the wild-type and mutant F40I enzymes do not differ. 2010 Wiley-Liss, Inc.

Kinetics of pack aluminization of nickel

NASA Technical Reports Server (NTRS)

Seigle, L. L.; Gupta, B. K.; Shankar, R.; Sarkhel, A. K.

1978-01-01

The kinetics of pack aluminization of unalloyed nickel in packs of varying aluminum activity with various halide activators were studied. Surface compositions of the coatings as functions of time, temperature, and pack composition were obtained in order to establish the boundary conditions for diffusion in the system. The structure of the packs was also examined in order to clarify the mechanism of aluminum transport. The results indicate that the kinetics of pack aluminization are controlled jointly by gas diffusion in the pack and solid diffusion in the coating. Levine and Caves' model for gas diffusion was combined with calculations of rates of diffusion in the solid to formulate a more complete theory for the kinetics of pack aluminization.

Determining Kinetic Parameters for Isothermal Crystallization of Glasses

NASA Technical Reports Server (NTRS)

Ray, C. S.; Zhang, T.; Reis, S. T.; Brow, R. K.

2006-01-01

Non-isothermal crystallization techniques are frequently used to determine the kinetic parameters for crystallization in glasses. These techniques are experimentally simple and quick compared to the isothermal techniques. However, the analytical models used for non-isothermal data analysis, originally developed for describing isothermal transformation kinetics, are fundamentally flawed. The present paper describes a technique for determining the kinetic parameters for isothermal crystallization in glasses, which eliminates most of the common problems that generally make the studies of isothermal crystallization laborious and time consuming. In this technique, the volume fraction of glass that is crystallized as a function of time during an isothermal hold was determined using differential thermal analysis (DTA). The crystallization parameters for the lithium-disilicate (Li2O.2SiO2) model glass were first determined and compared to the same parameters determined by other techniques to establish the accuracy and usefulness of the present technique. This technique was then used to describe the crystallization kinetics of a complex Ca-Sr-Zn-silicate glass developed for sealing solid oxide fuel cells.

Dynamic Covalent Synthesis of Aryleneethynylene Cages through Alkyne Metathesis: Dimer, Tetramer, or Interlocked Complex?

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

Wang, Qi; Yu, Chao; Zhang, Chenxi

A dynamic covalent approach towards rigid aryleneethynylene covalent organic polyhedrons (COPs) was explored. Our study on the relationship of the COP structures and the geometry of their building blocks reveals that the topology of aryleneethynylene COPs strongly depends on the size of the building blocks. A tetramer (D2h symmetric), dimer, or interlocked complex can be formed from monomers with the same face-to-edge angle but in different sizes. As alkyne metathesis is a self-exchange reaction and non-directional, the cyclooligomerization of multi-alkyne monomers involves both intramolecular cyclization and intermolecular metathesis reaction, resulting in complicated thermodynamic process disturbed by kinetic competition. Although amore » tetrahedron-shaped tetramer (Td symmetric) has comparable thermodynamic stability to a D2h symmetric tetramer, its formation is kinetically disfavored and was not observed experimentally. Aryleneethynylene COPs consist of purely unsaturated carbon backbones and exhibit large internal cavities, which would have interesting applications in host-guest chemistry and development of porous materials.« less

Cosmic ray sources, acceleration and propagation

NASA Technical Reports Server (NTRS)

Ptuskin, V. S.

1986-01-01

A review is given of selected papers on the theory of cosmic ray (CR) propagation and acceleration. The high isotropy and a comparatively large age of galactic CR are explained by the effective interaction of relativistic particles with random and regular electromagnetic fields in interstellar medium. The kinetic theory of CR propagation in the Galaxy is formulated similarly to the elaborate theory of CR propagation in heliosphere. The substantial difference between these theories is explained by the necessity to take into account in some cases the collective effects due to a rather high density of relativisitc particles. In particular, the kinetic CR stream instability and the hydrodynamic Parker instability is studied. The interaction of relativistic particles with an ensemble of given weak random magnetic fields is calculated by perturbation theory. The theory of CR transfer is considered to be basically completed for this case. The main problem consists in poor information about the structure of the regular and the random galactic magnetic fields. An account is given of CR transfer in a turbulent medium.

Pressure-Induced Amorphization in Single-Crystal Ta2O5 Nanowires: A Kinetic Mechanism and Improved Electrical Conductivity

NASA Astrophysics Data System (ADS)

Lu, Xujie; Hu, Qingyang; Yang, Wenge; Bai, Ligang; Sheng, Howard; Wang, Lin; Huang, Fuqiang; Wen, Jianguo; Miller, Dean; Zhao, Yusheng

2014-03-01

Pressure-induced amorphization (PIA) in single-crystal Ta2O5 nanowires is observed at 19 GPa and the obtained amorphous Ta2O5 nanowires show significant improvement in electrical conductivity. The phase transition process is unveiled by monitoring structural evolution with in-situ synchrotron XRD, PDF, Raman spectroscopy and TEM. The first principles calculations reveal the phonon modes softening during compression at particular bonds, and the analysis on the electron localization function also shows bond strength weakening at the same positions. Based on the experimental and theoretical results, a kinetic PIA mechanism is proposed and demonstrated systematically that amorphization is initiated by the disruption of connectivity between polyhedra at the particular weak-bonding positions along the a-axis in the unit cell. The one-dimensional morphology is well preserved for the pressure-induced amorphous Ta2O5 and the electrical conductivity is improved by an order of magnitude compared to traditional amorphous forms.

A first step towards a consensus static in vitro model for simulating full-term infant digestion.

PubMed

Ménard, O; Bourlieu, C; De Oliveira, S C; Dellarosa, N; Laghi, L; Carrière, F; Capozzi, F; Dupont, D; Deglaire, A

2018-02-01

In vitro alternatives to clinical trials are used for studying human food digestion. For simulating infant digestion, only a few models, lacking physiological relevance, are available. Thanks to an extensive literature review of the in vivo infant digestive conditions, a gastrointestinal static in vitro model was developed for infants born at term and aged 28days. The model was applied to the digestion of a commercial infant formula. Kinetics of digestion, as well as the structural evolution, were compared with those obtained while submitting the same formula to the adult international consensus protocol of in vitro static digestion. The kinetics of proteolysis and lipolysis differed according to the physiological stage resulting mainly from the reduced level of enzymes and bile salts, as well as the higher gastric pH in the infant model. This in vitro static model of infant digestion is of interest for scientists, food or pharmaceutical manufacturers. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tuning electronic properties of boron nitride nanoplate via doping carbon for enhanced adsorptive performance.

PubMed

Pang, Jingyu; Chao, Yanhong; Chang, Honghong; Li, Hongping; Xiong, Jun; He, Minqiang; Zhang, Qi; Li, Huaming; Zhu, Wenshuai

2017-12-15

In this paper, the carbon-doped boron nitride nanoplate (C-BNNP) was prepared by pyrolyzing the precursor under N 2 and served as an excellent adsorbent for removal of Rhodamine B (RhB). The structure and composition of C-BNNP were characterized and its adsorption behavior for RhB was investigated. Compared with boron nitride nanoplate (BNNP) which was synthesized under NH 3 , C-BNNP displayed an enhancement of the adsorption capacity for RhB (833mg/g). The adsorption activity was comprehensibly studied by kinetics, isotherm and thermodynamics. The adsorption kinetics followed pseudo-second-order model. The equilibrium adsorption data agreed well with the Langmuir isotherm. And the thermodynamics indicated that the adsorption process was a spontaneous, exothermic and physisorption process. In addition, the density functional theory was proposed that doping carbon in the BNNP decreased the chemical hardness of the adsorbent and enhanced the adsorption capacity of C-BNNP for RhB. Copyright © 2017 Elsevier Inc. All rights reserved.

Discovery of potent α-glucosidase inhibitor flavonols: Insights into mechanism of action through inhibition kinetics and docking simulations.

PubMed

Şöhretoğlu, Didem; Sari, Suat; Barut, Burak; Özel, Arzu

2018-05-17

Beside other pharmaceutical benefits, flavonoids are known for their potent α-glucosidase inhibition. In the present study, we investigated α-glucosidase inhibitory effects of structurally related 11 flavonols, among which quercetin-3-O-(3″-O-galloyl)-β-galactopyranoside (8) and quercetin 3-O-(6″-O-galloyl)-β-glucopyranoside (9) showed significant inhibition compared to the positive control, acarbose, with IC 50 values of 0.97 ± 0.02 and 1.35 ± 0.06 µM, respectively. It was found that while sugar substitution to C3-OH of C ring reduced the α-glucosidase inhibitory effect, galloyl substitution to these sugar units increased it. An enzyme kinetics analysis revealed that 7 was competitive, whereas 1, 2, 8, and 9 were uncompetitive inhibitors. In the light of these findings, we performed molecular docking studies to predict their inhibition mechanisms at atomic level. Copyright © 2018 Elsevier Inc. All rights reserved.

Current and turbulence measurements at the FINO1 offshore wind energy site: analysis using 5-beam ADCPs

NASA Astrophysics Data System (ADS)

Bakhoday-Paskyabi, Mostafa; Fer, Ilker; Reuder, Joachim

2018-01-01

We report concurrent measurements of ocean currents and turbulence at two sites in the North Sea, one site at upwind of the FINO1 platform and the other 200-m downwind of the Alpha Ventus wind farm. At each site, mean currents, Reynolds stresses, turbulence intensity and production of turbulent kinetic energy are obtained from two bottom-mounted 5-beam Nortek Signature1000s, high-frequency Doppler current profiler, at a water depth of approximately 30 m. Measurements from the two sites are compared to statistically identify the effects of wind farm and waves on ocean current variability and the turbulent structure in the water column. Profiles of Reynolds stresses are found to be sensible to both environmental forcing and the wind farm wake-induced distortions in both boundary layers near the surface and the seabed. Production of turbulent kinetic energy and turbulence intensity exhibit approximately similar, but less pronounced, patterns in the presence of farm wake effects.

Impacts of Spontaneous Hot Flow Anomalies on the Magnetosheath and Magnetopause

NASA Technical Reports Server (NTRS)

Omidi, N.; Berchem, J.; Sibeck, D.; Zhang, H.

2016-01-01

Spacecraft observations and global hybrid (kinetic ions and fluid electrons) simulations have demonstrated that ion dissipation processes at the quasi-parallel bow shock are associated with the formation of structures called spontaneous hot flow anomalies (SHFAs). Previous simulations and recent spacecraft observations have also established that SHFAs result in the formation of magnetosheath filamentary structures(MFS). In this paper we demonstrate that in addition to MFS, SHFAs also result in the formation of magnetos heath cavities that are associated with decreases in density, velocity, and magnetic field and enhancements in temperature. We use the results of a global MHD run to determine the change in the magnetosheath properties associated with cavities due to ion kinetic effects. The results also show the formation of regions of high flow speed called magnetosheath jets whose properties as a function of solar wind Mach number are described in this study. Comparing the properties of the simulated magnetosheath cavities and jets to past spacecraft observations provides good agreement in both cases. We also demonstrate that pressure variations associated with cavities and SHFAs in the sheath result in a continuous sunward and anti sunward magnetopause motion. This result is consistent with previous suggestions that SHFAs may be responsible for the generation of ion cyclotron waves and precipitation of ring current protons in the outer magnetosphere.

Structure and inhibition of orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum.

PubMed

Langley, David B; Shojaei, Maryam; Chan, Camilla; Lok, Hiu Chuen; Mackay, Joel P; Traut, Thomas W; Guss, J Mitchell; Christopherson, Richard I

2008-03-25

Orotidine 5'-monophosphate (OMP) decarboxylase from Plasmodium falciparum (PfODCase, EC 4.1.1.23) has been overexpressed, purified, subjected to kinetic and biochemical analysis, and crystallized. The native enzyme is a homodimer with a subunit molecular mass of 38 kDa. The saturation curve for OMP as a substrate conformed to Michaelis-Menten kinetics with K m = 350 +/- 60 nM and V max = 2.70 +/- 0.10 micromol/min/mg protein. Inhibition patterns for nucleoside 5'-monophosphate analogues were linear competitive with respect to OMP with a decreasing potency of inhibition of PfODCase in the order: pyrazofurin 5'-monophosphate ( K i = 3.6 +/- 0.7 nM) > xanthosine 5'-monophosphate (XMP, K i = 4.4 +/- 0.7 nM) > 6-azauridine 5'-monophosphate (AzaUMP, K i = 12 +/- 3 nM) > allopurinol-3-riboside 5'-monophosphate ( K i = 240 +/- 20 nM). XMP is an approximately 150-fold more potent inhibitor of PfODCase compared with the human enzyme. The structure of PfODCase was solved in the absence of ligand and displays a classic TIM-barrel fold characteristic of the enzyme. Both the phosphate-binding loop and the betaalpha5-loop have conformational flexibility, which may be associated with substrate capture and product release along the reaction pathway.

Protein adsorption on electrospun zinc doped hydroxyapatite containing nylon 6 membrane: kinetics and isotherm.

PubMed

Esfahani, Hamid; Prabhakaran, Molamma P; Salahi, Esmaeil; Tayebifard, Ali; Keyanpour-Rad, Mansour; Rahimipour, Mohamad Reza; Ramakrishna, Seeram

2015-04-01

Surface modification of electrospun polymeric membrane surfaces is a critical step towards the separation process including protein adsorption. In this study, the electrospun Nylon fibers was incorporated with positively charged zinc doped hydroxyapatite (HAp) nanoparticles to study the adsorption of negatively charged proteins, namely bovine serum albumin (BSA). Effects of zinc amount within the atomic structure of HAp (nZH; n=0, 4, 8 At.%) was evaluated on produced scaffolds and consequently protein adsorption. The results showed that the ability of Nylon membrane to adsorb BSA increased with incorporation of nZH nanoparticles within the nylon structure. This phenomenon is appeared to be relate to different electrostatic charge and not to physical characteristic of scaffolds. The incorporated membrane (N-4ZH) by nanoparticles with highest zeta (ξ) potential adsorbed the maximum amount of protein. The adsorption of BSA was best fitted with pseudo-second order kinetic model. The experimental isotherm data were further analyzed by using Langmuir and Freundlich equations. By comparing the correlation coefficients obtained for each linear transformation of isotherm analysis, it was found that the Langmuir equation was the best fit equilibrium model that described the adsorption of BSA on these membranes. Copyright © 2014 Elsevier Inc. All rights reserved.

Modeling time-coincident ultrafast electron transfer and solvation processes at molecule-semiconductor interfaces

NASA Astrophysics Data System (ADS)

Li, Lesheng; Giokas, Paul G.; Kanai, Yosuke; Moran, Andrew M.

2014-06-01

Kinetic models based on Fermi's Golden Rule are commonly employed to understand photoinduced electron transfer dynamics at molecule-semiconductor interfaces. Implicit in such second-order perturbative descriptions is the assumption that nuclear relaxation of the photoexcited electron donor is fast compared to electron injection into the semiconductor. This approximation breaks down in systems where electron transfer transitions occur on 100-fs time scale. Here, we present a fourth-order perturbative model that captures the interplay between time-coincident electron transfer and nuclear relaxation processes initiated by light absorption. The model consists of a fairly small number of parameters, which can be derived from standard spectroscopic measurements (e.g., linear absorbance, fluorescence) and/or first-principles electronic structure calculations. Insights provided by the model are illustrated for a two-level donor molecule coupled to both (i) a single acceptor level and (ii) a density of states (DOS) calculated for TiO2 using a first-principles electronic structure theory. These numerical calculations show that second-order kinetic theories fail to capture basic physical effects when the DOS exhibits narrow maxima near the energy of the molecular excited state. Overall, we conclude that the present fourth-order rate formula constitutes a rigorous and intuitive framework for understanding photoinduced electron transfer dynamics that occur on the 100-fs time scale.

Kinetically controlled indium surface coverage effects on PAMBE-growth of InN/GaN(0001) quantum well structures

NASA Astrophysics Data System (ADS)

Li, Chen; Maidaniuk, Yurii; Kuchuk, Andrian V.; Shetty, Satish; Ghosh, Pijush; White, Thomas P.; Morgan, Timothy Al.; Hu, Xian; Wu, Yang; Ware, Morgan E.; Mazur, Yuriy I.; Salamo, Gregory J.

2018-05-01

We report the effects of nitrogen (N) plasma and indium (In) flux on the In adatom adsorption/desorption kinetics on a GaN(0001) surface at the relatively high plasma-assisted molecular beam epitaxy-growth temperature of 680 °C. We experimentally demonstrate that under an active N flux, the (√{3 }×√{3 })R 30 ° surface reconstruction containing In and N quickly appears and the dynamically stable In adlayers sitting on this surface exhibit a continuous change from 0 to 2 MLs as a function of In flux. Compared to the bare GaN 1 ×1 surface which is stable during In exposure without an active N flux, we observed a much faster desorption for the bottom In adlayer and the absence of an In flux window corresponding to an In coverage of 1 ML. Moreover, when the In coverage exceeds 2 MLs, the desorption rates become identical for both surfaces. Finally, the importance of In surface coverage before GaN capping was shown by growing a series of InN/GaN multiple quantum well samples. The photoluminescence data show that a consistent quantum well structure is only formed if the surface is covered by excess In droplets before GaN capping.

Impacts of spontaneous hot flow anomalies on the magnetosheath and magnetopause

NASA Astrophysics Data System (ADS)

Omidi, N.; Berchem, J.; Sibeck, D.; Zhang, H.

2016-04-01

Spacecraft observations and global hybrid (kinetic ions and fluid electrons) simulations have demonstrated that ion dissipation processes at the quasi-parallel bow shock are associated with the formation of structures called spontaneous hot flow anomalies (SHFAs). Previous simulations and recent spacecraft observations have also established that SHFAs result in the formation of magnetosheath filamentary structures (MFS). In this paper we demonstrate that in addition to MFS, SHFAs also result in the formation of magnetosheath cavities that are associated with decreases in density, velocity, and magnetic field and enhancements in temperature. We use the results of a global MHD run to determine the change in the magnetosheath properties associated with cavities due to ion kinetic effects. The results also show the formation of regions of high flow speed called magnetosheath jets whose properties as a function of solar wind Mach number are described in this study. Comparing the properties of the simulated magnetosheath cavities and jets to past spacecraft observations provides good agreement in both cases. We also demonstrate that pressure variations associated with cavities and SHFAs in the sheath result in a continuous sunward and antisunward magnetopause motion. This result is consistent with previous suggestions that SHFAs may be responsible for the generation of ion cyclotron waves and precipitation of ring current protons in the outer magnetosphere.

Functional and Biochemical Characterization of Three Recombinant Human Glucose-6-Phosphate Dehydrogenase Mutants: Zacatecas, Vanua-Lava and Viangchan.

PubMed

Gómez-Manzo, Saúl; Marcial-Quino, Jaime; Vanoye-Carlo, America; Serrano-Posada, Hugo; González-Valdez, Abigail; Martínez-Rosas, Víctor; Hernández-Ochoa, Beatriz; Sierra-Palacios, Edgar; Castillo-Rodríguez, Rosa Angélica; Cuevas-Cruz, Miguel; Rodríguez-Bustamante, Eduardo; Arreguin-Espinosa, Roberto

2016-05-21

Glucose-6-phosphate dehydrogenase (G6PD) deficiency in humans causes severe disease, varying from mostly asymptomatic individuals to patients showing neonatal jaundice, acute hemolysis episodes or chronic nonspherocytic hemolytic anemia. In order to understand the effect of the mutations in G6PD gene function and its relation with G6PD deficiency severity, we report the construction, cloning and expression as well as the detailed kinetic and stability characterization of three purified clinical variants of G6PD that present in the Mexican population: G6PD Zacatecas (Class I), Vanua-Lava (Class II) and Viangchan (Class II). For all the G6PD mutants, we obtained low purification yield and altered kinetic parameters compared with Wild Type (WT). Our results show that the mutations, regardless of the distance from the active site where they are located, affect the catalytic properties and structural parameters and that these changes could be associated with the clinical presentation of the deficiency. Specifically, the structural characterization of the G6PD Zacatecas mutant suggests that the R257L mutation have a strong effect on the global stability of G6PD favoring an unstable active site. Using computational analysis, we offer a molecular explanation of the effects of these mutations on the active site.