Understanding Drug Release Data through Thermodynamic Analysis

PubMed Central

Freire, Marjorie Caroline Liberato Cavalcanti; Alexandrino, Francisco; Marcelino, Henrique Rodrigues; Picciani, Paulo Henrique de Souza; Silva, Kattya Gyselle de Holanda e; Genre, Julieta; de Oliveira, Anselmo Gomes; do Egito, Eryvaldo Sócrates Tabosa

2017-01-01

Understanding the factors that can modify the drug release profile of a drug from a Drug-Delivery-System (DDS) is a mandatory step to determine the effectiveness of new therapies. The aim of this study was to assess the Amphotericin-B (AmB) kinetic release profiles from polymeric systems with different compositions and geometries and to correlate these profiles with the thermodynamic parameters through mathematical modeling. Film casting and electrospinning techniques were used to compare behavior of films and fibers, respectively. Release profiles from the DDSs were performed, and the mathematical modeling of the data was carried out. Activation energy, enthalpy, entropy and Gibbs free energy of the drug release process were determined. AmB release profiles showed that the relationship to overcome the enthalpic barrier was PVA-fiber > PVA-film > PLA-fiber > PLA-film. Drug release kinetics from the fibers and the films were better fitted on the Peppas–Sahlin and Higuchi models, respectively. The thermodynamic parameters corroborate these findings, revealing that the AmB release from the evaluated systems was an endothermic and non-spontaneous process. Thermodynamic parameters can be used to explain the drug kinetic release profiles. Such an approach is of utmost importance for DDS containing insoluble compounds, such as AmB, which is associated with an erratic bioavailability. PMID:28773009

Elucidation of the naproxen sodium adsorption onto activated carbon prepared from waste apricot: kinetic, equilibrium and thermodynamic characterization.

PubMed

Onal, Y; Akmil-Başar, C; Sarici-Ozdemir, C

2007-09-30

In this study, activated carbon (WA11Zn5) was prepared from waste apricot, which is waste in apricot plants in Malatya, by chemical activation with ZnCl(2). BET surface area of activated carbon is determined as 1060 m(2)/g. The ability of WA11Zn5, to remove naproxen sodium from effluent solutions by adsorption has been studied. Equilibrium isotherms for the adsorption of naproxen sodium on activated carbon were measured experimentally. Results were analyzed by the Langmiur, Freundlich equation using linearized correlation coefficient at 298 K. The characteristic parameters for each isotherm have been determined. Langmiur equation is found to best represent the equilibrium data for naproxen sodium-WA11Zn5 systems. The monolayer adsorption capacity of WA11Zn5 for naproxen sodium was found to be 106.38 mg/g at 298 K. The process was favorable and spontaneous. The kinetics of adsorption of naproxen sodium have been discussed using three kinetic models, i.e., the pseudo first-order model, the pseudo second-order model, the intraparticle diffusion model. Kinetic parameters and correlation coefficients were determined. It was shown that the pseudo second-order kinetic equation could describe the adsorption kinetics for naproxen sodium onto WA11Zn5. The thermodynamic parameters, such as DeltaG degrees , DeltaS degrees and DeltaH degrees, were calculated. The thermodynamics of naproxen sodium-WA11Zn5 system indicates endothermic process.

Self-Assembly of Human Serum Albumin: A Simplex Phenomenon

PubMed Central

Thakur, Garima; Prashanthi, Kovur; Jiang, Keren; Thundat, Thomas

2017-01-01

Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is explained through thermodynamics and chemical kinetics. PMID:28930179

Kinetics of adsorption of dyes from aqueous solution using activated carbon prepared from waste apricot.

PubMed

Onal, Yunus

2006-10-11

Adsorbent (WA11Zn5) has been prepared from waste apricot by chemical activation with ZnCl(2). Pore properties of the activated carbon such as BET surface area, pore volume, pore size distribution, and pore diameter were characterized by N(2) adsorption and DFT plus software. Adsorption of three dyes, namely, Methylene Blue (MB), Malachite Green (MG), Crystal Violet (CV), onto activated carbon in aqueous solution was studied in a batch system with respect to contact time, temperature. The kinetics of adsorption of MB, MG and CV have been discussed using six kinetic models, i.e., the pseudo-first-order model, the pseudo-second-order model, the Elovich equation, the intraparticle diffusion model, the Bangham equation, the modified Freundlich equation. Kinetic parameters and correlation coefficients were determined. It was shown that the second-order kinetic equation could describe the adsorption kinetics for three dyes. The dyes uptake process was found to be controlled by external mass transfer at earlier stages (before 5 min) and by intraparticle diffusion at later stages (after 5 min). Thermodynamic parameters, such as DeltaG, DeltaH and DeltaS, have been calculated by using the thermodynamic equilibrium coefficient obtained at different temperatures and concentrations. The thermodynamics of dyes-WA11Zn5 system indicates endothermic process.

Thermodynamic Analysis of a Coupled Chemical Reaction.

ERIC Educational Resources Information Center

Trimm, Harold; And Others

1979-01-01

Describes a typical relaxation kinetic experiment using a sudden increase in the temperature of the system. Time involved is described as minimal and the approach as quicker, more accurate, sensitive, and producing simultaneous determination of several thermodynamic parameters. (Author/SA)

Mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis.

PubMed

Fang, Baishan; Niu, Jin; Ren, Hong; Guo, Yingxia; Wang, Shizhen

2014-01-01

Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH) from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA) and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated.

Evolution of a terrestrial magma ocean: Thermodynamics, kinetics, rheology, convection, differentiation

NASA Technical Reports Server (NTRS)

Solomatov, V. S.; Stevenson, D. J.

1992-01-01

The evolution of an initially totally molten magma ocean is constrained on the basis of analysis of various physical problems in the magma ocean. First of all an equilibrium thermodynamics of the magma ocean is developed in the melting temperature range. The equilibrium thermodynamical parameters are found as functions only of temperature and pressure and are used in the subsequent models of kinetics and convection. Kinematic processes determine the crystal size and also determine a non-equilibrium thermodynamics of the system. Rheology controls all dynamical regimes of the magma ocean. The thermal convection models for different rheological laws are developed for both the laminar convection and for turbulent convection in the case of equilibrium thermodynamics of the multiphase system. The evolution is estimated on the basis of all the above analysis.

Uniqueness of thermodynamic projector and kinetic basis of molecular individualism

NASA Astrophysics Data System (ADS)

Gorban, Alexander N.; Karlin, Iliya V.

2004-05-01

Three results are presented: First, we solve the problem of persistence of dissipation for reduction of kinetic models. Kinetic equations with thermodynamic Lyapunov functions are studied. Uniqueness of the thermodynamic projector is proven: There exists only one projector which transforms any vector field equipped with the given Lyapunov function into a vector field with the same Lyapunov function for a given anzatz manifold which is not tangent to the Lyapunov function levels. Second, we use the thermodynamic projector for developing the short memory approximation and coarse-graining for general nonlinear dynamic systems. We prove that in this approximation the entropy production increases. ( The theorem about entropy overproduction.) In example, we apply the thermodynamic projector to derive the equations of reduced kinetics for the Fokker-Planck equation. A new class of closures is developed, the kinetic multipeak polyhedra. Distributions of this type are expected in kinetic models with multidimensional instability as universally as the Gaussian distribution appears for stable systems. The number of possible relatively stable states of a nonequilibrium system grows as 2 m, and the number of macroscopic parameters is in order mn, where n is the dimension of configuration space, and m is the number of independent unstable directions in this space. The elaborated class of closures and equations pretends to describe the effects of “molecular individualism”. This is the third result.

Degradation kinetics of cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside during hot air and vacuum drying in mulberry (Morus alba L.) fruit: A comparative study based on solid food system.

PubMed

Zhou, Mo; Chen, Qinqin; Bi, Jinfeng; Wang, Yixiu; Wu, Xinye

2017-08-15

The aim of this study is to ascertain the degradation kinetic of anthocyanin in dehydration process of solid food system. Mulberry fruit was treated by hot air and vacuum drying at 60 and 75°C. The contents of cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside were determined by using high performance liquid chromatography. Kinetic and thermodynamic parameters were calculated for analysing the degradation characteristics. Model fitting results showed monomeric anthocyanin degradations were followed the second-order kinetic. Vacuum drying presented high kinetic rate constants and low t 1/2 values. Thermodynamic parameters including the activation energy, enthalpy change and entropy change appeared significant differences between hot air and vacuum drying. Both heating techniques showed similar effects on polyphenol oxidase activities. These results indicate the anthocyanin degradation kinetic in solid food system is different from that in liquid and the oxygen can be regarded as a catalyst to accelerate the degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

PubMed

Akiba, Hiroki; Tsumoto, Kouhei

2015-07-01

Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Chromium Biosorption from Cr(VI) Aqueous Solutions by Cupressus lusitanica Bark: Kinetics, Equilibrium and Thermodynamic Studies.

PubMed

Netzahuatl-Muñoz, Alma Rosa; Cristiani-Urbina, María del Carmen; Cristiani-Urbina, Eliseo

2015-01-01

The present study investigated the kinetics, equilibrium and thermodynamics of chromium (Cr) ion biosorption from Cr(VI) aqueous solutions by Cupressus lusitanica bark (CLB). CLB total Cr biosorption capacity strongly depended on operating variables such as initial Cr(VI) concentration and contact time: as these variables rose, total Cr biosorption capacity increased significantly. Total Cr biosorption rate also increased with rising solution temperature. The pseudo-second-order model described the total Cr biosorption kinetic data best. Langmuir´s model fitted the experimental equilibrium biosorption data of total Cr best and predicted a maximum total Cr biosorption capacity of 305.4 mg g(-1). Total Cr biosorption by CLB is an endothermic and non-spontaneous process as indicated by the thermodynamic parameters. Results from the present kinetic, equilibrium and thermodynamic studies suggest that CLB biosorbs Cr ions from Cr(VI) aqueous solutions predominantly by a chemical sorption phenomenon. Low cost, availability, renewable nature, and effective total Cr biosorption make CLB a highly attractive and efficient method to remediate Cr(VI)-contaminated water and wastewater.

Chromium Biosorption from Cr(VI) Aqueous Solutions by Cupressus lusitanica Bark: Kinetics, Equilibrium and Thermodynamic Studies

PubMed Central

Netzahuatl-Muñoz, Alma Rosa; Cristiani-Urbina, María del Carmen; Cristiani-Urbina, Eliseo

2015-01-01

The present study investigated the kinetics, equilibrium and thermodynamics of chromium (Cr) ion biosorption from Cr(VI) aqueous solutions by Cupressus lusitanica bark (CLB). CLB total Cr biosorption capacity strongly depended on operating variables such as initial Cr(VI) concentration and contact time: as these variables rose, total Cr biosorption capacity increased significantly. Total Cr biosorption rate also increased with rising solution temperature. The pseudo-second-order model described the total Cr biosorption kinetic data best. Langmuir´s model fitted the experimental equilibrium biosorption data of total Cr best and predicted a maximum total Cr biosorption capacity of 305.4 mg g-1. Total Cr biosorption by CLB is an endothermic and non-spontaneous process as indicated by the thermodynamic parameters. Results from the present kinetic, equilibrium and thermodynamic studies suggest that CLB biosorbs Cr ions from Cr(VI) aqueous solutions predominantly by a chemical sorption phenomenon. Low cost, availability, renewable nature, and effective total Cr biosorption make CLB a highly attractive and efficient method to remediate Cr(VI)-contaminated water and wastewater. PMID:26352933

Kinetic and thermodynamic studies of the Co(II) and Ni(II) ions removal from aqueous solutions by Ca-Mg phosphates.

PubMed

Ivanets, A I; Srivastava, V; Kitikova, N V; Shashkova, I L; Sillanpää, M

2017-03-01

The aim of this work was to study the sorption kinetics and thermodynamics of Co(II) and Ni(II) from aqueous solutions by sorbents on the basis of hydrogen (PD-1) and tertiary (PD-2) Ca-Mg phosphates depending on the solution temperature and sorbents chemical composition. Kinetic studies of adsorption of Co(II) and Ni(II) ions onto samples of phosphate sorbents were performed in batch experiment at the temperatures 288, 303, 318 and 333 K. The sorbent dose was fixed at 10 g L -1 , initial pH value 2.6, and contact time varied from 5 to 600 min. The kinetics of Co(II) and Ni(II) adsorption were analyzed by using pseudo-first order, pseudo-second order and intraparticle diffusion models. Thermodynamic parameters (ΔG°, ΔH° and ΔS°) for the sorption of Co(II) and Ni(II) were determined using the Gibbs-Helmholtz equation. The calculated kinetic parameters and corresponding correlation coefficients revealed that Co(II) and Ni(II) uptake process followed the pseudo-second order rate expression. Thermodynamic studies confirmed the spontaneous and endothermic nature of removal process which indicate that sorption of Co(II) and Ni(II) ions onto both phosphate sorbents is favoured at higher temperatures and has the chemisorptive mechanism. The data thus obtained would be useful for practical application of the low cost and highly effective Ca-Mg phosphate sorbents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative thermogravimetric analyses of co-combustion of textile dyeing sludge and sugarcane bagasse in carbon dioxide/oxygen and nitrogen/oxygen atmospheres: Thermal conversion characteristics, kinetics, and thermodynamics.

PubMed

Xie, Wenhao; Wen, Shaoting; Liu, Jingyong; Xie, Wuming; Kuo, Jiahong; Lu, Xingwen; Sun, Shuiyu; Chang, Kenlin; Buyukada, Musa; Evrendilek, Fatih

2018-05-01

Thermodynamic and kinetic parameters of co-combustion of textile dyeing sludge (TDS) and sugarcane bagasse (SB) were studied using thermogravimetric analysis in CO 2 /O 2 and N 2 /O 2 atmospheres. Our results showed that the comprehensive combustion characteristic index (CCI) of the blends was improved by 1.71-4.32 times. With the increased O 2 concentration, co-combustion peak temperature decreased from 329.7 to 318.2 °C, with an increase in its maximum weight loss rate from 10.04 to 14.99%/min and its CCI by 1.31 times (β = 20 °C·min -1 ). To evaluate the co-combustion characteristics, thermodynamic and kinetic parameters (entropy, Gibbs free energy and enthalpy changes, and apparent activation energy) were obtained in the five atmospheres. The lowest apparent activation energy of the TB64 blend was obtained in oxy-fuel atmosphere (CO 2 /O 2  = 7/3). Copyright © 2018 Elsevier Ltd. All rights reserved.

The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair

NASA Astrophysics Data System (ADS)

Wang, Yujie; Wang, Zhen; Wang, Yanli; Liu, Taigang; Zhang, Wenbing

2018-01-01

The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

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.

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.

PubMed

Liebermeister, Wolfram; Uhlendorf, Jannis; Klipp, Edda

2010-06-15

Standard rate laws are a key requisite for systematically turning metabolic networks into kinetic models. They should provide simple, general and biochemically plausible formulae for reaction velocities and reaction elasticities. At the same time, they need to respect thermodynamic relations between the kinetic constants and the metabolic fluxes and concentrations. We present a family of reversible rate laws for reactions with arbitrary stoichiometries and various types of regulation, including mass-action, Michaelis-Menten and uni-uni reversible Hill kinetics as special cases. With a thermodynamically safe parameterization of these rate laws, parameter sets obtained by model fitting, sampling or optimization are guaranteed to lead to consistent chemical equilibrium states. A reformulation using saturation values yields simple formulae for rates and elasticities, which can be easily adjusted to the given stationary flux distributions. Furthermore, this formulation highlights the role of chemical potential differences as thermodynamic driving forces. We compare the modular rate laws to the thermodynamic-kinetic modelling formalism and discuss a simplified rate law in which the reaction rate directly depends on the reaction affinity. For automatic handling of modular rate laws, we propose a standard syntax and semantic annotations for the Systems Biology Markup Language. An online tool for inserting the rate laws into SBML models is freely available at www.semanticsbml.org. Supplementary data are available at Bioinformatics online.

Adsorption laboratory experiment for undergraduate chemical engineering: Introducing kinetic, equilibrium and thermodynamic concepts

NASA Astrophysics Data System (ADS)

Muryanto, S.; Djatmiko Hadi, S.

2016-11-01

Adsorption laboratory experiment for undergraduate chemical engineering program is discussed. The experiment demonstrated adsorption of copper ions commonly found in wastewater using bio-sorbent, i.e. agricultural wastes. The adsorption was performed in a batch mode under various parameters: adsorption time (up to 120 min), initial pH (2 to 6), adsorbent dose (2.0 to 12.0 g L-1), adsorbent size (50 to 170 mesh), initial Cu2+ concentration (25 to 100 ppm) and temperatures (room temp to 40°C). The equilibrium and kinetic data of the experiments were calculated using the two commonly used isotherms: Langmuir and Lagergren pseudo-first-order kinetics. The maximum adsorption capacity for Cu2+ was found as 94.34 mg g-1. Thermodynamically, the adsorption process was spontaneous and endothermic. The calculated activation energy for the adsorption was observed as high as 127.94 kJ mol-1. Pedagogically, the experiment was assumed to be important in increasing student understanding of kinetic, equilibrium and thermodynamic concepts.

Thermodynamic stability and kinetic inertness of a Gd-DTPA bisamide complex grafted onto gold nanoparticles.

PubMed

Mogilireddy, Vijetha; Déchamps-Olivier, Isabelle; Alric, Christophe; Laurent, Gautier; Laurent, Sophie; Vander Elst, Luce; Muller, Robert; Bazzi, Rana; Roux, Stéphane; Tillement, Olivier; Chuburu, Françoise

2015-01-01

Gold nanoparticles coated by gadolinium (III) chelates (Au@DTDTPA) where DTDTPA is a dithiolated bisamide derivative of diethylenetriamine-N,N,N',N'',N''-pentaacetic acid (DTPA), constituted contrast agents for both X-ray computed tomography and magnetic resonance imaging. In an MRI context, highly stable Gd(3+) complexes are needed for in vivo applications. Thus, knowledge of the thermodynamic stability and kinetic inertness of these chelates, when grafted onto gold nanoparticles, is crucial since bisamide DTPA chelates are usually less suited for Gd(3+) coordination than DTPA. Therefore, these parameters were evaluated by means of potentiometric titrations and relaxivity measurements. The results showed that, when the chelates were grafted onto the nanoparticle, not only their thermodynamic stability but also their kinetic inertness were improved. These positive effects were correlated to the chelate packing at the nanoparticle surface that stabilized the corresponding Gd(3+) complexes and greatly enhanced their kinetic inertness. Copyright © 2014 John Wiley & Sons, Ltd.

Evaluation of agricultural residues pyrolysis under non-isothermal conditions: Thermal behaviors, kinetics, and thermodynamics.

PubMed

Chen, Jianbiao; Wang, Yanhong; Lang, Xuemei; Ren, Xiu'e; Fan, Shuanshi

2017-10-01

The thermal conversion characteristics, kinetics, and thermodynamics of agricultural residues, rape straw (RS) and wheat bran (WB), were investigated under non-isothermal conditions. TGA experiments showed that the pyrolysis characteristics of RS were quite different from those of WB. As reflected by the comprehensive devolatilization index, when the heating rate increased from 10 to 30Kmin -1 , the pyrolysis performance of RS and WB were improved 5.27 and 5.96 times, respectively. The kinetic triplets of the main pyrolysis process of agricultural residues were calculated by the Starink method and the integral master-plots method. Kinetic analysis results indicated that the most potential kinetic models for the pyrolysis of RS and WB were D 2 and F 2.7 , respectively. The thermodynamic parameters (ΔH, ΔG, and ΔS) were determined by the activated complex theory. The positive ΔH, positive ΔG, and negative ΔS at characteristic temperatures validated that the pyrolysis of agricultural residues was endothermic and non-spontaneous. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exhaustive Exercise-induced Oxidative Stress Alteration of Erythrocyte Oxygen Release Capacity.

PubMed

Xiong, Yanlian; Xiong, Yanlei; Wang, Yueming; Zhao, Yajin; Li, Yaojin; Ren, Yang; Wang, Ruofeng; Zhao, Mingzi; Hao, Yitong; Liu, Haibei; Wang, Xiang

2018-05-24

The aim of the present study is to explore the effect of exhaustive running exercise (ERE) in the oxygen release capacity of rat erythrocytes. Rats were divided into sedentary control (C), moderate running exercise (MRE) and exhaustive running exercise groups. The thermodynamics and kinetics properties of the erythrocyte oxygen release process of different groups were tested. We also determined the degree of band-3 oxidative and phosphorylation, anion transport activity and carbonic anhydrase isoform II(CAII) activity. Biochemical studies suggested that exhaustive running significantly increased oxidative injury parameters in TBARS and methaemoglobin levels. Furthermore, exhaustive running significantly decreased anion transport activity and carbonic anhydrase isoform II(CAII) activity. Thermodynamic analysis indicated that erythrocytes oxygen release ability also significantly increased due to elevated 2,3-DPG level after exhaustive running. Kinetic analysis indicated that exhaustive running resulted in significantly decreased T50 value. We presented evidence that exhaustive running remarkably impacted thermodynamics and kinetics properties of RBCs oxygen release. In addition, changes in 2,3-DPG levels and band-3 oxidation and phosphorylation could be the driving force for exhaustive running induced alterations in erythrocytes oxygen release thermodynamics and kinetics properties.

Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

PubMed

Exner, Kai S; Over, Herbert

2017-05-16

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

Kinetic, isotherm and thermodynamic studies of amaranth dye biosorption from aqueous solution onto water hyacinth leaves.

PubMed

Guerrero-Coronilla, Imelda; Morales-Barrera, Liliana; Cristiani-Urbina, Eliseo

2015-04-01

The present study explored the kinetics, equilibrium and thermodynamics of amaranth (acid red 27) anionic dye (AD) biosorption to water hyacinth leaves (LEC). The effect of LEC particle size, contact time, solution pH, initial AD concentration and temperature on AD biosorption was studied in batch experiments. AD biosorption increased with rising contact time and initial AD concentration, and with decreasing LEC particle size and solution pH. Pseudo-second-order chemical reaction kinetics provided the best correlation for the experimental data. Isotherm studies showed that the biosorption of AD onto LEC closely follows the Langmuir isotherm, with a maximum biosorption capacity of about 70 mg g(-1). The thermodynamic parameters confirm that AD biosorption by LEC is non-spontaneous and endothermic in nature. Results indicate that LEC is a strong biosorbent capable of effective detoxification of AD-laden wastewaters. Copyright © 2015 Elsevier Ltd. All rights reserved.

On the thermodynamic and kinetic investigations of a [c2]daisy chain polymer

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

Hmadeh, Mohamad; Fang, Lei; Trabolsi, Ali

2010-01-01

We report a variety of [c2]daisy chain molecules which undergo quantitative, efficient, and fully reversible molecular movements upon the addition of base/acid in organic solvents. Such externally triggered molecular movements can induce the contraction and extension of the [c2]daisy chain molecule as a whole. A linear polymer of such a bistable [c2]daisy chain exerts similar types of movements and can be looked upon as a candidate for the development of artificial muscles. The spectrophotometric investigations of both the monomeric and polymeric bistable [c2]daisy chains, as well as the corresponding model compounds, were performed in MeCN at room temperature, in ordermore » to obtain the thermodynamic parameters for these mechanically interlocked molecules. Based on their spectrophotometric and thermodynamic characteristics, kinetic analysis of the acid/base-induced contraction and extension of the [c2]daisy chain monomer and polymer were conducted by employing a stopped-flow technique. These kinetic data suggest that the rates of contraction and extension for these [c2]daisy chain molecules are determined by the thermodynamic stabilities of the corresponding kinetic intermediates. Faster switching rates for both the contraction and extension processes of the polymeric [c2]daisy chain were observed when compared to those of its monomeric counterpart. These kinetic and thermodynamic investigations on [c2]daisy chain-based muscle-like compounds provide important information for those seeking an understanding of the mechanisms of actuation in mechanically interlocked macromolecules.« less

Thermodynamic and kinetic analysis of the reaction between biological catecholamines and chlorinated methylperoxy radicals

NASA Astrophysics Data System (ADS)

Dimić, Dušan S.; Milenković, Dejan A.; Marković, Jasmina M. Dimitrić; Marković, Zoran S.

2018-05-01

The antiradical potency of catecholamines (dopamine, epinephrine, norepinephrine, L-DOPA), metabolites of dopamine (homovanillic acid, 3-methoxytyramine and 3,4-dihydroxyphenylacetic acid) and catechol towards substituted methylperoxy radicals is investigated. The thermodynamic parameters, together with the kinetic approach, are used to determine the most probable mechanism of action. The natural bond orbital and quantum theory of atoms in molecules are utilised to explain the highest reactivity of trichloromethylperoxy radical. The preferred mechanism is dependent both on the thermodynamic and kinetic parameters . The number of chlorine atoms on radical, the presence of intra-molecular hydrogen bond and number of hydroxy groups attached to the aromatic ring significantly influence the mechanism. The results suggest that sequential proton loss electron transfer (SPLET) is the most probable for reaction with methylperoxy and hydrogen atom transfer (HAT) for reaction with trichloromethylperoxy radicals, with a gradual transition between SPLET and HAT for other two radicals. Due to the significant deprotonation of molecules containing the carboxyl group, the respective anions are also investigated. The HAT and SPLET mechanisms are highly competitive in reaction with MP radical, while the dominant mechanism towards chlorinated radicals is HAT. The reactions in methanol and benzene are also discussed.

Shape-Controlled Synthesis of Colloidal Metal Nanocrystals: Thermodynamic versus Kinetic Products.

PubMed

Xia, Younan; Xia, Xiaohu; Peng, Hsin-Chieh

2015-07-01

This Perspective provides a contemporary understanding of the shape evolution of colloidal metal nanocrystals under thermodynamically and kinetically controlled conditions. It has been extremely challenging to investigate this subject in the setting of one-pot synthesis because both the type and number of seeds involved would be changed whenever the experimental conditions are altered, making it essentially impossible to draw conclusions when comparing the outcomes of two syntheses conducted under different conditions. Because of the uncertainty about seeds, most of the mechanistic insights reported in literature for one-pot syntheses of metal nanocrystals with different shapes are either incomplete or ambiguous, and some of them might be misleading or even wrong. Recently, with the use of well-defined seeds for such syntheses, it became possible to separate growth from nucleation and therefore investigate the explicit role(s) played by a specific thermodynamic or kinetic parameter in directing the evolution of colloidal metal nanocrystals into a specific shape. Starting from single-crystal seeds enclosed by a mix of {100}, {111}, and {110} facets, for example, one can obtain colloidal nanocrystals with diversified shapes by adjusting various thermodynamic or kinetic parameters. The mechanistic insights learnt from these studies can also be extended to account for the products of conventional one-pot syntheses that involve self-nucleation only. The knowledge can be further applied to many other types of seeds with twin defects or stacking faults, making it an exciting time to design and synthesize colloidal metal nanocrystals with the shapes sought for a variety of fundamental studies and technologically important applications.

Activation and thermodynamic parameter study of the heteronuclear C=O···H-N hydrogen bonding of diphenylurethane isomeric structures by FT-IR spectroscopy using the regularized inversion of an eigenvalue problem.

PubMed

Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

2012-08-02

The doublet of the ν(C=O) carbonyl band in isomeric urethane systems has been extensively discussed in qualitative terms on the basis of FT-IR spectroscopy of the macromolecular structures. Recently, a reaction extent model was proposed as an inverse kinetic problem for the synthesis of diphenylurethane for which hydrogen-bonded and non-hydrogen-bonded C=O functionalities were identified. In this article, the heteronuclear C=O···H-N hydrogen bonding in the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol was investigated via FT-IR spectroscopy, using a methodology of regularization for the inverse reaction extent model through an eigenvalue problem. The kinetic and thermodynamic parameters of this system were derived directly from the spectroscopic data. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied. The study determined the enthalpy (ΔH = 15.25 kJ/mol), entropy (TΔS = 14.61 kJ/mol), and free energy (ΔG = 0.6 kJ/mol) of heteronuclear C=O···H-N hydrogen bonding by FT-IR spectroscopy through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S, and δΔ(‡)G) at equilibrium in the chemical reaction system. The parameters obtained in this study may contribute toward a better understanding of the properties of, and interactions in, supramolecular systems, such as the switching behavior of hydrogen bonding.

Higher adsorption capacity of Spirulina platensis alga for Cr(VI) ions removal: parameter optimisation, equilibrium, kinetic and thermodynamic predictions.

PubMed

Gunasundari, Elumalai; Senthil Kumar, Ponnusamy

2017-04-01

This study discusses about the biosorption of Cr(VI) ion from aqueous solution using ultrasonic assisted Spirulina platensis (UASP). The prepared UASP biosorbent was characterised by Fourier transform infrared spectroscopy, X-ray diffraction, Brunauer-Emmet-Teller, scanning electron spectroscopy and energy dispersive X-ray and thermogravimetric analyses. The optimum condition for the maximum removal of Cr(VI) ions for an initial concentration of 50 mg/l by UASP was measured as: adsorbent dose of 1 g/l, pH of 3.0, contact time of 30 min and temperature of 303 K. Adsorption isotherm, kinetics and thermodynamic parameters were calculated. Freundlich model provided the best results for the removal of Cr(VI) ions by UASP. The adsorption kinetics of Cr(VI) ions onto UASP showed that the pseudo-first-order model was well in line with the experimental data. In the thermodynamic study, the parameters like Gibb's free energy, enthalpy and entropy changes were evaluated. This result explains that the adsorption of Cr(VI) ions onto the UASP was exothermic and spontaneous in nature. Desorption of the biosorbent was done using different desorbing agents in which NaOH gave the best result. The prepared material showed higher affinity for the removal of Cr(VI) ions and this may be an alternative material to the existing commercial adsorbents.

Metastable Solution Thermodynamic Properties and Crystal Growth Kinetics

NASA Technical Reports Server (NTRS)

Kim, Soojin; Myerson, Allan S.

1996-01-01

The crystal growth rates of NH4H2PO4, KH2PO4, (NH4)2SO4, KAl(SO4)2 central dot 12H2O, NaCl, and glycine and the nucleation rates of KBr, KCl, NaBr central dot 2H2O, (NH4)2Cl, and (NH4)2SO4 were expressed in terms of the fundamental driving force of crystallization calculated from the activity of supersaturated solutions. The kinetic parameters were compared with those from the commonly used kinetic expression based on the concentration difference. From the viewpoint of thermodynamics, rate expressions based on the chemical potential difference provide accurate kinetic representation over a broad range of supersaturation. The rates estimated using the expression based on the concentration difference coincide with the true rates of crystallization only in the concentration range of low supersaturation and deviate from the true kinetics as the supersaturation increases.

Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry

PubMed Central

Vander Meulen, Kirk A.; Butcher, Samuel E.

2012-01-01

A novel isothermal titration calorimetry (ITC) method was applied to investigate RNA helical packing driven by the GAAA tetraloop–receptor interaction in magnesium and potassium solutions. Both the kinetics and thermodynamics were obtained in individual ITC experiments, and analysis of the kinetic data over a range of temperatures provided Arrhenius activation energies (ΔH‡) and Eyring transition state entropies (ΔS‡). The resulting rich dataset reveals strongly contrasting kinetic and thermodynamic profiles for this RNA folding system when stabilized by potassium versus magnesium. In potassium, association is highly exothermic (ΔH25°C = −41.6 ± 1.2 kcal/mol in 150 mM KCl) and the transition state is enthalpically barrierless (ΔH‡ = −0.6 ± 0.5). These parameters are sigificantly positively shifted in magnesium (ΔH25°C = −20.5 ± 2.1 kcal/mol, ΔH‡ = 7.3 ± 2.2 kcal/mol in 0.5 mM MgCl2). Mixed salt solutions approximating physiological conditions exhibit an intermediate thermodynamic character. The cation-dependent thermodynamic landscape may reflect either a salt-dependent unbound receptor conformation, or alternatively and more generally, it may reflect a small per-cation enthalpic penalty associated with folding-coupled magnesium uptake. PMID:22058128

Kinetics and thermodynamics of Pb(II) adsorption onto modified spent grain from aqueous solutions

NASA Astrophysics Data System (ADS)

Li, Qingzhu; Chai, Liyuan; Yang, Zhihui; Wang, Qingwei

2009-01-01

Spent grain, a main by-product of the brewing industry, is available in large quantities, but its main application has been limited to animal feeding. Nevertheless, in this study, spent grain modified with 1 M NaCl solution as a novel adsorbent has been used for the adsorption of Pb(II) in aqueous solutions. Isotherms, kinetics and thermodynamics of Pb(II) adsorption onto modified spent grain were studied. The equilibrium data were well fitted with Langmuir, Freundlich and Dubinin-Radushkevick (D-R) isotherm models. The kinetics of Pb(II) adsorption followed pseudo-second-order model, using the rate constants of pseudo-second-order model, the activation energy ( Ea) of Pb(II) adsorption was determined as 12.33 kJ mol -1 according to the Arrhenius equation. Various thermodynamic parameters such as Δ Gads, Δ Hads and Δ Sads were also calculated. Thermodynamic results indicate that Pb(II) adsorption onto modified spent grain is a spontaneous and endothermic process. Therefore, it can be concluded that modified spent grain as a new effective adsorbent has potential for Pb(II) removal from aqueous solutions.

Radical kinetics in sub- and supercritical carbon dioxide: thermodynamic rate tuning.

PubMed

Ghandi, Khashayar; McFadden, Ryan M L; Cormier, Philip J; Satija, Paras; Smith, Marisa

2012-06-28

We report rate constants for muonium addition to 1,1-difluoroethylene (vinylidene fluoride) in CO2 at 290-530 K, 40-360 bar, and 0.05-0.90 g cm(-3). Rate constants are mapped against their thermodynamic conditions, demonstrating the kinetic tuning ability of the solvent. The reaction exhibits critical slowing near conditions of maximum solvent isothermal compressibility, where activation volumes of unprecedentedly large magnitudes on the order of ±10(6) cm(3) mol(-1) are observed. Such values are suggestive of pressure being a significant parameter for tuning fluorolkene reactivity.

Adsorptive Removal of Cadmium (II) from Aqueous Solution by Multi-Carboxylic-Functionalized Silica Gel: Equilibrium, Kinetics and Thermodynamics

NASA Astrophysics Data System (ADS)

Li, Min; Meng, Xiaojing; Yuan, Jinhai; Deng, Wenwen; Liang, Xiuke

2018-01-01

In the present study, the adsorption behavior of cadmium (II) ion from aqueous solution onto multi-carboxylic-functionalized silica gel (SG-MCF) has been investigated in detail by means of batch and column experiments. Batch experiments were performed to evaluate the effects of various experimental parameters such as pH value, contact time and initial concentration on adsorption capacity of cadmium (II) ion. The kinetic data were analyzed on the basis of the pseudo-first-order kinetic and the pseudo-second-order kinetic models and consequently, the pseudo-second-order kinetic can better describe the adsorption process than the pseudo-first-order kinetic model. Equilibrium isotherms for the adsorption of cadmium (II) ion were analyzed by Freundlich and Langmuir isotherm models, the results indicate that Langmuir isotherm model was found to be credible to express the data for cadmium (II) ion from aqueous solution onto the SG-MCF. Various thermodynamics parameters of the adsorption process, including free energy of adsorption (ΔG0 ), the enthalpy of adsorption (ΔH0 ) and standard entropy changes (ΔS0 ), were calculated to predict the nature of adsorption. The positive value of the enthalpy change and the negative value of free energy change indicate that the process is endothermic and spontaneous process.

Kinetics and Thermodynamics of Reserpine Adsorption onto Strong Acidic Cationic Exchange Fiber

PubMed Central

Guo, Zhanjing; Liu, Xiongmin; Huang, Hongmiao

2015-01-01

The kinetics and thermodynamics of the adsorption process of reserpine adsorbed onto the strong acidic cationic exchange fiber (SACEF) were studied by batch adsorption experiments. The adsorption capacity strongly depended on pH values, and the optimum reserpine adsorption onto the SACEF occurred at pH = 5 of reserpine solution. With the increase of temperature and initial concentration, the adsorption capacity increased. The equilibrium was attained within 20 mins. The adsorption process could be better described by the pseudo-second-order model and the Freundlich isotherm model. The calculated activation energy Ea was 4.35 kJ/mol. And the thermodynamic parameters were: 4.97<ΔH<7.44 kJ/mol, -15.29<ΔG<-11.87 kJ/mol and 41.97<ΔS<47.35 J/mol·K. The thermodynamic parameters demonstrated that the adsorption was an endothermic, spontaneous and feasible process of physisorption within the temperature range between 283 K and 323 K and the initial concentration range between 100 mg/L and 300 mg/L. All the results showed that the SACEF had a good adsorption performance for the adsorption of reserpine from alcoholic solution. PMID:26422265

Study of the Kinetics and Equilibrium of the Adsorption of Oils onto Hydrophobic Jute Fiber Modified via the Sol-Gel Method.

PubMed

Lv, Na; Wang, Xiaoli; Peng, Shitao; Zhang, Huaqin; Luo, Lei

2018-05-12

A new kind of hydrophobic and oil sorbent based on jute fiber was successfully prepared by the integration of silica onto a fiber surface via the sol-gel method and subsequent hydrophobic modification with octadecyltrichlorosilane (OTS). Compared with the hydrophilic raw fiber, the modified fiber had a water contact angle (CA) of 136.2°, suggesting that the material has good hydrophobicity. Furthermore, the ability of oil in the oil/water system (taking diesel for example) to absorb was revealed by the kinetics, the isotherm equation, and the thermodynamic parameters. Adsorption behavior was kinetically investigated using pseudo first-order and pseudo second-order models. The data mostly correlated with the pseudo first-order model. The equilibrium adsorption at 298 K was assessed by using the Langmuir and Freundlich isotherm models. The Freundlich model had greater consistency with the experimental data. The obtained thermodynamic parameters demonstrate that the adsorption of diesel is spontaneous, favorable, and exothermic.

The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2016-12-01

We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and activated complexes; and (4) shows direction and thermodynamic likelihood of each reaction branch within the transition state. The approach suites particularly well for calibration of kinetic parameters against experimentally acquired reaction dynamics measurements of nutrient biogeochemical cycles.

Isotherm, kinetic, and thermodynamic study of ciprofloxacin sorption on sediments.

PubMed

Mutavdžić Pavlović, Dragana; Ćurković, Lidija; Grčić, Ivana; Šimić, Iva; Župan, Josip

2017-04-01

In this study, equilibrium isotherms, kinetics and thermodynamics of ciprofloxacin on seven sediments in a batch sorption process were examined. The effects of contact time, initial ciprofloxacin concentration, temperature and ionic strength on the sorption process were studied. The K d parameter from linear sorption model was determined by linear regression analysis, while the Freundlich and Dubinin-Radushkevich (D-R) sorption models were applied to describe the equilibrium isotherms by linear and nonlinear methods. The estimated K d values varied from 171 to 37,347 mL/g. The obtained values of E (free energy estimated from D-R isotherm model) were between 3.51 and 8.64 kJ/mol, which indicated a physical nature of ciprofloxacin sorption on studied sediments. According to obtained n values as measure of intensity of sorption estimate from Freundlich isotherm model (from 0.69 to 1.442), ciprofloxacin sorption on sediments can be categorized from poor to moderately difficult sorption characteristics. Kinetics data were best fitted by the pseudo-second-order model (R 2  > 0.999). Thermodynamic parameters including the Gibbs free energy (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) were calculated to estimate the nature of ciprofloxacin sorption. Results suggested that sorption on sediments was a spontaneous exothermic process.

Influence of ultrasound pretreatment on enzymolysis kinetics and thermodynamics of sodium hydroxide extracted proteins from tea residue.

PubMed

Ayim, Ishmael; Ma, Haile; Alenyorege, Evans Adingba; Ali, Zeshan; Donkor, Prince Ofori

2018-03-01

The effect of ultrasound pretreatment using Single Frequency Counter Current Ultrasound (SFCCU) on the enzymolysis of tea residue protein (TRP) extracted with sodium hydroxide was investigated. The concentration of TRP hydrolysate, enzymolysis kinetics and thermodynamic parameters after SFCCU pretreatment were determined and compared with traditional enzymolysis. The results indicated that both ultrasound assisted and traditional enzymolysis conformed to first-order kinetics within the limits of the studied parameters. Temperature and sonication had affirmative effect on the enzymolysis of TRP with temperature yielding greater impact. Michaelis constant ( K M ) in ultrasonic pretreated enzymolysis decreased by 32.7% over the traditional enzymolysis. The highest polypeptide concentration of 24.12 mg ml -1 was obtained with the lowest energy requirement at improved conditions of 50 g L -1 of TRP, alcalase concentration of 2000 U g -1 , time of 10 min and temperature of 50 °C for the ultrasonic treated enzymolysis. The values of reaction rate constant ( k ) for TRP enzymolysis increased by 78, 40, 82 and 60% at 20, 30, 40 and 50 °C, respectively. The thermodynamic properties comprising activation energy ( Ea ), change in enthalpy (∆H ) and entropy (∆S ) were reduced by ultrasound pretreatment whereas Gibbs free energy (∆G ) was increased.

Removal of cadmium(II) ions from aqueous solution using Ni (15 wt.%)-doped α-Fe2O3 nanocrystals: equilibrium, thermodynamic, and kinetic studies.

PubMed

OuldM'hamed, Mohamed; Khezami, L; Alshammari, Abdulrahman G; Ould-Mame, S M; Ghiloufi, I; Lemine, O M

2015-01-01

The present publication investigates the performance of nanocrystalline Ni (15 wt.%)-doped α-Fe2O3 as an effective nanomaterial for the removal of Cd(II) ions from aqueous solutions. The nanocrystalline Ni-doped α-Fe2O3 powders were prepared by mechanical alloying, and characterized by X-ray diffraction and a vibrating sample magnetometer. Batch-mode experiments were realized to determine the adsorption equilibrium, kinetics, and thermodynamic parameters of toxic heavy metal ions by Ni (15 wt.%)-doped α-Fe2O3. The adsorption isotherms data were found to be in good agreement with the Langmuir model. The adsorption capacity of Cd(II) ion reached a maximum value of about 90.91 mg g(-1) at 328 K and pH 7. The adsorption process kinetics was found to comply with pseudo-second-order rate law. Thermodynamic parameters related to the adsorption reaction, free energy change, enthalpy change and entropy change, were evaluated. The found values of free energy and enthalpy revealed a spontaneous endothermic adsorption-process. Moreover, the positive entropy suggests an increase of randomness during the process of heavy metal removal at the adsorbent-solution interface.

Engineering of Organic Nanocrystals by Electrocrystallization

NASA Astrophysics Data System (ADS)

Kilani, Mohamed

This work discusses the experimental and theoretical methods used to control the morphology of nanocrystals. The hypothesis of the thermodynamic/kinetic control of the morphology was verified. We applied the electrocrystallization to make K(def)TCP nanocrystals and we tuned the electrochemical parameters to determine their influence on the nanocrystals morphologies. The characterization was mainly performed with AFM and FE-SEM. We presented in this work the possibility to control the morphology of K(def)TCP using the electrochemical parameters. The obtained shapes ranged from nanorods to rhombohedral shape, which is reported for the first time. The observed growth behavior was modeled and simulated with a method based on Monte-Carlo techniques. The simulation results show a qualitative match with the experimental findings. This work contributes to the understanding of the crystal growth behavior and the thermodynamic/kinetic morphology transition using electrocrystallization.

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.

Application of granular activated carbon/MnFe2O4 composite immobilized on C. glutamicum MTCC 2745 to remove As(III) and As(V): Kinetic, mechanistic and thermodynamic studies

NASA Astrophysics Data System (ADS)

Podder, M. S.; Majumder, C. B.

2016-01-01

The main objective of the present study was to investigate the efficiency of Corynebacterium glutamicum MTCC 2745 immobilized on granular activated carbon/MnFe2O4 (GAC/MnFe2O4) composite to treat high concentration of arsenic bearing wastewater. Non-linear regression analysis was done for determining the best-fit kinetic model on the basis of three correlation coefficients and three error functions and also for predicting the parameters involved in kinetic models. The results showed that Fractal-like mixed 1,2 order model for As(III) and Brouser-Weron-Sototlongo as well as Fractal-like pseudo second order models for As(V) were proficient to provide realistic description of biosorption/bioaccumulation kinetic. Applicability of mechanistic models in the current study exhibited that the rate governing step in biosorption/bioaccumulation of both As(III) and As(V) was film diffusion rather than intraparticle diffusion. The evaluated thermodynamic parameters ΔG0, ΔH0 and ΔS0 revealed that biosorption/bioaccumulation of both As(III) and As(V) was feasible, spontaneous and exothermic under studied conditions.

Phenol oxidation by mushroom waste extracts: a kinetic and thermodynamic study.

PubMed

Pigatto, Gisele; Lodi, Alessandra; Aliakbarian, Bahar; Converti, Attilio; da Silva, Regildo Marcio Gonçalves; Palma, Mauri Sérgio Alves

2013-09-01

Tyrosinase activity of mushroom extracts was checked for their ability to degrade phenol. Phenol oxidation kinetics was investigated varying temperature from 10 to 60 °C and the initial values of pH, enzyme activity and phenol concentration in the ranges 4.5-8.5, 1.43-9.54 U/mL and 50-600 mg/L, respectively. Thermodynamic parameters of phenol oxidation and tyrosinase reversible inactivation were estimated. Tyrosinase thermostability was also investigated through residual activity tests after extracts exposition at 20-50 °C, whose results allowed exploring the thermodynamics of enzyme irreversible thermoinactivation. This study is the first attempt to separate the effects of reversible unfolding and irreversible denaturation of tyrosinase on its activity. Extracts were finally tested on a real oil mill wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.

Parameter Balancing in Kinetic Models of Cell Metabolism†

PubMed Central

2010-01-01

Kinetic modeling of metabolic pathways has become a major field of systems biology. It combines structural information about metabolic pathways with quantitative enzymatic rate laws. Some of the kinetic constants needed for a model could be collected from ever-growing literature and public web resources, but they are often incomplete, incompatible, or simply not available. We address this lack of information by parameter balancing, a method to complete given sets of kinetic constants. Based on Bayesian parameter estimation, it exploits the thermodynamic dependencies among different biochemical quantities to guess realistic model parameters from available kinetic data. Our algorithm accounts for varying measurement conditions in the input data (pH value and temperature). It can process kinetic constants and state-dependent quantities such as metabolite concentrations or chemical potentials, and uses prior distributions and data augmentation to keep the estimated quantities within plausible ranges. An online service and free software for parameter balancing with models provided in SBML format (Systems Biology Markup Language) is accessible at www.semanticsbml.org. We demonstrate its practical use with a small model of the phosphofructokinase reaction and discuss its possible applications and limitations. In the future, parameter balancing could become an important routine step in the kinetic modeling of large metabolic networks. PMID:21038890

One-step synthesized calcium phosphate-based material for the removal of alizarin S dye from aqueous solutions: isothermal, kinetics, and thermodynamics studies

NASA Astrophysics Data System (ADS)

Adeogun, Abideen Idowu; Babu, Ramesh Balakrishnan

2015-07-01

Calcium phosphate hydroxyapatite (Ca-Hap) synthesized from CaCO3 and H3PO5, it was characterized by scanning electron microscopy, Fourier transform infrared, and X-ray diffraction. The Ca-Hap was used for the removal of Alizarin Red S dye from its aqueous solution. The kinetics, equilibrium, and thermodynamic of the adsorption of the dye onto the Ca-Hap were investigated. The effects of contact time, initial dye concentration, pH as well as temperature on adsorption capacity of Ca-Hap were studied. Experimental data were analyzed using six model equations: Langmuir, Freudlinch, Redlich-Peterson, Temkin, Dubinin-Radushkevich, and Sips isotherms and it was found that the data fitted well with Sips and Dubinin-Radushkevich isotherm models. Pseudo-first-order, pseudo-second-order, Elovic, and Avrami kinetic models were used to test the experimental data in order to elucidate the kinetic adsorption process and it was found that pseudo-second-order model best fit the data. The calculated thermodynamics parameters (∆G°, ∆H° and ∆S°) indicated that the process is spontaneous and endothermic in nature.

Discrete Thermodynamics

DOE PAGES

Margolin, L. G.; Hunter, A.

2017-10-18

Here, we consider the dependence of velocity probability distribution functions on the finite size of a thermodynamic system. We are motivated by applications to computational fluid dynamics, hence discrete thermodynamics. We then begin by describing a coarsening process that represents geometric renormalization. Then, based only on the requirements of conservation, we demonstrate that the pervasive assumption of local thermodynamic equilibrium is not form invariant. We develop a perturbative correction that restores form invariance to second-order in a small parameter associated with macroscopic gradients. Finally, we interpret the corrections in terms of unresolved kinetic energy and discuss the implications of ourmore » results both in theory and as applied to numerical simulation.« less

Discrete Thermodynamics

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

Margolin, L. G.; Hunter, A.

Here, we consider the dependence of velocity probability distribution functions on the finite size of a thermodynamic system. We are motivated by applications to computational fluid dynamics, hence discrete thermodynamics. We then begin by describing a coarsening process that represents geometric renormalization. Then, based only on the requirements of conservation, we demonstrate that the pervasive assumption of local thermodynamic equilibrium is not form invariant. We develop a perturbative correction that restores form invariance to second-order in a small parameter associated with macroscopic gradients. Finally, we interpret the corrections in terms of unresolved kinetic energy and discuss the implications of ourmore » results both in theory and as applied to numerical simulation.« less

Classical nucleation theory of homogeneous freezing of water: thermodynamic and kinetic parameters.

PubMed

Ickes, Luisa; Welti, André; Hoose, Corinna; Lohmann, Ulrike

2015-02-28

The probability of homogeneous ice nucleation under a set of ambient conditions can be described by nucleation rates using the theoretical framework of Classical Nucleation Theory (CNT). This framework consists of kinetic and thermodynamic parameters, of which three are not well-defined (namely the interfacial tension between ice and water, the activation energy and the prefactor), so that any CNT-based parameterization of homogeneous ice formation is less well-constrained than desired for modeling applications. Different approaches to estimate the thermodynamic and kinetic parameters of CNT are reviewed in this paper and the sensitivity of the calculated nucleation rate to the choice of parameters is investigated. We show that nucleation rates are very sensitive to this choice. The sensitivity is governed by one parameter - the interfacial tension between ice and water, which determines the energetic barrier of the nucleation process. The calculated nucleation rate can differ by more than 25 orders of magnitude depending on the choice of parameterization for this parameter. The second most important parameter is the activation energy of the nucleation process. It can lead to a variation of 16 orders of magnitude. By estimating the nucleation rate from a collection of droplet freezing experiments from the literature, the dependence of these two parameters on temperature is narrowed down. It can be seen that the temperature behavior of these two parameters assumed in the literature does not match with the predicted nucleation rates from the fit in most cases. Moreover a comparison of all possible combinations of theoretical parameterizations of the dominant two free parameters shows that one combination fits the fitted nucleation rates best, which is a description of the interfacial tension coming from a molecular model [Reinhardt and Doye, J. Chem. Phys., 2013, 139, 096102] in combination with the activation energy derived from self-diffusion measurements [Zobrist et al., J. Phys. Chem. C, 2007, 111, 2149]. However, some fundamental understanding of the processes is still missing. Further research in future might help to tackle this problem. The most important questions, which need to be answered to constrain CNT, are raised in this study.

Thermodynamic and kinetic studies of As2O3 toxicological effects on human insulin in generation diabetes mellitus

NASA Astrophysics Data System (ADS)

Mohsennia, Mohsen; Motaharinejad, Atieh; Rafiee-Pour, Hossain-Ali; Torabbeigi, Marzieh

2017-12-01

The interaction of arsenic trioxide with human insulin was investigated by circular dichroism (CD), cyclic voltammetry and electrophoresis techniques. The interfacial behavior of insulin in presence of As2O3 onto the Ag electrode surface was studied at 310 K in phosphate buffer solution (PBS). According to Far-UV CD spectroscopy results, As2O3 caused to decrease in structural compactness and variety of alpha helix into beta structures. Near-UV CD indicated that As2O3 dissociates disulfide linkage in insulin structure. The kinetic parameters, including charge-transfer coefficient and apparent heterogeneous electron transfer rate constant were also determined. The thermodynamic parameters of insulin denaturation in presence of arsenic trioxide were calculated and reported. The obtained results indicated strong adsorption of insulin in presence of arsenic trioxide onto the Ag surface via chemisorptions.

Kinetics, isothermal and thermodynamics studies of electrocoagulation removal of basic dye rhodamine B from aqueous solution using steel electrodes

NASA Astrophysics Data System (ADS)

Adeogun, Abideen Idowu; Balakrishnan, Ramesh Babu

2017-07-01

Electrocoagulation was used for the removal of basic dye rhodamine B from aqueous solution, and the process was carried out in a batch electrochemical cell with steel electrodes in monopolar connection. The effects of some important parameters such as current density, pH, temperature and initial dye concentration, on the process, were investigated. Equilibrium was attained after 10 min at 30 °C. Pseudo-first-order, pseudo-second-order, Elovich and Avrami kinetic models were used to test the experimental data in order to elucidate the kinetic adsorption process; pseudo-first-order and Avrami models best fitted the data. Experimental data were analysed using six model equations: Langmuir, Freudlinch, Redlich-Peterson, Temkin, Dubinin-Radushkevich and Sips isotherms and it was found that the data fitted well with Sips isotherm model. The study showed that the process depends on current density, temperature, pH and initial dye concentration. The calculated thermodynamics parameters (Δ G°, Δ H° and Δ S°) indicated that the process is spontaneous and endothermic in nature.

Combined Yamamoto approach for simultaneous estimation of adsorption isotherm and kinetic parameters in ion-exchange chromatography.

PubMed

Rüdt, Matthias; Gillet, Florian; Heege, Stefanie; Hitzler, Julian; Kalbfuss, Bernd; Guélat, Bertrand

2015-09-25

Application of model-based design is appealing to support the development of protein chromatography in the biopharmaceutical industry. However, the required efforts for parameter estimation are frequently perceived as time-consuming and expensive. In order to speed-up this work, a new parameter estimation approach for modelling ion-exchange chromatography in linear conditions was developed. It aims at reducing the time and protein demand for the model calibration. The method combines the estimation of kinetic and thermodynamic parameters based on the simultaneous variation of the gradient slope and the residence time in a set of five linear gradient elutions. The parameters are estimated from a Yamamoto plot and a gradient-adjusted Van Deemter plot. The combined approach increases the information extracted per experiment compared to the individual methods. As a proof of concept, the combined approach was successfully applied for a monoclonal antibody on a cation-exchanger and for a Fc-fusion protein on an anion-exchange resin. The individual parameter estimations for the mAb confirmed that the new approach maintained the accuracy of the usual Yamamoto and Van Deemter plots. In the second case, offline size-exclusion chromatography was performed in order to estimate the thermodynamic parameters of an impurity (high molecular weight species) simultaneously with the main product. Finally, the parameters obtained from the combined approach were used in a lumped kinetic model to simulate the chromatography runs. The simulated chromatograms obtained for a wide range of gradient lengths and residence times showed only small deviations compared to the experimental data. Copyright © 2015 Elsevier B.V. All rights reserved.

Total solids content and degree of hydrolysis influence proteolytic inactivation kinetics following whey protein hydrolysate manufacture.

PubMed

Conesa, Celia; FitzGerald, Richard J

2013-10-23

The kinetics and thermodynamics of the thermal inactivation of Corolase PP in two different whey protein concentrate (WPC) hydrolysates with degree of hydrolysis (DH) values of ~10 and 21%, and at different total solids (TS) levels (from 5 to 30% w/v), were studied. Inactivation studies were performed in the temperature range from 60 to 75 °C, and residual enzyme activity was quantified using the azocasein assay. The inactivation kinetics followed a first-order model. Analysis of the activation energy, thermodynamic parameters, and D and z values, demonstrated that the inactivation of Corolase PP was dependent on solution TS. The intestinal enzyme preparation was more heat sensitive at low TS. Moreover, it was also found that the enzyme was more heat sensitive in solutions at higher DH.

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.

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

Metronidazole removal in powder-activated carbon and concrete-containing graphene adsorption systems: Estimation of kinetic, equilibrium and thermodynamic parameters and optimization of adsorption by a central composite design.

PubMed

Manjunath, S V; Kumar, S Mathava; Ngo, Huu Hao; Guo, Wenshan

2017-12-06

Metronidazole (MNZ) removal by two adsorbents, i.e., concrete-containing graphene (CG) and powder-activated carbon (PAC), was investigated via batch-mode experiments and the outcomes were used to analyze the kinetics, equilibrium and thermodynamics of MNZ adsorption. MNZ sorption on CG and PAC has followed the pseudo-second-order kinetic model, and the thermodynamic parameters revealed that MNZ adsorption was spontaneous on PAC and non-spontaneous on CG. Subsequently, two-parameter isotherm models, i.e., Langmuir, Freundlich, Temkin, Dubinin-Radushkevich and Elovich models, were applied to evaluate the MNZ adsorption capacity. The maximum MNZ adsorption capacities ([Formula: see text]) of PAC and CG were found to be between 25.5-32.8 mg/g and 0.41-0.002 mg/g, respectively. Subsequently, the effects of pH, temperature and adsorbent dosage on MNZ adsorption were evaluated by a central composite design (CCD) approach. The CCD experiments have pointed out the complete removal of MNZ at a much lower PAC dosage by increasing the system temperature (i.e., from 20°C to 40°C). On the other hand, a desorption experiment has shown 3.5% and 1.7% MNZ removal from the surface of PAC and CG, respectively, which was insignificant compared to the sorbed MNZ on the surface by adsorption. The overall findings indicate that PAC and CG with higher graphene content could be useful in MNZ removal from aqueous systems.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

PubMed

Cotten, Cameron; Reed, Jennifer L

2013-01-30

Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

PubMed Central

2013-01-01

Background Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. Results In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. Conclusions This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets. PMID:23360254

Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches

PubMed Central

Guedich, Sondés; Puffer-Enders, Barbara; Baltzinger, Mireille; Hoffmann, Guillaume; Da Veiga, Cyrielle; Jossinet, Fabrice; Thore, Stéphane; Bec, Guillaume; Ennifar, Eric; Burnouf, Dominique; Dumas, Philippe

2016-01-01

ABSTRACT Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations. PMID:26932506

Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches.

PubMed

Guedich, Sondés; Puffer-Enders, Barbara; Baltzinger, Mireille; Hoffmann, Guillaume; Da Veiga, Cyrielle; Jossinet, Fabrice; Thore, Stéphane; Bec, Guillaume; Ennifar, Eric; Burnouf, Dominique; Dumas, Philippe

2016-01-01

Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations.

Kinetic and thermodynamic parameters for heat denaturation of human recombinant lactoferrin from rice.

PubMed

Castillo, Eduardo; Pérez, María Dolores; Franco, Indira; Calvo, Miguel; Sánchez, Lourdes

2012-06-01

Heat denaturation of recombinant human lactoferrin (rhLf) from rice with 3 different iron-saturation degrees, holo rhLf (iron-saturated), AsIs rhLf (60% iron saturation), and apo rhLf (iron-depleted), was studied. The 3 forms of rhLf were subjected to heat treatment, and the kinetic and thermodynamic parameters of the denaturation process were determined. Thermal denaturation of rhLf was assessed by measuring the loss of reactivity against specific antibodies. D(t) values (time to reduce 90% of immunoreactivity) decreased with increasing temperature of treatment for apo and holo rhLf, those values being higher for the iron-saturated form, which indicates that iron confers thermal stability to rhLf. However, AsIs rhLf showed a different behaviour with an increase in resistance to heat between 79 °C and 84 °C, so that the kinetic parameters could not be calculated. The heat denaturation process for apo and holo rhLf was best described assuming a reaction order of 1.5. The activation energy of the denaturation process was 648.20 kJ/mol for holo rhLf and 406.94 kJ/mol for apo rhLf, confirming that iron-depleted rhLf is more sensitive to heat treatment than iron-saturated rhLf.

Understanding Product Optimization: Kinetic versus Thermodynamic Control.

ERIC Educational Resources Information Center

Lin, King-Chuen

1988-01-01

Discusses the concept of kinetic versus thermodynamic control of reactions. Explains on the undergraduate level (1) the role of kinetic and thermodynamic control in kinetic equations, (2) the influence of concentration and temperature upon the reaction, and (3) the application of factors one and two to synthetic chemistry. (MVL)

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

PubMed

Du, Bin; Zielinski, Daniel C; Kavvas, Erol S; Dräger, Andreas; Tan, Justin; Zhang, Zhen; Ruggiero, Kayla E; Arzumanyan, Garri A; Palsson, Bernhard O

2016-06-06

The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question. In this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations. Overall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches.

Thermodynamics and kinetics parameters of co-combustion between sewage sludge and water hyacinth in CO2/O2 atmosphere as biomass to solid biofuel.

PubMed

Huang, Limao; Liu, Jingyong; He, Yao; Sun, Shuiyu; Chen, Jiacong; Sun, Jian; Chang, KenLin; Kuo, Jiahong; Ning, Xun'an

2016-10-01

Thermodynamics and kinetics of sewage sludge (SS) and water hyacinth (WH) co-combustion as a blend fuel (SW) for bioenergy production were studied through thermogravimetric analysis. In CO2/O2 atmosphere, the combustion performance of SS added with 10-40wt.% WH was improved 1-1.97 times as revealed by the comprehensive combustion characteristic index (CCI). The conversion of SW in different atmospheres was identified and their thermodynamic parameters (ΔH,ΔS,ΔG) were obtained. As the oxygen concentration increased from 20% to 70%, the ignition temperature of SW decreased from 243.1°C to 240.3°C, and the maximum weight loss rate and CCI increased from 5.70%·min(-1) to 7.26%·min(-1) and from 4.913%(2)·K(-3)·min(-2) to 6.327%(2)·K(-3)·min(-2), respectively, which corresponded to the variation in ΔS and ΔG. The lowest activation energy (Ea) of SW was obtained in CO2/O2=7/3 atmosphere. Copyright © 2016 Elsevier Ltd. All rights reserved.

Application of activated carbon derived from scrap tires for adsorption of Rhodamine B.

PubMed

Li, Li; Liu, Shuangxi; Zhu, Tan

2010-01-01

Activated carbon derived from solid hazardous waste scrap tires was evaluated as a potential adsorbent for cationic dye removal. The adsorption process with respect to operating parameters was investigated to evaluate the adsorption characteristics of the activated pyrolytic tire char (APTC) for Rhodamine B (RhB). Systematic research including equilibrium, kinetics and thermodynamic studies was performed. The results showed that APTC was a potential adsorbent for RhB with a higher adsorption capacity than most adsorbents. Solution pH and temperature exert significant influence while ionic strength showed little effect on the adsorption process. The adsorption equilibrium data obey Langmuir isotherm and the kinetic data were well described by the pseudo second-order kinetic model. The adsorption process followed intra-particle diffusion model with more than one process affecting the adsorption process. Thermodynamic study confirmed that the adsorption was a physisorption process with spontaneous, endothermic and random characteristics.

Kinetics and thermodynamics studies of silver ions adsorption onto coconut shell activated carbon.

PubMed

Silva-Medeiros, Flávia V; Consolin-Filho, Nelson; Xavier de Lima, Mateus; Bazzo, Fernando Previato; Barros, Maria Angélica S D; Bergamasco, Rosângela; Tavares, Célia R G

2016-12-01

The presence of silver in the natural water environment has been of great concern because of its toxicity, especially when it is in the free ion form (Ag(+)). This paper aims to study the adsorption kinetics of silver ions from an aqueous solution onto coconut shell activated carbon using batch methods. Batch kinetic data were fitted to the first-order model and the pseudo-second-order model, and this last equation fits correctly the experimental data. Equilibrium experiments were carried out at 30°C, 40°C, and 50°C. The adsorption isotherms were reasonably fit using Langmuir model, and the adsorption process was slightly influenced by changes in temperature. Thermodynamic parameters (ΔH°, ΔG°, and ΔS°) were determined. The adsorption process seems to be non-favorable, exothermic, and have an increase in the orderness.

Insight into biosorption equilibrium, kinetics and thermodynamics of crystal violet onto Ananas comosus (pineapple) leaf powder

NASA Astrophysics Data System (ADS)

Chakraborty, Sagnik; Chowdhury, Shamik; Saha, Papita Das

2012-06-01

Biosorption performance of pineapple leaf powder (PLP) for removal of crystal violet (CV) from its aqueous solutions was investigated. To this end, the influence of operational parameters such as pH, biosorbent dose, initial dye concentration and temperature were studied employing a batch experimental setup. The biosorption process followed the Langmuir isotherm model with high correlation coefficients ( R 2 > 0.99) at different temperatures. The maximum monolayer biosorption capacity was found to be 78.22 mg g-1 at 293 K. The kinetic data conformed to the pseudo-second-order kinetic model. The activation energy of the system was calculated as 58.96 kJ mol- 1 , indicating chemisorption nature of the ongoing biosorption process. A thermodynamic study showed spontaneous and exothermic nature of the biosorption process. Owing to its low cost and high dye uptake capacity, PLP has potential for application as biosorbent for removal of CV from aqueous solutions.

Vacuum drying of apples (cv. Golden Delicious): drying characteristics, thermodynamic properties, and mass transfer parameters

NASA Astrophysics Data System (ADS)

Nadi, Fatemeh; Tzempelikos, Dimitrios

2018-01-01

In this work, apples of cv. Golden Delicious were cut into slices that were 5 and 7 mm thick and then vacuum dried at 50, 60 and 70 °C and pressure of 0.02 bar. The thin layer model drying kinetics was studied, and mass transfer properties, specifically effective moisture diffusivity and convective mass transfer coefficient, were evaluated using the Fick's equation of diffusion. Also, thermodynamic parameters of the process, i.e. enthalpy (ΔH), entropy (ΔS) and Gibbs free energy (ΔG), were determined. Colour properties were evaluated as one of the important indicators of food quality and marketability. Determination of mass transfer parameters and thermodynamic properties of vacuum dried apple slices has not been discussed much in the literature. In conclusion, the Nadi's model fitted best the observed data that represent the drying process. Thermodynamic properties were determined based on the dependence of the drying constant of the Henderson and Pabis model on temperature, and it was concluded that the variation in drying kinetics depends on the energy contribution of the surrounding environment. The enthalpy and entropy diminished, while the Gibbs free energy increased with the increase of the temperature of drying; therefore, it was possible to verify that variation in the diffusion process in the apple during drying depends on energetic contributions of the environment. The obtained results showed that diffusivity increased for 69%, while the mass transfer coefficient increase was even higher, 75%, at the variation of temperature of 20 °C. The increase in the dimensionless Biot number was 20%.

Vacuum drying of apples (cv. Golden Delicious): drying characteristics, thermodynamic properties, and mass transfer parameters

NASA Astrophysics Data System (ADS)

Nadi, Fatemeh; Tzempelikos, Dimitrios

2018-07-01

In this work, apples of cv. Golden Delicious were cut into slices that were 5 and 7 mm thick and then vacuum dried at 50, 60 and 70 °C and pressure of 0.02 bar. The thin layer model drying kinetics was studied, and mass transfer properties, specifically effective moisture diffusivity and convective mass transfer coefficient, were evaluated using the Fick's equation of diffusion. Also, thermodynamic parameters of the process, i.e. enthalpy ( ΔH), entropy ( ΔS) and Gibbs free energy ( ΔG), were determined. Colour properties were evaluated as one of the important indicators of food quality and marketability. Determination of mass transfer parameters and thermodynamic properties of vacuum dried apple slices has not been discussed much in the literature. In conclusion, the Nadi's model fitted best the observed data that represent the drying process. Thermodynamic properties were determined based on the dependence of the drying constant of the Henderson and Pabis model on temperature, and it was concluded that the variation in drying kinetics depends on the energy contribution of the surrounding environment. The enthalpy and entropy diminished, while the Gibbs free energy increased with the increase of the temperature of drying; therefore, it was possible to verify that variation in the diffusion process in the apple during drying depends on energetic contributions of the environment. The obtained results showed that diffusivity increased for 69%, while the mass transfer coefficient increase was even higher, 75%, at the variation of temperature of 20 °C. The increase in the dimensionless Biot number was 20%.

Radiation processed polychloroprene-co-ethylene-propene diene terpolymer blends: Effect of radiation vulcanization on solvent transport kinetics

NASA Astrophysics Data System (ADS)

Dubey, K. A.; Bhardwaj, Y. K.; Chaudhari, C. V.; Kumar, Virendra; Goel, N. K.; Sabharwal, S.

2009-03-01

Blends of polychloroprene rubber (PCR) and ethylene propylene diene terpolymer rubber (EPDM) of different compositions were made and exposed to different gamma radiation doses. The radiation sensitivity and radiation vulcanization efficiency of blends was estimated by gel-content analysis, Charlesby-Pinner parameter determination and crosslinking density measurements. Gamma radiation induced crosslinking was most efficient for EPDM ( p0/ q0 ˜ 0.08), whereas it was the lowest for blends containing 40% PCR ( p0/ q0 ˜ 0.34). The vulcanized blends were characterized for solvent diffusion characteristics by following the swelling dynamics. Blends with higher PCR content showed anomalous swelling. The sorption and permeability of the solvent were not strictly in accordance with each other and the extent of variation in two parameters was found to be a function of blend composition. The Δ G values for solvent diffusion were in the range -2.97 to -9.58 kJ/mol and indicated thermodynamically favorable sorption for all blends. These results were corroborated by dynamic swelling, experimental as well as simulated profiles and have been explained on the basis of correlation between crosslinking density, diffusion kinetics, thermodynamic parameters and polymer-polymer interaction parameter.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics.

PubMed

Chapman, Brian

2017-06-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis- substrate binding, cis → trans bound enzyme shuttling, trans -substrate dissociation and trans → cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive 'tuning' of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force-flux relations, with only a minority of cases having their quasi -linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically 'tuned' to its particular task, dependent on the cis- and trans- substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport.

A facilitated diffusion model constrained by the probability isotherm: a pedagogical exercise in intuitive non-equilibrium thermodynamics

PubMed Central

2017-01-01

This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis–Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action. Rapid equilibration scenarios require sensitive ‘tuning’ of the thermodynamic binding parameters to the equilibrium substrate concentration. All non-equilibrium scenarios show sigmoidal force–flux relations, with only a minority of cases having their quasi-linear portions close to equilibrium. Few cases fulfil the expectations of MMK relating reaction rates to enzyme saturation. This new approach illuminates and extends the concept of rate-limiting steps by focusing on the free energy dissipation associated with each reaction step and thereby deducing its respective relative chemical impedance. The crucial importance of an enzyme's being thermodynamically ‘tuned’ to its particular task, dependent on the cis- and trans-substrate concentrations with which it deals, is consistent with the occurrence of numerous isoforms for enzymes that transport a given substrate in physiologically different circumstances. This approach to kinetic modelling, being aligned with neither MMK nor LNET, is best described as intuitive non-equilibrium thermodynamics, and is recommended as a useful adjunct to the design and interpretation of experiments in biotransport. PMID:28680687

Kinetic and thermodynamic studies of a novel acid protease from Aspergillus foetidus.

PubMed

Souza, Paula Monteiro; Aliakbarian, Bahar; Filho, Edivaldo Ximenes Ferreira; Magalhães, Pérola Oliveira; Junior, Adalberto Pessoa; Converti, Attilio; Perego, Patrizia

2015-11-01

The kinetics of a thermostable extracellular acid protease produced by an Aspergillus foetidus strain was investigated at different pH, temperatures and substrate concentrations. The enzyme exhibited maximal activity at pH 5.0 and 55°C, and its irreversible deactivation was well described by first-order kinetics. When temperature was raised from 55 to 70°C, the deactivation rate constant increased from 0.018 to 5.06h(-1), while the half-life decreased from 37.6 to 0.13h. The results of activity collected at different temperatures were then used to estimate, the activation energy of the hydrolysis reaction (E*=19.03kJ/mol) and the standard enthalpy variation of reversible enzyme unfolding (ΔH°U=19.03kJ/mol). The results of residual activity tests carried out in the temperature range 55-70°C allowed estimating the activation energy (E(*)d=314.12kJ/mol), enthalpy (311.27≤(ΔH°d≤311.39kJ/mol), entropy (599.59≤ΔS(*)d≤610.49kJ/mol K) and Gibbs free energy (103.18≤ΔG(*)d≤113.87kJ/mol) of the enzyme irreversible denaturation. These thermodynamic parameters suggest that this new protease is highly thermostable and could be important for industrial applications. To the best of our knowledge, this is the first report on thermodynamic parameters of an acid protease produced by A. foetidus. Copyright © 2015 Elsevier B.V. All rights reserved.

iSCHRUNK--In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks.

PubMed

Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

2016-01-01

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-based metabolic flux analysis contribute to improved understanding of steady-state properties of metabolism. However, knowledge about kinetics and enzyme activities though essential for quantitative understanding of metabolic dynamics remains scarce and involves uncertainty. Here, we present a computational methodology that allow us to determine and quantify the kinetic parameters that correspond to a certain physiology as it is described by a given metabolic flux profile and a given metabolite concentration vector. Though we initially determine kinetic parameters that involve a high degree of uncertainty, through the use of kinetic modeling and machine learning principles we are able to obtain more accurate ranges of kinetic parameters, and hence we are able to reduce the uncertainty in the model analysis. We computed the distribution of kinetic parameters for glucose-fed E. coli producing 1,4-butanediol and we discovered that the observed physiological state corresponds to a narrow range of kinetic parameters of only a few enzymes, whereas the kinetic parameters of other enzymes can vary widely. Furthermore, this analysis suggests which are the enzymes that should be manipulated in order to engineer the reference state of the cell in a desired way. The proposed approach also sets up the foundations of a novel type of approaches for efficient, non-asymptotic, uniform sampling of solution spaces. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Thermodynamic and kinetic analysis of heterogeneous photocatalysis for semiconductor systems.

PubMed

Liu, Baoshun; Zhao, Xiujian; Terashima, Chiaki; Fujishima, Akira; Nakata, Kazuya

2014-05-21

Since the report of the Honda-Fujishima effect, heterogeneous photocatalysis has attracted much attention around the world because of its potential energy and environmental applications. Although great progresses have been made in recent years, most were focused on preparing highly-active photocatalysts and investigating visible light utilization. In fact, we are still unclear on the thermodynamic and kinetic nature of photocatalysis to date, which sometimes leads to misunderstandings for experimental results. It is timely to give a review and discussion on the thermodynamics and kinetics of photocatalysis, so as to direct future researches. However, there is an absence of a detailed review on this topic until now. In this article, we tried to review and discuss the thermodynamics and kinetics of photocatalysis. We explained the thermodynamic driving force of photocatalysis, and distinguished the functions of light and heat in photocatalysis. The Langmuir-Hinshelwood kinetic model, the ˙OH oxidation mechanism, and the direct-indirect (D-I) kinetic model were reviewed and compared. Some applications of the D-I model to study photocatalytic kinetics were also discussed. The electron transport mode and its importance in photocatalysis were investigated. Finally, the intrinsic relation between the kinetics and the thermodynamics of photocatalytic reactions was discussed.

Comparative 4f-4f absorption spectral study for the interactions of Nd(III) with some amino acids: Preliminary thermodynamics and kinetic studies of interaction of Nd(III):glycine with Ca(II)

NASA Astrophysics Data System (ADS)

Moaienla, T.; Bendangsenla, N.; David Singh, Th.; Sumitra, Ch.; Rajmuhon Singh, N.; Indira Devi, M.

2012-02-01

Spectral analysis of Nd(III) complexes with some amino acids viz.; glycine, L-alanine, L-phenylalanine and L-aspartic acid in the presence and absence of Ca 2+ was carried out in some organic solvents; CH 3OH, CH 3CN, DMF and dioxane using comparative absorption spectra of 4f-4f transitions. The study was carried out by evaluating various energy interaction parameters like Slator-Condon ( Fk), Lande factor ( ξ4f), nephelauxetic ratio ( β), bonding parameter ( b1/2), percent-covalency ( δ) by applying partial and multiple regression analysis. The values of oscillator strength ( Pobs) and Judd-Ofelt electric dipole intensity parameter Tλ ( λ = 2, 4, 6) for different 4f-4f transitions have been calculated. On analysis of the variation of the various energy interaction parameters as well as the changes in the oscillator strength ( Pobs) and Tλ values, reveal the mode of binding with the different ligands. Kinetic studies for the complexation of Nd(III):glycine:Ca(II) have also been discussed at different temperatures in DMF medium and from it the values of activation energy ( Ea) and thermodynamic parameters like Δ H°, Δ S° and Δ G° for the complexation are evaluated.

Dependence of the kinetic and thermodynamic parameters on hydrophilic-lipophilic character of alprazolam, clonazepam, diazepam, doxepin and haloperidol in alkaline environment.

PubMed

Maślanka, Anna; Krzek, Jan; Szlósarczyk, Marek; Żmudzki, Paweł; Wach, Katarzyna

2013-10-15

Examination of the stability of clonazepam, diazepam, alprazolam, haloperidol, and doxepin in basic solutions was performed, together with an assessment of the kinetic (k, t0.1i t0.5) and thermodynamic (Ea, ΔH(++)i ΔS(++)) stability-indicating parameters, which were compared with the lipophilicity (logP) of the studied drugs. It was observed that the calculated values of Ea, ΔH(++) and ΔS(++) for the studied drugs increased from 41.04 kJ/mol to 125.50 kJ/mol, from 37.82 kJ/mol to 122.24 kJ/mol and from -167.09 J/Kmol to 53.02 J/Kmol, respectively, along with an increase of lipophilicity (logP) from 2.12 to 4.30 for the most hydrophilic alprazolam to the most lipophilic haloperidol. The degradation products were identified using UPLC/MS/MS method. Copyright © 2013 Elsevier B.V. All rights reserved.

Thermodynamics of axial substitution and kinetics of reactions with amino acids for the paddlewheel complex tetrakis(acetato)chloridodiruthenium(II,III).

PubMed

Santos, Rodrigo L S R; van Eldik, Rudi; de Oliveira Silva, Denise

2012-06-18

The known paddlewheel, tetrakis(acetato)chloridodiruthenium(II,III), offers a versatile synthetic route to a novel class of antitumor diruthenium(II,III) metallo drugs, where the equatorial ligands are nonsteroidal anti-inflammatory carboxylates. This complex was studied here as a soluble starting prototype model for antitumor analogues to elucidate the reactivity of the [Ru(2)(CH(3)COO)(4)](+) framework. Thermodynamic studies on equilibration reactions for axial substitution of water by chloride and kinetic studies on reactions of the diaqua complexes with the amino acids glycine, cysteine, histidine, and tryptophan were performed. The standard thermodynamic reaction parameters ΔH°, ΔS°, and ΔV° were determined and showed that both of the sequential axial substitution reactions are enthalpy driven. Kinetic rate laws and rate constants were determined for the axial substitution reactions of coordinated water by the amino acids that gave the corresponding aqua(amino acid)-Ru(2) substituted species. The results revealed that the [Ru(2)(CH(3)COO)(4)](+) paddlewheel framework remained stable during the axial ligand substitution reactions and was also mostly preserved in the presence of the amino acids.

Improving the enzymolysis efficiency of potato protein by simultaneous dual-frequency energy-gathered ultrasound pretreatment: Thermodynamics and kinetics.

PubMed

Cheng, Yu; Liu, Yun; Wu, Juan; Ofori Donkor, Prince; Li, Ting; Ma, Haile

2017-07-01

The thermodynamics and kinetics of traditional and simultaneous dual frequency energy-gathered ultrasound (SDFU) assisted enzymolysis of potato protein were investigated to get the knowledge of the mechanisms on the SDFU's promoting efficiency during enzymolysis. The concentration of potato protein hydrolysate and parameters of thermodynamic and kinetic during traditional and SDFU assisted enzymolysis were determined. The results showed that potato protein hydrolysate concentration of SDFU assisted enzymolysis was higher than traditional enzymolysis at the hydrolysis time of 60min (p<0.05) whereas not significantly different at 120min (p>0.05). In some cases, SDFU assisted enzymolysis took less hydrolysis time than traditional enzymolysis when the similar conversion rates of potato protein were obtained. The thermodynamic papameters including the energy of activation (E a ), enthalpy of activation (△H), entropy of activation (△S) were reduced by ultrasound pretreatment while Gibbs free energy of activation (△G) increased little (1.6%). Also, kinetic papameters including Michaelis constant (K M ) and catalytic rate constant (k cat ) decreased by ultrasound pretreatment. On the contrary, reaction rate constants (k) of SDFU assisted enzymolysis were higher than that of traditional enzymolysis (p<0.05). It was indicated that the efficiency of SDFU assisted enzymolysis was higher than traditional enzymolysis in a limited time. The higher efficiency of SDFU assisted enzymolysis was related with the decrease of E a and K M by lowering the energy barrier between ground and active state and increasing affinity between substrate and enzyme. Copyright © 2017 Elsevier B.V. All rights reserved.

Calculation of kinetic rate constants from thermodynamic data

NASA Technical Reports Server (NTRS)

Marek, C. John

1995-01-01

A new scheme for relating the absolute value for the kinetic rate constant k to the thermodynamic constant Kp is developed for gases. In this report the forward and reverse rate constants are individually related to the thermodynamic data. The kinetic rate constants computed from thermodynamics compare well with the current kinetic rate constants. This method is self consistent and does not have extensive rules. It is first demonstrated and calibrated by computing the HBr reaction from H2 and Br2. This method then is used on other reactions.

Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c3sc53331j Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

PubMed Central

Hariadi, Rizal F.; Yurke, Bernard

2015-01-01

DNA nanotubes provide a programmable architecture for molecular self-assembly and can serve as model systems for one-dimensional biomolecular assemblies. While a variety of DNA nanotubes have been synthesized and employed as models for natural biopolymers, an extensive investigation of DNA nanotube kinetics and thermodynamics has been lacking. Using total internal reflection microscopy, DNA nanotube polymerization was monitored in real time at the single filament level over a wide range of free monomer concentrations and temperatures. The measured polymerization rates were subjected to a global nonlinear fit based on polymerization theory in order to simultaneously extract kinetic and thermodynamic parameters. For the DNA nanotubes used in this study, the association rate constant is (5.99 ± 0.15) × 105 M–1 s–1, the enthalpy is 87.9 ± 2.0 kcal mol–1, and the entropy is 0.252 ± 0.006 kcal mol–1 K–1. The qualitative and quantitative similarities between the kinetics of DNA nanotubes, actin filaments, and microtubules polymerization highlight the prospect of building complex dynamic systems from DNA molecules inspired by biological architecture. PMID:29308139

Future constraints on halo thermodynamics from combined Sunyaev-Zel'dovich measurements

NASA Astrophysics Data System (ADS)

Battaglia, Nicholas; Ferraro, Simone; Schaan, Emmanuel; Spergel, David N.

2017-11-01

The improving sensitivity of measurements of the kinetic Sunyaev-Zel'dovich (SZ) effect opens a new window into the thermodynamic properties of the baryons in halos. We propose a methodology to constrain these thermodynamic properties by combining the kinetic SZ, which is an unbiased probe of the free electron density, and the thermal SZ, which probes their thermal pressure. We forecast that our method constrains the average thermodynamic processes that govern the energetics of galaxy evolution like energetic feedback across all redshift ranges where viable halos sample are available. Current Stage-3 cosmic microwave background (CMB) experiments like AdvACT and SPT-3G can measure the kSZ and tSZ to greater than 100σ if combined with a DESI-like spectroscopic survey. Such measurements translate into percent-level constraints on the baryonic density and pressure profiles and on the feedback and non-thermal pressure support parameters for a given ICM model. This in turn will provide critical thermodynamic tests for sub-grid models of feedback in cosmological simulations of galaxy formation. The high fidelity measurements promised by the next generation CMB experiment, CMB-S4, allow one to further sub-divide these constraints beyond redshift into other classifications, like stellar mass or galaxy type.

Modeling the complete Otto cycle: Preliminary version. [computer programming

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.; Mcbride, B. J.

1977-01-01

A description is given of the equations and the computer program being developed to model the complete Otto cycle. The program incorporates such important features as: (1) heat transfer, (2) finite combustion rates, (3) complete chemical kinetics in the burned gas, (4) exhaust gas recirculation, and (5) manifold vacuum or supercharging. Changes in thermodynamic, kinetic and transport data as well as model parameters can be made without reprogramming. Preliminary calculations indicate that: (1) chemistry and heat transfer significantly affect composition and performance, (2) there seems to be a strong interaction among model parameters, and (3) a number of cycles must be calculated in order to obtain steady-state conditions.

Theoretical study of gas hydrate decomposition kinetics--model development.

PubMed

Windmeier, Christoph; Oellrich, Lothar R

2013-10-10

In order to provide an estimate of the order of magnitude of intrinsic gas hydrate dissolution and dissociation kinetics, the "Consecutive Desorption and Melting Model" (CDM) is developed by applying only theoretical considerations. The process of gas hydrate decomposition is assumed to comprise two consecutive and repetitive quasi chemical reaction steps. These are desorption of the guest molecule followed by local solid body melting. The individual kinetic steps are modeled according to the "Statistical Rate Theory of Interfacial Transport" and the Wilson-Frenkel approach. All missing required model parameters are directly linked to geometric considerations and a thermodynamic gas hydrate equilibrium model.

Estimation of the viscosities of liquid binary alloys

NASA Astrophysics Data System (ADS)

Wu, Min; Su, Xiang-Yu

2018-01-01

As one of the most important physical and chemical properties, viscosity plays a critical role in physics and materials as a key parameter to quantitatively understanding the fluid transport process and reaction kinetics in metallurgical process design. Experimental and theoretical studies on liquid metals are problematic. Today, there are many empirical and semi-empirical models available with which to evaluate the viscosity of liquid metals and alloys. However, the parameter of mixed energy in these models is not easily determined, and most predictive models have been poorly applied. In the present study, a new thermodynamic parameter Δ G is proposed to predict liquid alloy viscosity. The prediction equation depends on basic physical and thermodynamic parameters, namely density, melting temperature, absolute atomic mass, electro-negativity, electron density, molar volume, Pauling radius, and mixing enthalpy. Our results show that the liquid alloy viscosity predicted using the proposed model is closely in line with the experimental values. In addition, if the component radius difference is greater than 0.03 nm at a certain temperature, the atomic size factor has a significant effect on the interaction of the binary liquid metal atoms. The proposed thermodynamic parameter Δ G also facilitates the study of other physical properties of liquid metals.

Characterizations of strontium(II) and barium(II) adsorption from aqueous solutions using dolomite powder.

PubMed

Ghaemi, Ahad; Torab-Mostaedi, Meisam; Ghannadi-Maragheh, Mohammad

2011-06-15

In this research, adsorption technique was applied for strontium and barium removal from aqueous solution using dolomite powder. The process has been investigated as a function of pH, contact time, temperature and adsorbate concentration. The experimental data was analyzed using equilibrium isotherm, kinetic and thermodynamic models. The isotherm data was well described by Langmuir isotherm model. The maximum adsorption capacity was found to be 1.172 and 3.958 mg/g for Sr(II) and Ba(II) from the Langmuir isotherm model at 293 K, respectively. The kinetic data was tested using first and pseudo-second order models. The results indicated that adsorption fitted well with the pseudo-second order kinetic model. The thermodynamic parameters (ΔG°, ΔH°, and ΔS°) were also determined using the equilibrium constant value obtained at different temperatures. The results showed that the adsorption for both ions was feasible and exothermic. Copyright © 2011 Elsevier B.V. All rights reserved.

Adsorption kinetics, isotherm, and thermodynamics studies of acetyl-11-keto-β-boswellic acids (AKBA) from Boswellia serrata extract using macroporous resin.

PubMed

Niphadkar, Sonali S; Rathod, Virendra K

2017-09-14

An acetyl-11-keto-β-boswellic acid (AKBA) is potent anti-inflammatory agent found in Boswellia serrata oleogum resin. Adsorption characteristics of AKBA from B. serrata were studied using macroporous adsorbent resin to understand separation and adsorption mechanism of targeted molecules. Different macroporous resins were screened for adsorption and desorption of AKBA and Indion 830 was screened as it showed higher adsorption capacity. The kinetic equations were studied and results showed that the adsorption of AKBA on Indion 830 was well fitted to the pseudo first-order kinetic model. The influence of two parameters such as temperature (298, 303, and 308 K) and pH (5-8) on the adsorption process was also studied. The experimental data was further investigated using Langmuir, Freundlich, and Temkin isotherm models. It was observed that Langmuir isotherm model was found to be the best fit for AKBA adsorption by Indion 830 and highest adsorption capacity (50.34 mg/g) was obtained at temperature of 303 K. The values of thermodynamic parameters such as the change of Gibbs free energy (ΔG*), entropy (ΔS*), and enthalpy (ΔH*), indicated that the process of adsorption was spontaneous, favourable, and exothermic.

Equilibrium, kinetic and thermodynamic studies on the removal of U(VI) by low cost agricultural waste.

PubMed

Kausar, Abida; Bhatti, Haq Nawaz; MacKinnon, Gillian

2013-11-01

In this research, biosorption efficiency of different agro-wastes was evaluated with rice husk showing maximum biosorption capacity among the selected biosorbents. Optimization of native, SDS-treated and immobilized rice husk adsorption parameters including pH, biosorbent amount, contact time, initial U(VI) concentration and temperature for maximum U(VI) removal was investigated. Maximum biosorption capacity for native (29.56 mg g(-1)) and immobilized biomass (17.59 mg g(-1)) was observed at pH 4 while SDS-treated biomass showed maximum removal (28.08 mg g(-1)) at pH 5. The Langmuir sorption isotherm model correlated best with the U(IV) biosorption equilibrium data for the 10-100 mg L(-1) concentration range. The kinetics of the reaction followed pseudo-second order kinetic model. Thermodynamic parameters like free energy (ΔG(0)) and enthalpy (ΔH°) confirmed the spontaneous and exothermic nature of the process. Experiments to determine the regeneration capacity of the selected biosorbents and the effect of competing metal ions on biosorption capacity were also conducted. The biomass was characterized using scanning electron microscopy, surface area analysis, Fourier transformed infra-red spectroscopy and thermal gravimetric analysis. The study proved that rice husk has potential to treat uranium in wastewater. Copyright © 2013 Elsevier B.V. All rights reserved.

Kinetics, equilibrium and thermodynamic studies on biosorption of Ag(I) from aqueous solution by macrofungus Pleurotus platypus.

PubMed

Das, Devlina; Das, Nilanjana; Mathew, Lazar

2010-12-15

Reports are available on silver binding capacity of some microorganisms. However, reports on the equilibrium studies on biosorption of silver by macrofungi are seldom known. The present study was carried out in a batch system using dead biomass of macrofungus Pleurotus platypus for the sorption of Ag(I). P. platypus exhibited the highest silver uptake of 46.7 mg g(-1) of biomass at pH 6.0 in the presence of 200 mg L(-1) Ag(I) at 20°C. Kinetic studies based on fractional power, zero order, first order, pseudo-first order, Elovich, second order and pseudo-second order rate expressions have been carried out. The results showed a very good compliance with the pseudo-first order model. The experimental data were analyzed using two parameter isotherms (Langmuir, Freundlich, Dubinin-Radushkevich, Temkin and Halsey), three parameter isotherms (Redlich-Peterson, Sips, Khan, Koble-Corrigan, Hill, Toth, Radke-Prausmitz, Jossens, Langmuir-Freundlich), four parameter isotherms (Weber-van Vliet, Fritz-Schlunder, Baudu) and five parameter isotherm (Fritz-Schlunder). Thermodynamic parameters of the biosorption (ΔG, ΔH and ΔS) were also determined. The present study confirmed that macrofungus P. platypus may be used as a cost effective efficient biosorbent for the removal of Ag(I) ions from aqueous solution. Copyright © 2010 Elsevier B.V. All rights reserved.

Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

PubMed

Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

2008-12-25

Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

Consequences of inducing intrinsic disorder in a high-affinity protein-protein interaction.

PubMed

Papadakos, Grigorios; Sharma, Amit; Lancaster, Lorna E; Bowen, Rebecca; Kaminska, Renata; Leech, Andrew P; Walker, Daniel; Redfield, Christina; Kleanthous, Colin

2015-04-29

The kinetic and thermodynamic consequences of intrinsic disorder in protein-protein recognition are controversial. We address this by inducing one partner of the high-affinity colicin E3 rRNase domain-Im3 complex (K(d) ≈ 10(-12) M) to become an intrinsically disordered protein (IDP). Through a variety of biophysical measurements, we show that a single alanine mutation at Tyr507 within the hydrophobic core of the isolated colicin E3 rRNase domain causes the enzyme to become an IDP (E3 rRNase(IDP)). E3 rRNase(IDP) binds stoichiometrically to Im3 and forms a structure that is essentially identical to the wild-type complex. However, binding of E3 rRNase(IDP) to Im3 is 4 orders of magnitude weaker than that of the folded rRNase, with thermodynamic parameters reflecting the disorder-to-order transition on forming the complex. Critically, pre-steady-state kinetic analysis of the E3 rRNase(IDP)-Im3 complex demonstrates that the decrease in affinity is mostly accounted for by a drop in the electrostatically steered association rate. Our study shows that, notwithstanding the advantages intrinsic disorder brings to biological systems, this can come at severe kinetic and thermodynamic cost.

Thermodynamics and Kinetics of Chemical Equilibrium in Solution.

ERIC Educational Resources Information Center

Leenson, I. A.

1986-01-01

Discusses theory of thermodynamics of the equilibrium in solution and dissociation-dimerization kinetics. Describes experimental procedure including determination of molar absorptivity and equilibrium constant, reaction enthalpy, and kinetics of the dissociation-dimerization reaction. (JM)

Dynamic and thermodynamic mechanisms of TFA adsorption by particulate matter.

PubMed

Guo, Junyu; Zhai, Zihan; Wang, Lei; Wang, Ziyuan; Wu, Jing; Zhang, Boya; Zhang, Jianbo

2017-06-01

Trifluoroacetic acid (TFA) in the atmosphere is produced by degradation of hydrochlorofluorocarbons and hydrofluorocarbons. In recent years, TFA has attracted global attention because of increased environmental concentrations, biological toxicity and accumulation in aqueous environments. This study focused on the mechanisms underlying the adsorption of TFA by particulate matter to identify the appropriate descriptive model for this process and thus improve estimation of TFA adsorption in future environmental monitoring. Onsite gas and particle phase sampling in Beijing, China, and subsequent measurement of TFA concentrations indicated that the TFA concentration in the gas phase (1396 ± 225 pg m -3 ) was much higher than that in the particle phase (62 ± 8 pg m -3 ) and that monthly concentrations varied seasonally with temperature. Based on the field results and analysis, an adsorption experiment of TFA on soot was then conducted at three different temperatures (293, 303, and 313 K) to provide parameters for kinetic and thermodynamic modelling. The proportion of atmospheric TFA concentration in the gas phase increased with temperature, indicating that temperature affected the phase distribution of TFA. The subsequent kinetic and thermodynamic modelling showed that the adsorption of TFA by soot could be described well by the Bangham kinetic model. The adsorption was controlled by diffusion, and the key mechanism was physical adsorption. The adsorption behavior can be well described by the Langmuir isotherm model. The calculated thermodynamic parameters ΔG° (-2.34, -1.25, and -0.15 kJ mol -1  at 293, 303, and 313 K, respectively), ΔH° (-34.34 kJ mol -1 ), and ΔS° (-109.22 J mol -1  K -1 ) for TFA adsorption by soot were negative, indicating that adsorption was a spontaneous, exothermic process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kinetics and thermodynamics of oxidation mediated reaction in L-cysteine and its methyl and ethyl esters in dimethyl sulfoxide-d6 by NMR spectroscopy

NASA Astrophysics Data System (ADS)

Dougherty, Ryan J.; Singh, Jaideep; Krishnan, V. V.

2017-03-01

L-Cysteine (L-Cys), L-Cysteine methyl ester (L-CysME) or L-Cysteine ethyl ester (L-CysEE), when dissolved in dimethyl sulfoxide, undergoes an oxidation process. This process is slow enough and leads to nuclear magnetic resonance (NMR) spectral changes that could be monitored in real time. The oxidation mediated transition is modeled as a pseudo-first order kinetics and the thermodynamic parameters are estimated using the Eyring's formulation. L-Cysteine and their esters are often used as biological models due to the remarkable thiol group that can be found in different oxidation states. This oxidation mediated transition is due to the combination of thiol oxidation to a disulfide followed by solvent-induced effects may be relevant in designing cysteine-based molecular models.

Determination of Kinetic and Thermodynamic Parameters that Describe Isothermal Seed Germination: A Student Research Project.

ERIC Educational Resources Information Center

Hageseth, Gaylord T.

1982-01-01

Describes a project for students to collect and fit data to a theoretical mathematical model that describes the rate of isothermal seed germination, including activation energy for substrate and produce and the autocatalytic reaction, and changes in enthalpy, entropy, and the Gibb's free energy. (Author/SK)

Mechanistic information from the first volume profile analysis for a reversible intermolecular electron-transfer reaction involving pentaammine(isonicotinamide)ruthenium and cytochrome c

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

Baensch, B.; Meier, M.; Martinez, P.

1994-10-12

The reversible intermolecular electron-transfer reaction between pentaammine(isonicotinamide)ruthenium(II/III) and horse-heart cytochrome c iron(III/II) was subjected to a detailed kinetic and thermodynamic study as a function of temperature and pressure. Theoretical calculations based on the Marcus-Hush theory were employed to predict all rate and equilibrium constants as well as activation parameters. There is an excellent agreement between the kinetically and thermodynamically determined equilibrium constants and associated pressure parameters. These data are used to construct a volume profile for the overall process, from which it follows that the transition state lies halfway between the reactant and product states on a volume basis. Themore » reorganization in the transition state has reached a similar degree in both directions of the electron-transfer process and corresponds to a {lambda}{sup {double_dagger}} value of 0.44 for this reversible reaction. This is the first complete volume profile analysis for a reversible intermolecular electron-transfer reaction.« less

Study of production and pyrolysis characteristics of sweet orange flavor-β-cyclodextrin inclusion complex.

PubMed

Zhu, Guangyong; Xiao, Zuobing; Zhou, Rujun; Zhu, Yalun

2014-05-25

Flavor plays an important role and has been widely used in foods. Encapsulation can prevent the loss of volatile aromatic ingredients, provide protection and enhance the stability of the flavor. Kinetic and thermodynamic parameters are helpful in understanding the mechanism of molecular recognition between hosts and guests. This work focused on the study of production of a sweet orange flavor-β-cyclodextrin (CD) inclusion complex, and investigated the combination of flavor and β-CD by thermogravimetric analysis. Pyrolysis characteristics, kinetic and thermodynamic parameters of the flavor-β-CD inclusion complex were determined. The results showed that the flavor-β-CD inclusion complexes can form large aggregates in water. During thermal degradation of blank β-CD and flavor-β-CD inclusion complex, three main stages can be distinguished. The thermogravimetric (TG) curve of blank β-CD shows a leveling-off from room temperature to 250°C, while the TG curve of flavor-β-CD inclusion complex is downward sloping in this temperature range. Copyright © 2014 Elsevier Ltd. All rights reserved.

Removal of Congo Red from Aqueous Solution by Anion Exchange Membrane (EBTAC): Adsorption Kinetics and Themodynamics.

PubMed

Khan, Muhammad Imran; Akhtar, Shahbaz; Zafar, Shagufta; Shaheen, Aqeela; Khan, Muhammad Ali; Luque, Rafael; Rehman, Aziz Ur

2015-07-08

The adsorption behavior of anionic dye congo red (CR) from aqueous solutions using an anion exchange membrane (EBTAC) has been investigated at room temperature. The effect of several factors including contact time, membrane dosage, ionic strength and temperature were studied. Kinetic models, namely pseudo-first-order and pseudo-second-order, liquid film diffusion and Elovich models as well as Bangham and modified freundlich Equations, were employed to evaluate the experimental results. Parameters such as adsorption capacities, rate constant and related correlation coefficients for every model were calculated and discussed. The adsorption of CR on anion exchange membranes followed pseudo-second-order Kinetics. Thermodynamic parameters, namely changes in Gibbs free energy ( ∆G° ), enthalpy ( ∆H° ) and entropy ( ∆S° ) were calculated for the adsorption of congo red, indicating an exothermic process.

Removal of Congo Red from Aqueous Solution by Anion Exchange Membrane (EBTAC): Adsorption Kinetics and Themodynamics

PubMed Central

Khan, Muhammad Imran; Akhtar, Shahbaz; Zafar, Shagufta; Shaheen, Aqeela; Khan, Muhammad Ali; Luque, Rafael; ur Rehman, Aziz

2015-01-01

The adsorption behavior of anionic dye congo red (CR) from aqueous solutions using an anion exchange membrane (EBTAC) has been investigated at room temperature. The effect of several factors including contact time, membrane dosage, ionic strength and temperature were studied. Kinetic models, namely pseudo-first-order and pseudo-second-order, liquid film diffusion and Elovich models as well as Bangham and modified freundlich Equations, were employed to evaluate the experimental results. Parameters such as adsorption capacities, rate constant and related correlation coefficients for every model were calculated and discussed. The adsorption of CR on anion exchange membranes followed pseudo-second-order Kinetics. Thermodynamic parameters, namely changes in Gibbs free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) were calculated for the adsorption of congo red, indicating an exothermic process. PMID:28793430

Errors in Sounding of the Atmosphere Using Broadband Emission Radiometry (SABER) Kinetic Temperature Caused by Non-Local Thermodynamic Equilibrium Model Parameters

NASA Technical Reports Server (NTRS)

Garcia-Comas, Maya; Lopez-Puertas, M.; Funke, B.; Bermejo-Pantaleon, D.; Marshall, Benjamin T.; Mertens, Christopher J.; Remsberg, Ellis E.; Mlynczak, Martin G.; Gordley, L. L.; Russell, James M.

2008-01-01

The vast set of near global and continuous atmospheric measurements made by the SABER instrument since 2002, including daytime and nighttime kinetic temperature (T(sub k)) from 20 to 105 km, is available to the scientific community. The temperature is retrieved from SABER measurements of the atmospheric 15 micron CO2 limb emission. This emission separates from local thermodynamic equilibrium (LTE) conditions in the rarefied mesosphere and thermosphere, making it necessary to consider the CO2 vibrational state non-LTE populations in the retrieval algorithm above 70 km. Those populations depend on kinetic parameters describing the rate at which energy exchange between atmospheric molecules take place, but some of these collisional rates are not well known. We consider current uncertainties in the rates of quenching of CO2 (v2 ) by N2 , O2 and O, and the CO2 (v2 ) vibrational-vibrational exchange to estimate their impact on SABER T(sub k) for different atmospheric conditions. The T(sub k) is more sensitive to the uncertainty in the latter two and their effects depend on altitude. The T(sub k) combined systematic error due to non-LTE kinetic parameters does not exceed +/- 1.5 K below 95 km and +/- 4-5 K at 100 km for most latitudes and seasons (except for polar summer) if the Tk profile does not have pronounced vertical structure. The error is +/- 3 K at 80 km, +/- 6 K at 84 km and +/- 18 K at 100 km under the less favourable polar summer conditions. For strong temperature inversion layers, the errors reach +/- 3 K at 82 km and +/- 8 K at 90 km. This particularly affects tide amplitude estimates, with errors of up to +/- 3 K.

Global investigation of potential energy surfaces for the pyrolysis of C(1)-C(3) hydrocarbons: toward the development of detailed kinetic models from first principles.

PubMed

Ryazantsev, Mikhail N; Jamal, Adeel; Maeda, Satoshi; Morokuma, Keiji

2015-11-07

Detailed kinetic models (DKMs) are the most fundamental "bottom-up" approaches to computational investigation of the pyrolysis and oxidation of fuels. The weakest points of existing DKMs are incomplete information about the reaction types that can be involved in the potential energy surfaces (PESs) in pyrolysis and oxidation processes. Also, the computational thermodynamic parameters available in the literature vary widely with the level of theory employed. More sophisticated models require improvement both in our knowledge of the type of the reactions involved and the consistency of thermodynamic and kinetic parameters. In this paper, we aim to address these issues by developing ab initio models that can be used to describe early stages of pyrolysis of C1-C3 hydrocarbons. We applied a recently developed global reaction route mapping (GRRM) strategy to systematically investigate the PES of the pyrolysis of C1-C3 hydrocarbons at a consistent level of theory. The reactions are classified into 14 reaction types. The critical points on the PES for all reactions in the network are calculated at the highly accurate UCCSD(T)-F12b/cc-pVTZ//UM06-2X/cc-pVTZ level of theory. The data reported in this paper can be used for first principle calculations of kinetic constants and for a subsequent study on modeling the evolution of the species from the reaction network of the pyrolysis and oxidation of C1-C3 hydrocarbons.

Effects of multi-frequency power ultrasound on the enzymolysis of corn gluten meal: Kinetics and thermodynamics study.

PubMed

Jin, Jian; Ma, Haile; Qu, Wenjuan; Wang, Kai; Zhou, Cunshan; He, Ronghai; Luo, Lin; Owusu, John

2015-11-01

The effects of multi-frequency power ultrasound (MPU) pretreatment on the kinetics and thermodynamics of corn gluten meal (CGM) were investigated in this research. The apparent constant (KM), apparent break-down rate constant (kA), reaction rate constants (k), energy of activation (Ea), enthalpy of activation (ΔH), entropy of activation (ΔS) and Gibbs free energy of activation (ΔG) were determined by means of the Michaelis-Menten equation, first-order kinetics model, Arrhenius equation and transition state theory, respectively. The results showed that MPU pretreatment can accelerate the enzymolysis of CGM under different enzymolysis conditions, viz. substrate concentration, enzyme concentration, pH, and temperature. Kinetics analysis revealed that MPU pretreatment decreased the KM value by 26.1% and increased the kA value by 7.3%, indicating ultrasound pretreatment increased the affinity between enzyme and substrate. In addition, the values of k for ultrasound pretreatment were increased by 84.8%, 41.9%, 28.9%, and 18.8% at the temperature of 293, 303, 313 and 323 K, respectively. For the thermodynamic parameters, ultrasound decreased Ea, ΔH and ΔS by 23.0%, 24.3% and 25.3%, respectively, but ultrasound had little change in ΔG value in the temperature range of 293-323 K. In conclusion, MPU pretreatment could remarkably enhance the enzymolysis of CGM, and this method can be applied to protein proteolysis industry to produce peptides. Copyright © 2015 Elsevier B.V. All rights reserved.

Oxidation kinetics of crystal violet by potassium permanganate in acidic medium

NASA Astrophysics Data System (ADS)

Khan, Sameera Razi; Ashfaq, Maria; Mubashir; Masood, Summyia

2016-05-01

The oxidation kinetics of crystal violet (a triphenylmethane dye) by potassium permanganate was focused in an acidic medium by the spectrophotometric method at 584 nm. The oxidation reaction of crystal violet by potassium permanganate is carried out in an acidic medium at different temperatures ranging within 298-318 K. The kinetic study was carried out to investigate the effect of the concentration, ionic strength and temperature. The reaction followed first order kinetics with respect to potassium permanganate and crystal violet and the overall rate of the reaction was found to be second order. Thermodynamic activation parameters like the activation energy ( E a), enthalpy change (Δ H*), free energy change (Δ G*), and entropy change (Δ S*) have also been evaluated.

Kinetics of enzymatic synthesis of liquid wax ester from oleic acid and oleyl alcohol.

PubMed

Radzi, Salina Mat; Mohamad, Rosfarizan; Basri, Mahiran; Salleh, Abu Bakar; Ariff, Arbakariya; Rahman, Mohammad Basyaruddin Abdul; Rahman, Raja Noor Zaliha Raja Abdul

2010-01-01

The kinetics of wax ester synthesis from oleic acid and oleyl alcohol using immobilized lipase from Candida antartica as catalyst was studied with different types of impeller (Rushton turbine and AL-hydrofoil) to create different mixing conditions in 2l stirred tank reactor. The effects of catalyst concentration, reaction temperature, and impeller tip speed on the synthesis were also evaluated. Rushton turbine impeller exhibited highest conversion rate at lower impeller tip speed as compared to AL-hydrofoil impeller. A second-order reversible kinetic model from single progress curve for the prediction of fractional conversion at given reaction time was proposed and the corresponding kinetic parameter values were calculated by non-linear regression method. The results from the simulation using the proposed model showed satisfactory agreement with the experimental data. Activation energy shows a value of 21.77 Kcal/mol. The thermodynamic parameters of the process, enthalpy and entropy, were 21.15 Kcal/mol and 52.07 cal/mol.K, respectively.

Strain E?ect on the Instability of Island Formation in Submonolayer Heteroepitaxy

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

Yao, yugui; Li, Maozhi; Wu, Biao

2009-01-01

Strain e ect on the instability of island formation in submonolayer heteroepitaxy is studied in both thermodynamic and kinetic regimes. By using linear stability analysis, the energy change of an island due to small perturbations is analyzed. A phase diagram is constructed to illustrate the interplay between kinetic processes and strain e ect on the shape instability. Critical island sizes beyond which islands grow unstable are also derived for various growth conditions and can be used to estimate energy parameters. The scaling forms of shape instability are also discussed.

Modeling and experimental characterization of Blackglas(TM) polymer pyrolysis to ceramic and thermodynamic characterization of Blackglas(TM) ceramic

NASA Astrophysics Data System (ADS)

Wang, Feng

2000-10-01

The transformation of Blackglas(TM) polymer to ceramic is characterized by TGA-RGA/MS, Si29 and C13 NMR. Si29 NMR reveals a dependence between the postcure temperature and the microstructure of the resin. The postcure temperature that appears to give optimal mechanical and oxidative properties of Blackglas(TM) ceramic is around 150°C. The pyrolysis processing models, which are the Lumped Parameters Model (LPM), the Mechanistic Kinetic Model (MKM) and the Redistribution Reaction Model (RRM), are developed to provide an effective window of processing parameters rather than a costly, time-consuming trial and error approach. The Lumped Parameters Model (LPM) is developed to study the effects of various parameters such as temperature, curing conditions and heating rates on mass loss during the pyrolysis of resin and green composites. It can be used for the model-predictive control of the pyrolysis process; The Mechanistic Kinetic Model (MKM) is developed on the basis of known chemistry and architecture of the polysiloxane for the transformation of Blackglas(TM) polymer to ceramic and the evolution of gases. The effects of various heating protocols on the outgassing kinetics have been studied to develop an optimum protocol for a rapid pyrolysis process which gives a composite with desirable mechanical properties; The Redistribution Reaction Model (RRM) is proposed to describe how the microcompositions of silicon oxycarbide change with respect to temperature, and to the ratio O/Si in the polymer precursor. A Thermodynamic Additivity Model (TAM) is developed to estimate the heat capacity, standard heat of formation and entropy of Blackglas(TM) ceramic by means of the Neumann Kopp rule and the available thermodynamic data of the Si-C and Si-O systems. Thermal stability of this ceramic is investigated by constructing predominance diagrams, and it is shown that the internal degradation reactions, which account for a significant loss of strength, will proceed further in the Blackglas(TM) matrix than in the Nicalon fibers. This probably will induce failure in the matrix at lower temperatures than in the fibers. The predominance diagrams also explain the high temperature oxidation, reduction and volatilization experiments on silicon and silicon carbide in high vacuum.

Use of Physicochemical Parameters to Assess the Environmental Fate of Organic Pollutants: The Fugacity Model

ERIC Educational Resources Information Center

Domenech, Xavier; Ayllon, Jose Antonio; Peral, Jose

2006-01-01

The environmental fate and behavior of different organic pollutants based on the qualitative analysis of thermodynamic and kinetic data is presented. The Fugacity model allows the use of different partition constants in an easy way, to determine the distribution of chemical between different phases in equilibrium of an environmental system.

Reduced chemical kinetic model of detonation combustion of one- and multi-fuel gaseous mixtures with air

NASA Astrophysics Data System (ADS)

Fomin, P. A.

2018-03-01

Two-step approximate models of chemical kinetics of detonation combustion of (i) one hydrocarbon fuel CnHm (for example, methane, propane, cyclohexane etc.) and (ii) multi-fuel gaseous mixtures (∑aiCniHmi) (for example, mixture of methane and propane, synthesis gas, benzene and kerosene) are presented for the first time. The models can be used for any stoichiometry, including fuel/fuels-rich mixtures, when reaction products contain molecules of carbon. Owing to the simplicity and high accuracy, the models can be used in multi-dimensional numerical calculations of detonation waves in corresponding gaseous mixtures. The models are in consistent with the second law of thermodynamics and Le Chatelier's principle. Constants of the models have a clear physical meaning. The models can be used for calculation thermodynamic parameters of the mixture in a state of chemical equilibrium.

Kinetic Reaction Mechanism of Sinapic Acid Scavenging NO2 and OH Radicals: A Theoretical Study

PubMed Central

Lu, Yang; Wang, AiHua; Shi, Peng; Zhang, Hui; Li, ZeSheng

2016-01-01

The mechanism and kinetics underlying reactions between the naturally-occurring antioxidant sinapic acid (SA) and the very damaging ·NO2 and ·OH were investigated through the density functional theory (DFT). Two most possible reaction mechanisms were studied: hydrogen atom transfer (HAT) and radical adduct formation (RAF). Different reaction channels of neutral and anionic sinapic acid (SA-) scavenging radicals in both atmosphere and water medium were traced independently, and the thermodynamic and kinetic parameters were calculated. We find the most active site of SA/SA- scavenging ·NO2 and ·OH is the –OH group in benzene ring by HAT mechanism, while the RAF mechanism for SA/SA- scavenging ·NO2 seems thermodynamically unfavorable. In water phase, at 298 K, the total rate constants of SA eliminating ·NO2 and ·OH are 1.30×108 and 9.20×109 M-1 S-1 respectively, indicating that sinapic acid is an efficient scavenger for both ·NO2 and ·OH. PMID:27622460

Thermodynamics and kinetics of protein folding on the ribosome: Alteration in energy landscapes, denatured state, and transition state ensembles

NASA Astrophysics Data System (ADS)

O'Brien, Edward; Vendruscolo, Michele; Dobson, Christopher

2010-03-01

In vitro experiments examining cotranslational folding utilize ribosome-nascent chain complexes (RNCs) in which the nascent chain is stalled at different points of its biosynthesis on the ribosome. We investigate the thermodynamics, kinetics, and structural properties of RNCs containing five different globular and repeat proteins stalled at ten different nascent chain lengths using coarse grained replica exchange simulations. We find that when the proteins are stalled near the ribosome exit tunnel opening they exhibit altered folding coopserativity, quantified by the van't Hoff enthalpy criterion; a significantly altered denatured state ensemble, in terms of Rg and shape parameters (Rg tensor); and the appearance of partially folded intermediates during cotranslation, evidenced by the appearance of a third basin in the free energy profile. These trends are due in part to excluded volume (crowding) interactions between the ribosome and nascent chain. We perform in silico temperature-jump experiments on the RNCs and examine nascent chain folding kinetics and structural changes in the transition state ensemble at various stall lengths.

Efficient removal of cadmium using magnetic multiwalled carbon nanotube nanoadsorbents: equilibrium, kinetic, and thermodynamic study

NASA Astrophysics Data System (ADS)

Pashai Gatabi, Maliheh; Milani Moghaddam, Hossain; Ghorbani, Mohsen

2016-07-01

Adsorptive potential of maghemite decorated multiwalled carbon nanotubes (MWCNTs) for the removal of cadmium ions from aqueous solution was investigated. The magnetic nanoadsorbent was synthesized using a versatile and cost effective chemical route. Structural, magnetic and surface charge properties of the adsorbent were characterized using FTIR, XRD, TEM, VSM analysis and pHPZC determination. Batch adsorption experiments were performed under varied system parameters such as pH, contact time, initial cadmium concentration and temperature. Highest cadmium adsorption was obtained at pH 8.0 and contact time of 30 min. Adsorption behavior was kinetically studied using pseudo first-order, pseudo second-order, and Weber-Morris intra particle diffusion models among which data were mostly correlated to pseudo second-order model. Adsorbate-adsorbent interactions as a function of temperature was assessed by Langmuir, Freundlich, Dubinin-Radushkevich (D-R) and Temkin isotherm models from which Freundlich model had the highest consistency with the data. The adsorption capacity increased with increasing temperature and maximum Langmuir's adsorption capacity was found to be 78.81 mg g-1 at 298 K. Thermodynamic parameters and activation energy value suggest that the process of cadmium removal was spontaneous and physical in nature, which lead to fast kinetics and high regeneration capability of the nanoadsorbent. Results of this work are of great significance for environmental applications of magnetic MWCNTs as promising adsorbent for heavy metals removal from aqueous solutions.

Understanding the Elementary Steps in DNA Tile-Based Self-Assembly.

PubMed

Jiang, Shuoxing; Hong, Fan; Hu, Huiyu; Yan, Hao; Liu, Yan

2017-09-26

Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.

Kinetics and mechanisms of thiol-disulfide exchange covering direct substitution and thiol oxidation-mediated pathways.

PubMed

Nagy, Péter

2013-05-01

Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol-disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. This review is focused on the kinetics and mechanisms of thiol-disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery.

Improving the Kinetics and Thermodynamics of Mg(BH 4) 2 for Hydrogen Storage

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

Wood, Brandon; Klebanoff, Lennie; Stavila, Vitalie

The objective of this project is to (1) combine theory, synthesis, and characterization across multiple scales to understand the intrinsic kinetic and thermodynamic limitations in MgB 2/Mg(BH 4) 2; (2) construct and apply a flexible, validated, multiscale theoretical framework for modeling (de)hydrogenation kinetics of the Mg-B-H system and related metal hydrides; and (3) devise strategies for improving kinetics and thermodynamics, particularly through nanostructuring and doping. The project has an emphasis on understanding and improving rehydrogenation of MgB 2, which has generally been less explored and is key to enabling practical use.

Misconceptions regarding basic thermodynamics and enzyme kinetics have led to erroneous conclusions regarding the metabolic importance of lactate dehydrogenase isoenzyme expression.

PubMed

Bak, Lasse K; Schousboe, Arne

2017-11-01

Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate involving the coenzyme NAD + . Part of the foundation for the proposed shuttling of lactate from astrocytes to neurons during brain activation is the differential distribution of LDH isoenzymes between the two cell types. In this short review, we outline the basic kinetic properties of the LDH isoenzymes expressed in neurons and astrocytes, and argue that the distribution of LDH isoenzymes does not in any way govern directional flow of lactate between the two cellular compartments. The two main points are as follows. First, in line with the general concept of chemical catalysis, enzymes do not influence the thermodynamic equilibrium of a chemical reaction but merely the speed at which equilibrium is obtained. Thus, differential distribution of LDH isoenzymes with different kinetic parameters does not predict which cells are producing and which are consuming lactate. Second, the thermodynamic equilibrium of the reaction is toward the reduced substrate (i.e., lactate), which is reflected in the concentrations measured in brain tissue, suggesting that the reaction is at near-equilibrium at steady state. To conclude, the cellular distribution of LDH isoenzymes is of little if any consequence in determining any directional flow of lactate between neurons and astrocytes. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Irreversible thermodynamics of Poisson processes with reaction.

PubMed

Méndez, V; Fort, J

1999-11-01

A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.

MnFe2O4-graphene oxide magnetic nanoparticles as a high-performance adsorbent for rare earth elements: Synthesis, isotherms, kinetics, thermodynamics and desorption.

PubMed

Ghobadi, Misagh; Gharabaghi, Mahdi; Abdollahi, Hadi; Boroumand, Zohreh; Moradian, Marzieh

2018-06-05

In recent decades, considerable amounts of rare earth elements have been used and then released into industrial wastewater, which caused serious environmental problems. In this work, in order to recycle rare earth cations (La 3+ and Ce 3+ ) from aqueous solutions, MnFe 2 O 4 -Graphene oxide magnetic nanoparticles were synthesized and after characterization studies, their adsorption isotherms, kinetics, thermodynamics and desorption were comprehensively investigated. Characterized was performed using XRD, FE-SEM, FT-IR, Raman spectroscopy, VSM, BET and DLS. REE adsorption on MnFe 2 O 4 -GO was studied for the first time in the present work and the maximum adsorption capacity at the optimum condition (room temperature and pH = 7) for La 3+ and Ce 3+ were 1001 and 982 mg/g respectively, and the reactions were completed within 20 min. In addition, the adsorption data were well matched with the Langmuir model and the adsorption kinetics were fitted with the pseudo-second order model. The thermodynamic parameters were calculated and the reactions were found to be endothermic and spontaneous. Moreover, the Dubinin-Radushkevich model predicted chemical ion-exchange adsorption. Desorption studies also demonstrated that MnFe 2 O 4 -GO can be regenerated for multiple reuses. Overall, high adsorption capacity, chemical stability, reusability, fast kinetics, easy magnetic separation, and simple synthesis method indicated that MnFe 2 O 4 -GO is a high-performance adsorbent for REE. Copyright © 2018. Published by Elsevier B.V.

Kinetics of azathioprine metabolism in fresh human blood.

PubMed

Chrzanowska, M; Hermann, T; Gapińska, M

1985-01-01

Azathioprine (AZA) is transformed in the whole fresh human blood in vitro to 6-mercaptopurine (6-MP). The rate of the above reaction was followed as a function of time at 25, 30 and 37 degrees C. Pseudo-first-order rate constants and thermodynamic parameters were calculated. The statistical evaluation of the parameters calculated was provided. Half-life time of 6-MP formation in blood from AZA at e.g. 37 degrees C was equal to 28.9 +/- 2.8 min.

Interpreting equilibrium-conductivity and conductivity-relaxation measurements to establish thermodynamic and transport properties for multiple charged defect conducting ceramics.

PubMed

Zhu, Huayang; Ricote, Sandrine; Coors, W Grover; Kee, Robert J

2015-01-01

A model-based interpretation of measured equilibrium conductivity and conductivity relaxation is developed to establish thermodynamic, transport, and kinetics parameters for multiple charged defect conducting (MCDC) ceramic materials. The present study focuses on 10% yttrium-doped barium zirconate (BZY10). In principle, using the Nernst-Einstein relationship, equilibrium conductivity measurements are sufficient to establish thermodynamic and transport properties. However, in practice it is difficult to establish unique sets of properties using equilibrium conductivity alone. Combining equilibrium and conductivity-relaxation measurements serves to significantly improve the quantitative fidelity of the derived material properties. The models are developed using a Nernst-Planck-Poisson (NPP) formulation, which enables the quantitative representation of conductivity relaxations caused by very large changes in oxygen partial pressure.

Dyes removal using activated carbon from palm oil waste with digital image colorimetry quantification

NASA Astrophysics Data System (ADS)

Firdaus, M. Lutfi; Puspita, Melfi; Alwi, Wiwit; Ghufira, Nurhamidah, Elvia, Rina

2017-11-01

In the present study, activated carbon prepared from palm oil husk was used as adsorbent to remove synthetic dyes of Reactive Red 120 (RR) and Direct Green 26 (DG) from aqueous solution. The effects of solution pH, contact time, adsorbent weight, dyes concentration, and temperature on adsorption were evaluated based on batch experiments along with determination of the adsorption isotherms, kinetics, and thermodynamics parameters. Visible spectrophotometry was used for the quantification of dyes concentration, in conjunction with digital image colorimetry as a novel quantification method. Compared to visible spectrophotometry, the results of digital image colorimetry were accurate. In addition, improved sensitivity was achieved using this new colorimetry method. At equilibrium, dyes adsorption onto activated carbon followed Freundlich model, with adsorption capacities for RR and DG were 32 and 27 mg/g, respectively. The adsorption kinetics study showed a pseudo-second-order model with thermodynamic parameters of ΔG°, ΔH°, and ΔS° were -1.8 to -3.8 kJ/mol, -13.5 to -24.38 kJ/mol, and 0.001 J/mol, respectively. Therefore, the process of adsorption was exothermic and spontaneous with an increase in the disorder or entropy of the system.

Mechanisms of kinetic stabilization by the drugs paclitaxel and vinblastine

PubMed Central

Castle, Brian T.; McCubbin, Seth; Prahl, Louis S.; Bernens, Jordan N.; Sept, David; Odde, David J.

2017-01-01

Microtubule-targeting agents (MTAs), widely used as biological probes and chemotherapeutic drugs, bind directly to tubulin subunits and “kinetically stabilize” microtubules, suppressing the characteristic self-assembly process of dynamic instability. However, the molecular-level mechanisms of kinetic stabilization are unclear, and the fundamental thermodynamic and kinetic requirements for dynamic instability and its elimination by MTAs have yet to be defined. Here we integrate a computational model for microtubule assembly with nanometer-scale fluorescence microscopy measurements to identify the kinetic and thermodynamic basis of kinetic stabilization by the MTAs paclitaxel, an assembly promoter, and vinblastine, a disassembly promoter. We identify two distinct modes of kinetic stabilization in live cells, one that truly suppresses on-off kinetics, characteristic of vinblastine, and the other a “pseudo” kinetic stabilization, characteristic of paclitaxel, that nearly eliminates the energy difference between the GTP- and GDP-tubulin thermodynamic states. By either mechanism, the main effect of both MTAs is to effectively stabilize the microtubule against disassembly in the absence of a robust GTP cap. PMID:28298489

Efficacy of mangrove leaf powder for bioremediation of chromium (VI) from aqueous solutions: kinetic and thermodynamic evaluation

NASA Astrophysics Data System (ADS)

Sathish, Thadikamala; Vinithkumar, N. V.; Dharani, G.; Kirubagaran, R.

2015-06-01

Biosorption of heavy metals by bio-materials has been posited as a potential alternative to the existing physicochemical technologies for detoxification and recovery of toxic and valuable metals from wastewaters. In this context, the role of mangrove leaf powder (MLP) as biosorbent for chromium removal was investigated. In the present study, the effect of process parameters such as particle size, solution pH, initial concentration of Cr(VI) ion and adsorbent dose on chromium removal by MLP was investigated. The maximum sorption was observed at particle size 0.5 mm and pH 2.0. The adsorption data follow the pseudo second-order kinetics model. The isotherms denote that Langmuir model is the best fitted than Freundlich model. The maximum adsorption capacity ( Q 0) of 60.24 mg/g of Cr(VI) at 30 min on MLP was determined using the Langmuir model. The adsorption isotherm model indicates that the chromium is adsorbing as monolayer on the surface of MLP with heterogeneous energetic distribution of active sites. Various thermodynamic parameters, such as Gibb's free energy (∆ G °), enthalpy (∆ H °) and entropy (∆ S °) have been calculated. The thermodynamic data revealed that the adsorption of chromium ions onto MLP is endothermic in nature and a spontaneous process. The results of the present study suggest that MLP is an effective bioremediation measure for removal of high concentration of Cr(VI) in waste waters.

Thermodynamic and kinetic studies of As(V) removal from water by zirconium oxide-coated marine sand.

PubMed

Khan, Tabrez Alam; Chaudhry, Saif Ali; Ali, Imran

2013-08-01

Arsenic contamination of groundwater is a major threat to human beings globally. Among various methods available for arsenic removal, adsorption is fast, inexpensive, selective, accurate, reproducible and eco-friendly in nature. The present paper describes removal of arsenate from water on zirconium oxide-coated sand (novel adsorbent). In the present work, zirconium oxide-coated sand was prepared and characterised by infrared and X-ray diffraction techniques. Batch experiments were performed to optimise different adsorption parameters such as initial arsenate concentration (100-1,000 μg/L), dose (1-8 g/L), pH of the solution (2-14), contact time (15-150 min.), and temperature (20, 30, 35 and 40 °C). The experimental data were analysed by Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherm models. Furthermore, thermodynamic and kinetic parameters were evaluated to know the mode of adsorption between ZrOCMS and As(V). The maximum removal of arsenic, 97 %, was achieved at initial arsenic concentration of 200 μg/L, after 75 min at dosage of 5.0 g/L, pH 7.0 and 27 ± 2 °C. For 600 μg/L concentration, the maximum Langmuir monolayer adsorption capacity was found to be 270 μg/g at 35 °C. Kinetic modelling data indicated that adsorption process followed pseudo-second-order kinetics. The mechanism is controlled by liquid film diffusion model. Thermodynamic parameter, ΔH°, was -57.782, while the values of ΔG° were -9.460, -12.183, -13.343 and -13.905 kJ/mol at 20, 30, 35 and 40 °C, respectively, suggesting exothermic and spontaneous nature of the process. The change in entropy, ΔS°= -0.23 kJ/mol indicated that the entropy decreased due to adsorption of arsenate ion onto the solid adsorbent. The results indicated that the reported zirconium oxide-coated marine sand (ZrOCMS) was good adsorbent with 97 % removal capacity at 200 μg/L concentration. It is interesting to note that the permissible limit of arsenic as per World Health Organization is 10 μg/L, and in real situation, this low concentration can be achieved through this adsorbent. Besides, the adsorption capacity showed that this adsorbent may be used for the removal of arsenic from any natural water resource.

Real-time and label-free analysis of binding thermodynamics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a QCM biosensor

PubMed Central

Li, Xueming; Song, Siyu; Shuai, Qi; Pei, Yihan; Aastrup, Teodor; Pei, Yuxin; Pei, Zhichao

2015-01-01

A novel approach to the study of binding thermodynamics and kinetics of carbohydrate-protein interactions on unfixed cancer cell surfaces using a quartz crystal microbalance (QCM) biosensor was developed, in which binding events take place at the cell surface, more closely mimicking a biologically relevant environment. In this study, colon adenocarcinoma cells (KM-12) and ovary adenocarcinoma cells (SKOV-3) grew on the optimized polystyrene-coated biosensor chip without fixation. The association and dissociation between the cell surface carbohydrates and a range of lectins, including WGA, Con A, UEA-I, GS-II, PNA and SBA, were monitored in real time and without label for evaluation of cell surface glycosylation. Furthermore, the thermodynamic and kinetic parameters of the interaction between lectins and cell surface glycan were studied, providing detailed information about the interactions, such as the association rate constant, dissociation rate constant, affinity constant, as well as the changes of entropy, enthalpy and Gibbs free energy. This application provides an insight into the cell surface glycosylation and the complex molecular recognition on the intact cell surface, which may have impacts on disease diagnosis and drug discovery. PMID:26369583

Nonextensive kinetic theory and H-theorem in general relativity

NASA Astrophysics Data System (ADS)

Santos, A. P.; Silva, R.; Alcaniz, J. S.; Lima, J. A. S.

2017-11-01

The nonextensive kinetic theory for degenerate quantum gases is discussed in the general relativistic framework. By incorporating nonadditive modifications in the collisional term of the relativistic Boltzmann equation and entropy current, it is shown that Tsallis entropic framework satisfies a H-theorem in the presence of gravitational fields. Consistency with the 2nd law of thermodynamics is obtained only whether the entropic q-parameter lies in the interval q ∈ [ 0 , 2 ] . As occurs in the absence of gravitational fields, it is also proved that the local collisional equilibrium is described by the extended Bose-Einstein (Fermi-Dirac) q-distributions.

Thermodynamical transcription of density functional theory with minimum Fisher information

NASA Astrophysics Data System (ADS)

Nagy, Á.

2018-03-01

Ghosh, Berkowitz and Parr designed a thermodynamical transcription of the ground-state density functional theory and introduced a local temperature that varies from point to point. The theory, however, is not unique because the kinetic energy density is not uniquely defined. Here we derive the expression of the phase-space Fisher information in the GBP theory taking the inverse temperature as the Fisher parameter. It is proved that this Fisher information takes its minimum for the case of constant temperature. This result is consistent with the recently proven theorem that the phase-space Shannon information entropy attains its maximum at constant temperature.

Hot, cold, and annual reference atmospheres for Edwards Air Force Base, California (1975 version)

NASA Technical Reports Server (NTRS)

Johnson, D. L.

1975-01-01

Reference atmospheres pertaining to summer (hot), winter (cold), and mean annual conditions for Edwards Air Force Base, California, are presented from surface to 90 km altitude (700 km for the annual model). Computed values of pressure, kinetic temperature, virtual temperature, and density and relative differences percentage departure from the Edwards reference atmospheres, 1975 (ERA-75) of the atmospheric parameters versus altitude are tabulated in 250 m increments. Hydrostatic and gas law equations were used in conjunction with radiosonde and rocketsonde thermodynamic data in determining the vertical structure of these atmospheric models. The thermodynamic parameters were all subjected to a fifth degree least-squares curve-fit procedure, and the resulting coefficients were incorporated into Univac 1108 computer subroutines so that any quantity may be recomputed at any desired altitude using these subroutines.

Predicting Grain Growth in Nanocrystalline Materials: A Thermodynamic and Kinetic-Based Model Informed by High Temperature X-ray Diffraction Experiments

DTIC Science & Technology

2014-10-01

and d) Γb0. The scatter of the data points is due to the variation in the other parameters at 1 h. The line represents a best fit linear regression...parameters: a) Hseg, b) QL, c) γ0, and d) Γb0. The scatter of the data points is due to the variation in the other parameters at 1 h. The line represents...concentration x0 for the nanocrystalline Fe–Zr system. The white square data point shows the location of the experimental data used for fitting the

Thermodynamics and simulation of hard-sphere fluid and solid: Kinetic Monte Carlo method versus standard Metropolis scheme

NASA Astrophysics Data System (ADS)

Ustinov, E. A.

2017-01-01

The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure-chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs-Duhem equation as a constraint. A detailed thermodynamic analysis of the hard-sphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems.

Nanotransition Materials (NTMs): Photocatalysis, Validated High Effective Sorbent Models Study for Organic Dye Degradation and Precise Mathematical Data’s at Standardized Level

PubMed Central

Khan, Farheen; Wahab, Rizwan; Hagar, Mohamed; Alnoman, Rua; Lutfullah; Rashid, Mohd

2018-01-01

The present work describes the synthesis of copper oxide nanoparticles (CuONPs) via a solution process with the aim of applying the nano-adsorbent for the reduction of methylene blue (MB) dye in alkaline media. These NPs were characterized via Field emission scanning electron microscopy (FE-SEM), X-ray diffraction, high-resolution Transmission electron microscopy (TEM), and ultra violet UV-visible spectroscopy to confirm their morphology and crystalline and optical properties in order to design an adsorption-degradation process. The photocatalytic CuONPs exhibited dynamic properties, great adsorption affinity during the chemisorption process, and operated at various modes with a strong interaction between the adsorbent and the adsorptive species, and equilibrium isotherm, kinetic isotherm, and thermodynamic activities in the presence of UV light. All basic quantities, such as concentration, pH, adsorbent dose, time, and temperature, were determined by an optimization process. The best-fitted adsorption Langmuir model (R2 = 0.9988) and performance, including adsorption capacity (350.87 mg/g), photocatalytic efficiency (90.74%), and degradation rate constant (Ks = 2.23 ×10−2 min−1), illustrate good feasibility with respect to sorption-reduction reactions but followed a pseudo-second-order kinetic on the adsorbent surface, reaching an equilibrium point in 80 min. The thermodynamic analysis suggests that the adsorption reaction is spontaneous and endothermic in nature. The thermodynamic parameters such as enthalpy (∆H°), entropy (∆S°), and Gibbs free energy (∆G°) give effective results to support a chemical reduction reaction at 303 K temperature. The equilibrium isotherm and kinetic and thermodynamic models with error function analysis explore the potential, acceptability, accuracy, access to adsorbents, and novelty of an unrivaled-sorption system. PMID:29495511

Kinetics and Mechanisms of Thiol–Disulfide Exchange Covering Direct Substitution and Thiol Oxidation-Mediated Pathways

PubMed Central

2013-01-01

Abstract Significance: Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol–disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. Critical Issues: This review is focused on the kinetics and mechanisms of thiol–disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Recent Advances and Future Directions: Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery. Antioxid. Redox Signal. 18, 1623–1641. PMID:23075118

Thermodynamics and Kinetics of Sulfide Oxidation by Oxygen: A Look at Inorganically Controlled Reactions and Biologically Mediated Processes in the Environment

PubMed Central

Luther, George W.; Findlay, Alyssa J.; MacDonald, Daniel J.; Owings, Shannon M.; Hanson, Thomas E.; Beinart, Roxanne A.; Girguis, Peter R.

2011-01-01

The thermodynamics for the first electron transfer step for sulfide and oxygen indicates that the reaction is unfavorable as unstable superoxide and bisulfide radical ions would need to be produced. However, a two-electron transfer is favorable as stable S(0) and peroxide would be formed, but the partially filled orbitals in oxygen that accept electrons prevent rapid kinetics. Abiotic sulfide oxidation kinetics improve when reduced iron and/or manganese are oxidized by oxygen to form oxidized metals which in turn oxidize sulfide. Biological sulfur oxidation relies on enzymes that have evolved to overcome these kinetic constraints to affect rapid sulfide oxidation. Here we review the available thermodynamic and kinetic data for H2S and HS• as well as O2, reactive oxygen species, nitrate, nitrite, and NOx species. We also present new kinetic data for abiotic sulfide oxidation with oxygen in trace metal clean solutions that constrain abiotic rates of sulfide oxidation in metal free solution and agree with the kinetic and thermodynamic calculations. Moreover, we present experimental data that give insight on rates of chemolithotrophic and photolithotrophic sulfide oxidation in the environment. We demonstrate that both anaerobic photolithotrophic and aerobic chemolithotrophic sulfide oxidation rates are three or more orders of magnitude higher than abiotic rates suggesting that in most environments biotic sulfide oxidation rates will far exceed abiotic rates due to the thermodynamic and kinetic constraints discussed in the first section of the paper. Such data reshape our thinking about the biotic and abiotic contributions to sulfide oxidation in the environment. PMID:21833317

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.

Uncovering the self-assembly of DNA nanostructures by thermodynamics and kinetics.

PubMed

Wei, Xixi; Nangreave, Jeanette; Liu, Yan

2014-06-17

CONSPECTUS: DNA nanotechnology is one of the most flourishing interdisciplinary research fields. DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales. They can be used as scaffolds for organizing other nanoparticles, proteins, and chemical groups, leveraging their functions for creating complex bioinspired materials that may serve as smart drug delivery systems, in vitro or in vivo biomolecular computing platforms, and diagnostic devices. Achieving optimal structural features, efficient assembly protocols, and precise functional group positioning and modification requires a thorough understanding of the thermodynamics and kinetics of the DNA nanostructure self-assembly process. The most common real-time measurement strategies include monitoring changes in UV absorbance based on the hyperchromic effect of DNA, and the emission signal changes of DNA intercalating dyes or covalently conjugated fluorescent dyes/pairs that accompany temperature dependent structural changes. Thermodynamic studies of a variety of DNA nanostructures have been performed, from simple double stranded DNA formation to more complex origami assembly. The key parameters that have been evaluated in terms of stability and cooperativity include the overall dimensions, the folding path of the scaffold, crossover and nick point arrangement, length and sequence of single strands, and salt and ion concentrations. DNA tile-tile interactions through sticky end hybridization have also been analyzed, and the steric inhibition and rigidity of tiles turn out to be important factors. Many kinetic studies have also been reported, and most are based on double stranded DNA formation. A two-state assumption and the hypothesis of several intermediate states have been applied to determine the rate constant and activation energy of the DNA hybridization process. A few simulated models were proposed to represent the structural, mechanical, and kinetic properties of DNA hybridization. The kinetics of strand displacement reactions has also been studied as a special case of DNA hybridization. The thermodynamic and kinetic characteristics of DNA nanostructures have been exploited to develop rapid and isothermal annealing protocols. It is conceivable that a more thorough understanding of the DNA assembly process could be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications.

Kinetics and thermodynamics of living copolymerization processes

PubMed Central

2016-01-01

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’. PMID:27698043

Kinetics and thermodynamics of living copolymerization processes.

PubMed

Gaspard, Pierre

2016-11-13

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Kinetics and thermodynamics of living copolymerization processes

NASA Astrophysics Data System (ADS)

Gaspard, Pierre

2016-11-01

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Kinetics and Thermochemistry of ClCO Formation from the Cl + CO Association Reaction

NASA Technical Reports Server (NTRS)

Nicovich, J. M.; Kreutter, K. D.; Wine, P. H.

1997-01-01

Laser flash photolysis of Cl2/CO/M mixtures (M = N2, CO, Ar, CO2) has been employed in conjunction with Cl((sup 2)P(sub J)) detection by time-resolved resonance fluorescence spectroscopy to investigate equilibration kinetics in the reactions Cl((sup 2)P(sub J)) + CO ClCO as a function of temperature (185-260 K) and pressure (14-200 Torr). The association and dissociation reactions are found to be in the low-pressure limit over the range of experimental conditions investigated. In N2 and/or CO buffer gases, the temperature dependences of the ClCO formation and dissociation reaction rate constants are described by the Arrhenius expressions k(sub 1) = (1.05 +/- 0.36) x 10(exp -34) exp[(810 +/- 70)/T] cm(exp 6)/molecules(exp 2).s and k(sub -1) = (4.1 +/- 3.1) x 10(exp -10) exp[(-2960 +/- 60)/T]cu cm/(molecule.s) (errors are 2 sigma). Second- and third-law analyses of the temperature dependence of the equilbrium constant (k/k-1) lead to the following thermodynamic parameters for the association reaction: Delta-H(sub 298) = -7.7 +/- 0.6 kcal/mol, Delta-H(sub 0) = -6.9 +/- 0.7 kcal/mol, Delta-S(sub 298) = -23.8 +/- 2.0 cal/mole.K, Delta-H(sub f,298)(ClCO) = 5.2 +/- 0.6 kcal/mol (errors are 2 sigma). The results repported in this study significantly reduce the uncertainties in all reported kinetic and thermodynamic parameters.

Adsorption of methyl orange from aqueous solution by aminated pumpkin seed powder: Kinetics, isotherms, and thermodynamic studies.

PubMed

Subbaiah, Munagapati Venkata; Kim, Dong-Su

2016-06-01

Present research discussed the utilization of aminated pumpkin seed powder (APSP) as an adsorbent for methyl orange (MO) removal from aqueous solution. Batch sorption experiments were carried to evaluate the influence of pH, initial dye concentration, contact time, and temperature. The APSP was characterized by using Fourier Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscopy (SEM). The experimental equilibrium adsorption data were fitted using two two-parameter models (Langmuir and Freundlich) and two three-parameter models (Sips and Toth). Langmuir and Sips isotherms provided the best model for MO adsorption data. The maximum monolayer sorption capacity was found to be 200.3mg/g based on the Langmuir isotherm model. The pseudo-first-order and pseudo-second-order model equations were used to analyze the kinetic data of the adsorption process and the data was fitted well with the pseudo-second-order kinetic model (R(2)>0.97). The calculated thermodynamic parameters such as ΔG(0), ΔH(0) and ΔS(0) from experimental data showed that the sorption of MO onto APSP was feasible, spontaneous and endothermic in the temperature range 298-318 K. The FTIR results revealed that amine and carboxyl functional groups present on the surface of APSP. The SEM results show that APSP has an irregular and porous surface which is adequate morphology for dye adsorption. Desorption experiments were carried to explore the feasibility of adsorbent regeneration and the adsorbed MO from APSP was desorbed using 0.1M NaOH with an efficiency of 93.5%. Findings of the present study indicated that APSP can be successfully used for removal of MO from aqueous solution. Copyright © 2016 Elsevier Inc. All rights reserved.

Theory of the milieu dependent isomerisation dynamics of reducing sugars applied to d-erythrose.

PubMed

Kaufmann, Martin; Mügge, Clemens; Kroh, Lothar W

2015-12-11

Quantitative (1)H selective saturation transfer NMR spectroscopy ((1)H SST qNMR) was used to fully describe the milieu dependent dynamics of the isomeric system of d-erythrose. Thermodynamic activation parameters are calculated for acidic as well as for basic catalysis combining McConnell's modified Bloch equations for the chemical exchange solved for the constraint of saturating the non-hydrated acyclic isomer, the Eyring equation and Hudson's equation for pH dependent catalysis. A detailed mathematical examination describing the milieu dependent dynamics of sugar isomerisation is provided. Thermodynamic data show evidence that photo-catalysed sugar isomerisation as well as degradation has to be considered. Approximations describing the pH and temperature dependence of thermodynamic activation parameters are derived that indicate the possibility of photo-affecting equilibrium constants. Moreover, the results show that isomerisation dynamics are closely related to degradation kinetics and that sugars' reactivities are altered by the concentration of acyclic carbonyl isomer and the sum of its ring closing rate constants. Additionally, it is concluded that sugar solutions show a limited self-stabilising behaviour. Copyright © 2015 Elsevier Ltd. All rights reserved.

Thermodynamics and kinetics of binary nucleation in ideal-gas mixtures.

PubMed

Alekseechkin, Nikolay V

2015-08-07

The nonisothermal single-component theory of droplet nucleation [N. V. Alekseechkin, Physica A 412, 186 (2014)] is extended to binary case; the droplet volume V, composition x, and temperature T are the variables of the theory. An approach based on macroscopic kinetics (in contrast to the standard microscopic model of nucleation operating with the probabilities of monomer attachment and detachment) is developed for the droplet evolution and results in the derived droplet motion equations in the space (V, x, T)—equations for V̇≡dV/dt, ẋ, and Ṫ. The work W(V, x, T) of the droplet formation is obtained in the vicinity of the saddle point as a quadratic form with diagonal matrix. Also, the problem of generalizing the single-component Kelvin equation for the equilibrium vapor pressure to binary case is solved; it is presented here as a problem of integrability of a Pfaffian equation. The equation for Ṫ is shown to be the first law of thermodynamics for the droplet, which is a consequence of Onsager's reciprocal relations and the linked-fluxes concept. As an example of ideal solution for demonstrative numerical calculations, the o-xylene-m-xylene system is employed. Both nonisothermal and enrichment effects are shown to exist; the mean steady-state overheat of droplets and their mean steady-state enrichment are calculated with the help of the 3D distribution function. Some qualitative peculiarities of the nucleation thermodynamics and kinetics in the water-sulfuric acid system are considered in the model of regular solution. It is shown that there is a small kinetic parameter in the theory due to the small amount of the acid in the vapor and, as a consequence, the nucleation process is isothermal.

Kinetics and thermodynamic analysis in one-pot pyrolysis of rice hull using renewable calcium oxide based catalysts.

PubMed

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

2018-06-06

Thermodynamic and kinetic parameters of catalytic pyrolysis of rice hull (RH) pyrolysis using two different types of renewable catalysts namely natural limestone (LS) and eggshells (ES) using thermogravimetric analysis (TG) approach at different heating rates of 10-100 K min -1 in temperature range of 323-1173 K are investigated. Catalytic pyrolysis mechanism of both catalysts had shown significant effect on the degradation of RH. Model free kinetic of iso-conversional method (Flynn-Wall-Ozawa) and multi-step reaction model (Distributed Activation Energy Model) were employed into present study. The average activation energy was found in the range of 175.4-177.7 kJ mol -1 (RH), 123.3-132.5 kJ mol -1 (RH-LS), and 96.1-100.4 kJ mol -1 (RH-ES) respectively. The syngas composition had increased from 60.05 wt% to 63.1 wt% (RH-LS) and 63.4 wt% (RH-ES). However, the CO 2 content had decreased from 24.1 wt% (RH) to 20.8 wt% (RH-LS) and 19.9 wt% (RH-ES). Copyright © 2018 Elsevier Ltd. All rights reserved.

Removal of methylene blue from aqueous solution by a solvothermal-synthesized graphene/magnetite composite.

PubMed

Ai, Lunhong; Zhang, Chunying; Chen, Zhonglan

2011-09-15

In this study, we have demonstrated a facile one-step solvothermal method for the synthesis of the graphene nanosheet (GNS)/magnetite (Fe(3)O(4)) composite. During the solvothermal treatment, in situ conversion of FeCl(3) to Fe(3)O(4) and simultaneous reduction of graphene oxide (GO) into graphene in ethylene glycol solution were achieved. Electron microscopy study suggests the Fe(3)O(4) spheres with a size of about 200 nm are uniformly distributed and firmly anchored on the wrinkled graphene layers with a high density. The resulting GNS/Fe(3)O(4) composite shows extraordinary adsorption capacity and fast adsorption rates for removal of organic dye, methylene blue (MB), in water. The adsorption kinetics, isotherms and thermodynamics were investigated in detail to reveal that the kinetics and equilibrium adsorptions are well-described by pseudo-second-order kinetic and Langmuir isotherm model, respectively. The thermodynamic parameters reveal that the adsorption process is spontaneous and endothermic in nature. This study shows that the as-prepared GNS/Fe(3)O(4) composite could be utilized as an efficient, magnetically separable adsorbent for the environmental cleanup. Copyright © 2011 Elsevier B.V. All rights reserved.

Biosorption of As(III) and As(V) on the surface of TW/MnFe2O4 composite from wastewater: kinetics, mechanistic and thermodynamics

NASA Astrophysics Data System (ADS)

Podder, M. S.; Majumder, C. B.

2017-10-01

In the present study, TW/MnFe2O4 composite (MTW) was synthesized and estimated as an effective biosorbent for removing As (III) and As(V) from wastewater. Physicochemical analysis of composite was performed through SEM-EDX. 86.615 and 83.478% removal efficiency were obtained by composite dosage of 2 g/L at contact time 120 min at temperature 30 °C and pH 7.0 and 4.0 for As(III) and As(V), respectively. Kinetic results study showed that Brouers-Weron-Sotolongo and Ritchie second-order for As(III) and Brouers-Weron-Sotolongo model for As(V) were capable to describe an accurate explanation of adsorption kinetic. Applicability of mechanistic models in the current study exposed that the rate-controlling step in the biosorption of both As(III) and As(V) on the surface of composite was film diffusion rather than intraparticle diffusion. The estimated thermodynamic parameters Δ G 0, Δ H 0 and Δ S 0 revealed that the biosorption of both As(III) and As(V) on the composite was feasible, spontaneous and exothermic.

Thermodynamic, electronic and magnetic properties of intermetallic compounds through statistical models

NASA Astrophysics Data System (ADS)

Cadeville, M. C.; Pierron-Bohnes, V.; Bouzidi, L.; Sanchez, J. M.

1993-01-01

Local and average electronic and magnetic properties of transition metal alloys are strongly correlated to the distribution of atoms on the lattice sites. The ability of some systems to form long range ordered structures at low temperature allows to discuss their properties in term of well identified occupation operators as those related to long range order (LRO) parameters. We show that using theoretical determinations of these LRO parameters through statistical models like the cluster variation method (CVM) developed to simulate the experimental phase diagrams, we are able to reproduce a lot of physical properties. In this paper we focus on two points: (i) a comparison between CVM results and an experimental determination of the LRO parameter by NMR at 59Co in a CoPt3 compound, and (ii) the modelling of the resistivity of ferromagnetic and paramagnetic intermetallic compounds belonging to Co-Pt, Ni-Pt and Fe-Al systems. All experiments were performed on samples in identified thermodynamic states, implying that kinetic effects are thoroughly taken into account.

Removal of Direct Red 12B by garlic peel as a cheap adsorbent: Kinetics, thermodynamic and equilibrium isotherms study of removal

NASA Astrophysics Data System (ADS)

Asfaram, A.; Fathi, M. R.; Khodadoust, S.; Naraki, M.

2014-06-01

The removal of dyes from industrial waste is very important from health and hygiene point of view and for environmental protection. In this work, efficiency and performance of garlic peel (GP) adsorbent for the removal of Direct Red 12B (DR12B) from wastewater was investigated. The influence of variables including pH, concentration of the dye and amount of adsorbent, particle size, contact time and temperature on the dye removal has been investigated. It was observed that the pseudo-second-order kinetic model fits better with good correlation coefficient and the equilibrium data fitted well with the Langmuir model. More than 99% removal efficiency was obtained within 25 min at adsorbent dose of 0.2 g per 50 ml for initial dye concentration of 50 mg L-1. Calculation of various thermodynamic parameters such as, Gibb's free energy, entropy and enthalpy of the on-going adsorption process indicate feasibility and endothermic nature of DR12B adsorption.

Transport properties of dilute α -Fe (X ) solid solutions (X = C, N, O)

NASA Astrophysics Data System (ADS)

Schuler, Thomas; Nastar, Maylise

2016-06-01

We extend the self-consistent mean field (SCMF) method to the calculation of the Onsager matrix of Fe-based interstitial solid solutions. Both interstitial jumps and substitutional atom-vacancy exchanges are accounted for. A general procedure is introduced to split the Onsager matrix of a dilute solid solution into intrinsic cluster Onsager matrices, and extract from them flux-coupling ratios, mobilities, and association-dissociation rates for each cluster. The formalism is applied to vacancy-interstitial solute pairs in α -Fe (V X pairs, X = C, N, O), with ab initio based thermodynamic and kinetic parameters. Convergence of the cluster mobility contribution gives a controlled estimation of the cluster definition distance, taking into account both its thermodynamic and kinetic properties. Then, the flux-coupling behavior of each V X pair is discussed, and qualitative understanding is achieved from the comparison between various contributions to the Onsager matrix. Also, the effect of low-activation energy second-nearest-neighbor interstitial solute jumps around a vacancy on these results is addressed.

Grain formation in astronomical systems: A critical review of condensation processes

NASA Technical Reports Server (NTRS)

Donn, B.

1978-01-01

An analysis is presented of the assumption and the applicability of the three theoretical methods for calculating condensations in cosmic clouds where no pre-existing nuclei exist. The three procedures are: thermodynamic equilibrium calculations, nucleation theory, and a kinetic treatment which would take into account the characteristics of each individual collision. Thermodynamics provide detailed results on the composition temperature and composition of the condensate provided the system attains equilibrium. Because of the cosmic abundance mixture of elements, large supersaturations in some cases and low pressures, equilibrium is not expected in astronomical clouds. Nucleation theory, a combination of thermodynamics and kinetics, has the limitations of each scheme. Kinetics, not requiring equilibrium, avoids nearly all the thermodynamics difficulties but requires detailed knowledge of many reactions which thermodynamics avoids. It appears to be the only valid way to treat grain formation in space. A review of experimental studies is given.

Sensitivity of predicted scaling and permeability in Enhanced Geothermal Systems to Thermodynamic Data and Activity Models

NASA Astrophysics Data System (ADS)

Hingerl, Ferdinand F.; Wagner, Thomas; Kulik, Dmitrii A.; Kosakowski, Georg; Driesner, Thomas; Thomsen, Kaj

2010-05-01

A consortium of research groups from ETH Zurich, EPF Lausanne, the Paul Scherrer Institut and the University of Bonn collaborates in a comprehensive program of basic research on key aspects of the Enhanced Geothermal Systems (EGSs). As part of this GEOTHERM project (www.geotherm.ethz.ch), we concentrate on the fundamental investigation of thermodynamic models suitable for describing fluid-rock interactions at geothermal conditions. Predictions of the fluid-rock interaction in EGS still face several major challenges. Slight variations in the input thermodynamic and kinetic parameters may result in significant differences in the predicted mineral solubilities and stable assemblage. Realistic modeling of mineral precipitation in turn has implications onto our understanding of the permeability evolution of the geothermal reservoir, as well as the scaling in technical installations. In order to reasonably model an EGS, thermodynamic databases and activity models must be tailored to geothermal conditions. We therefore implemented in GEMS code the Pitzer formalism, which is the standard model used for computing thermodynamic excess properties of brines at elevated temperatures and pressures. This model, however, depends on a vast amount of interaction parameters, which are to a substantial extend unknown. Furthermore, a high order polynomial temperature interpolation makes extrapolation unreliable if not impossible. As an alternative we additionally implemented the EUNIQUAC activity model. EUNIQUAC requires fewer empirical fit parameters (only binary interaction parameters needed) and uses simpler and more stable temperature and pressure extrapolations. This results in an increase in computation speed, which is of crucial importance when performing coupled long term simulations of geothermal reservoirs. To achieve better performance under geothermal conditions, we are currently partly reformulating EUNIQUAC and refitting the existing parameter set. First results of the Pitzer-EUNIQUAC benchmark applied to relevant aqueous solutions at elevated temperature, pressure and ionic strength will be presented.

Bayesian Calibration of Thermodynamic Databases and the Role of Kinetics

NASA Astrophysics Data System (ADS)

Wolf, A. S.; Ghiorso, M. S.

2017-12-01

Self-consistent thermodynamic databases of geologically relevant materials (like Berman, 1988; Holland and Powell, 1998, Stixrude & Lithgow-Bertelloni 2011) are crucial for simulating geological processes as well as interpreting rock samples from the field. These databases form the backbone of our understanding of how fluids and rocks interact at extreme planetary conditions. Considerable work is involved in their construction from experimental phase reaction data, as they must self-consistently describe the free energy surfaces (including relative offsets) of potentially hundreds of interacting phases. Standard database calibration methods typically utilize either linear programming or least squares regression. While both produce a viable model, they suffer from strong limitations on the training data (which must be filtered by hand), along with general ignorance of many of the sources of experimental uncertainty. We develop a new method for calibrating high P-T thermodynamic databases for use in geologic applications. The model is designed to handle pure solid endmember and free fluid phases and can be extended to include mixed solid solutions and melt phases. This new calibration effort utilizes Bayesian techniques to obtain optimal parameter values together with a full family of statistically acceptable models, summarized by the posterior. Unlike previous efforts, the Bayesian Logistic Uncertain Reaction (BLUR) model directly accounts for both measurement uncertainties and disequilibrium effects, by employing a kinetic reaction model whose parameters are empirically determined from the experiments themselves. Thus, along with the equilibrium free energy surfaces, we also provide rough estimates of the activation energies, entropies, and volumes for each reaction. As a first application, we demonstrate this new method on the three-phase aluminosilicate system, illustrating how it can produce superior estimates of the phase boundaries by incorporating constraints from all available data, while automatically handling variable data quality due to a combination of measurement errors and kinetic effects.

The Kinetics and Thermodynamics of the Phenol from Cumene Process: A Physical Chemistry Experiment.

ERIC Educational Resources Information Center

Chen, Edward C. M.; Sjoberg, Stephen L.

1980-01-01

Presents a physical chemistry experiment demonstrating the differences between thermodynamics and kinetics. The experiment used the formation of phenol and acetone from cumene hydroperoxide, also providing an example of an industrially significant process. (CS)

Equilibrium, kinetic and thermodynamic studies of uranium biosorption by calcium alginate beads.

PubMed

Bai, Jing; Fan, Fangli; Wu, Xiaolei; Tian, Wei; Zhao, Liang; Yin, Xiaojie; Fan, Fuyou; Li, Zhan; Tian, Longlong; Wang, Yang; Qin, Zhi; Guo, Junsheng

2013-12-01

Calcium alginate beads are potential biosorbent for radionuclides removal as they contain carboxyl groups. However, until now limited information is available concerning the uptake behavior of uranium by this polymer gel, especially when sorption equilibrium, kinetics and thermodynamics are concerned. In present work, batch experiments were carried out to study the equilibrium, kinetics and thermodynamics of uranium sorption by calcium alginate beads. The effects of initial solution pH, sorbent amount, initial uranium concentration and temperature on uranium sorption were also investigated. The determined optimal conditions were: initial solution pH of 3.0, added sorbent amount of 40 mg, and uranium sorption capacity increased with increasing initial uranium concentration and temperature. Equilibrium data obtained under different temperatures were fitted better with Langmuir model than Freundlich model, uranium sorption was dominated by a monolayer way. The kinetic data can be well depicted by the pseudo-second-order kinetic model. The activation energy derived from Arrhenius equation was 30.0 kJ/mol and the sorption process had a chemical nature. Thermodynamic constants such as ΔH(0), ΔS(0) and ΔG(0) were also evaluated, results of thermodynamic study showed that the sorption process was endothermic and spontaneous. Copyright © 2013 Elsevier Ltd. All rights reserved.

Binding kinetics of five drugs to beta2-adrenoceptor using peak profiling method and nonlinear chromatography.

PubMed

Liang, Yuan; Wang, Jing; Fei, Fuhuan; Sun, Huanmei; Liu, Ting; Li, Qian; Zhao, Xinfeng; Zheng, Xiaohui

2018-02-23

Investigations of drug-protein interactions have advanced our knowledge of ways to design more rational drugs. In addition to extensive thermodynamic studies, ongoing works are needed to enhance the exploration of drug-protein binding kinetics. In this work, the beta2-adrenoceptor (β 2 -AR) was immobilized on N, N'-carbonyldiimidazole activated amino polystyrene microspheres to prepare an affinity column (4.6 mm × 5.0 cm, 8 μm). The β 2 -AR column was utilized to determine the binding kinetics of five drugs to the receptor. Introducing peak profiling method into this receptor chromatographic analysis, we determined the dissociation rate constants (k d ) of salbutamol, terbutaline, methoxyphenamine, isoprenaline hydrochloride and ephedrine hydrochloride to β 2 -AR to be 15 (±1), 22 (±1), 3.3 (±0.2), 2.3 (±0.2) and 2.1 (±0.1) s -1 , respectively. The employment of nonlinear chromatography (NLC) in this case exhibited the same rank order of k d values for the five drugs bound to β 2 -AR. We confirmed that both the peak profiling method and NLC were capable of routine measurement of receptor-drug binding kinetics. Compared with the peak profiling method, NLC was advantageous in the simultaneous assessment of the kinetic and apparent thermodynamic parameters. It will become a powerful method for high throughput drug-receptor interaction analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Thermodynamic and Kinetic Properties of Shocks in Two-Dimensional Yukawa Systems [Thermodynamic and Kinetic Properties of Shocks in 2D Yukawa Systems

DOE PAGES

Marciante, Mathieu; Murillo, Michael Sean

2017-01-10

Particle-level simulations of shocked plasmas are carried out to examine kinetic properties not captured by hydrodynamic models. In particular, molecular dynamics simulations of 2D Yukawa plasmas with variable couplings and screening lengths are used to examine shock features unique to plasmas, including the presence of dispersive shock structures for weak shocks. A phase-space analysis reveals several kinetic properties, including anisotropic velocity distributions, non-Maxwellian tails, and the presence of fast particles ahead of the shock, even for moderately low Mach numbers. As a result, we also examine the thermodynamics (Rankine-Hugoniot relations) of recent experiments and find no anomalies in their equationsmore » of state.« less

Thermodynamic and Kinetic Properties of Shocks in Two-Dimensional Yukawa Systems [Thermodynamic and Kinetic Properties of Shocks in 2D Yukawa Systems

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

Marciante, Mathieu; Murillo, Michael Sean

Particle-level simulations of shocked plasmas are carried out to examine kinetic properties not captured by hydrodynamic models. In particular, molecular dynamics simulations of 2D Yukawa plasmas with variable couplings and screening lengths are used to examine shock features unique to plasmas, including the presence of dispersive shock structures for weak shocks. A phase-space analysis reveals several kinetic properties, including anisotropic velocity distributions, non-Maxwellian tails, and the presence of fast particles ahead of the shock, even for moderately low Mach numbers. As a result, we also examine the thermodynamics (Rankine-Hugoniot relations) of recent experiments and find no anomalies in their equationsmore » of state.« less

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

Wang, Yujie; Gong, Sha; Wang, Zhen

The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption ofmore » hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.« less

Chemistry and Environments of Dolomitization —A Reappraisal

NASA Astrophysics Data System (ADS)

Machel, Hans-G.; Mountjoy, Eric W.

1986-05-01

Dolomitization of calcium carbonate can best be expressed by mass transfer reactions that allow for volume gain, preservation, or loss during the replacement process. Experimental data, as well as textures and porosities of natural dolomites, indicate that these reactions must include CO 32- and/or HCO 3- supplied by the solution to the reaction site. Since dolomite formation is thermodynamically favoured in solutions of (a) low Ca 2+/Mg 2+ ratios, (b) low Ca 2+/CO 32- (or Ca 2+/HCO 3-) ratios, and (c) high temperatures, the thermodynamic stability for the system calcite-dolomite-water is best represented in a diagram with these three parameters as axes. Kinetic considerations favour dolomitization under the same conditions, and additionally at low as well as at high salinities. If thermodynamic and kinetic considerations are combined, the following conditions and environments are considered chemically conducive to dolomitization: (1) environments of any salinity above thermodynamic and kinetic saturation with respect to dolomite (i.e. freshwater/seawater mixing zones, normal saline to hypersaline subtidal environments, hypersaline supratidal environments, schizohaline environments); (2) alkaline environments (i.e. those under the influence of bacterial reduction and/or fermentation processes, or with high input of alkaline continental groundwaters); and (3) many environments with temperatures greater than about 50°C (subsurface and hydrothermal environments). Whether or not massive, replacive dolostones are formed in these environments depends on a sufficient supply of magnesium, and thus on hydrologic parameters. Most massive dolostones, particularly those consisting of shallowing-upward cycles and capped by regional unconformities, have been interpreted to be formed according to either the freshwater/seawater mixing model or the sabkha with reflux model. However, close examination of natural mixing zones and exposed evaporitic environments reveals that the amounts of dolomite formed are small and texturally different from the massive, replacive dolostones commonly inferred to have been formed in these environments. Many shallowing-upward sequences are devoid of dolomite. It is therefore suggested that massive, replacive dolomitization during exposure is rare, if not impossible. Rather, only small quantities of dolomite (cement or replacement) are formed which may act as nuclei for later subsurface dolomitization. Alternatively, large-scale dolomitization may take place in shallow subtidal environments of moderate to strong hypersalinity. The integration of stratigraphic, petrographic, geochemical, and hydrological parameters suggests that the only environments capable of forming massive, replacive dolostones on a large scale are shallow, hypersaline subtidal environments and certain subsurface environments.

Determination of kinetic and equilibrium parameters of the batch adsorption of Mn(II), Co(II), Ni(II) and Cu(II) from aqueous solution by black carrot (Daucus carota L.) residues.

PubMed

Güzel, Fuat; Yakut, Hakan; Topal, Giray

2008-05-30

In this study, the effect of temperature on the adsorption of Mn(II), Ni(II), Co(II) and Cu(II) from aqueous solution by modified carrot residues (MCR) was investigated. The equilibrium contact times of adsorption process for each heavy metals-MCR systems were determined. Kinetic data obtained for each heavy metal by MCR at different temperatures were applied to the Lagergren equation, and adsorption rate constants (kads) at these temperatures were determined. These rate constants related to the adsorption of heavy metal by MCR were applied to the Arrhenius equation, and activation energies (Ea) were determined. In addition, the isotherms for adsorption of each heavy metal by MCR at different temperatures were also determined. These isothermal data were applied to linear forms of isotherm equations that they fit the Langmuir adsorption isotherm, and the Langmuir constants (qm and b) were calculated. b constants determined at different temperatures were applied to thermodynamic equations, and thermodynamic parameters such as enthalpy (Delta H), free energy (Delta G), and entropy (Delta S) were calculated and these values show that adsorption of heavy metal on MCR was an endothermic process and process of adsorption was favoured at high temperatures.

Green Synthesis of Zinc Oxide Nanoparticles for Enhanced Adsorption of Lead Ions from Aqueous Solutions: Equilibrium, Kinetic and Thermodynamic Studies.

PubMed

Azizi, Susan; Mahdavi Shahri, Mahnaz; Mohamad, Rosfarizan

2017-06-08

In the present study, ZnO nanoparticles (NPs) were synthesized in zerumbone solution by a green approach and appraised for their ability to absorb Pb(II) ions from aqueous solution. The formation of as-synthesized NPs was established by X-ray diffraction (XRD), Transmission Electron Microscopy (TEM), and UV-visible studies. The XRD and TEM analyses revealed high purity and wurtzite hexagonal structure of ZnO NPs with a mean size of 10.01 ± 2.6 nm. Batch experiments were performed to investigate the impact of process parameters viz. Pb(II) concentration, pH of solution, adsorbent mass, solution temperature, and contact time variations on the removal efficiency of Pb(II). The adsorption isotherm data provided that the adsorption process was mainly monolayer on ZnO NPs. The adsorption process follows pseudo-second-order reaction kinetic. The maximum removal efficiencies were 93% at pH 5. Thermodynamic parameters such as enthalpy change (ΔH⁰), free energy change (ΔG⁰), and entropy change (ΔS⁰) were calculated; the adsorption process was spontaneous and endothermic. The good efficiency of the as-synthesized NPs makes them attractive for applications in water treatment, for removal of heavy metals from aqueous system.

The surface characteristics of hyperbranched polyamide modified corncob and its adsorption property for Cr(VI)

NASA Astrophysics Data System (ADS)

Lin, Hai; Han, Shaoke; Dong, Yingbo; He, Yinhai

2017-08-01

A low-cost anion adsorbent for Cr(VI) effectively removing was synthesized by hyperbranched polyamide modified corncob (HPMC). Samples were characterized by Brunauer-Emmett-Teller (BET) surface area analysis, field-emission scanning electron microscopy (FE-SEM) with energy-dispersive X-ray spectroscopy, Fourier transform infrared (FTIR) and zeta potential analysis. Kinetics, isotherms and thermodynamics studies of HPMC for Cr(VI) adsorption were investigated in batch static experiments, in the temperature range of 25-45 °C, pH = 2.0. Results showed that the adsorption was rapid and stable, with the uptake capacity higher than 80% after 30 min. Adsorption behavior and rate-controlling mechanisms were analyzed using three kinetic models (pseudo-first order, pseudo-second order, intra-particle kinetic model). Kinetic studies showed that the adsorption of HPMC to Cr(VI) relied the pseudo-second-order model, and controlled both by the intra-particle diffusion and film diffusion. Equilibrium data was tested by Langmuir and Freundlich adsorption isotherm models. Langmuir model was more suitable to indicate a homogeneous distribution of active sites on HPMC and monolayer adsorption. The maximum adsorption capacity from the Langmuir model, qmax, was 131.6 mg/g at pH 2.0 and 45 °C for HPMC. Thermodynamic parameters revealed spontaneous and endothermic nature of the Cr(VI) adsorption onto HPMC.

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

PubMed Central

Smallbone, Kieran; Klipp, Edda; Mendes, Pedro; Liebermeister, Wolfram

2013-01-01

The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments. PMID:24324546

Hungarian University Students' Misunderstandings in Thermodynamics and Chemical Kinetics

ERIC Educational Resources Information Center

Turanyi, Tamas; Toth, Zoltan

2013-01-01

The misunderstandings related to thermodynamics (including chemical equilibrium) and chemical kinetics of first and second year Hungarian students of chemistry, environmental science, biology and pharmacy were investigated. We demonstrated that Hungarian university students have similar misunderstandings in physical chemistry to those reported in…

Zirconium-nickel crystals—hydrogen accumulators: Dissolution and penetration of hydrogen atoms in alloys

NASA Astrophysics Data System (ADS)

Matysina, Z. A.; Zaginaichenko, S. Yu.; Shchur, D. V.; Gabdullin, M. T.; Kamenetskaya, E. A.

2016-07-01

The calculation of the free energy, thermodynamic equilibrium equations, and kinetic equations of the intermetallic compound Zr2NiH x has been carried out based on molecular-kinetic concepts. The equilibrium hydrogen concentration depending on the temperature, pressure, and energy parameters has been calculated. The absorption-desorption of hydrogen has been studied, and the possibility of the realization of the hysteresis effect has been revealed. The kinetics of the dissolution and permeability of hydrogen is considered, the time dependence of these values has been found, and conditions for the extremum character of their time dependence have been determined. Relaxation times of the dissolution and permeability of hydrogen into the alloy have been calculated. The calculation results are compared with the experimental data available in the literature.

Design of a new integrated chitosan-PAMAM dendrimer biosorbent for heavy metals removing and study of its adsorption kinetics and thermodynamics.

PubMed

Zarghami, Zabihullah; Akbari, Ahmad; Latifi, Ali Mohammad; Amani, Mohammad Ali

2016-04-01

In this research, different generations of PAMAM-grafted chitosan as integrated biosorbents were successfully synthesized via step by step divergent growth approach of dendrimer. The synthesized products were utilized as adsorbents for heavy metals (Pb(2+) in this study) removing from aqueous solution and their reactive Pb(2+) removal potential was evaluated. The results showed that as-synthesized products with higher generations of dendrimer, have more adsorption capacity compared to products with lower generations of dendrimer and sole chitosan. Adsorption capacity of as-prepared product with generation 3 of dendrimer is 18times more than sole chitosan. Thermodynamic and kinetic studies were performed for understanding equilibrium data of the uptake capacity and kinetic rate uptake, respectively. Thermodynamic and kinetic studies showed that Langmuir isotherm model and pseudo second order kinetic model are more compatible for describing equilibrium data of the uptake capacity and kinetic rate of the Pb(2+) uptake, respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

Exploring the kinetic and thermodynamic aspects of four-electron electrochemical reactions: electrocatalysis of oxygen evolution by metal oxides and biological systems.

PubMed

Wang, Vincent C-C

2016-08-10

Finding fundamental and general mechanisms for electrochemical reactions, such as the oxygen evolution reaction (OER) from water and reduction of CO2, plays vital roles in developing the desired electrocatalysts for facilitating solar fuel production. Recently, density functional theory (DFT) calculations have shown that there is a universal scaling relation of adsorption energy between key intermediate species, HO(ad) and HOO(ad), on the surface of metal oxides as OER electrocatalysts. In this paper, a kinetic and thermodynamic model for the four-electron electrochemical reaction based on previous OER mechanisms proposed by DFT calculations is developed to further investigate the electrocatalytic properties over a wide range of metal oxides and photosystem II. The OER activity of metal oxides (i.e. electrocatalytic current) calculated from the DFT-calculated equilibrium potentials with kinetic properties, such as the rate constants for interfacial electron transfer and catalytic turnover, can lead to a volcano-shaped trend that agrees with the results observed in experiments. In addition, the kinetic aspects of the impact on the electrocatalysts are evaluated. Finally, comparing the results of metal oxides and photosystem II, and fitting experimental voltammograms give further insights into kinetic and thermodynamic roles. Here, the general guidelines for designing OER electrocatalysts with unified kinetic and thermodynamic properties are presented.

Tested Demonstrations: Thermodynamic Changes, Kinetics, Equilibrium, and LeChatelier's Principle.

ERIC Educational Resources Information Center

Gilbert, George L., Ed.

1984-01-01

Procedures for demonstrating thermodynamic changes, kinetics and reaction mechanisms, equilibrium, and LeChatelier's principle are presented. The only materials needed for these demonstrations are beakers, water, assorted wooden blocks of varying thickness, assorted rubber tubing, and a sponge. The concepts illustrated in each demonstration are…

Optimization of methylene blue using Ca(2+) and Zn(2+) bio-polymer hydrogel beads: A comparative study.

PubMed

Kumar, M; Tamilarasan, R; Arthanareeswaran, G; Ismail, A F

2015-11-01

Recently noted that the methylene blue cause severe central nervous system toxicity. It is essential to optimize the methylene blue from aqueous environment. In this study, a comparison of an optimization of methylene blue was investigated by using modified Ca(2+) and Zn(2+) bio-polymer hydrogel beads. A batch mode study was conducted using various parameters like time, dye concentration, bio-polymer dose, pH and process temperature. The isotherms, kinetics, diffusion and thermodynamic studies were performed for feasibility of the optimization process. Freundlich and Langmuir isotherm equations were used for the prediction of isotherm parameters and correlated with dimensionless separation factor (RL). Pseudo-first order and pseudo-second order Lagegren's kinetic equations were used for the correlation of kinetic parameters. Intraparticle diffusion model was employed for diffusion of the optimization process. The Fourier Transform Infrared Spectroscopy (FTIR) shows different absorbent peaks of Ca(2+) and Zn(2+) beads and the morphology of the bio-polymer material analyzed with Scanning Electron Microscope (SEM). The TG & DTA studies show that good thermal stability with less humidity without production of any non-degraded products. Copyright © 2015 Elsevier Inc. All rights reserved.

Thermodynamics and computation during collective motion near criticality

NASA Astrophysics Data System (ADS)

Crosato, Emanuele; Spinney, Richard E.; Nigmatullin, Ramil; Lizier, Joseph T.; Prokopenko, Mikhail

2018-01-01

We study self-organization of collective motion as a thermodynamic phenomenon in the context of the first law of thermodynamics. It is expected that the coherent ordered motion typically self-organises in the presence of changes in the (generalized) internal energy and of (generalized) work done on, or extracted from, the system. We aim to explicitly quantify changes in these two quantities in a system of simulated self-propelled particles and contrast them with changes in the system's configuration entropy. In doing so, we adapt a thermodynamic formulation of the curvatures of the internal energy and the work, with respect to two parameters that control the particles' alignment. This allows us to systematically investigate the behavior of the system by varying the two control parameters to drive the system across a kinetic phase transition. Our results identify critical regimes and show that during the phase transition, where the configuration entropy of the system decreases, the rates of change of the work and of the internal energy also decrease, while their curvatures diverge. Importantly, the reduction of entropy achieved through expenditure of work is shown to peak at criticality. We relate this both to a thermodynamic efficiency and the significance of the increased order with respect to a computational path. Additionally, this study provides an information-geometric interpretation of the curvature of the internal energy as the difference between two curvatures: the curvature of the free entropy, captured by the Fisher information, and the curvature of the configuration entropy.

Adsorption of Pb(II) ions from aqueous environment using eco-friendly chitosan schiff's base@Fe3O4 (CSB@Fe3O4) as an adsorbent; kinetics, isotherm and thermodynamic studies.

PubMed

Weijiang, Zhang; Yace, Zhang; Yuvaraja, Gutha; Jiao, Xu

2017-12-01

Chitosan and its derivatives can be used to modify magnetic materials to promote the adsorption properties of the magnetic materials for the removal of meal ions. In this study a novel CSB@Fe 3 O 4 was prepared, characterized by XRD, FTIR, SEM, TEM, and VSM analysis and utilized as an adsorbent material for the removal of Pb(II) ions from aqueous solution. Batch studies were performed to evaluate the influences of various experimental parameters like pH, adsorbent dosage, contact time, initial concentration, and the effect of temperature. Optimum conditions for Pb(II) removal were found to be pH 5, adsorbent dosage 0.5g and equilibrium time of 105min. The pseudo-first-order, pseudo-second-order and intraparticle diffusion models were used to analyze kinetic data. The data fit well with the second-order kinetic model. The equilibrium data were analyzed using the Langmuir, and Freundlich isotherm models. The best interpretation for the equilibrium data was given by Langmuir isotherm, and the maximum adsorption capacity was found to be 83.33mg/g for CSB@Fe 3 O 4 . The calculated thermodynamic parameters ΔG°(-9.728, -9.034 and -7.883kJ/mol for 303, 313, and 323K), ΔH° (20.39kJ/mol) and ΔS° (0.0947J/molK) showed that the adsorption of Pb(II) ions were feasible, spontaneous and endothermic in nature. Copyright © 2017 Elsevier B.V. All rights reserved.

Oxygen reduction reaction catalyzed by platinum nanonetwork prepared by template free one step synthesis for polymer electrolyte membrane fuel cells

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

Narayanamoorthy, B.; Kumar, B.V.V.S. Pavan; Eswaramoorthy, M.

2014-07-01

Highlights: • Supportless Pt nanonetwork (Pt NN) synthesized by novel template free one step method as per our earlier reported procedure. • Electrocatalytic activity of Pt NN studied taking oxygen reduction reaction in acid medium. • Kinetic and thermodynamic parameters were deduced under hydrodynamic conditions. • ORR mechanistic pathway was proposed based on kinetic rate constants. • ADT analysis found enhanced stability (5000 cycles) for Pt NN than Pt NN/VC and reported Pt/C. - Abstract: The reduction reaction of molecular oxygen (ORR) was investigated using supportless Pt nanonetwork (Pt NN) electrocatalyst in sulfuric acid medium. Pt NN was prepared bymore » template free borohydride reduction. The transmission electron microscope images revealed a network like nano-architecture having an average cluster size of 30 nm. The electrochemical characterization of supportless and Vulcan carbon supported Pt NN (Pt NN/VC) was carried out using rotating disc and ring disc electrodes at various temperatures. Kinetic and thermodynamic parameters were estimated under hydrodynamic conditions and compared with Pt NN/VC and reported Pt/C catalysts. The accelerated durability test revealed that supportless Pt NN is quite stable for 5000 potential cycles with 22% reduction in electrochemical surface area (ECSA). While the initial limiting current density has in fact increased by 11.6%, whereas Pt NN/VC suffered nearly 55% loss in ECSA and 13% loss in limiting current density confirming an enhanced stability of supportless Pt NN morphology for ORR compared to conventional Pt/C ORR catalysts in acid medium.« less

Equilibrium, kinetic and thermodynamic studies on aluminum biosorption by a mycelial biomass (Streptomyces rimosus).

PubMed

Tassist, Amina; Lounici, Hakim; Abdi, Nadia; Mameri, Nabil

2010-11-15

This work focused on kinetic, equilibrium and thermodynamic studies on aluminum biosorption by Streptomyces rimosus biomass. Infrared spectroscopy analysis shows that S. rimosus present some groups: hydroxyl, methyl, carboxyl, amine, thiol and phosphate. The maximum biosorption capacity of S. rimosus biomass was found to be 11.76 mg g(-1) for the following optimum conditions: particle size, [250-560] μm, pH 4-4.25, biomass content of 25 g L(-1), agitation of 250 rpm and temperature of 25 °C. Langmuir, Freundlich and Dubinin-Radushkevich (D-R) models were applied to describe the biosorption isotherms at free pH (pH(i) 4) and fixed pH (pH(f) 4). Langmuir model is the most adequate. With fixed pH, the maximum biosorption capacity is enhanced from 6.62 mg g(-1) to 11.76 mg g(-1). The thermodynamic parameters (ΔG°, ΔH° and ΔS°) showed the feasibility, endothermic and spontaneous nature of the biosorption at 10-80 °C. The activation energy (Ea) was determined as 52.18 kJ mol(-1) using the Arrhenius equation and the rate constant of pseudo-second-order model (the most adequate kinetic model). The mean free energy was calculated as 12.91 kJ mol(-1) using the D-R isotherm model. The mechanism of Al(III) biosorption on S. rimosus could be a chemical ion exchange and carboxyl groups are mainly involved in this mechanism. Copyright © 2010 Elsevier B.V. All rights reserved.

Kinetic study on bonding reaction of gelatin with CdS nanopaticles by UV-visible spectroscopy.

PubMed

Tang, Shihua; Wang, Baiyang; Li, Youqun

2015-04-15

The chemical kinetics on gelatin-CdS direct conjugates has been systematically investigated as a function of different temperature and reactant concentration (i.e. Cd(2+), S(2-) and gelatin) by UV-visible spectroscopy, for the first time. The nonlinear fitting and the differential method were used to calculate the initial rate based on the absorbance-time data. A double logarithmic linear equation for calculating the rate constant (k) and the reaction order (n) was introduced. The reaction kinetic parameters (n, k, Ea, and Z) and activation thermodynamic parameters (ΔG(≠), ΔH(≠), and ΔS(≠)) were obtained from variable temperature kinetic studies. The overall rate equation allowing evaluation of conditions that provide required reaction rate could be expressed as: r = 1.11 × 10(8) exp(-4971/T)[Cd(2+)][gelatin](0.6)[S(2-)](0.6) (M/S) The calculated values of the reaction rate are well coincide with the experimental results. A suitable kinetic model is also proposed. This work will provide guidance for the rational design of gelatin-directed syntheses of metal sulfide materials, and help to understand the biological effects of nanoparticles at the molecular level. Copyright © 2015 Elsevier B.V. All rights reserved.

Demonstration of Thermodynamics and Kinetics Using FriXion Erasable Pens

ERIC Educational Resources Information Center

Campbell, Dean J.; Bosma, Wayne B.; Bannon, Stephen J.; Gunter, Molly M.; Hammar, Margaret K.

2012-01-01

FriXion erasable pens contain thermochromic inks that have colored low-temperature forms and colorless high-temperature forms. Liquid nitrogen can be used to kinetically trap the high-temperature forms of the ink at temperatures at which ordinarily the low-temperature forms are more thermodynamically stable. (Contains 2 figures.)

Thermodynamics and Kinetics of Ligand Binding to Vitamin B-12a: A Laboratory Experiment

ERIC Educational Resources Information Center

Sweigart, D. A.

1975-01-01

Describes an open-ended experiment involving a bioinorganic system that provides the student a direct link between thermodynamics and kinetics. It utilizes a rapid reaction technique and requires one to clearly understand the relationship of experimental observable (absorbance) to a mechanism. (GS)

Entropy is in Flux V3.4

NASA Astrophysics Data System (ADS)

Kadanoff, Leo P.

2017-05-01

The science of thermodynamics was put together in the Nineteenth Century to describe large systems in equilibrium. One part of thermodynamics defines entropy for equilibrium systems and demands an ever-increasing entropy for non-equilibrium ones. Since thermodynamics does not define entropy out of equilibrium, pure thermodynamics cannot follow the details of how this increase occurs. However, starting with the work of Ludwig Boltzmann in 1872, and continuing to the present day, various models of non-equilibrium behavior have been put together with the specific aim of generalizing the concept of entropy to non-equilibrium situations. This kind of entropy has been termed kinetic entropy to distinguish it from the thermodynamic variety. Knowledge of kinetic entropy started from Boltzmann's insight about his equation for the time dependence of gaseous systems. In this paper, his result is stated as a definition of kinetic entropy in terms of a local equation for the entropy density. This definition is then applied to Landau's theory of the Fermi liquid thereby giving the kinetic entropy within that theory. The dynamics of many condensed matter systems including Fermi liquids, low temperature superfluids, and ordinary metals lend themselves to the definition of kinetic entropy. In fact, entropy has been defined and used for a wide variety of situations in which a condensed matter system has been allowed to relax for a sufficient period so that the very most rapid fluctuations have been ironed out. One of the broadest applications of non-equilibrium analysis considers quantum degenerate systems using Martin-Schwinger Green's functions (Phys Rev 115:1342-1373, 1959) as generalized Wigner functions, g^<({p},ω ,{R},T) and g^>({p},ω ,{R},T). This paper describes once again how the quantum kinetic equations for these functions give locally defined conservation laws for mass momentum and energy. In local thermodynamic equilibrium, this kinetic theory enables a reasonable definition of the density of kinetic entropy. However, when the system is outside of local equilibrium, this definition fails. It is speculated that quantum entanglement is the source of this failure.

The applications of chemical thermodynamics and chemical kinetics to planetary atmospheres research

NASA Technical Reports Server (NTRS)

Fegley, Bruce, Jr.

1990-01-01

A review of the applications of chemical thermodynamics and chemical kinetics to planetary atmospheres research during the past four decades is presented with an emphasis on chemical equilibrium models and thermochemical kinetics. Several current problems in planetary atmospheres research such as the origin of the atmospheres of the terrestrial planets, atmosphere-surface interactions on Venus and Mars, deep mixing in the atmospheres of the gas giant planets, and the origin of the atmospheres of outer planet satellites all require laboratory data on the kinetics of thermochemical reactions for their solution.

Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

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

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

2011-06-15

Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubblemore » evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink strength of interstitial loop for interstitials. In part II, we present a generic phase field model and discuss the thermodynamic and kinetic properties in phase-field models including the reaction kinetics of radiation defects and local free energy of irradiated materials. In particular, a two-sublattice thermodynamic model is suggested to describe the local free energy of alloys with irradiated defects. Fe-Cr alloy is taken as an example to explain the required thermodynamic and kinetic properties for quantitative phase-field modeling. Finally the great challenges in phase-field modeling will be discussed.« less

Thermodynamic and kinetic characterization of polycyclic aromatic hydrocarbons in reversed-phase liquid chromatography.

PubMed

Howerton, Samuel B; McGuffin, Victoria L

2003-07-15

The retention of six polycyclic aromatic hydrocarbons (PAHs) was characterized by reversed-phase liquid chromatography. The PAHs were detected by laser-induced fluorescence at four points along an optically transparent capillary column. The profiles were characterized in space and time using an exponentially modified Gaussian equation. The resulting parameters were used to calculate the retention factors, as well as the concomitant changes in molar enthalpy and molar volume, for each PAH on monomeric (2.7 micromol/m2) and polymeric (5.4 micromol/m2) octadecylsilica. The changes in molar enthalpy become more exothermic as ring number increases and as annelation structure becomes less condensed. The changes in molar volume become more negative as ring number increases for the planar PAHs, but are positive for the nonplanar solutes. In addition, the rate constants, as well as the concomitant activation enthalpy and activation volume, are calculated for the first time. The kinetic data demonstrate that many of the PAHs exhibit very fast transitions between the mobile and stationary phases. The transition state is very high in energy, and the activation enthalpies and volumes become greater as ring number increases and as annelation structure becomes less condensed. The changes in thermodynamic and kinetic behavior are much more pronounced for the polymeric phase than for the monomeric phase.

Sorption behavior of nano-TiO2 for the removal of selenium ions from aqueous solution.

PubMed

Zhang, Lei; Liu, Na; Yang, Lijun; Lin, Qing

2009-10-30

Titanium dioxide nanoparticles were employed for the sorption of selenium ions from aqueous solution. The process was studied in detail by varying the sorption time, pH, and temperature. The sorption was found to be fast, and to reach equilibrium basically within 5.0 min. The sorption has been optimized with respect to the pH, maximum sorption has been achieved from solution of pH 2-6. Sorbed Se(IV) and Se(VI) were desorbed with 2.0 mL 0.1 mol L(-1) NaOH. The kinetics and thermodynamics of the sorption of Se(IV) onto nano-TiO2 have been studied. The kinetic experimental data properly correlate with the second-order kinetic model (k(2)=0.69 g mg(-1) min(-1), 293 K). The overall rate process appears to be influenced by both boundary layer diffusion and intraparticle diffusion. The sorption data could be well interpreted by the Langmuir sorption isotherm. The mean energy of adsorption (14.46 kJ mol(-1)) was calculated from the Dubinin-Radushkevich (D-R) adsorption isotherm at room temperature. The thermodynamic parameters for the sorption were also determined, and the DeltaH(0) and DeltaG(0) values indicate exothermic behavior.

Thermodynamic and Kinetics Analysis of Peptides Derived from CapZ, NDR, p53, HDM2, and HDM4 Binding to Human S100B

PubMed Central

Wafer, Lucas N.; Streicher, Werner W.; McCallum, Scott A.; Makhatadze, George I.

2012-01-01

S100B is a member of the S100 subfamily of EF-hand proteins that has been implicated in malignant melanoma and neurodegenerative conditions such as Alzheimer's and Parkinson's disease. Calcium-induced conformational changes expose a hydrophobic binding cleft, facilitating interactions with a wide variety of nuclear, cytoplasmic, and extracellular target proteins. Previously, peptides derived from CapZ, p53, NDR, HDM2 and HDM4 have been shown to interact with S100B in a calcium-dependent manner. However, the thermodynamic and kinetic basis of these interactions remains largely unknown. To gain further insight, these peptides were screened against the S100B protein using isothermal titration calorimetry and nuclear magnetic resonance. All peptides were found to have binding affinities in the low micromolar to nanomolar range. Binding-induced changes in the line shapes of S100B backbone 1H and 15N were monitored to obtain the dissociation constants and the kinetic binding parameters. The large microscopic Kon rate constants observed in this study, Kon ≥1×107 M-1s-1, suggest that S100B utilizes a “fly casting mechanism” in the recognition of these peptide targets. PMID:22913742

Impact of biochar produced from post-harvest residue on the adsorption behavior of diesel oil on loess soil.

PubMed

Jiang, Yu Feng; Sun, Hang; Yves, Uwamungu J; Li, Hong; Hu, Xue Fei

2016-02-01

The primary objective of this study was to investigate the effect of biochar, produced from wheat residue at different temperatures, on the adsorption of diesel oil by loess soil. Kinetic and equilibrium data were processed to understand the adsorption mechanism of diesel by biochar-affected loess soil; dynamic and thermodynamic adsorption experiments were conducted to characterize this adsorption. The surface features and chemical structure of biochar, modified at varying pyrolytic temperatures, were investigated using surface scanning electron microscopy and Fourier transform infrared analysis. The kinetic data showed that the adsorption of diesel oil onto loess soil could be described by a pseudo-second-order kinetic model, with the rate-controlling step being intraparticle diffusion. However, in the presence of biochar, boundary layer control and intraparticle diffusion were both involved in the adsorption. Besides, the adsorption equilibrium data were well described by the Freundlich isothermal model. The saturated adsorption capacity weakened as temperature increased, suggesting a spontaneous exothermic process. Thermodynamic parameter analysis showed that adsorption was mainly a physical process and was enhanced by chemical adsorption. The adsorption capacity of loess soil for diesel oil was weakened with increasing pH. The biochar produced by pyrolytic wheat residue increased the adsorption behavior of petroleum pollutants in loess soil.

Crystallization kinetics and molecular mobility of an amorphous active pharmaceutical ingredient: A case study with Biclotymol.

PubMed

Schammé, Benjamin; Couvrat, Nicolas; Malpeli, Pascal; Delbreilh, Laurent; Dupray, Valérie; Dargent, Éric; Coquerel, Gérard

2015-07-25

The present case study focuses on the crystallization kinetics and molecular mobility of an amorphous mouth and throat drug namely Biclotymol, through differential scanning calorimetry (DSC), temperature resolved X-ray powder diffraction (TR-XRPD) and hot stage microscopy (HSM). Kinetics of crystallization above the glass transition through isothermal and non-isothermal cold crystallization were considered. Avrami model was used for isothermal crystallization process. Non-isothermal cold crystallization was investigated through Augis and Bennett model. Differences between crystallization processes have been ascribed to a site-saturated nucleation mechanism of the metastable form, confirmed by optical microscopy images. Regarding molecular mobility, a feature of molecular dynamics in glass-forming liquids as thermodynamic fragility index m was determined through calorimetric measurements. It turned out to be around m=100, describing Biclotymol as a fragile glass-former for Angell's classification. Relatively long-term stability of amorphous Biclotymol above Tg was analyzed indirectly by calorimetric monitoring to evaluate thermodynamic parameters and crystallization behavior of glassy Biclotymol. Within eight months of storage above Tg (T=Tg+2°C), amorphous Biclotymol does not show a strong inclination to crystallize and forms a relatively stable glass. This case study, involving a multidisciplinary approach, points out the importance of continuing looking for stability predictors. Copyright © 2015 Elsevier B.V. All rights reserved.

Encapsulation of Ionic Liquids with an Aprotic Heterocyclic Anion (AHA-IL) for CO2 Capture: Preserving the Favorable Thermodynamics and Enhancing the Kinetics of Absorption.

PubMed

Moya, Cristian; Alonso-Morales, Noelia; de Riva, Juan; Morales-Collazo, Oscar; Brennecke, Joan F; Palomar, Jose

2018-03-08

The performance of an ionic liquid with an aprotic heterocyclic anion (AHA-IL), trihexyl(tetradecyl)phosphonium 2-cyanopyrrolide ([P 66614 ][2-CNPyr]), for CO 2 capture has been evaluated considering both the thermodynamics and the kinetics of the phenomena. Absorption gravimetric measurements of the gas-liquid equilibrium isotherms of CO 2 -AHA-IL systems were carried out from 298 to 333 K and at pressures up to 15 bar, analyzing the role of both chemical and physical absorption phenomena in the overall CO 2 solubility in the AHA-IL, as has been done previously. In addition, the kinetics of the CO 2 chemical absorption process was evaluated by in situ Fourier transform infrared spectroscopy-attenuated total reflection, following the characteristic vibrational signals of the reactants and products over the reaction time. A chemical absorption model was used to describe the time-dependent concentration of species involved in the reactive absorption, obtaining kinetic parameters (such as chemical reaction kinetic constants and diffusion coefficients) as a function of temperatures and pressures. As expected, the results demonstrate that the CO 2 absorption rate is mass-transfer-controlled because of the relatively high viscosity of AHA-IL. The AHA-IL was encapsulated in a porous carbon sphere (Encapsulated Ionic Liquid, ENIL) to improve the kinetic performance of the AHA-IL for CO 2 capture. The newly synthesized AHA-ENIL material was evaluated as a CO 2 sorbent with gravimetric absorption measurements. AHA-ENIL systems preserve the good CO 2 absorption capacity of the AHA-IL but drastically enhance the CO 2 absorption rate because of the increased gas-liquid surface contact area achieved by solvent encapsulation.

Thermodynamic Modeling of Gas Transport in Glassy Polymeric Membranes.

PubMed

Minelli, Matteo; Sarti, Giulio Cesare

2017-08-19

Solubility and permeability of gases in glassy polymers have been considered with the aim of illustrating the applicability of thermodynamically-based models for their description and prediction. The solubility isotherms are described by using the nonequilibrium lattice fluid (NELF) (model, already known to be appropriate for nonequilibrium glassy polymers, while the permeability isotherms are described through a general transport model in which diffusivity is the product of a purely kinetic factor, the mobility coefficient, and a thermodynamic factor. The latter is calculated from the NELF model and mobility is considered concentration-dependent through an exponential relationship containing two parameters only. The models are tested explicitly considering solubility and permeability data of various penetrants in three glassy polymers, PSf, PPh and 6FDA-6FpDA, selected as the reference for different behaviors. It is shown that the models are able to calculate the different behaviors observed, and in particular the permeability dependence on upstream pressure, both when it is decreasing as well as when it is increasing, with no need to invoke the onset of additional plasticization phenomena. The correlations found between polymer and penetrant properties with the two parameters of the mobility coefficient also lead to the predictive ability of the transport model.

Thermodynamic Modeling of Gas Transport in Glassy Polymeric Membranes

PubMed Central

Minelli, Matteo; Sarti, Giulio Cesare

2017-01-01

Solubility and permeability of gases in glassy polymers have been considered with the aim of illustrating the applicability of thermodynamically-based models for their description and prediction. The solubility isotherms are described by using the nonequilibrium lattice fluid (NELF) (model, already known to be appropriate for nonequilibrium glassy polymers, while the permeability isotherms are described through a general transport model in which diffusivity is the product of a purely kinetic factor, the mobility coefficient, and a thermodynamic factor. The latter is calculated from the NELF model and mobility is considered concentration-dependent through an exponential relationship containing two parameters only. The models are tested explicitly considering solubility and permeability data of various penetrants in three glassy polymers, PSf, PPh and 6FDA-6FpDA, selected as the reference for different behaviors. It is shown that the models are able to calculate the different behaviors observed, and in particular the permeability dependence on upstream pressure, both when it is decreasing as well as when it is increasing, with no need to invoke the onset of additional plasticization phenomena. The correlations found between polymer and penetrant properties with the two parameters of the mobility coefficient also lead to the predictive ability of the transport model. PMID:28825619

Mechanisms of kinetic stabilization by the drugs paclitaxel and vinblastine.

PubMed

Castle, Brian T; McCubbin, Seth; Prahl, Louis S; Bernens, Jordan N; Sept, David; Odde, David J

2017-05-01

Microtubule-targeting agents (MTAs), widely used as biological probes and chemotherapeutic drugs, bind directly to tubulin subunits and "kinetically stabilize" microtubules, suppressing the characteristic self-assembly process of dynamic instability. However, the molecular-level mechanisms of kinetic stabilization are unclear, and the fundamental thermodynamic and kinetic requirements for dynamic instability and its elimination by MTAs have yet to be defined. Here we integrate a computational model for microtubule assembly with nanometer-scale fluorescence microscopy measurements to identify the kinetic and thermodynamic basis of kinetic stabilization by the MTAs paclitaxel, an assembly promoter, and vinblastine, a disassembly promoter. We identify two distinct modes of kinetic stabilization in live cells, one that truly suppresses on-off kinetics, characteristic of vinblastine, and the other a "pseudo" kinetic stabilization, characteristic of paclitaxel, that nearly eliminates the energy difference between the GTP- and GDP-tubulin thermodynamic states. By either mechanism, the main effect of both MTAs is to effectively stabilize the microtubule against disassembly in the absence of a robust GTP cap. © 2017 Castle et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Perform Thermodynamics Measurements on Fuel Cycle Case Study Systems

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

Martin, Leigh R.

This document was prepared to meet FCR&D level 3 milestone M3FT-14IN0304022, “Perform Thermodynamics Measurements on Fuel Cycle Case Study Systems.” This work was carried out under the auspices of the Thermodynamics and Kinetics FCR&D work package. This document reports preliminary work in support of determining the thermodynamic parameters for the ALSEP process. The ALSEP process is a mixed extractant system comprised of a cation exchanger 2-ethylhexyl-phosphonic acid mono-2-ethylhexyl ester (HEH[EHP]) and a neutral solvating extractant N,N,N’,N’-tetraoctyldiglycolamide (TODGA). The extractant combination produces complex organic phase chemistry that is challenging for traditional measurement techniques. To neutralize the complexity, temperature dependent solvent extractionmore » experiments were conducted with neat TODGA and scaled down concentrations of the ALSEP formulation to determine the enthalpies of extraction for the two conditions. A full set of thermodynamic data for Eu, Am, and Cm extraction by TODGA from 3.0 M HNO3 is reported. These data are compared to previous extraction results from a 1.0 M HNO3 aqueous medium, and a short discussion of the mixed HEH[EHP]/TODGA system results is offered.« less

Sorption and desorption studies of a reactive azo dye on effective disposal of redundant material.

PubMed

Çelekli, Abuzer; Bozkurt, Hüseyin

2013-07-01

The effective disposal of redundant elephant dung (ED) is important for environmental protection and utilization of resource. The aim of this study was to remove a toxic-azo dye, Reactive Red (RR) 120, using this relatively cheap material as a new adsorbent. The FTIR-ATR spectra of ED powders before and after the sorption of RR 120 and zero point charge (pHzpc) of ED were determined. The sorption capacity of ED for removing of RR 120 were carried out as functions of particle size, adsorbent dose, pH, temperature, ionic strength, initial dye concentration, and contact time. Sorption isotherm, kinetic, activation energy, thermodynamic, and desorption parameters of RR 120 on ED were studied. The sorption process was found to be dependent on particle size, adsorbent dose, pH, temperature, ionic strength, initial dye concentration, and contact time. FTIR-ATR spectroscopy indicated that amine and amide groups have significant role on the sorption of RR 120 on ED. The pHzpc of ED was found to be 7.3. Sorption kinetic of RR 120 on ED was well described by sigmoidal Logistic model. The Langmuir isotherm was well fitted to the equilibrium data. The maximum sorption capacity was 95.71 mg g(-1). The sorption of RR 120 on ED was mainly physical and exothermic according to results of D-R isotherm, Arrhenius equation, thermodynamic, and desorption studies. The thermodynamic parameters showed that this process was feasible and spontaneous. This study showed that ED as a low-cost adsorbent had a great potential for the removal of RR 120 as an alternative eco-friendly process.

Marcus Theory: Thermodynamics CAN Control the Kinetics of Electron Transfer Reactions

ERIC Educational Resources Information Center

Silverstein, Todd P.

2012-01-01

Although it is generally true that thermodynamics do not influence kinetics, this is NOT the case for electron transfer reactions in solution. Marcus Theory explains why this is so, using straightforward physical chemical principles such as transition state theory, Arrhenius' Law, and the Franck-Condon Principle. Here the background and…

Serial sectioning of grain microstructures under junction control: An old problem in a new guise

NASA Astrophysics Data System (ADS)

Zöllner, D.; Streitenberger, P.

2015-04-01

In the present work the importance of 3D and 4D microstructure analyses are shown. To that aim, we study polycrystalline grain microstructures obtained by grain growth under grain boundary, triple line and quadruple point control. The microstructures themselves are obtained by mesoscopic computer simulations, which enjoy a far greater control over the kinetic and thermodynamic parameters affecting grain growth than can be realized experimentally. In extensive simulation studies we find by 3D respectively 4D microstructure analyses that metrical and topological properties of the microstructures depend strongly on the microstructural feature controlling the growth kinetics. However, the differences between the growth kinetics vanish when we look at classical 2D sections of the 3D ensembles making a differentiation of the controlling grain feature near impossible.

Kinetic and mechanism of the oxidation of chromium(III) complex with anthranil- N, N-diacetic acid by periodate ion in acidic aqueous solutions

NASA Astrophysics Data System (ADS)

Ali, Ismat H.

2015-06-01

The kinetics of oxidation of [CrIII(atda)(H2O)2] (atda = anthranil- N, N-diacetato) complex by IO{4/-} was studied spectrophotometrically in aqueous solutions with pH range 2.20-3.34, 0.30 M ionic strength and in 20.0-40.0°C temperature range. The rate law of the reaction exhibited saturation kinetics. Values of the rate constant for the electron transfer process, the equilibrium constant for dissociation of [CrIII (atda)(H2O)2] to [CrIII (atda) (H2O)OH]+ + H+ and the pre-equilibrium formation constant were calculated. The thermodynamic activation parameters are reported. It is proposed that electron transfer proceeds through an inner-sphere mechanism via coordination of the IVII to chromium(III).

Kinetic, equilibrium and thermodynamic studies on sorption of uranium and thorium from aqueous solutions by a selective impregnated resin containing carminic acid.

PubMed

Rahmani-Sani, Abolfazl; Hosseini-Bandegharaei, Ahmad; Hosseini, Seyyed-Hossein; Kharghani, Keivan; Zarei, Hossein; Rastegar, Ayoob

2015-04-09

In this work, the removal of uranium and thorium ions from aqueous solutions was studied by solid-liquid extraction using an advantageous extractant-impregnated resin (EIR) prepared by loading carminic acid (CA) onto Amberlite XAD-16 resin beads. Batch sorption experiments using CA/XAD-16 beads for the removal of U(VI) and Th(IV) ions were carried out as a function of several parameters, like equilibration time, metal ion concentration, etc. The equilibrium data obtained from the sorption experiments were adjusted to the Langmuir isotherm model and the calculated maximum sorption capacities in terms of monolayer sorption were in agreement with those obtained from the experiments. The experimental data on the sorption behavior of both metal ions onto the EIR beads fitted well in both Bangham and intra-particle diffusion kinetic models, indicating that the intra-particle diffusion is the rate-controlling step. The thermodynamic studies at different temperatures revealed the feasibility and the spontaneous nature of the sorption process for both uranium and thorium ions. Copyright © 2014 Elsevier B.V. All rights reserved.

Novel biosynthesized silver nanoparticles from cobweb as adsorbent for Rhodamine B: equilibrium isotherm, kinetic and thermodynamic studies

NASA Astrophysics Data System (ADS)

Azeez, Luqmon; Lateef, Agbaje; Adebisi, Segun A.; Oyedeji, Abdulrasaq O.

2018-03-01

This study has investigated the adsorption of Rhodamine B (Rh-B) dye on novel biosynthesized silver nanoparticles (AgNPs) from cobweb. The effects of contact time, initial pH, initial dye concentration, adsorbent dosage and temperature were studied on the removal of Rh-B and they significantly affected its uptake. Adsorption isotherms were evaluated using Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherm models. The adsorption process was best described by Langmuir isotherm with R 2 of 0.9901, indicating monolayer adsorption. The maximum adsorption capacity ( q max) of 59.85 mg/g showed that it has relatively high performance, while adsorption intensity showed a favourable adsorption process. Pseudo-second-order kinetics fitted best the rate of adsorption and intra-particle diffusion revealed both surface adsorption and intra-particle diffusion-controlled adsorption process. Negative values of thermodynamic parameters (Δ H°, Δ S° and Δ G°) indicated an exothermic and spontaneous adsorption process. The mean sorption energy ( E) and activation energy ( E a) suggested the uptake of Rh-B onto AgNPs was chemical in nature (chemosorption).

Thermodynamic and kinetic analyses of curcumin and bovine serum albumin binding.

PubMed

Hudson, Eliara Acipreste; de Paula, Hauster Maximiler Campos; Ferreira, Guilherme Max Dias; Ferreira, Gabriel Max Dias; Hespanhol, Maria do Carmo; da Silva, Luis Henrique Mendes; Pires, Ana Clarissa Dos S

2018-03-01

Bovine serum albumin (BSA)/curcumin binding and dye photodegradation stability were evaluated. BSA/curcumin complex showed 1:1 stoichiometry, but the thermodynamic binding parameters depended on the technique used and BSA conformation. The binding constant was of the order of 10 5 L·mol -1 by fluorescence and microcalorimetric, and 10 3 and 10 4 L·mol -1 by surface plasmon resonance (steady-state equilibrium and kinetic experiments, respectively). For native BSA/curcumin, fluorescence indicated an enthalpic and entropic driven process based on the standard enthalpy change (ΔH ○ F =-8.67kJ·mol -1 ), while microcalorimetry showed an entropic driven binding process (ΔH ○ cal =29.11kJ·mol -1 ). For the unfolded BSA/curcumin complex, it was found thatp ΔH ○ F =-16.12kJ·mol -1 and ΔH ○ cal =-42.63kJ·mol -1 . BSA (mainly native) increased the curcumin photodegradation stability. This work proved the importance of using different techniques to characterize the protein-ligand binding. Copyright © 2017 Elsevier Ltd. All rights reserved.

Equilibrium, kinetic and thermodynamic studies for adsorption of BTEX onto Ordered Mesoporous Carbon (OMC).

PubMed

Konggidinata, Mas Iwan; Chao, Bing; Lian, Qiyu; Subramaniam, Ramalingam; Zappi, Mark; Gang, Daniel Dianchen

2017-08-15

Chemical and petrochemical industries produce substantial amounts of wastewater everyday. This wastewater contains organic pollutants such as benzene, toluene, ethylbenzene and xylenes (BTEX) that are toxic to human and aquatic life. Ordered Mesoporous Carbon (OMC), the adsorbent that possesses the characteristics of an ideal adsorbent was investigated to understand its properties and suitability for BTEX removal. Adsorption isotherms, adsorption kinetics, the effects of initial BTEX concentrations and temperatures on the adsorption process were studied. The OMCs were characterized using surface area and pore size analyzer, transmission electron microscopy (TEM), elemental analysis, thermogravimetric analysis (TGA) and fourier transform infrared spectroscopy (FTIR). The results suggested that the Langmuir Isotherm and Pseudo-Second-Order Models described the experimental data well. The thermodynamic parameters, Gibbs free energy (ΔG°), the enthalpy change (ΔH°) and the entropy change (ΔS°) of adsorption indicated that the adsorption processes were physical, endothermic, and spontaneous. In addition, OMC had 27% higher overall adsorption capacities compared to granular activated carbon (GAC). Copyright © 2017 Elsevier B.V. All rights reserved.

Utilization of Waste Biomass (Kitchen Waste) Hydrolysis Residue as Adsorbent for Dye Removal: Kinetic, Equilibrium, and Thermodynamic Studies.

PubMed

Li, Panyu; Chen, Xi; Zeng, Xiaotong; Zeng, Yu; Xie, Yi; Li, Xiang; Wang, Yabo; Xie, Tonghui; Zhang, Yongkui

2018-02-02

Kitchen waste hydrolysis residue (KWHR), which is produced in the bioproduction process from kitchen waste (KW), is usually wasted with potential threats to the environment. Herein, experiments were carried out to evaluate the potential of KWHR as adsorbent for dye (methylene blue, MB) removal from aqueous solution. The adsorbent was characterized using FT-IR and SEM. Adsorption results showed that the operating variables had great effects on the removal efficiency of MB. Kinetic study indicated pseudo-second-order model was suitable to describe the adsorption process. Afterwards, the equilibrium data were well fitted by using Langmuir isotherm model, suggesting a monolayer adsorption. The Langmuir monolayer adsorption capacity was calculated to be 110.13 mg/g, a level comparable to some other low-cost adsorbents. It was found that the adsorption process of MB onto KWHR was spontaneous and exothermic through the estimation of thermodynamic parameters. Thus, KWHR was of great potential to be an alternative adsorbent material to improve the utilization efficiency of bioresource (KW) and lower the cost of adsorbent for color treatment.

Kinetic and thermodynamic studies on the adsorption of anionic surfactant on quaternary ammonium cationic cellulose.

PubMed

Zhang, Yuanzhang; Shi, Wenjian; Zhou, Hualan; Fu, Xing; Chen, Xuan

2010-06-01

Removal of anionic surfactants from aqueous solutions by adsorption onto quaternary ammonium cationic cellulose (QACC) was investigated. The effects of solution acidity, initial concentration, adsorption time, and temperature on the adsorption of sodium dodecyl-benzene sulfonate (SDBS), sodium lauryl sulfate (SLS), and sodium dodecyl sulfonate (SDS) were studied. The kinetic experimental data fit well with the pseudo-second-order model; the rate constant of the adsorption increased with temperature. The values of apparent activation energy for the adsorption were calculated as ranging from 10.2 to 17.4 kJ/ mol. The adsorption isotherm can be described by the Langmuir isotherm. The values of thermodynamic parameters (deltaH0, deltaS0, and deltaG0) for the adsorption indicated that this process was spontaneous and endothermic. At 318 K, the saturated adsorption capacities of QACC for SDBS, SLS, and SDS were 1.75, 1.53, and 1.39 mmol/g, respectively. The adsorption process was mainly chemisorption and partially physisorption. The results show that QACC is effective for the removal of anionic surfactants.

Bistable or oscillating state depending on station and temperature in three-station glycorotaxane molecular machines.

PubMed

Busseron, Eric; Romuald, Camille; Coutrot, Frédéric

2010-09-03

High-yield, straightforward synthesis of two- and three-station [2]rotaxane molecular machines based on an anilinium, a triazolium, and a mono- or disubstituted pyridinium amide station is reported. In the case of the pH-sensitive two-station molecular machines, large-amplitude movement of the macrocycle occurred. However, the presence of an intermediate third station led, after deprotonation of the anilinium station, and depending on the substitution of the pyridinium amide, either to exclusive localization of the macrocycle around the triazolium station or to oscillatory shuttling of the macrocycle between the triazolium and monosubstituted pyridinium amide station. Variable-temperature (1)H NMR investigation of the oscillating system was performed in CD(2)Cl(2). The exchange between the two stations proved to be fast on the NMR timescale for all considered temperatures (298-193 K). Interestingly, decreasing the temperature displaced the equilibrium between the two translational isomers until a unique location of the macrocycle around the monosubstituted pyridinium amide station was reached. Thermodynamic constants K were evaluated at each temperature: the thermodynamic parameters DeltaH and DeltaS were extracted from a Van't Hoff plot, and provided the Gibbs energy DeltaG. Arrhenius and Eyring plots afforded kinetic parameters, namely, energies of activation E(a), enthalpies of activation DeltaH( not equal), and entropies of activation DeltaS( not equal). The DeltaG values deduced from kinetic parameters match very well with the DeltaG values determined from thermodynamic parameters. In addition, whereas signal coalescence of pyridinium hydrogen atoms located next to the amide bond was observed at 205 K in the oscillating rotaxane and at 203 K in the two-station rotaxane with a unique location of the macrocycle around the pyridinium amide, no separation of (1)H NMR signals of the considered hydrogen atoms was seen in the corresponding nonencapsulated thread. It is suggested that the macrocycle acts as a molecular brake for the rotation of the pyridinium-amide bond when it interacts by hydrogen bonding with both the amide NH and the pyridinium hydrogen atoms at the same time.

Application of a single model to study the adsorption equilibrium of prednisolone on six carbonaceous materials.

PubMed

Valenzuela-Calahorro, C; Cuerda-Correa, E; Navarrete-Guijosa, A; Gonzalez-Pradas, E

2002-06-01

The knowledge of sorption processes of nonelectrolytes in solution by solid adsorbents implies the study of kinetics, equilibrium, and thermodynamic functions. However, quite frequently the equilibrium isotherms are studied by comparing them with those corresponding to the Giles et al. classification (1); these isotherms are also analyzed by fitting them to equations based on thermodynamic or kinetic criteria, and even to empirical equations. Nevertheless, information obtained is more coherent and satisfactory if the adsorption isotherms are fitted by using an equation describing the equilibrium isotherms according to the kinetic laws. These mentioned laws would determine each one of the unitary processes (one or more) which condition the global process. In this paper, an adsorption process of prednisolone in solution by six carbonaceous materials is explained according to a previously proposed single model, which allows to establish a kinetic law which fits satisfactorily most of C vs t isotherms (2). According to the above-mentioned kinetic law, equations describing sorption equilibrium processes have been deducted, and experimental data points have been fitted to these equations; such a fitting yields to different values of adsorption capacity and kinetic equilibrium constants for the different processes at several temperatures. However, in spite of their practical interest, these constants have no thermodynamic signification. Thus, the thermodynamic equilibrium constant (K) has been calculated by using a modified expression of the Gaines et al. equation (3). Global average values of the thermodynamic functions have also been calculated from the K values. Information related to variations of DeltaH and DeltaS with the surface coverage fraction was obtained by using the corresponding Clausius-Clapeyron equations.

Application of green seaweed biomass for MoVI sorption from contaminated waters. Kinetic, thermodynamic and continuous sorption studies.

PubMed

Bertoni, Fernando A; Medeot, Anabela C; González, Juan C; Sala, Luis F; Bellú, Sebastián E

2015-05-15

Spongomorpha pacifica biomass was evaluated as a new sorbent for Mo(VI) removal from aqueous solution. The maximum sorption capacity was found to be 1.28×10(6)±1×10(4) mg kg(-1) at 20°C and pH 2.0. Sorption kinetics and equilibrium studies followed pseudo-first order and Langmuir adsorption isotherm models, respectively. FTIR analysis revealed that carboxyl and hydroxyl groups were mainly responsible for the sorption of Mo(VI). SEM images show that morphological changes occur at the biomass surface after Mo(VI) sorption. Activation parameters and mean free energies obtained with Dubinin-Radushkevich isotherm model demonstrate that the mechanism of sorption process was chemical sorption. Thermodynamic parameters demonstrate that the sorption process was spontaneous, endothermic and the driven force was entropic. The isosteric heat of sorption decreases with surface loading, indicating that S. pacifica has an energetically non-homogeneous surface. Experimental breakthrough curves were simulated by Thomas and modified dose-response models. The bed depth service time (BDST) model was employed to scale-up the continuous sorption experiments. The critical bed depth, Z0 was determined to be 1.7 cm. S.pacifica biomass showed to be a good sorbent for Mo(VI) and it can be used in continuous treatment of effluent polluted with molybdate ions. Copyright © 2015 Elsevier Inc. All rights reserved.

Removal of tetracycline from wastewater using pumice stone: equilibrium, kinetic and thermodynamic studies

PubMed Central

2014-01-01

In this study, pumice stone was used for the removal of tetracyline (TC) from aqueous solutions. It was characterized by XRD, FT-IR, SEM and BET analyses. Cation exchange capacity of pumice stone was found to be 9.9 meq/100 g. Effect of various parameters such as solution pH (2–11), adsorbent dosage (0.5-10 g/L), contact time (2.5-120 min), initial TC concentration (5–300 mg/L) and temperature (20–50°C) on TC adsorption onto pumice was investigated. Also the adsorption of TC on pumice stone was studied as a function of Na+ and Cu2+ cations changing pH from 2 to 11 using batch experiments. The best removal efficiency performance was exhibited at adsorbent dosage 10 g/L, pH 3, contact time 120 min. Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherm models were applied to the equilibrium data. The result has shown that the adsorption was favorable, physicochemical in nature and agrees well with Langmuir and Freundlich models. The maximum Langmuir adsorption capacity was found to be 20.02 mg/g. The adsorption behavior of TC on pumices stone was fitted well in the pseudo-second order kinetics model. Thermodynamic parameters calculated from the adsorption data at different temperature showed that the adsorption reaction was feasible, spontaneous and exothermic. PMID:24936305

The temperature dependence of the BK channel activity - kinetics, thermodynamics, and long-range correlations.

PubMed

Wawrzkiewicz-Jałowiecka, Agata; Dworakowska, Beata; Grzywna, Zbigniew J

2017-10-01

Large-conductance, voltage dependent, Ca 2+ -activated potassium channels (BK) are transmembrane proteins that regulate many biological processes by controlling potassium flow across cell membranes. Here, we investigate to what extent temperature (in the range of 17-37°C with ΔT=5°C step) is a regulating parameter of kinetic properties of the channel gating and memory effect in the series of dwell-time series of subsequent channel's states, at membrane depolarization and hyperpolarization. The obtained results indicate that temperature affects strongly the BK channels' gating, but, counterintuitively, it exerts no effect on the long-range correlations, as measured by the Hurst coefficient. Quantitative differences between dependencies of appropriate channel's characteristics on temperature are evident for different regimes of voltage. Examining the characteristics of BK channel activity as a function of temperature allows to estimate the net activation energy (E act ) and changes of thermodynamic parameters (ΔH, ΔS, ΔG) by channel opening. Larger E act corresponds to the channel activity at membrane hyperpolarization. The analysis of entropy and enthalpy changes of closed to open channel's transition suggest the entropy-driven nature of the increase of open state probability during voltage activation and supports the hypothesis about the voltage-dependent geometry of the channel vestibule. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of different isotherm models, kinetic, thermodynamic, and copper biosorption efficiency of Lobaria pulmonaria (L.) Hoffm.

PubMed

Kiliç, Zeynep; Atakol, Orhan; Aras, Sümer; Cansaran-Duman, Demet; Celikkol, Pelin; Emregul, Emel

2014-01-01

The biosorption characteristics of Cu(II) ions from aqueous solution using Lobaria pulmonaria (L.) Hoffm. biomass were investigated. The biosorption efficiency of Cu(II) onto biomass was significantly influenced by the operating parameters. The maximum biosorption efficiency of L. pulmonaria was 65.3% at 10 mg/L initial metal concentration for 5 g/L lichen biomass dosage. The biosorption of Cu(II) ions onto biomass fits the Langmuir isotherm model and the pseudo-second-order kinetic model well. The thermodynamic parameters indicate the feasibility and exothermic and spontaneous nature of the biosorption. The effective desorption achieved with HCl was 96%. Information on the nature of possible interactions between the functional groups of the L. pulmonaria biomass and Cu(II) ions was obtained via Fourier transform infrared (FTIR) spectroscopy. The results indicated that the carboxyl (-COOH) and hydroxyl (-OH) groups of the biomass were mainly involved in the biosorption of Cu(II) onto L. pulmonaria biomass. The L. pulmonaria is a promising biosorbent for Cu(lI) ions because of its availability, low cost, and high metal biosorption and desorption capacities. Lobaria pulmonaria is a promising biosorbent for Cu(II) ions because of its availability, low cost, and high metal biosorption and desorption capacities. To the best of our knowledge, this is the first paper on the biosorption Cu by L. pulmonaria.

The Compositional Dependence of the Microstructure and Properties of CMSX-4 Superalloys

NASA Astrophysics Data System (ADS)

Yu, Hao; Xu, Wei; Van Der Zwaag, Sybrand

2018-01-01

The degradation of creep resistance in Ni-based single-crystal superalloys is essentially ascribed to their microstructural evolution. Yet there is a lack of work that manages to predict (even qualitatively) the effect of alloying element concentrations on the rate of microstructural degradation. In this research, a computational model is presented to connect the rafting kinetics of Ni superalloys to their chemical composition by combining thermodynamics calculation and a modified microstructural model. To simulate the evolution of key microstructural parameters during creep, the isotropic coarsening rate and γ/ γ' misfit stress are defined as composition-related parameters, and the effect of service temperature, time, and applied stress are taken into consideration. Two commercial superalloys, for which the kinetics of the rafting process are selected as the reference alloys, and the corresponding microstructural parameters are simulated and compared with experimental observations reported in the literature. The results confirm that our physical model not requiring any fitting parameters manages to predict (semiquantitatively) the microstructural parameters for different service conditions, as well as the effects of alloying element concentrations. The model can contribute to the computational design of new Ni-based superalloys.

Experiments in Thermodynamics and Kinetics of Phosphine Substitution in (p-Cymene)RuCl[subscript 2](PR[subscript 3])

ERIC Educational Resources Information Center

Ozerov, Oleg V.; Fafard, Claudia M.; Hoffman, Norris W.

2007-01-01

This manuscript describes a set of three experiments that investigates the thermodynamic and kinetic aspects of phosphine substitution at a Ru center. In the first experiment, the students synthesize a Ru organometallic complex containing a phosphine ligand. In the second, equilibria for phosphine substitution involving several different…

Kinetics and thermodynamics of bovine serum albumin interactions with Congo red dye.

PubMed

de Paula, Hauster Maximiler Campos; Coelho, Yara Luiza; Agudelo, Alvaro Javier Patiño; Rezende, Jaqueline de Paula; Ferreira, Gabriel Max Dias; Ferreira, Guilherme Max Dias; Pires, Ana Clarissa Dos Santos; da Silva, Luis Henrique Mendes

2017-11-01

To optimize the therapeutic applications of Congo red (CR), a potential inhibitor of protein aggregation, the kinetics and thermodynamics of the interactions between CR and a model protein need to be understood. We used surface plasmon resonance (SPR) and fluorescence techniques to determine the dynamics and thermodynamic parameters for the formation of complexes between CR and bovine serum albumin (BSA). CR interacts with BSA through a transition complex; the activation energy for association (E act(a) ) was determined to be 35.88kJmol -1 , while the activation enthalpy (ΔH ‡ ), entropy (ΔS ‡ ), and Gibbs free energy (ΔG ‡ ) are 33.41kJmol -1 , 0.18Jmol -1 K -1 , and 33.35kJmol -1 , respectively. When this intermediate transforms into the final CR-BSA complex, the entropy of the system increases and part of the absorbed energy is released; this process is associated with a reverse activation energy (E act(d) ) of 20.17kJmol -1 , and values of ΔH ‡ , ΔS ‡ , and ΔG ‡ of 17.69kJmol -1 , -162.86Jmol -1 K -1 , and 66.25kJmol -1 , respectively. A comparison of the SPR and fluorescence results suggests that there is more than one site where BSA interacts with CR. Copyright © 2017 Elsevier B.V. All rights reserved.

Removal of anionic dye Congo red from aqueous solution by raw pine and acid-treated pine cone powder as adsorbent: equilibrium, thermodynamic, kinetics, mechanism and process design.

PubMed

Dawood, Sara; Sen, Tushar Kanti

2012-04-15

Pine cone a natural, low-cost agricultural by-product in Australia has been studied for its potential application as an adsorbent in its raw and hydrochloric acid modified form. Surface study of pine cone and treated pine cone was investigated using Fourier transform infrared (FTIR) and scanning electron microscopy (SEM). The modification process leads to increases in the specific surface area and decreases mean particle sizes of acid-treated pine cone when compared to raw pine cone biomass. Batch adsorption experiments were performed to remove anionic dye Congo red from aqueous solution. It was found that the extent of Congo red adsorption by both raw pine cone biomass and acid-treated biomass increased with initial dye concentration, contact time, temperature but decreased with increasing solution pH and amount of adsorbent of the system. Overall, kinetic studies showed that the dye adsorption process followed pseudo-second-order kinetics based on pseudo-first-order and intra-particle diffusion models. The different kinetic parameters including rate constant, half-adsorption time, and diffusion coefficient were determined at different physico-chemical conditions. Equilibrium data were best represented by Freundlich isotherm model among Langmuir and Freundlich adsorption isotherm models. It was observed that the adsorption was pH dependent and the maximum adsorption of 32.65 mg/g occurred at pH of 3.55 for an initial dye concentration of 20 ppm by raw pine cone, whereas for acid-treated pine cone the maximum adsorption of 40.19 mg/g for the same experimental conditions. Freundlich constant 'n' also indicated favourable adsorption. Thermodynamic parameters such as ∆G(0), ∆H(0), and ∆S(0) were calculated. A single-stage batch absorber design for the Congo red adsorption onto pine cone biomass also presented based on the Freundlich isotherm model equation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Thermodynamic Tuning of Mg-Based Hydrogen Storage Alloys: A Review

PubMed Central

Zhu, Min; Lu, Yanshan; Ouyang, Liuzhang; Wang, Hui

2013-01-01

Mg-based hydrides are one of the most promising hydrogen storage materials because of their relatively high storage capacity, abundance, and low cost. However, slow kinetics and stable thermodynamics hinder their practical application. In contrast to the substantial progress in the enhancement of the hydrogenation/dehydrogenation kinetics, thermodynamic tuning is still a great challenge for Mg-based alloys. At present, the main strategies to alter the thermodynamics of Mg/MgH2 are alloying, nanostructuring, and changing the reaction pathway. Using these approaches, thermodynamic tuning has been achieved to some extent, but it is still far from that required for practical application. In this article, we summarize the advantages and disadvantages of these strategies. Based on the current progress, finding reversible systems with high hydrogen capacity and effectively tailored reaction enthalpy offers a promising route for tuning the thermodynamics of Mg-based hydrogen storage alloys. PMID:28788353

Kinetic and Thermodynamic Characterization of Dihydrotestosterone-Induced Conformational Perturbations in Androgen Receptor Ligand-Binding Domain

PubMed Central

Jasuja, Ravi; Ulloor, Jagadish; Yengo, Christopher M.; Choong, Karen; Istomin, Andrei Y.; Livesay, Dennis R.; Jacobs, Donald J.; Swerdloff, Ronald S.; Mikšovská, Jaroslava; Larsen, Randy W.; Bhasin, Shalender

2009-01-01

Ligand-induced conformational perturbations in androgen receptor (AR) are important in coactivator recruitment and transactivation. However, molecular rearrangements in AR ligand-binding domain (AR-LBD) associated with agonist binding and their kinetic and thermodynamic parameters are poorly understood. We used steady-state second-derivative absorption and emission spectroscopy, pressure and temperature perturbations, and 4,4′-bis-anilinonaphthalene 8-sulfonate (bis-ANS) partitioning to determine the kinetics and thermodynamics of the conformational changes in AR-LBD after dihydrotestosterone (DHT) binding. In presence of DHT, the second-derivative absorption spectrum showed a red shift and a change in peak-to-peak distance. Emission intensity increased upon DHT binding, and center of spectral mass was blue shifted, denoting conformational changes resulting in more hydrophobic environment for tyrosines and tryptophans within a more compact DHT-bound receptor. In pressure perturbation calorimetry, DHT-induced energetic stabilization increased the Gibbs free energy of unfolding to 8.4 ± 1.3 kcal/mol from 3.5 ± 1.6 kcal/mol. Bis-ANS partitioning studies revealed that upon DHT binding, AR-LBD underwent biphasic rearrangement with a high activation energy (13.4 kcal/mol). An initial, molten globule-like burst phase (k ∼30 sec−1) with greater solvent accessibility was followed by rearrangement (k ∼0.01 sec−1), leading to a more compact conformation than apo-AR-LBD. Molecular simulations demonstrated unique sensitivity of tyrosine and tryptophan residues during pressure unfolding with rearrangement of residues in the coactivator recruitment surfaces distant from the ligand-binding pocket. In conclusion, DHT binding leads to energetic stabilization of AR-LBD domain and substantial rearrangement of residues distant from the ligand-binding pocket. DHT binding to AR-LBD involves biphasic receptor rearrangement including population of a molten globule-like intermediate state. PMID:19443608

Nanoscale Zero-Valent Iron (NZVI) supported on sineguelas waste for Pb(II) removal from aqueous solution: kinetics, thermodynamic and mechanism.

PubMed

Arshadi, M; Soleymanzadeh, M; Salvacion, J W L; SalimiVahid, F

2014-07-15

In this study, the synthesis and characterization of a new adsorbent containing nanoscale zerovalent iron particles (NZVI) decorated sineguelas waste (S-NaOH-NZVI) from agriculture biomass was investigated for the adsorption/reduction of inorganic pollution such as Pb(II) ions. The combination of ZVI particles on the surface of sineguelas waste can help to overcome the disadvantage of ultra-fine powders which may have strong tendency to agglomerate into larger particles, resulting in an adverse effect on both effective surface area and catalyst performance. The synthesized materials were characterized with different methods such as FT-IR, BET, XRD, TEM and pHPZC. Good dispersion of NZVI particles (ca. 10-70nm) on the sineguelas waste was observed. The effects of various parameters, such as contact time, pH, concentration, adsorbent dosage and temperature were studied. The adsorption of Pb(II) ions has been studied in terms of pseudo-first- and second-order kinetics, and the Freundlich, Langmuir and Langmuir-Freundlich isotherms models have also been used to the equilibrium adsorption data. The adsorption kinetics followed the mechanism of the pseudo-second-order equation. The thermodynamic parameters (ΔG, ΔH and ΔS) indicated that the adsorption of Pb(II) ions were feasible, spontaneous and endothermic at 25-80°C. XRD analysis indicated the presence of Pb(0) on the S-NaOH-NZVI surface. This study suggests that the modified sineguelas waste by NZVI particles can be prepared at low cost and the materials are environmentally benign for the removal of Pb(II) ions, and likely many other heavy metal ions, from water. Copyright © 2014 Elsevier Inc. All rights reserved.

Biosorptive uptake of arsenic(V) by steam activated carbon from mung bean husk: equilibrium, kinetics, thermodynamics and modeling

NASA Astrophysics Data System (ADS)

Mondal, Sandip; Aikat, Kaustav; Halder, Gopinath

2017-12-01

The present investigation emphasizes on the biosorptive removal of toxic pentavalent arsenic from water using steam activated carbon prepared from mung bean husk (SAC-MBH). Characterization of the synthesized sorbent was done using different instrumental techniques, i.e., SEM, BET and point of zero charge. Sorptive uptake of As(V) over steam activated MBH as a function of pH (3-9), agitation speed (40-200 rpm), dosage (50-1000 mg) and temperature (298-313 K) was studied by batch process at arsenic concentration of 2 mg L-1. Lower pH increases the arsenic removal over the pH range of 3-9. Among three adsorption isotherm models examined, Langmuir model was observed to show superior results over Freundlich model. The mean sorption energy (E) estimated by Dubinin-Radushkevich model suggested that the process of adsorption was chemisorption. Thermodynamic parameters confer that the sorption process was spontaneous, exothermic and feasible in nature. The pseudo-second-order rate kinetics of arsenic gave better correlation coefficients as compared to pseudo-first-order kinetics equation. Three process parameters, viz. adsorbent dosage, agitation speed and pH were opted for optimizing As(V) elimination using central composite design matrix of response surface methodology (RSM). The identical design setup was used for artificial neural network (ANN) for comparing its prediction capability with RSM towards As(V) removal. Maximum arsenic removal was observed to be 98.75% at sorbent dosage 0.75 gm L-1, pH 3.0, agitation speed 160 rpm and temperature 308 K. The study concluded that SAC-MBH could be a competent adsorbent for As(V) removal and ANN model was better in arsenic removal predictability results than RSM model.

Computation of Kinetics for the Hydrogen/Oxygen System Using the Thermodynamic Method

NASA Technical Reports Server (NTRS)

Marek, C. John

1996-01-01

A new method for predicting chemical rate constants using thermodynamics has been applied to the hydrogen/oxygen system. This method is based on using the gradient of the Gibbs free energy and a single proportionality constant D to determine the kinetic rate constants. Using this method the rate constants for any gas phase reaction can be computed from thermodynamic properties. A modified reaction set for the H/O system is determined. A11 of the third body efficiencies M are taken to be unity. Good agreement was obtained between the thermodynamic method and the experimental shock tube data. In addition, the hydrogen bromide experimental data presented in previous work is recomputed with M's of unity.

Kinetics of the cellular decomposition of supersaturated solid solutions

NASA Astrophysics Data System (ADS)

Ivanov, M. A.; Naumuk, A. Yu.

2014-09-01

A consistent description of the kinetics of the cellular decomposition of supersaturated solid solutions with the development of a spatially periodic structure of lamellar (platelike) type, which consists of alternating phases of precipitates on the basis of the impurity component and depleted initial solid solution, is given. One of the equations, which determines the relationship between the parameters that describe the process of decomposition, has been obtained from a comparison of two approaches in order to determine the rate of change in the free energy of the system. The other kinetic parameters can be described with the use of a variational method, namely, by the maximum velocity of motion of the decomposition boundary at a given temperature. It is shown that the mutual directions of growth of the lamellae of different phases are determined by the minimum value of the interphase surface energy. To determine the parameters of the decomposition, a simple thermodynamic model of states with a parabolic dependence of the free energy on the concentrations has been used. As a result, expressions that describe the decomposition rate, interlamellar distance, and the concentration of impurities in the phase that remain after the decomposition have been derived. This concentration proves to be equal to the half-sum of the initial concentration and the equilibrium concentration corresponding to the decomposition temperature.

Equilibrium, kinetics and process design of acid yellow 132 adsorption onto red pine sawdust.

PubMed

Can, Mustafa

2015-01-01

Linear and non-linear regression procedures have been applied to the Langmuir, Freundlich, Tempkin, Dubinin-Radushkevich, and Redlich-Peterson isotherms for adsorption of acid yellow 132 (AY132) dye onto red pine (Pinus resinosa) sawdust. The effects of parameters such as particle size, stirring rate, contact time, dye concentration, adsorption dose, pH, and temperature were investigated, and interaction was characterized by Fourier transform infrared spectroscopy and field emission scanning electron microscope. The non-linear method of the Langmuir isotherm equation was found to be the best fitting model to the equilibrium data. The maximum monolayer adsorption capacity was found as 79.5 mg/g. The calculated thermodynamic results suggested that AY132 adsorption onto red pine sawdust was an exothermic, physisorption, and spontaneous process. Kinetics was analyzed by four different kinetic equations using non-linear regression analysis. The pseudo-second-order equation provides the best fit with experimental data.

Ultrasonic evidence of hydrophobic interactions. Effect of ultrasound on benzoin condensation and some other reactions in aqueous ethanol.

PubMed

Tuulmets, Ants; Hagu, Hannes; Salmar, Siim; Cravotto, Giancarlo; Järv, Jaak

2007-03-29

The kinetics of KCN-catalyzed benzoin condensation of benzaldehyde in water and ethanol-water binary mixtures was investigated both under ultrasound at 22 kHz and without sonication. Thermodynamic activation parameters were calculated from kinetic data obtained at 35, 50, and 65 degrees C. Evidence that ultrasound can retard reactions is reported and hence a direct proof that sonochemical processes occur in the bulk solution. Former results and literature data for ester hydrolyses and tert-butyl chloride solvolysis are involved in the discussion. A quantitative relationship between sonication effects and the hydrophobicity of reagents is presented for the first time. Ultrasound affects hydrophobic interactions with the solvent, which are not manifested in conventional kinetics. When it suppresses the stabilization of the encounter complexes between reagents, sonication hinders the reaction but accelerates it when it perturbs the hydrophobic stabilization of the ground state of a reagent.

NMR reaction monitoring in flow synthesis

PubMed Central

Gomez, M Victoria

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed. PMID:28326137

NMR reaction monitoring in flow synthesis.

PubMed

Gomez, M Victoria; de la Hoz, Antonio

2017-01-01

Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways

PubMed Central

Vinnakota, Kalyan C.; Wu, Fan; Kushmerick, Martin J.; Beard, Daniel A.

2009-01-01

The operation of biochemical systems in vivo and in vitro is strongly influenced by complex interactions between biochemical reactants and ions such as H+, Mg2+, K+, and Ca2+. These are important second messengers in metabolic and signaling pathways that directly influence the kinetics and thermodynamics of biochemical systems. Herein we describe the biophysical theory and computational methods to account for multiple ion binding to biochemical reactants and demonstrate the crucial effects of ion binding on biochemical reaction kinetics and thermodynamics. In simulations of realistic systems, the concentrations of these ions change with time due to dynamic buffering and competitive binding. In turn, the effective thermodynamic properties vary as functions of cation concentrations and important environmental variables such as temperature and overall ionic strength. Physically realistic simulations of biochemical systems require incorporating all of these phenomena into a coherent mathematical description. Several applications to physiological systems are demonstrated based on this coherent simulation framework. PMID:19216922

A Computational Framework for Identifiability and Ill-Conditioning Analysis of Lithium-Ion Battery Models

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

López C, Diana C.; Wozny, Günter; Flores-Tlacuahuac, Antonio

2016-03-23

The lack of informative experimental data and the complexity of first-principles battery models make the recovery of kinetic, transport, and thermodynamic parameters complicated. We present a computational framework that combines sensitivity, singular value, and Monte Carlo analysis to explore how different sources of experimental data affect parameter structural ill conditioning and identifiability. Our study is conducted on a modified version of the Doyle-Fuller-Newman model. We demonstrate that the use of voltage discharge curves only enables the identification of a small parameter subset, regardless of the number of experiments considered. Furthermore, we show that the inclusion of a single electrolyte concentrationmore » measurement significantly aids identifiability and mitigates ill-conditioning.« less

Removal of Pb(II) ions from aqueous solution by a waste mud from copper mine industry: equilibrium, kinetic and thermodynamic study.

PubMed

Ozdes, Duygu; Gundogdu, Ali; Kemer, Baris; Duran, Celal; Senturk, Hasan Basri; Soylak, Mustafa

2009-07-30

The objective of this study was to assess the adsorption potential of a waste mud (WM) for the removal of lead (Pb(II)) ions from aqueous solutions. The WM was activated with NaOH in order to increase its adsorption capacity. Adsorption studies were conducted in a batch system as a function of solution pH, contact time, initial Pb(II) concentration, activated-waste mud (a-WM) concentration, temperature, etc. Optimum pH was specified as 4.0. The adsorption kinetic studies indicated that the overall adsorption process was best described by pseudo-second-order kinetics. The equilibrium adsorption capacity of a-WM was obtained by using Langmuir and Freundlich isotherm models and both models fitted well. Adsorption capacity for Pb(II) was found to be 24.4 mg g(-1) for 10 g L(-1) of a-WM concentration. Thermodynamic parameters including the Gibbs free energy (Delta G degrees), enthalpy (Delta H degrees), and entropy (DeltaS degrees) indicated that the adsorption of Pb(II) ions on the a-WM was feasible, spontaneous and endothermic, at temperature range of 0-40 degrees C. Desorption studies were carried out successfully with diluted HCl solutions. The results indicate that a-WM can be used as an effective and no-cost adsorbent for the treatment of industrial wastewaters contaminated with Pb(II) ions.

Comparative studies on adsorptive removal of heavy metal ions by biosorbent, bio-char and activated carbon obtained from low cost agro-residue.

PubMed

Kırbıyık, Çisem; Pütün, Ayşe Eren; Pütün, Ersan

2016-01-01

In this study, Fe(III) and Cr(III) metal ion adsorption processes were carried out with three adsorbents in batch experiments and their adsorption performance was compared. These adsorbents were sesame stalk without pretreatment, bio-char derived from thermal decomposition of biomass, and activated carbon which was obtained from chemical activation of biomass. Scanning electron microscopy and Fourier transform-infrared techniques were used for characterization of adsorbents. The optimum conditions for the adsorption process were obtained by observing the influences of solution pH, adsorbent dosage, initial solution concentration, contact time and temperature. The optimum adsorption efficiencies were determined at pH 2.8 and pH 4.0 for Fe(III) and Cr(III) metal ion solutions, respectively. The experimental data were modelled by different isotherm models and the equilibriums were well described by the Langmuir adsorption isotherm model. The pseudo-first-order, pseudo-second-order kinetic, intra-particle diffusion and Elovich models were applied to analyze the kinetic data and to evaluate rate constants. The pseudo-second-order kinetic model gave a better fit than the others. The thermodynamic parameters, such as Gibbs free energy change ΔG°, standard enthalpy change ΔH° and standard entropy change ΔS° were evaluated. The thermodynamic study showed the adsorption was a spontaneous endothermic process.

A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis.

PubMed

Jones, Hannah B L; Wells, Stephen A; Prentice, Erica J; Kwok, Anthony; Liang, Liyin L; Arcus, Vickery L; Pudney, Christopher R

2017-09-01

Our understanding of how enzymes work is coloured by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins, however, exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover. Herein we apply combined pressure and temperature kinetics studies to elucidate the full suite of thermodynamic parameters defining an enzyme FEL as it relates to enzyme turnover. We find that the key thermodynamic parameters governing vibrational modes related to enzyme turnover are the isobaric expansivity term and the change in heat capacity for enzyme catalysis. Variation in the enzyme FEL affects these terms. Our analysis is supported by a range of biophysical and computational approaches that specifically capture information on protein vibrational modes and the FEL (all atom flexibility calculations, red edge excitation shift spectroscopy and viscosity studies) that provide independent evidence for our findings. Our data suggest that restricting the enzyme FEL may be a powerful strategy when attempting to rationally engineer enzymes, particularly to alter thermal activity. Moreover, we demonstrate how rational predictions can be made with a rapid computational approach. © 2017 Federation of European Biochemical Societies.

Ultrasound assisted intensification of enzyme activity and its properties: a mini-review.

PubMed

Nadar, Shamraja S; Rathod, Virendra K

2017-08-22

Over the last decade, ultrasound technique has emerged as the potential technology which shows large applications in food and biotechnology processes. Earlier, ultrasound has been employed as a method of enzyme inactivation but recently, it has been found that ultrasound does not inactivate all enzymes, particularly, under mild conditions. It has been shown that the use of ultrasonic treatment at appropriate frequencies and intensity levels can lead to enhanced enzyme activity due to favourable conformational changes in protein molecules without altering its structural integrity. The present review article gives an overview of influence of ultrasound irradiation parameters (intensity, duty cycle and frequency) and enzyme related factors (enzyme concentration, temperature and pH) on the catalytic activity of enzyme during ultrasound treatment. Also, it includes the effect of ultrasound on thermal kinetic parameters and Michaelis-Menten kinetic parameters (k m and V max ) of enzymes. Further, in this review, the physical and chemical effects of ultrasound on enzyme have been correlated with thermodynamic parameters (enthalpy and entropy). Various techniques used for investigating the conformation changes in enzyme after sonication have been highlighted. At the end, different techniques of immobilization for ultrasound treated enzyme have been summarized.

pH-dependent relationship between thermodynamic and kinetic stability in the denaturation of human phosphoglycerate kinase 1.

PubMed

Pey, Angel L

2014-08-01

Human phosphoglycerate kinase 1 (hPGK1) is a glycolytic enzyme essential for ATP synthesis, and it is implicated in different pathological conditions such as inherited diseases, oncogenesis and activation of drugs for cancer and viral treatments. Particularly, mutations in hPGK1 cause human PGK1 deficiency, a rate metabolic conformational disease. We have recently found that most of these mutations cause protein kinetic destabilization by significant changes in the structure/energetics of the transition state for irreversible denaturation. In this work, we explore the relationships between protein conformation, thermodynamic and kinetic stability in hPGK1 by performing comprehensive analyses in a wide pH range (2.5-8). hPGK1 remains in a native conformation at pH 5-8, but undergoes a conformational transition to a molten globule-like state at acidic pH. Interestingly, hPGK1 kinetic stability remains essentially constant at pH 6-8, but is significantly reduced when pH is decreased from 6 to 5. We found that this decrease in kinetic stability is caused by significant changes in the energetic/structural balance of the denaturation transition state, which diverge from those found for disease-causing mutations. We also show that protein kinetic destabilization by acidic pH is strongly linked to lower thermodynamic stability, while in disease-causing mutations seems to be linked to lower unfolding cooperativity. These results highlight the plasticity of the hPGK1 denaturation mechanism that responds differently to changes in pH and in disease-causing mutations. New insight is presented into the different factors contributing to hPGK1 thermodynamic and kinetic stability and the role of denaturation mechanisms in hPGK1 deficiency. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction

ERIC Educational Resources Information Center

Jeffery, Kathleen A.; Pelaez, Nancy; Anderson, Trevor R.

2018-01-01

To keep biochemistry instruction current and relevant, it is crucial to expose students to cutting-edge scientific research and how experts reason about processes governed by thermodynamics and kinetics such as protein folding and dynamics. This study focuses on how experts explain their research into this topic with the intention of informing…

Teaching Thermodynamics and Kinetics to Advanced General Chemistry Students and to Upper-Level Undergraduate Students Using PV Diagrams

ERIC Educational Resources Information Center

Iyengar, Srinivasan S.; deSouza, Romualdo T.

2014-01-01

We describe how complex concepts in macroscopic chemistry, namely, thermodynamics and kinetics, can be taught at considerable depth both at the first-year undergraduate as well as upper levels. We begin with a careful treatment of PV diagrams, and by pictorially integrating the appropriate area in a PV diagram, we introduce work. This starting…

Tailoring Thermodynamics and Kinetics for Hydrogen Storage in Complex Hydrides towards Applications.

PubMed

Liu, Yongfeng; Yang, Yaxiong; Gao, Mingxia; Pan, Hongge

2016-02-01

Solid-state hydrogen storage using various materials is expected to provide the ultimate solution for safe and efficient on-board storage. Complex hydrides have attracted increasing attention over the past two decades due to their high gravimetric and volumetric hydrogen densities. In this account, we review studies from our lab on tailoring the thermodynamics and kinetics for hydrogen storage in complex hydrides, including metal alanates, borohydrides and amides. By changing the material composition and structure, developing feasible preparation methods, doping high-performance catalysts, optimizing multifunctional additives, creating nanostructures and understanding the interaction mechanisms with hydrogen, the operating temperatures for hydrogen storage in metal amides, alanates and borohydrides are remarkably reduced. This temperature reduction is associated with enhanced reaction kinetics and improved reversibility. The examples discussed in this review are expected to provide new inspiration for the development of complex hydrides with high hydrogen capacity and appropriate thermodynamics and kinetics for hydrogen storage. © 2015 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetics and thermodynamics studies on the BMP-2 adsorption onto hydroxyapatite surface with different multi-morphological features.

PubMed

Lu, Zhiwei; Huangfu, Changxin; Wang, Yanying; Ge, Hongwei; Yao, Yao; Zou, Ping; Wang, Guangtu; He, Hua; Rao, Hanbing

2015-01-01

The effect of the surface topography on protein adsorption process is of great significance for designing hydroxyapatite (HA) ceramic material surfaces. In this work, three different topographies of HA materials HA-sheet, HA-rod, and HA-whisker were synthesized and testified by X-ray diffraction (XRD), Fourier transform infrared (FT-IR), Brunauer-Emmett-Teller (BET) and a field emission scanning electron microscopy (FE-SEM). We have systematically investigated the adsorption kinetics and thermodynamics of bone morphogenetic proteins (BMP-2) on the three different topography surfaces of HA, respectively. The results showed that the maximum adsorption capacities of HA-sheet, HA-rod and HA-whisker were (219.96 ± 10.18), (247.13 ± 12.35), and (354.67 ± 17.73) μg · g(-1), respectively. Kinetic parameters, rate constants, equilibrium adsorption capacities and related correlation coefficients, for each kinetic model were calculated as well as discussed. It demonstrated that the adsorption of BMP-2 onto HA could be described by the pseudo second-order equation. Adsorption of BMP-2 onto HA followed the Langmuir isotherm. It confirmed that compared with other samples HA-whisker had more adsorption sites for its high specific surface area which could provide more opportunities for protein molecules. The adsorption processes were endothermic (ΔH > 0), spontaneous (ΔG < 0) and entropy increasing (ΔS > 0). A possible adsorption mechanism has been proposed. In addition, the BMP-2 could be adsorbed to the surface which existed slight conformational changes by FT-IR. Copyright © 2015 Elsevier B.V. All rights reserved.

Kinetic Study on the CsXH3−X PW12O40/Fe-SiO2 Nanocatalyst for Biodiesel Production

PubMed Central

Feyzi, Mostafa; Norouzi, Leila; Rafiee, Hamid Reza

2013-01-01

The kinetic of the transesterification reaction over the CsXH3−XPW12O40/Fe-SiO2 catalyst prepared using sol-gel and impregnation procedures was investigated in different operational conditions. Experimental conditions were varied as follows: reaction temperature 323–333 K, methanol/oil molar ratio = 12/1, and the reaction time 0–240 min. The H3PW12O40 heteropolyacid has recently attracted significant attention due to its potential for application in the production of biodiesel, in either homogeneous or heterogeneous catalytic conditions. Although fatty acids esterification reaction has been known for some time, data is still scarce regarding kinetic and thermodynamic parameters, especially when catalyzed by nonconventional compounds such as H3PW12O40. Herein, a kinetic study utilizing Gc-Mas in situ allows for evaluating the effects of operation conditions on reaction rate and determining the activation energy along with thermodynamic constants including ΔG, ΔS, and ΔH. It indicated that the CsXH3−XPW12O40/Fe-SiO2 magnetic nanocatalyst can be easily recycled with a little loss by magnetic field and can maintain higher catalytic activity and higher recovery even after being used 5 times. Characterization of catalyst was carried out by using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform-infrared spectroscopy (FT-IR), N2 adsorption-desorption measurements methods, thermal gravimetric analysis (TGA), and differential scanning calorimetry (DSC). PMID:24391465

Preparation, characterization, non-isothermal reaction kinetics, thermodynamic properties, and safety performances of high nitrogen compound: hydrazine 3-nitro-1,2,4-triazol-5-one complex.

PubMed

Yi, Jian-Hua; Zhao, Feng-Qi; Gao, Hong-Xu; Xu, Si-Yu; Wang, Min-Chang; Hu, Rong-Zu

2008-05-01

A new high nitrogen compound hydrazine 3-nitro-1,2,4-triazol-5-one complex (HNTO) was prepared by the reaction of 3-nitro-1,2,4-triazol-5-one with hydrazine hydrate, and its structure was characterized by means of organic elemental analyzer, FT-IR, XRD, (13)C NMR and (15)N NMR. The non-isothermal reaction kinetics of the main exothermic decomposition reaction of HNTO was investigated by means of DSC. The thermodynamic properties of HNTO were calculated. The results showed that the formation of HNTO is achieved by proton transfer of N(4) atom, and it makes a higher nitrogen content and lower acidity. The reaction mechanism of HNTO is classified as nucleation and growth, and the mechanism function is Avramo-Erofeev equation with n=2/5. The kinetic parameters of the reaction are E(a)=195.29 kJ mol(-1), lg(A (s(-1)))=19.37, respectively. The kinetic equation can be expressed as: d(alpha)/d(t) = 10(18.97)(1 - alpha)[-ln(1 - alpha)](3/5) e(-2.35 x 10(4)/T). The safety performances of HNTO were carried out. The critical temperature of thermal explosion are 464.26 and 474.37 K, the adiabatic time-to-explosion is 262s, the impact sensitivity H(50)=45.7 cm, the friction sensitivity P=20% and the electrostatic spark sensitivity E(50)>5.4J (no ignition). It shows that HNTO has an insensitive nature as RDX and NTO, etc.

Spontaneous Unfolding-Refolding of Fibronectin Type III Domains Assayed by Thiol Exchange

PubMed Central

Shah, Riddhi; Ohashi, Tomoo; Erickson, Harold P.; Oas, Terrence G.

2017-01-01

Globular proteins are not permanently folded but spontaneously unfold and refold on time scales that can span orders of magnitude for different proteins. A longstanding debate in the protein-folding field is whether unfolding rates or folding rates correlate to the stability of a protein. In the present study, we have determined the unfolding and folding kinetics of 10 FNIII domains. FNIII domains are one of the most common protein folds and are present in 2% of animal proteins. FNIII domains are ideal for this study because they have an identical seven-strand β-sandwich structure, but they vary widely in sequence and thermodynamic stability. We assayed thermodynamic stability of each domain by equilibrium denaturation in urea. We then assayed the kinetics of domain opening and closing by a technique known as thiol exchange. For this we introduced a buried Cys at the identical location in each FNIII domain and measured the kinetics of labeling with DTNB over a range of urea concentrations. A global fit of the kinetics data gave the kinetics of spontaneous unfolding and refolding in zero urea. We found that the folding rates were relatively similar, ∼0.1–1 s−1, for the different domains. The unfolding rates varied widely and correlated with thermodynamic stability. Our study is the first to address this question using a set of domains that are structurally homologous but evolved with widely varying sequence identity and thermodynamic stability. These data add new evidence that thermodynamic stability correlates primarily with unfolding rate rather than folding rate. The study also has implications for the question of whether opening of FNIII domains contributes to the stretching of fibronectin matrix fibrils. PMID:27909052

The atmospheric heat engine response to climate change

NASA Astrophysics Data System (ADS)

Pauluis, O. M.

2014-12-01

Moist convection is characterized by complex interactions between dynamics and thermodynamics. As air parcels within the atmosphere, they experience multiple thermodynamic transformations, such as compression and expansion, diabatic heating and cooling, condensation and mixing. These transformations correspond to those of a heat engine that produces kinetic energy while transporting energy from a warm source to a colder sink. This atmospheric heat engine is however directly affected by moist processes. First, falling precipitation acts as a break on the circulation by dissipating a significant amount of kinetic energy. Second, evaporation of unsaturated water and diffusion of water vapor are irrevesible processes that also reduce the amount of work that can be produced. An important challenge is to quantify the impacts that these two effects have on the generation of kinetic energy. Here, I will introduce a new technique - the Mean Air Flow As Lagragian Dynamics Approximation (MAFALDA) - that can be used to systematically analyze the thermodynamic behavior of complex atmospheric flows. This approach relies on sorting the upward mass transport in terms of the equivalent potential temperature of the air parcels to obtain an isentropic streamfunction. This streamfunction is then used to determine the thermodynamic evolution of air parcels as they move through the atmosphere. This approach is applied to analyze how convective systems would behave in a warmer climate. It is shown that an increase in atmospheric temperature lead to a significant increase of the amount of kinetic energy that is produced per unit of mass of air transported. At the same time, the total generation of kinetic energy is only slightly affected. Taken together, these findings imply that, in a warming atmosphere, the number of intense convective events will be reduced, while their intensity should increase. I will also discuss the new possibility of systematically studying the thermodynamic transformation in atmospheric models.

An Intuitive Approach to Steady-State Kinetics.

ERIC Educational Resources Information Center

Raines, Ronald T.; Hansen, David E.

1988-01-01

Attempts to provide an intuitive understanding of steady state kinetics. Discusses the meaning of steady state and uses free energy profiles to illustrate and follow complex kinetic and thermodynamic relationships. Provides examples with explanations. (MVL)

Classical and Quantum Thermal Physics

NASA Astrophysics Data System (ADS)

Prasad, R.

2016-11-01

List of figures; List of tables; Preface; Acknowledgement; Dedication; 1. The kinetic theory of gases; 2. Ideal to real gas, viscosity, conductivity and diffusion; 3. Thermodynamics: definitions and Zeroth law; 4. First Law of Thermodynamics and some of its applications; 5. Second Law of Thermodynamics and some of its applications; 6. TdS equations and their applications; 7. Thermodynamic functions, potentials, Maxwell equations, the Third Law and equilibrium; 8. Some applications of thermodynamics to problems of physics and engineering; 9. Application of thermodynamics to chemical reactions; 10. Quantum thermodynamics; 11. Some applications of quantum thermodynamics; 12. Introduction to the thermodynamics of irreversible processes; Index.

Microbial respiration and dissolution precipitation reactions of minerals: thermo-kinetics and reactive transport modelling

NASA Astrophysics Data System (ADS)

Azaroual, M. M.; Parmentier, M.; Andre, L.; Croiset, N.; Pettenati, M.; Kremer, S.

2010-12-01

Microbial processes interact closely with abiotic geochemical reactions and mineralogical transformations in several hydrogeochemical systems. Reactive transport models are aimed to analyze these complex mechanisms integrating as well as the degradation of organic matter as the redox reactions involving successive terminal electron acceptors (TEAPs) mediated by microbes through the continuum of unsaturated zone (soil) - saturated zone (aquifer). The involvement of microbial processes in reactive transport in soil and subsurface geologic greatly complicates the mastery of the major mechanisms and the numerical modelling of these systems. The introduction of kinetic constraints of redox reactions in aqueous phase requires the decoupling of equilibrium reactions and the redefinition of mass balance of chemical elements including the concept of basis species and secondary species of thermodynamic databases used in geochemical modelling tools. An integrated methodology for modelling the reactive transport has been developed and implemented to simulate the transfer of arsenic, denitrification processes and the role of metastable aqueous sulfur species with pyrite and organic matter as electron donors entities. A mechanistic rate law of microbial respiration in various geochemical environments was used to simulate reactive transport of arsenic, nitrate and organic matter combined to the generalized rate law of mineral dissolution - precipitation reactions derived from the transition state theory was used for dissolution - precipitation of silica, aluminosilicate, carbonate, oxyhydroxide, and sulphide minerals. The kinetic parameters are compiled from the literature measurements based on laboratory constrained experiments and field observations. Numerical simulations, using the geochemical software PHREEQC, were performed aiming to identify the key reactions mediated by microbes in the framework of in the first hand the concept of the unsaturated - saturated zones of an artificial recharge of deep aquifers system and in a second hand an acid mine drainage system. A large amount of data is available on the old mine site of Cheni (France). This field data on acid mine drainage are compared to a thermokinetic model including biological kinetics, precipitation-dissolution kinetics and surface complexation on ferrihydrite. The kinetic parameters are from literature and from a fitting on batch biological experiments. The integrated approach combining reaction kinetics and biogeochemical thermodynamic constraints is successfully applied to denitrification experiments in the presence of acetate and pyrite conducted in the laboratory for batch and column systems. The powerful of this coupled approach allows a fine description of the different transition species from nitrate to nitrogen. The fitted kinetic parameters established for modelling these laboratory results are thus extended to simulate the denitrification processes in a field case where organic matter and pyrite FeS2 are the electron donors and O2, NO3, Fe(OH)3, SO4 are the electron acceptors in the framework of a continuum UZ - SZ aiming to identify the stabilized redox zones of acid mine drainage. The detailed results obtained on two actual case studies will be presented.

Derived and thiourea-functionalized silica for cadmium removal: isotherm, kinetic and thermodynamic studies

NASA Astrophysics Data System (ADS)

Omotunde, Iyanu; Okoronkwo, Afamefuna; Oluwashina, Olugbenga

2018-03-01

The present study explored the feasibility of using derived and thiourea-functionalized silica as adsorbent for the removal of cadmium under different experimental conditions. Effects of various parameters such as function of point of zero charge (pHPZC), solution pH, sorbent-sorbate resident time and ratio, concentration and temperature were investigated. The sorption of cadmium followed the pseudo-second-order rate kinetics. Thermodynamic studies revealed that the sorption of cadmium was endothermic and spontaneous, with good affinity toward the sorbent. Various isotherm models, viz. Langmuir, Freundlich, Temkin, Dubinin-Radushkevich, Harkins-Jura, and Halsey isotherms were used to analyze the equilibrium data at different temperatures. The Freundlich, Halsey, Langmuir, and Temkin models were found to be in good agreement with the experimental data with high R 2, low RMSE, and low χ 2 values. The results show that the sorption capacity increases with an increase in solution temperature from 28 to 65 °C. The maximum sorption capacity calculated from Langmuir isotherm was 27.55 and 28.41 mg g-1 for derived and thiourea-functionalized silica, respectively, at optimum condition of pH 5 and contact time of 120 min.

Theories of binary fluid mixtures: from phase-separation kinetics to active emulsions

NASA Astrophysics Data System (ADS)

Cates, Michael E.; Tjhung, Elsen

2018-02-01

Binary fluid mixtures are examples of complex fluids whose microstructure and flow are strongly coupled. For pairs of simple fluids, the microstructure consists of droplets or bicontinuous demixed domains and the physics is controlled by the interfaces between these domains. At continuum level, the structure is defined by a composition field whose gradients which are steep near interfaces drive its diffusive current. These gradients also cause thermodynamic stresses which can drive fluid flow. Fluid flow in turn advects the composition field, while thermal noise creates additional random fluxes that allow the system to explore its configuration space and move towards the Boltzmann distribution. This article introduces continuum models of binary fluids, first covering some well-studied areas such as the thermodynamics and kinetics of phase separation, and emulsion stability. We then address cases where one of the fluid components has anisotropic structure at mesoscopic scales creating nematic (or polar) liquid-crystalline order; this can be described through an additional tensor (or vector) order parameter field. We conclude by outlining a thriving area of current research, namely active emulsions, in which one of the binary components consists of living or synthetic material that is continuously converting chemical energy into mechanical work.

Mutational analysis of the antigenomic trans-acting delta ribozyme: the alterations of the middle nucleotides located on the P1 stem.

PubMed Central

Ananvoranich, S; Lafontaine, D A; Perreault, J P

1999-01-01

Our previous report on delta ribozyme cleavage using a trans -acting antigenomic delta ribozyme and a collection of short substrates showed that the middle nucleotides of the P1 stem, the substrate binding site, are essential for the cleavage activity. Here we have further investigated the effect of alterations in the P1 stem on the kinetic and thermodynamic parameters of delta ribozyme cleavage using various ribozyme variants carrying single base mutations at putative positions reported. The kinetic and thermodynamic values obtained in mutational studies of the two middle nucleotides of the P1 stem suggest that the binding and active sites of the delta ribozyme are uniquely formed. Firstly, the substrate and the ribozyme are engaged in the formation of a helix, known as the P1 stem, which may contain a weak hydrogen bond(s) or a bulge. Secondly, a tertiary interaction involving the base moieties in the middle of the P1 stem likely plays a role in defining the chemical environment. As a con-sequence, the active site might form simultaneously or subsequently to the binding site during later steps of the pathway. PMID:10037808

Adsorption of methyl orange from aqueous solution using chitosan/diatomite composite.

PubMed

Zhao, Peng; Zhang, Runhu; Wang, Jianglin

2017-04-01

A novel chitosan/diatomite composite was prepared by a simple mixture in the mass ratio to remove methyl orange (MO) from aqueous media in this study. The composite adsorbent was characterized by Fourier transform infrared spectroscopy and scanning electron microscopy analysis. The parameters to influence the adsorption of MO were studied under such conditions as kinetics, adsorption isotherm, pH effect, and thermodynamics. The results revealed that adsorption of MO was initially rapid and the equilibrium time was reached after 40 min. The optimal value of the pH was 5.0 for better adsorption. The equilibrium data were well fitted to the Langmuir isotherm compared to the Freundlich isotherm, and exhibited the highest capacity and a removal rate of 88.37% under an initial dye concentration of 50 mg/L. The kinetic data were well described by the pseudo-second order model. The thermodynamic calculations revealed that the sorption was viable, spontaneous, and exothermic under the conditions studied. In addition, the chitosan/diatomite composite had good adsorption and desorption performance with respect to reusability after six cycles. These results showed that the chitosan/diatomite could be considered as a potential adsorbent for the removal of MO in aqueous solution.

A study of equilibrium and FTIR, SEM/EDS analysis of trimethoprim adsorption onto K10

NASA Astrophysics Data System (ADS)

Bekçi, Zehra; Seki, Yoldaş; Kadir Yurdakoç, M.

2007-02-01

The sorption behavior of K10, a type of montmorillonite for trimethoprim (TMP) drug, was studied by using batch technique under different pH and temperature. The interaction between K10 and TMP was investigated using SEM, and FTIR. It was observed that adsorption was increased between pH 2.5 and 6.3. By performing kinetic experiments, the pseudo-second-order kinetic model provides the best fit for TMP adsorption onto K10 montmorillonite. The sorption of TMP reached the equilibrium state after 6 h sorption time and has been described by using Langmuir, Freundlich and Dubinin-Radushkevich equations to obtain adsorption capacity values. The results indicate that the relative adsorption capacity values ( Kf) are decreasing with the increase of temperature in the range of 298-318 K. The sorption energy values obtained from DR isotherm show that sorption of TMP onto K10 can be explained by ion exchange mechanism at 298, 308 and 318 K. The thermodynamic studies were conducted to find the thermodynamic parameters Δ H°, Δ S° and Δ G°. It was determined that adsorption process is spontaneous and exothermic in nature.

DFT analysis of the reaction paths of formaldehyde decomposition on silver.

PubMed

Montoya, Alejandro; Haynes, Brian S

2009-07-16

Periodic density functional theory is used to study the dehydrogenation of formaldehyde (CH(2)O) on the Ag(111) surface and in the presence of adsorbed oxygen or hydroxyl species. Thermodynamic and kinetic parameters of elementary surface reactions have been determined. The dehydrogenation of CH(2)O on clean Ag(111) is thermodynamically and kinetically unfavorable. In particular, the activation energy for the first C-H bond scission of adsorbed CH(2)O (25.8 kcal mol(-1)) greatly exceeds the desorption energy for molecular CH(2)O (2.5 kcal mol(-1)). Surface oxygen promotes the destruction of CH(2)O through the formation of CH(2)O(2), which readily decomposes to CHO(2) and then in turn to CO(2) and adsorbed hydrogen. Analysis of site selectivity shows that CH(2)O(2), CHO(2), and CHO are strongly bound to the surface through the bridge sites, whereas CO and CO(2) are weakly adsorbed with no strong preference for a particular surface site. Dissociation of CO and CO(2) on the Ag(111) surface is highly activated and therefore unfavorable with respect to their molecular desorption.

Monodisperse self-assembly in a model with protein-like interactions

NASA Astrophysics Data System (ADS)

Wilber, Alex W.; Doye, Jonathan P. K.; Louis, Ard A.; Lewis, Anna C. F.

2009-11-01

We study the self-assembly behavior of patchy particles with "proteinlike" interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parameters of the model and find robust assembly of all target structures considered. Optimal assembly occurs in the region of parameter space where a free energy barrier regulates the rate of nucleation, thus preventing the premature exhaustion of the supply of monomers that can lead to the formation of incomplete shells. The interactions also need to be specific enough to prevent the assembly of malformed shells, but while maintaining kinetic accessibility. Free energy landscapes computed for our model have a funnel-like topography guiding the system to form the target structure and show that the torsional component of the interparticle interactions prevents the formation of disordered aggregates that would otherwise act as kinetic traps.

A breakthrough biosorbent in removing heavy metals: Equilibrium, kinetic, thermodynamic and mechanism analyses in a lab-scale study.

PubMed

Abdolali, Atefeh; Ngo, Huu Hao; Guo, Wenshan; Lu, Shaoyong; Chen, Shiao-Shing; Nguyen, Nguyen Cong; Zhang, Xinbo; Wang, Jie; Wu, Yun

2016-01-15

A breakthrough biosorbent namely multi-metal binding biosorbent (MMBB) made from a combination of tea wastes, maple leaves and mandarin peels, was prepared to evaluate their biosorptive potential for removal of Cd(II), Cu(II), Pb(II) and Zn(II) from multi-metal aqueous solutions. FTIR and SEM were conducted, before and after biosorption, to explore the intensity and position of the available functional groups and changes in adsorbent surface morphology. Carboxylic, hydroxyl and amine groups were found to be the principal functional groups for the sorption of metals. MMBB exhibited best performance at pH 5.5 with maximum sorption capacities of 31.73, 41.06, 76.25 and 26.63 mg/g for Cd(II), Cu(II), Pb(II) and Zn(II), respectively. Pseudo-first and pseudo-second-order models represented the kinetic experimental data in different initial metal concentrations very well. Among two-parameter adsorption isotherm models, the Langmuir equation gave a better fit of the equilibrium data. For Cu(II) and Zn(II), the Khan isotherm describes better biosorption conditions while for Cd(II) and Pb(II), the Sips model was found to provide the best correlation of the biosorption equilibrium data. The calculated thermodynamic parameters indicated feasible, spontaneous and exothermic biosorption process. Overall, this novel MMBB can effectively be utilized as an adsorbent to remove heavy metal ions from aqueous solutions. Copyright © 2015 Elsevier B.V. All rights reserved.

Thermodynamic and kinetic analyses of the CO2 chemisorption mechanism on Na2TiO3: Experimental and theoretical evidences

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

Duan, Yuhua

2014-01-01

ABSTRACT: Sodium metatitanate (Na2TiO3) was successfully synthesized via a solid-state reaction. The Na2TiO3 structure and microstructure were characterized using X-ray diffraction, scanning and transmission electron microscopy, and N2 adsorption. Then, the CO2 chemisorption mechanism on Na2TiO3 was systematically analyzed to determine the influence of temperature. The CO2 chemisorption capacity of Na2TiO3 was evaluated both dynamically and isothermally, and the products were reanalyzed to elucidate the Na2TiO3-CO2 reaction mechanism. Different chemical species (Na2CO3, Na2O, and Na4Ti5O12 or Na16Ti10O28) were identified during the CO2 capture process in Na2TiO3. In addition, some CO2 chemisorption kinetic parameters were determined. The ΔH‡ was found tomore » be 140.9 kJ/mol, to the Na2TiO3-CO2 system, between 600 and 780 °C. Results evidenced that CO2 chemisorption on Na2TiO3 highly depends on the reaction temperature. Furthermore, the experiments were theoretically supported by different thermodynamic calculations. The calculated thermodynamic properties of CO2 capture reactions by (Na2TiO3, Na4Ti5O12, and Na16Ti10O28) sodium titanates were fully investigated.« less

Removal of Direct Red 23 from aqueous solution using corn stalks: Isotherms, kinetics and thermodynamic studies

NASA Astrophysics Data System (ADS)

Fathi, M. R.; Asfaram, A.; Farhangi, A.

2015-01-01

The objective of this study was to assess the suitability and efficiency of corn stalk (CS) for the removal of diazo dye Direct Red 23 (DR23) from aqueous solutions. The effect of different variables in the batch method as a function of solution pH, contact time, initial dye concentration, CS amount, temperature, and so forth by the optimization method has been investigated. The color reduction was monitored by spectrophotometry at 503 nm before and after DR23 adsorption on the CS, and the removal percentage was calculated using the difference in absorbance. The sorption processes followed the pseudo second order in addition to intraparticle diffusion kinetics models with a good correlation coefficient with the overall entire adsorption of DR23 on adsorbent. The experimental equilibrium data were tested by four widely used isotherm models namely, Langmuir, Freundlich, Tempkin and Dubinin-Radushkevich (D-R). It was found that adsorption of DR23 on CS well with the Freindlich isotherm model, implying monolayer coverage of dye molecules onto the surface of the adsorbent. More than 99% removal efficiency was obtained within 10 min at adsorbent dose of 0.2 g for initial dye concentration of 10-90 mg L-1 at pH 3. Various thermodynamic parameters, such as Gibbs free energy, entropy, and enthalpy, of the ongoing adsorption process have been calculated. Judgment based on the obtained results of thermodynamic values shows the spontaneous and endothermic nature adsorption processes on adsorbent.

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

PubMed Central

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

2010-01-01

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

Thermodynamic and kinetic anisotropies in octane thin films.

PubMed

Haji-Akbari, Amir; Debenedetti, Pablo G

2015-12-07

Confinement breaks the translational symmetry of materials, making all thermodynamic and kinetic quantities functions of position. Such symmetry breaking can be used to obtain configurations that are not otherwise accessible in the bulk. Here, we use computer simulations to explore the effect of substrate-liquid interactions on thermodynamic and kinetic anisotropies induced by a solid substrate. We consider n-octane nano-films that are in contact with substrates with varying degrees of attraction, parameterized by an interaction parameter ϵS. Complete freezing of octane nano-films is observed at low temperatures, irrespective of ϵS, while at intermediate temperatures, a frozen monolayer emerges at solid-liquid and vapor-liquid interfaces. By carefully inspecting the profiles of translational and orientational relaxation times, we confirm that the translational and orientational degrees of freedom are decoupled at these frozen monolayers. At sufficiently high temperatures, however, free interfaces and solid-liquid interfaces close to loose (low-ϵS) substrates undergo "pre-freezing," characterized by mild peaks in several thermodynamic quantities. Two distinct dynamic regimes are observed at solid-liquid interfaces. The dynamics is accelerated in the vicinity of loose substrates, while sticky (high-ϵS) substrates decelerate dynamics, sometimes by as much as two orders of magnitude. These two distinct dynamical regimes have been previously reported by Haji-Akbari and Debenedetti [J. Chem. Phys. 141, 024506 (2014)] for a model atomic glass-forming liquid. We also confirm the existence of two correlations-proposed in the above-mentioned work-in solid-liquid subsurface regions of octane thin films, i.e., a correlation between atomic density and normal stress, and between atomic translational relaxation time and lateral stress. Finally, we inspect the ability of different regions of an octane film to explore the potential energy landscape by performing inherent structure calculations, and observe no noticeable difference between the free surface and the bulk in efficiently exploring the potential energy landscape. This is unlike the films of model atomic glass formers that tend to sample their respective landscape more efficiently at free surfaces. We discuss the implications of this finding to the ability of octane-and other n-alkanes-to form ultrastable glasses.

Contact Angle and Adhesion Dynamics and Hysteresis on Molecularly Smooth Chemically Homogeneous Surfaces.

PubMed

Chen, Szu-Ying; Kaufman, Yair; Schrader, Alex M; Seo, Dongjin; Lee, Dong Woog; Page, Steven H; Koenig, Peter H; Isaacs, Sandra; Gizaw, Yonas; Israelachvili, Jacob N

2017-09-26

Measuring truly equilibrium adhesion energies or contact angles to obtain the thermodynamic values is experimentally difficult because it requires loading/unloading or advancing/receding boundaries to be measured at rates that can be slower than 1 nm/s. We have measured advancing-receding contact angles and loading-unloading adhesion energies for various systems and geometries involving molecularly smooth and chemically homogeneous surfaces moving at different but steady velocities in both directions, ±V, focusing on the thermodynamic limit of ±V → 0. We have used the Bell Theory (1978) to derive expressions for the dynamic (velocity-dependent) adhesion energies and contact angles suitable for both (i) dynamic adhesion measurements using the classic Johnson-Kendall-Roberts (JKR, 1971) theory of "contact mechanics" and (ii) dynamic contact angle hysteresis measurements of both rolling droplets and syringe-controlled (sessile) droplets on various surfaces. We present our results for systems that exhibited both steady and varying velocities from V ≈ 10 mm/s to 1 nm/s, where in all cases but one, the advancing (V > 0) and receding (V < 0) adhesion energies and/or contact angles converged toward the same theoretical (thermodynamic) values as V → 0. Our equations for the dynamic contact angles are similar to the classic equations of Blake & Haynes (1969) and fitted the experimental adhesion data equally well over the range of velocities studied, although with somewhat different fitting parameters for the characteristic molecular length/dimension or area and characteristic bond formation/rupture lifetime or velocity. Our theoretical and experimental methods and results unify previous kinetic theories of adhesion and contact angle hysteresis and offer new experimental methods for testing kinetic models in the thermodynamic, quasi-static, limit. Our analyses are limited to kinetic effects only, and we conclude that hydrodynamic, i.e., viscous, and inertial effects do not play a role at the interfacial velocities of our experiments, i.e., V < (1-10) mm/s (for water and hexadecane, but for viscous polymers it may be different), consistent with previously reported studies.

Comparative absorption spectroscopy involving 4f-4f transitions to explore the kinetics of simultaneous coordination of uracil with Nd(III) and Zn(II) and its associated thermodynamics

NASA Astrophysics Data System (ADS)

Victory Devi, Ch.; Rajmuhon Singh, N.

2011-10-01

The interaction of uracil with Nd(III) has been explored in presence and absence of Zn(II) using the comparative absorption spectroscopy involving the 4f-4f transitions in different solvents. The complexation of uracil with Nd(III) is indicated by the change in intensity of 4f-4f bands expressing in terms of significant change in oscillator strength and Judd-Ofelt parameters. Intensification of this bands became more prominent in presence of Zn(II) suggesting the stimulative effect of Zn(II) towards the complexation of Nd(III) with uracil. Other spectral parameters namely Slator-Condon ( Fk's), nephelauxetic effect ( β), bonding ( b1/2) and percent covalency ( δ) parameters are computed to correlate their simultaneous binding of metal ions with uracil. The sensitivities of the observed 4f-4f transitions towards the minor coordination changes around Nd(III) has been used to monitor the simultaneous coordination of uracil with Nd(III) and Zn(II). The variation of intensities (oscillator strengths and Judd-Ofelt parameters) of 4f-4f bands during the complexation has helped in following the heterobimetallic complexation of uracil. Rate of complexation with respect to hypersensitive transition was evaluated. Energy of activation and thermodynamic parameters for the complexation reaction were also determined.

Theoretical prediction of crystallization kinetics of a supercooled Lennard-Jones fluid

NASA Astrophysics Data System (ADS)

Gunawardana, K. G. S. H.; Song, Xueyu

2018-05-01

The first order curvature correction to the crystal-liquid interfacial free energy is calculated using a theoretical model based on the interfacial excess thermodynamic properties. The correction parameter (δ), which is analogous to the Tolman length at a liquid-vapor interface, is found to be 0.48 ± 0.05 for a Lennard-Jones (LJ) fluid. We show that this curvature correction is crucial in predicting the nucleation barrier when the size of the crystal nucleus is small. The thermodynamic driving force (Δμ) corresponding to available simulated nucleation conditions is also calculated by combining the simulated data with a classical density functional theory. In this paper, we show that the classical nucleation theory is capable of predicting the nucleation barrier with excellent agreement to the simulated results when the curvature correction to the interfacial free energy is accounted for.

Study of Adsorption Mechanism of Congo Red on Graphene Oxide/PAMAM Nanocomposite

PubMed Central

Rafi, Mohammad; Samiey, Babak; Cheng, Chil-Hung

2018-01-01

Graphene oxide/poly(amidoamine) (GO/PAMAM) nanocomposite adsorbed high quantities of congo red (CR) anionic dye in 0.1 M NaCl solution, with the maximum adsorption capacity of 198 mg·g−1. The kinetics and thermodynamics of adsorption were investigated to elucidate the effects of pH, temperature, shaking rate, ionic strength, and contact time. Kinetic data were analyzed by the KASRA model and the KASRA, ISO, and pore-diffusion equations. Adsorption adsorption isotherms were studied by the ARIAN model and the Henry, Langmuir, and Temkin equations. It was shown that adsorption sites of GO/PAMAM at experimental conditions were phenolic hydroxyl groups of GO sheets and terminal amine groups of PAMAM dendrimer. Analysis of kinetic data indicated that amine sites were located on the surface, and that hydroxyl sites were placed in the pores of adsorbent. CR molecules interacted with the adsorption sites via hydrogen bonds. The molecules were adsorbed firstly on the amine sites, and then on the internal hydroxyl sites. Adsorption kinetic parameters indicated that the interaction of CR to the –NH3+ sites was the rate-controlling step of adsorption of CR on this site and adsorption activation energies calculated for different parts of this step. On the other hand, kinetic parameters showed that the intraparticle diffusion was the rate-controlling step during the interaction of CR molecules to –OH sites and activation energy of this step was not calculable. Finally, the used GO/PAMAM was completely regenerated by using ethylenediamine. PMID:29587463

Force feedback effects on single molecule hopping and pulling experiments

NASA Astrophysics Data System (ADS)

Rico-Pasto, M.; Pastor, I.; Ritort, F.

2018-03-01

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments.

Force feedback effects on single molecule hopping and pulling experiments.

PubMed

Rico-Pasto, M; Pastor, I; Ritort, F

2018-03-28

Single-molecule experiments with optical tweezers have become an important tool to study the properties and mechanisms of biological systems, such as cells and nucleic acids. In particular, force unzipping experiments have been used to extract the thermodynamics and kinetics of folding and unfolding reactions. In hopping experiments, a molecule executes transitions between the unfolded and folded states at a preset value of the force [constant force mode (CFM) under force feedback] or trap position [passive mode (PM) without feedback] and the force-dependent kinetic rates extracted from the lifetime of each state (CFM) and the rupture force distributions (PM) using the Bell-Evans model. However, hopping experiments in the CFM are known to overestimate molecular distances and folding free energies for fast transitions compared to the response time of the feedback. In contrast, kinetic rate measurements from pulling experiments have been mostly done in the PM while the CFM is seldom implemented in pulling protocols. Here, we carry out hopping and pulling experiments in a short DNA hairpin in the PM and CFM at three different temperatures (6 °C, 25 °C, and 45 °C) exhibiting largely varying kinetic rates. As expected, we find that equilibrium hopping experiments in the CFM and PM perform well at 6 °C (where kinetics are slow), whereas the CFM overestimates molecular parameters at 45 °C (where kinetics are fast). In contrast, nonequilibrium pulling experiments perform well in both modes at all temperatures. This demonstrates that the same kind of feedback algorithm in the CFM leads to more reliable determination of the folding reaction parameters in irreversible pulling experiments.

Thermal degradation of ternary blend films containing PVA/chitosan/vanillin

NASA Astrophysics Data System (ADS)

Kasai, Deepak; Chougale, Ravindra; Masti, Saraswati; Narasgoudar, Shivayogi

2018-05-01

The ternary chitosan/poly (vinyl alcohol)/vanillin blend films were prepared by solution casting method. The influence of equal weight percent of poly (vinyl alcohol) and vanillin on thermal stability of the chitosan blend films were investigated by using thermogravimetric analysis (TGA). The kinetic parameters such as enthalpy (ΔH*), entropy (ΔS*), and Gibbs free energy (ΔG*) in the first and second decomposition steps based on the thermogravimetric data were calculated. The thermal stabilities of the blend films were confirmed by thermodynamic parameters obtained in the activation energies, which indicated that increase in the equal weight percent of PVA/vanillin decreased the thermal stability of the chitosan film.

Phase transitions in tumor growth: V what can be expected from cancer glycolytic oscillations?

NASA Astrophysics Data System (ADS)

Martin, R. R.; Montero, S.; Silva, E.; Bizzarri, M.; Cocho, G.; Mansilla, R.; Nieto-Villar, J. M.

2017-11-01

Experimental evidence confirms the existence of glycolytic oscillations in cancer, which allows it to self-organize in time and space far from thermodynamic equilibrium, and provides it with high robustness, complexity and adaptability. A kinetic model is proposed for HeLa tumor cells grown in hypoxia conditions. It shows oscillations in a wide range of parameters. Two control parameters (glucose and inorganic phosphate concentration) were varied to explore the phase space, showing also the presence of limit cycles and bifurcations. The complexity of the system was evaluated by focusing on stationary state stability and Lempel-Ziv complexity. Moreover, the calculated entropy production rate was demonstrated behaving as a Lyapunov function.

Adsorption Properties of Low-Cost Biomaterial Derived from Prunus amygdalus L. for Dye Removal from Water

PubMed Central

Deniz, Fatih

2013-01-01

The capability of Prunus amygdalus L. (almond) shell for dye removal from aqueous solutions was investigated and methyl orange was used as a model compound. The effects of operational parameters including pH, ionic strength, adsorbent concentration and mesh size, dye concentration, contact time, and temperature on the removal of dye were evaluated. The adsorption kinetics conformed to the pseudo-second-order kinetic model. The equilibrium data pointed out excellent fit to the Langmuir isotherm model with maximum monolayer adsorption capacity of 41.34 mg g−1 at 293 K. Thermodynamic analysis proved a spontaneous, favorable, and exothermic process. It can be concluded that almond shell might be a potential low-cost adsorbent for methyl orange removal from aqueous media. PMID:23935442

Kinetics and mechanism of degradation of some 2-sulfanilamidopyrimidine derivatives. Part III. The use of Hammett equation for kinetic investigation of 2-sulfanilamidopyrimidine derivatives autoxidation.

PubMed

Zajac, M

1977-01-01

General first-order rate constants for autoxidation of sulfadiazine, sulfamerazine, sulfadimidine, sulfaperine and sulfamethoxydiazine in the air oxygen atmosphere, in solutions of pH 4-7, at 403, 411 and 418 K were determined from the absorbance measurements in 0-1 mole/dm3 HCl at 243 or 333 nm, using the so-called "subtraction technique". The thermodynamic parameters of this reaction were determined (deltaHa, deltaH not equal to, deltaS not equal to, deltaG not equal to and logA). The effect of the substituents in positions 4, 5 and 6 of the pyrimidine ring on the rate of autoxidation was interpreted in terms of the Hammett equation.

Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

NASA Astrophysics Data System (ADS)

Asgharzadeh, Somaie; Vahedpour, Morteza

2018-06-01

Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.

Biosorption of formic and acetic acids from aqueous solution using activated carbon from shea butter seed shells

NASA Astrophysics Data System (ADS)

Adekola, Folahan A.; Oba, Ismaila A.

2017-10-01

The efficiency of prepared activated carbon from shea butter seed shells (SB-AC) for the adsorption of formic acid (FA) and acetic acid (AA) from aqueous solution was investigated. The effect of optimization parameters including initial concentration, agitation time, adsorbent dosage and temperature of adsorbate solution on the sorption capacity were studied. The SB-AC was characterized for the following parameters: bulk density, moisture content, ash content, pH, Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The optimal conditions for the adsorption were established and the adsorption data for AA fitted Dubinin-Radushkevich (D-R) isotherm well, whereas FA followed Langmuir isotherm. The kinetic data were examined. It was found that pseudo-second-order kinetic model was found to adequately explain the sorption kinetic of AA and FA from aqueous solution. It was again found that intraparticle diffusion was found to explain the adsorption mechanism. Adsorption thermodynamic parameters were estimated and the negative values of Δ G showed that the adsorption process was feasible and spontaneous in nature, while the negative values of Δ H indicate that the adsorption process was exothermic. It is therefore established that SB-AC has good potential for the removal of AA and FA from aqueous solution. Hence, it should find application in the regular treatment of polluted water in aquaculture and fish breeding system.

Nickel(II) biosorption by Rhodotorula glutinis.

PubMed

Suazo-Madrid, Alicia; Morales-Barrera, Liliana; Aranda-García, Erick; Cristiani-Urbina, Eliseo

2011-01-01

The present study reports the feasibility of using Rhodotorula glutinis biomass as an alternative low-cost biosorbent to remove Ni(II) ions from aqueous solutions. Acetone-pretreated R. glutinis cells showed higher Ni(II) biosorption capacity than untreated cells at pH values ranging from 3 to 7.5, with an optimum pH of 7.5. The effects of other relevant environmental parameters, such as initial Ni(II) concentration, shaking contact time and temperature, on Ni(II) biosorption onto acetone-pretreated R. glutinis were evaluated. Significant enhancement of Ni(II) biosorption capacity was observed by increasing initial metal concentration and temperature. Kinetic studies showed that the kinetic data were best described by a pseudo-second-order kinetic model. Among the two-, three-, and four-parameter isotherm models tested, the Fritz-Schluender model exhibited the best fit to experimental data. Thermodynamic parameters (activation energy, and changes in activation enthalpy, activation entropy, and free energy of activation) revealed that the biosorption of Ni(II) ions onto acetone-pretreated R. glutinis biomass is an endothermic and non-spontaneous process, involving chemical sorption with weak interactions between the biosorbent and Ni(II) ions. The high sorption capacity (44.45 mg g(-1) at 25°C, and 63.53 mg g(-1) at 70°C) exhibited by acetone-pretreated R. glutinis biomass places this biosorbent among the best adsorbents currently available for removal of Ni(II) ions from aqueous effluents.

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.

Peptide self-assembly: thermodynamics and kinetics.

PubMed

Wang, Juan; Liu, Kai; Xing, Ruirui; Yan, Xuehai

2016-10-21

Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.

Comparisons of kinetics, thermodynamics and regeneration of tetramethylammonium hydroxide adsorption in aqueous solution with graphene oxide, zeolite and activated carbon

NASA Astrophysics Data System (ADS)

Chang, Shenteng; Lu, Chungsying; Lin, Kun-Yi Andrew

2015-01-01

Graphene oxide (GO), sodium Y-type zeolite (NaY) and granular activated carbon (GAC) are selected as adsorbents to study their kinetics, thermodynamics and regeneration of tetramethylammonium hydroxide (TMAH) adsorption from water. The adsorption kinetics follows the pseudo-second-order rate law while the adsorption thermodynamics shows an exothermic reaction with GO and GAC but displays an endothermic reaction with NaY. The adsorbed TMAH can be readily desorbed from the surface of GO and NaY by 0.05 M NaCl solution. A comparative study on the cyclic TMAH adsorption with GO, NaY and GAC is also conducted and the results reveal that GO exhibits the greatest TMAH adsorption capacity as well as superior reversibility of TMAH adsorption over 10 cycles of adsorption and desorption process. These features indicate that GO is a promising and efficient adsorbent for TMAH removal in wastewater treatment.

Thermodynamic and kinetic theory of nucleation, deliquescence and efflorescence transitions in the ensemble of droplets on soluble particles.

PubMed

Shchekin, Alexander K; Shabaev, Ilya V; Hellmuth, Olaf

2013-02-07

Thermodynamic and kinetic peculiarities of nucleation, deliquescence and efflorescence transitions in the ensemble of droplets formed on soluble condensation nuclei from a solvent vapor have been considered. The interplay of the effects of solubility and the size of condensation nuclei has been analyzed. Activation barriers for the deliquescence and phase transitions and for the reverse efflorescence transition have been determined as functions of the relative humidity of the vapor-gas atmosphere, initial size, and solubility of condensation nuclei. It has been demonstrated that, upon variations in the relative humidity of the atmosphere, the crossover in thermodynamically stable and unstable variables of the droplet state takes place. The physical meaning of stable and unstable variables has been clarified. The kinetic equations for establishing equilibrium and steady distributions of binary droplets have been solved. The specific times for relaxation, deliquescence and efflorescence transitions have been calculated.

Thermodynamics and kinetics of graphene chemistry: a graphene hydrogenation prototype study.

PubMed

Pham, Buu Q; Gordon, Mark S

2016-12-07

The thermodynamic and kinetic controls of graphene chemistry are studied computationally using a graphene hydrogenation reaction and polyaromatic hydrocarbons to represent the graphene surface. Hydrogen atoms are concertedly chemisorped onto the surface of graphene models of different shapes (i.e., all-zigzag, all-armchair, zigzag-armchair mixed edges) and sizes (i.e., from 16-42 carbon atoms). The second-order Z-averaged perturbation theory (ZAPT2) method combined with Pople double and triple zeta basis sets are used for all calculations. It is found that both the net enthalpy change and the barrier height of graphene hydrogenation at graphene edges are lower than at their interior surfaces. While the thermodynamic product distribution is mainly determined by the remaining π-islands of functionalized graphenes (Phys. Chem. Chem. Phys., 2013, 15, 3725-3735), the kinetics of the reaction is primarily correlated with the localization of the electrostatic potential of the graphene surface.

Kinetics and thermodynamics of chemical reactions in Li/SOCl2 cells

NASA Technical Reports Server (NTRS)

Hansen, Lee D.; Frank, Harvey

1987-01-01

Work is described that was designed to determine the kinetic constants necessary to extrapolate kinetic data on Li/SOCl2 cells over the temperature range from 25 to 75 C. A second objective was to characterize as far as possible the chemical reactions that occur in the cells since these reactions may be important in understanding the potential hazards of these cells. The kinetics of the corrosion processes in undischarged Li/SOCl2 cells were determined and separated according to their occurrence at the anode and cathode; the effects that switching the current on and off has on the corrosion reactions was determined; and the effects of discharge state on the kinetics of the corrosion process were found. A thermodynamic analysis of the current-producing reactions in the cell was done and is included.

Studies on Thorium Adsorption Characteristics upon Activated Titanium Hydroxide Prepared from Rosetta Ilmenite Concentrate

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

Gado, M, E-mail: parq28@yahoo.com; Zaki, S

2016-01-01

The titanium hydroxide prepared from Rosetta ilmenite concentrate has been applied for Th (IV) adsorption from its acid aqueous solutions. The prepared hydroxide is first characterized by both Fourier transform infrared (FT-IR) spectrum and thermogravimetric analysis. The relevant factors affecting the adsorption process have been studied. The obtained equilibrium data fits well with the Langmuir isotherm rather than Freundlich isotherm, while the adsorption kinetic data follow the pseudo-second order model. The different thermodynamic parameters have also been calculated and indicate that the adsorption process is spontaneous.

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

Reiche, Helmut Matthias; Vogel, Sven C.

New in situ data for the U-C system are presented, with the goal of improving knowledge of the phase diagram to enable production of new ceramic fuels. The none quenchable, cubic, δ-phase, which in turn is fundamental to computational methods, was identified. Rich datasets of the formation synthesis of uranium carbide yield kinetics data which allow the benchmarking of modeling, thermodynamic parameters etc. The order-disorder transition (carbon sublattice melting) was observed due to equal sensitivity of neutrons to both elements. This dynamic has not been accurately described in some recent simulation-based publications.

Combined Homogeneous Surface Diffusion Model - Design of experiments approach to optimize dye adsorption considering both equilibrium and kinetic aspects.

PubMed

Muthukkumaran, A; Aravamudan, K

2017-12-15

Adsorption, a popular technique for removing azo dyes from aqueous streams, is influenced by several factors such as pH, initial dye concentration, temperature and adsorbent dosage. Any strategy that seeks to identify optimal conditions involving these factors, should take into account both kinetic and equilibrium aspects since they influence rate and extent of removal by adsorption. Hence rigorous kinetics and accurate equilibrium models are required. In this work, the experimental investigations pertaining to adsorption of acid orange 10 dye (AO10) on activated carbon were carried out using Central Composite Design (CCD) strategy. The significant factors that affected adsorption were identified to be solution temperature, solution pH, adsorbent dosage and initial solution concentration. Thermodynamic analysis showed the endothermic nature of the dye adsorption process. The kinetics of adsorption has been rigorously modeled using the Homogeneous Surface Diffusion Model (HSDM) after incorporating the non-linear Freundlich adsorption isotherm. Optimization was performed for kinetic parameters (color removal time and surface diffusion coefficient) as well as the equilibrium affected response viz. percentage removal. Finally, the optimum conditions predicted were experimentally validated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermal degradation kinetics of all-trans and cis-carotenoids in a light-induced model system.

PubMed

Xiao, Ya-Dong; Huang, Wu-Yang; Li, Da-Jing; Song, Jiang-Feng; Liu, Chun-Quan; Wei, Qiu-Yu; Zhang, Min; Yang, Qiu-Ming

2018-01-15

Thermal degradation kinetics of lutein, zeaxanthin, β-cryptoxanthin, β-carotene was studied at 25, 35, and 45°C in a model system. Qualitative and quantitative analyses of all-trans- and cis-carotenoids were conducted using HPLC-DAD-MS technologies. Kinetic and thermodynamic parameters were calculated by non-linear regression. A total of 29 geometrical isomers and four oxidation products were detected, including all-trans-, keto compounds, mono-cis- and di-cis-isomers. Degradations of all-trans-lutein, zeaxanthin, β-cryptoxanthin, and β-carotene were described by a first-order kinetic model, with the order of rate constants as k β -carotene >k β -cryptoxanthin >k lutein >k zeaxanthin . Activation energies of zeaxanthin, lutein, β-cryptoxanthin, and β-carotene were 65.6, 38.9, 33.9, and 8.6kJ/moL, respectively. cis-carotenoids also followed with the first-order kinetic model, but they did not show a defined sequence of degradation rate constants and activation energies at different temperatures. A possible degradation pathway of four carotenoids was identified to better understand the mechanism of carotenoid degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

A minimal dissipation type-based classification in irreversible thermodynamics and microeconomics

NASA Astrophysics Data System (ADS)

Tsirlin, A. M.; Kazakov, V.; Kolinko, N. A.

2003-10-01

We formulate the problem of finding classes of kinetic dependencies in irreversible thermodynamic and microeconomic systems for which minimal dissipation processes belong to the same type. We show that this problem is an inverse optimal control problem and solve it. The commonality of this problem in irreversible thermodynamics and microeconomics is emphasized.

Affinity, Avidity, and Kinetics of Target Sequence Binding to LC8 Dynein Light Chain Isoforms*

PubMed Central

Radnai, László; Rapali, Péter; Hódi, Zsuzsa; Süveges, Dániel; Molnár, Tamás; Kiss, Bence; Bécsi, Bálint; Erdödi, Ferenc; Buday, László; Kardos, József; Kovács, Mihály; Nyitray, László

2010-01-01

LC8 dynein light chain (DYNLL) is a highly conserved eukaryotic hub protein with dozens of binding partners and various functions beyond being a subunit of dynein and myosin Va motor proteins. Here, we compared the kinetic and thermodynamic parameters of binding of both mammalian isoforms, DYNLL1 and DYNLL2, to two putative consensus binding motifs (KXTQTX and XG(I/V)QVD) and report only subtle differences. Peptides containing either of the above motifs bind to DYNLL2 with micromolar affinity, whereas a myosin Va peptide (lacking the conserved Gln) and the noncanonical Pak1 peptide bind with Kd values of 9 and 40 μm, respectively. Binding of the KXTQTX motif is enthalpy-driven, although that of all other peptides is both enthalpy- and entropy-driven. Moreover, the KXTQTX motif shows strikingly slower off-rate constant than the other motifs. As most DYNLL partners are homodimeric, we also assessed the binding of bivalent ligands to DYNLL2. Compared with monovalent ligands, a significant avidity effect was found as follows: Kd values of 37 and 3.5 nm for a dimeric myosin Va fragment and a Leu zipper dimerized KXTQTX motif, respectively. Ligand binding kinetics of DYNLL can best be described by a conformational selection model consisting of a slow isomerization and a rapid binding step. We also studied the binding of the phosphomimetic S88E mutant of DYNLL2 to the dimeric myosin Va fragment, and we found a significantly lower apparent Kd value (3 μm). We conclude that the thermodynamic and kinetic fine-tuning of binding of various ligands to DYNLL could have physiological relevance in its interaction network. PMID:20889982

Kinetics and thermodynamics of exonuclease-deficient DNA polymerases

NASA Astrophysics Data System (ADS)

Gaspard, Pierre

2016-04-01

A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependencies on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production are calculated analytically in terms of the rate constants and the concentrations. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

Protein control of true, gated, and coupled electron transfer reactions.

PubMed

Davidson, Victor L

2008-06-01

Electron transfer (ET) through and between proteins is a fundamental biological process. The rates of ET depend upon the thermodynamic driving force, the reorganization energy, and the degree of electronic coupling between the reactant and product states. The analysis of protein ET reactions is complicated by the fact that non-ET processes might influence the observed ET rate in kinetically complex biological systems. This Account describes studies of the methylamine dehydrogenase-amicyanin-cytochrome c-551i protein ET complex that have revealed the influence of several features of the protein structure on the magnitudes of the physical parameters for true ET reactions and how they dictate the kinetic mechanisms of non-ET processes that sometimes influence protein ET reactions. Kinetic and thermodynamic studies, coupled with structural information and biochemical data, are necessary to fully describe the ET reactions of proteins. Site-directed mutagenesis can be used to elucidate specific structure-function relationships. When mutations selectively alter the electronic coupling, reorganization energy, or driving force for the ET reaction, it becomes possible to use the parameters of the ET process to determine how specific amino acid residues and other features of the protein structure influence the ET rates. When mutations alter the kinetic mechanism for ET, one can determine the mechanisms by which non-ET processes, such as protein conformational changes or proton transfers, control the rates of ET reactions and how specific amino acid residues and certain features of the protein structure influence these non-ET reactions. A complete description of the mechanism of regulation of biological ET reactions enhances our understanding of metabolism, respiration, and photosynthesis at the molecular level. Such information has important medical relevance. Defective protein ET leads to production of the reactive oxygen species and free radicals that are associated with aging and many disease states. Defective ET within the respiratory chain also causes certain mitochondrial myopathies. An understanding of the mechanisms of regulation of protein ET is also of practical value because it provides a logical basis for the design of applications utilizing redox enzymes, such as enzyme-based electrode sensors and fuel cells.

Solute induced relaxation in glassy polymers: Experimental measurements and nonequilibrium thermodynamic model

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

Minelli, Matteo; Doghieri, Ferruccio

2014-05-15

Data for kinetics of mass uptake from vapor sorption experiments in thin glassy polymer samples are here interpreted in terms of relaxation times for volume dilation. To this result, both models from non-equilibrium thermodynamics and from mechanics of volume relaxation contribute. Different kind of sorption experiments have been considered in order to facilitate the direct comparison between kinetics of solute induced volume dilation and corresponding data from process driven by pressure or temperature jumps.

Impact of Alkyl Spacer Length on Aggregation Pathways in Kinetically Controlled Supramolecular Polymerization.

PubMed

Ogi, Soichiro; Stepanenko, Vladimir; Thein, Johannes; Würthner, Frank

2016-01-20

We have investigated the kinetic and thermodynamic supramolecular polymerizations of a series of amide-functionalized perylene bisimide (PBI) organogelator molecules bearing alkyl spacers of varied lengths (ethylene to pentylene chains, PBI-1-C2 to PBI-1-C5) between the amide and PBI imide groups. These amide-functionalized PBIs form one-dimensional fibrous nanostructures as the thermodynamically favored states in solvents of low polarity. Our in-depth studies revealed, however, that the kinetic behavior of their supramolecular polymerization is dependent on the spacer length. Propylene- and pentylene-tethered PBIs follow a similar polymerization process as previously observed for the ethylene-tethered PBI. Thus, the monomers of these PBIs are kinetically trapped in conformationally restricted states through intramolecular hydrogen bonding between the amide and imide groups. In contrast, the intramolecularly hydrogen-bonded monomers of butylene-tethered PBI spontaneously self-assemble into nanoparticles, which constitute an off-pathway aggregate state with regard to the thermodynamically stable fibrous supramolecular polymers obtained. Thus, for this class of π-conjugated system, an unprecedented off-pathway aggregate with high kinetic stability could be realized for the first time by introducing an alkyl linker of optimum length (C4 chain) between the amide and imide groups. Our current system with an energy landscape of two competing nucleated aggregation pathways is applicable to the kinetic control over the supramolecular polymerization by the seeding approach.

Improvement in low-temperature and instantaneous high-rate output performance of Al-free AB5-type hydrogen storage alloy for negative electrode in Ni/MH battery: Effect of thermodynamic and kinetic regulation via partial Mn substituting

NASA Astrophysics Data System (ADS)

Zhou, Wanhai; Zhu, Ding; Tang, Zhengyao; Wu, Chaoling; Huang, Liwu; Ma, Zhewen; Chen, Yungui

2017-03-01

A series of Al-free Mn-modified AB5-type hydrogen storage alloys have been designed and the effects of thermodynamic stability and electrochemical kinetics on electrochemical performance via Mn substituting have been investigated. Compared with high-Al alloys, the Al-free alloys in this study have better low-temperature performance and instantaneous high-rate output because of the higher surface catalytic ability. After partial substitution of Ni by Mn, both the hydrogen desorption capacity and plateau pressure decrease, and correspondingly results in an improved thermodynamic stability which is adverse to low-temperature delivery. Additionally, with the improvement of charge acceptance ability and anti-corrosion property via Mn substitution, the room-temperature discharge capacity and cycling stability increase slightly. However, Mn adversely affects the electrochemical kinetics and deteriorates both the surface catalytic ability and the bulk hydrogen diffusion ability, leading to the drop of low-temperature dischargeability, high-rate dischargeability and peak power (Ppeak). Based on the thermodynamic and kinetic regulation and overall electrochemical properties, the optimal composition is obtained when x = 0.2, the discharge capacity is 243.6 mAh g-1 at -40 °C with 60 mA g-1, and the Ppeak attains to 969.6 W kg-1 at -40 °C.

Ab Initio-Based Kinetic Modeling for the Design of Molecular Catalysts: The Case of H 2 Production Electrocatalysts

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

Ho, Ming-Hsun; Rousseau, Roger; Roberts, John A. S.

2015-09-04

Design of fast, efficient electrocatalysts for energy production and energy utilization requires a systematic approach to predict and tune the energetics of reaction intermediates and the kinetic barriers between them as well as to tune reaction conditions (e.g., concentration of reactants, acidity of the reaction medium, and applied electric potential). Thermodynamics schemes based on the knowledge of pKa values, hydride donor ability, redox potentials, and other relevant thermodynamic properties have been demonstrated to be very effective for exploring possible reaction pathways. We seek to identify high-energy intermediates, which may represent a catalytic bottleneck, and low-energy intermediates, which may represent amore » thermodynamic sink. In this study, working on a well-established Ni-based bioinspired electrocatalyst for H2 production, we performed a detailed kinetic analysis of the catalytic pathways to assess the limitations of our current (standard state) thermodynamic analysis with respect to prediction of optimal catalyst performance. To this end, we developed a microkinetic model based on extensive ab initio simulations. The model was validated against available experimental data, and it reproduces remarkably well the observed turnover rate as a function of the acid concentration and catalytic conditions, providing valuable information on the main factors limiting catalysis. Using this kinetic analysis as a reference, we show that indeed a purely thermodynamic analysis of the possible reaction pathways provides us with valuable information, such as a qualitative picture of the species involved during catalysis, identification of the possible branching points, and the origin of the observed overpotential, which are critical insights for electrocatalyst design. However, a significant limitation of this approach is understanding how these insights relate to rate, which is an equally critical piece of information. Taking our analysis a step further, we show that the kinetic model can easily be extended to different catalytic conditions by using linear free energy relationships for activation barriers based on simple thermodynamics quantities, such as pKa values. We also outline a possible procedure to extend it to other catalytic platforms, making it a general and effective way to design catalysts with improved performance.« less

Kinetics and equilibrium models for the sorption of tributyltin to nZnO, activated carbon and nZnO/activated carbon composite in artificial seawater.

PubMed

Ayanda, Olushola S; Fatoki, Olalekan S; Adekola, Folahan A; Ximba, Bhekumusa J

2013-07-15

The removal of tributyltin (TBT) from artificial seawater using nZnO, activated carbon and nZnO/activated carbon composite was systematically studied. The equilibrium and kinetics of adsorption were investigated in a batch adsorption system. Equilibrium adsorption data were analyzed using Langmuir, Freundlich, Temkin and Dubinin-Radushkevich (D-R) isotherm models. Pseudo first- and second-order, Elovich, fractional power and intraparticle diffusion models were applied to test the kinetic data. Thermodynamic parameters such as ΔG°, ΔS° and ΔH° were also calculated to understand the mechanisms of adsorption. Optimal conditions for the adsorption of TBT from artificial seawater were then applied to TBT removal from natural seawater. A higher removal efficiency of TBT (>99%) was obtained for the nZnO/activated carbon composite material and for activated carbon but not for nZnO. Copyright © 2013 Elsevier Ltd. All rights reserved.

Stepwise Adaptations to Low Temperature as Revealed by Multiple Mutants of Psychrophilic α-Amylase from Antarctic Bacterium*

PubMed Central

Cipolla, Alexandre; D'Amico, Salvino; Barumandzadeh, Roya; Matagne, André; Feller, Georges

2011-01-01

The mutants Mut5 and Mut5CC from a psychrophilic α-amylase bear representative stabilizing interactions found in the heat-stable porcine pancreatic α-amylase but lacking in the cold-active enzyme from an Antarctic bacterium. From an evolutionary perspective, these mutants can be regarded as structural intermediates between the psychrophilic and the mesophilic enzymes. We found that these engineered interactions improve all the investigated parameters related to protein stability as follows: compactness; kinetically driven stability; thermodynamic stability; resistance toward chemical denaturation, and the kinetics of unfolding/refolding. Concomitantly to this improved stability, both mutants have lost the kinetic optimization to low temperature activity displayed by the parent psychrophilic enzyme. These results provide strong experimental support to the hypothesis assuming that the disappearance of stabilizing interactions in psychrophilic enzymes increases the amplitude of concerted motions required by catalysis and the dynamics of active site residues at low temperature, leading to a higher activity. PMID:21900238

Revisiting kinetic boundary conditions at the surface of fuel droplet hydrocarbons: An atomistic computational fluid dynamics simulation

PubMed Central

Nasiri, Rasoul

2016-01-01

The role of boundary conditions at the interface for both Boltzmann equation and the set of Navier-Stokes equations have been suggested to be important for studying of multiphase flows such as evaporation/condensation process which doesn’t always obey the equilibrium conditions. Here we present aspects of transition-state theory (TST) alongside with kinetic gas theory (KGT) relevant to the study of quasi-equilibrium interfacial phenomena and the equilibrium gas phase processes, respectively. A two-state mathematical model for long-chain hydrocarbons which have multi-structural specifications is introduced to clarify how kinetics and thermodynamics affect evaporation/condensation process at the surface of fuel droplet, liquid and gas phases and then show how experimental observations for a number of n-alkane may be reproduced using a hybrid framework TST and KGT with physically reasonable parameters controlling the interface, gas and liquid phases. The importance of internal activation dynamics at the surface of n-alkane droplets is established during the evaporation/condensation process. PMID:27215897

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

PubMed Central

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

2014-01-01

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

The novel kinetics expression of Cadmium (II) removal using green adsorbent horse dung humic acid (Hd-Ha)

NASA Astrophysics Data System (ADS)

Basuki, Rahmat; Santosa, Sri Juari; Rusdiarso, Bambang

2017-03-01

Humic acid from dry horse dung powder has been prepared and this horse dung humic acid (HD-HA) was then applied as a sorbent to adsorb Cadmium(II) from a solution. Characterization of HD-HA was conducted by detection of its functional group, UV-Vis spectra, ash level, and total acidity. Result of the work showed that HD-HA had similar character compared with peat soil humic acid (PS-HA) and previous researchers. The adsorption study of this work was investigated by batch experiment in pH 5. The thermodynamics parameters in this work were determined by the Langmuir isotherm model for monolayer sorption and Freundlich isotherm model multilayer sorption. Monolayer sorption capacity (b) for HD-HA was 1.329 × 10-3 mol g-1, equilibrium constant (K) was 5.651 (mol/L)-1, and multilayer sorption capacity was 2.646 × 10-2 mol g-1. The kinetics parameters investigated in this work were determined by the novel kinetics expression resulted from the mathematical derivation the availability of binding sites of sorbent. Adsorption rate constant (ka) from this novel expression was 43.178 min-1 (mol/L)-1 and desorption rate constant (kd) was 1.250 × 10-2 min-1. Application of the kinetics model on sorption Cd(II) onto HD-HA showed the nearly all of models gave a good linearity. However, only this proposed kinetics expression has good relation with Langmuir model. The novel kinetics expression proposed in this paper seems to be more realistic and reasonable and close to the experimental real condition because the value of ka/kd (3452 (mol/L)-1) was fairly close with K from Langmuir isotherm model (5651 (mol/L)-1). Comparison of this novel kinetics expression with well-known Lagergren pseudo-first order kinetics and Ho pseudo-second order kinetics was also critically discussed in this paper.

Mathematical Modeling of Ammonia Electro-Oxidation on Polycrystalline Pt Deposited Electrodes

NASA Astrophysics Data System (ADS)

Diaz Aldana, Luis A.

The ammonia electrolysis process has been proposed as a feasible way for electrochemical generation of fuel grade hydrogen (H2). Ammonia is identified as one of the most suitable energy carriers due to its high hydrogen density, and its safe and efficient distribution chain. Moreover, the fact that this process can be applied even at low ammonia concentration feedstock opens its application to wastewater treatment along with H 2 co-generation. In the ammonia electrolysis process, ammonia is electro-oxidized in the anode side to produce N2 while H2 is evolved from water reduction in the cathode. A thermodynamic energy requirement of just five percent of the energy used in hydrogen production from water electrolysis is expected from ammonia electrolysis. However, the absence of a complete understanding of the reaction mechanism and kinetics involved in the ammonia electro-oxidation has not yet allowed the full commercialization of this process. For that reason, a kinetic model that can be trusted in the design and scale up of the ammonia electrolyzer needs to be developed. This research focused on the elucidation of the reaction mechanism and kinetic parameters for the ammonia electro-oxidation. The definition of the most relevant elementary reactions steps was obtained through the parallel analysis of experimental data and the development of a mathematical model of the ammonia electro-oxidation in a well defined hydrodynamic system, such as the rotating disk electrode (RDE). Ammonia electro-oxidation to N 2 as final product was concluded to be a slow surface confined process where parallel reactions leading to the deactivation of the catalyst are present. Through the development of this work it was possible to define a reaction mechanism and values for the kinetic parameters for ammonia electro-oxidation that allow an accurate representation of the experimental observations on a RDE system. Additionally, the validity of the reaction mechanism and kinetic parameters were supplemented by means of process scale up, performance evaluation, and hydrodynamic analysis in a flow cell electrolyzer. An adequate simulation of the flow electrolyzer performance was accomplished using the obtained kinetic parameters.

Kinetic and thermodynamic studies of AISI 4130 steel alloy corrosion in ethylene glycol-water mixture in presence of inhibitors

NASA Astrophysics Data System (ADS)

Khomami, M. Niknejad; Danaee, I.; Attar, A. A.; Peykari, M.

2013-05-01

The electrochemical behavior of steel alloy in ethylene glycol-water mixture was investigated by electrochemical methods. The results obtained showed that corrosion rate was decreased with increasing ethylene glycol concentration. The effect of inorganic inhibitors including NO3 -, NO2 -, Cr2O7 2- and CrO4 2- were studied using electrochemical techniques where the highest inhibition efficiency was obtained for CrO4 2-. In the presence of chromate the inhibitor efficiency increased with its concentration. The inhibiting effect of the chromate was explained on the basis of the competitive adsorption between the inorganic anions and the aggressive Cl- ions, and the adsorption isotherm basically obeys the Langmuir adsorption isotherm. Thermodynamic parameters for steel corrosion and inhibitor adsorption were determined and reveal that the adsorption process is spontaneous. Also, a phenomenon of both physical and chemical adsorption is proposed.

Conformational stability and thermodynamic characterization of the lipoic acid bearing domain of human mitochondrial branched chain α-ketoacid dehydrogenase

PubMed Central

Naik, Mandar T.; Huang, Tai-Huang

2004-01-01

The lipoic acid bearing domain (hbLBD) of human mitochondrial branched chain α-ketoacid dehydrogenase (BCKD) plays important role of substrate channeling in oxidative decarboxylation of the branched chain α-ketoacids. Recently hbLBD has been found to follow two-step folding mechanism without detectable presence of stable or kinetic intermediates. The present study describes the conformational stability underlying the folding of this small β-barrel domain. Thermal denaturation in presence of urea and isothermal urea denaturation titrations are used to evaluate various thermodynamic parameters defining the equilibrium unfolding. The linear extrapolation model successfully describes the two-step; native state ↔denatured state unfolding transition of hbLBD. The average temperature of maximum stability of hbLBD is estimated as 295.6 ± 0.9 K. Cold denaturation of hbLBD is also predicted and discussed. PMID:15322287

Numerical simulation by the molecular collision theory of two-phase mixture explosion characteristics in closed or vented vessels

NASA Astrophysics Data System (ADS)

Pascaud, J. M.; Brossard, J.; Lombard, J. M.

1999-09-01

The aim of this work consists in presenting a simple modelling (the molecular collision theory), easily usable in an industrial environment in order to predict the evolution of thermodynamical characteristics of the combustion of two-phase mixtures in a closed or a vented vessel. Basic characteristics of the modelling have been developed for ignition and combustion of propulsive powders and adapted with appropriate parameters linked to simplified kinetics. A simple representation of the combustion phenomena based on energy transfers and the action of specific molecules is presented. The model is generalized to various mixtures such as dust suspensions, liquid fuel drops and hybrid mixtures composed of dust and a gaseous supply such as methane or propane in the general case of vented explosions. The pressure venting due to the vent breaking is calculated from thermodynamical characteristics given by the model and taking into account, the mass rate of discharge of the different products deduced from the standard orifice equations. The application conditions determine the fuel ratio of the used mixtures, the nature of the chemical kinetics and the calculation of a universal set of parameters. The model allows to study the influence of the fuel concentration and the supply of gaseous additives, the influence of the vessel volume (2400ell leq V_bleq 250 000ell) and the influence of the venting pressure or the vent area. The first results have been compared with various experimental works available for two phase mixtures and indicate quite correct predictions.

CHEMKIN2. General Gas-Phase Chemical Kinetics

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

Rupley, F.M.

1992-01-24

CHEMKIN is a high-level tool for chemists to use to describe arbitrary gas-phase chemical reaction mechanisms and systems of governing equations. It remains, however, for the user to select and implement a solution method; this is not provided. It consists of two major components: the Interpreter and the Gas-phase Subroutine Library. The Interpreter reads a symbolic description of an arbitrary, user-specified chemical reaction mechanism. A data file is generated which forms a link to the Gas-phase Subroutine Library, a collection of about 200 modular subroutines which may be called to return thermodynamic properties, chemical production rates, derivatives of thermodynamic properties,more » derivatives of chemical production rates, or sensitivity parameters. Both single and double precision versions of CHEMKIN are included. Also provided is a set of FORTRAN subroutines for evaluating gas-phase transport properties such as thermal conductivities, viscosities, and diffusion coefficients. These properties are an important part of any computational simulation of a chemically reacting flow. The transport properties subroutines are designed to be used in conjunction with the CHEMKIN Subroutine Library. The transport properties depend on the state of the gas and on certain molecular parameters. The parameters considered are the Lennard-Jones potential well depth and collision diameter, the dipole moment, the polarizability, and the rotational relaxation collision number.« less

Modeling CO{sub 2} and H{sub 2}S solubility in MDEA and DEA: Design implications

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

Rochelle, G.T.; Posey, M.

1996-12-31

The solubility of H{sub 2}S and CO{sub 2} in aqueous alkanolamines affects solution capacity and the required circulation rate for acid gas absorption. These thermodynamics also determine the relationship of steam rate and the lean loading of the solution which in turn sets the leak of acid gas from the top of the absorber. Finally, the mechanisms of mass transfer and the role of kinetics, especially in stripping, depend on the vapor/liquid equilibria. Published measurements of CO{sub 2} and H{sub 2}S solubility in methyldiethanolamine (MDEA) and diethanolamine (DEA) are not in general agreement, especially at low loading of acid gas.more » The available sets of solubility data have been regressed with the AspenPlus electrolyte/NRTL model. All of the parameters and constants that make up this model have been carefully evaluated. Independent thermodynamic data such as freezing point and heat of mixing have been included in the regression to strengthen the estimates of model parameters. The parameters for each set of solubility data have been evaluated in an attempt to determine which set is correct. Each evaluated model has been used to calculate the acid gas capacity and minimum stripping steam rate for several industrial cases of acid gas absorption/stripping.« less

Thermodynamic and kinetic modeling of Mn-Ni-Si precipitates in low-Cu reactor pressure vessel steels

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

Ke, Huibin; Wells, Peter; Edmondson, Philip D.

Formation of large volume fractions of Mn-Ni-Si precipitates (MNSPs) causes excess irradiation embrittlement of reactor pressure vessel (RPV) steels at high, extended-life fluences. Thus, a new and unique, semi-empirical cluster dynamics model was developed to study the evolution of MNSPs in low-Cu RPV steels. The model is based on CALPHAD thermodynamics and radiation enhanced diffusion kinetics. The thermodynamics dictates the compositional and temperature dependence of the free energy reductions that drive precipitation. The model treats both homogeneous and heterogeneous nucleation, where the latter occurs on cascade damage, like dislocation loops. The model has only four adjustable parameters that were fitmore » to an atom probe tomography (APT) database. The model predictions are in semi-quantitative agreement with systematic Mn, Ni and Si composition variations in alloys characterized by APT, including a sensitivity to local tip-to-tip variations even in the same steel. The model predicts that heterogeneous nucleation plays a critical role in MNSP formation in lower alloy Ni contents. Single variable assessments of compositional effects show that Ni plays a dominant role, while even small variations in irradiation temperature can have a large effect on the MNSP evolution. Within typical RPV steel ranges, Mn and Si have smaller effects. Furthermore, the delayed but then rapid growth of MNSPs to large volume fractions at high fluence is well predicted by the model. For purposes of illustration, the effect of MNSPs on transition temperature shifts are presented based on well-established microstructure-property and property-property models.« less

Recommendations for terminology and databases for biochemical thermodynamics.

PubMed

Alberty, Robert A; Cornish-Bowden, Athel; Goldberg, Robert N; Hammes, Gordon G; Tipton, Keith; Westerhoff, Hans V

2011-05-01

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature. Copyright © 2011 Elsevier B.V. All rights reserved.

Effect of Fe3O4 addition on removal of ammonium by zeolite NaA.

PubMed

Liu, Haibo; Peng, Shuchuan; Shu, Lin; Chen, Tianhu; Bao, Teng; Frost, Ray L

2013-01-15

Magnetic zeolite NaA with different Fe(3)O(4) loadings was prepared by hydrothermal synthesis based on metakaolin and Fe(3)O(4). The effect of added Fe(3)O(4) on the removal of ammonium by zeolite NaA was investigated by varying the Fe(3)O(4) loading, pH, adsorption temperature, initial concentration, adsorption time. Langmuir, Freundlich, and pseudo-second-order modeling were used to describe the nature and mechanism of ammonium ion exchange using both zeolite and magnetic zeolite. Thermodynamic parameters such as change in Gibbs free energy, enthalpy and entropy were calculated. The results show that all the selected factors affect the ammonium ion exchange by zeolite and magnetic zeolite, however, the added Fe(3)O(4) apparently does not affect the ion exchange performance of zeolite to the ammonium ion. Freundlich model provides a better description of the adsorption process than Langmuir model. Moreover, kinetic analysis indicates the exchange of ammonium on the two materials follows a pseudo-second-order model. Thermodynamic analysis makes it clear that the adsorption process of ammonium is spontaneous and exothermic. Regardless of kinetic or thermodynamic analysis, all the results suggest that no considerable effect on the adsorption of the ammonium ion by zeolite is found after the addition of Fe(3)O(4). According to the results, magnetic zeolite NaA can be used for the removal of ammonium due to the good adsorption performance and easy separation method from aqueous solution. Copyright © 2012 Elsevier Inc. All rights reserved.

Thermodynamic and kinetic modeling of Mn-Ni-Si precipitates in low-Cu reactor pressure vessel steels

DOE PAGES

Ke, Huibin; Wells, Peter; Edmondson, Philip D.; ...

2017-07-12

Formation of large volume fractions of Mn-Ni-Si precipitates (MNSPs) causes excess irradiation embrittlement of reactor pressure vessel (RPV) steels at high, extended-life fluences. Thus, a new and unique, semi-empirical cluster dynamics model was developed to study the evolution of MNSPs in low-Cu RPV steels. The model is based on CALPHAD thermodynamics and radiation enhanced diffusion kinetics. The thermodynamics dictates the compositional and temperature dependence of the free energy reductions that drive precipitation. The model treats both homogeneous and heterogeneous nucleation, where the latter occurs on cascade damage, like dislocation loops. The model has only four adjustable parameters that were fitmore » to an atom probe tomography (APT) database. The model predictions are in semi-quantitative agreement with systematic Mn, Ni and Si composition variations in alloys characterized by APT, including a sensitivity to local tip-to-tip variations even in the same steel. The model predicts that heterogeneous nucleation plays a critical role in MNSP formation in lower alloy Ni contents. Single variable assessments of compositional effects show that Ni plays a dominant role, while even small variations in irradiation temperature can have a large effect on the MNSP evolution. Within typical RPV steel ranges, Mn and Si have smaller effects. Furthermore, the delayed but then rapid growth of MNSPs to large volume fractions at high fluence is well predicted by the model. For purposes of illustration, the effect of MNSPs on transition temperature shifts are presented based on well-established microstructure-property and property-property models.« less

Enantiomeric separation of volatile organics by gas chromatography for the in situ analysis of extraterrestrial materials: kinetics and thermodynamics investigation of various chiral stationary phases.

PubMed

Freissinet, C; Buch, A; Szopa, C; Sternberg, R

2013-09-06

The performances of several commercial chiral capillary columns have been evaluated with the aim of determining the one most suitable for enantiomeric separation in a gas chromatograph onboard a space probe. We compared the GC-MS response of three capillary columns coated with different chiral stationary phases (CSP) using volatile chiral organic molecules which are potential markers of a prebiotic organic chemistry. The three different chiral capillary columns are Chirasil-Val, with an amino acid derivative CSP, ChiralDex-β-PM, with a CSP composed of dissolved permethylated β-cyclodextrins in polysiloxane, and Chirasil-Dex, with a CSP made of modified cyclodextrins chemically bonded to the polysiloxane backbone. Both kinetics and thermodynamics studies have been carried out to evaluate the chiral recognition potential in these different types of columns. The thermodynamic parameters also allow a better understanding of the driving forces affecting the retention and separation of the enantiomers. The Chirasil-Dex-CSP displays the best characteristics for an optimal resolution of the chiral compounds, without preliminary derivatization. This CSP had been chosen to be the only chiral column in the Sample Analysis at Mars (SAM) experiment onboard the current Mars Science Laboratory (MSL) mission, and is also part of the Mars Organic Molecules Analyzer (MOMA) gas chromatograph onboard the next Martian mission ExoMars. The use of this column could also be extended to all space missions aimed at studying chirality in space. Copyright © 2013 Elsevier B.V. All rights reserved.

Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading

NASA Astrophysics Data System (ADS)

Gaspard, Pierre

2016-04-01

Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorporated nucleotide. The replication fidelity is shown to increase significantly thanks to this dependence at the basis of the mechanism of exonuclease proofreading. In particular, this dependence can provide up to a 100-fold lowering of the error probability under physiological conditions. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

Thermodynamic and Kinetic Behavior of the Polystyrene/Poly(vinyl methyl ether) Blend as Studied by Excimer Fluorescence.

DTIC Science & Technology

1986-01-02

AD-A±63 895 THERMODYNAMIC AND KINETIC BEHAVIOR OF THE / POLYSTYRENE/POLY(YINYL METHYL E..(U) STANFORD UNIY CALIFDEPT OF CHEMICAL ENGINEERING C N...Polystyrene/Poly(vinyl methyl ether) Blend 7. DEcFRMN 81 toOR 30USptE8 00~ as Studied by Excimer Fluorescence 6 EFRIGOG EOTNME *AUTHOR() a. CONTRACT OR GRANT...werea fondoare ihemoriisof * ~ Ex e sp fluodecositionsdu to deud Gen e and hoog Pinus Florsneis shownhase migrationprocSECURITY CLASIFICTIO OFd

Swelling-induced optical anisotropy of thermoresponsive hydrogels based on poly(2-(2-methoxyethoxy)ethyl methacrylate): deswelling kinetics probed by quantitative Mueller matrix polarimetry.

PubMed

Patil, Nagaraj; Soni, Jalpa; Ghosh, Nirmalya; De, Priyadarsi

2012-11-29

Thermodynamically favored polymer-water interactions below the lower critical solution temperature (LCST) caused swelling-induced optical anisotropy (linear retardance) of thermoresponsive hydrogels based on poly(2-(2-methoxyethoxy)ethyl methacrylate). This was exploited to study the macroscopic deswelling kinetics quantitatively by a generalized polarimetry analysis method, based on measurement of the Mueller matrix and its subsequent inverse analysis via the polar decomposition approach. The derived medium polarization parameters, namely, linear retardance (δ), diattenuation (d), and depolarization coefficient (Δ), of the hydrogels showed interesting differences between the gels prepared by conventional free radical polymerization (FRP) and reversible addition-fragmentation chain transfer polymerization (RAFT) and also between dry and swollen state. The effect of temperature, cross-linking density, and polymerization technique employed to synthesize hydrogel on deswelling kinetics was systematically studied via conventional gravimetry and corroborated further with the corresponding Mueller matrix derived quantitative polarimetry characteristics (δ, d, and Δ). The RAFT gels exhibited higher swelling ratio and swelling-induced optical anisotropy compared to FRP gels and also deswelled faster at 30 °C. On the contrary, at 45 °C, deswelling was significantly retarded for the RAFT gels due to formation of a skin layer, which was confirmed and quantified via the enhanced diattenuation and depolarization parameters.

Reactive transport modelling of groundwater chemistry in a chalk aquifer at the watershed scale

NASA Astrophysics Data System (ADS)

Mangeret, A.; De Windt, L.; Crançon, P.

2012-09-01

This study investigates thermodynamics and kinetics of water-rock interactions in a carbonate aquifer at the watershed scale. A reactive transport model is applied to the unconfined chalk aquifer of the Champagne Mounts (France), by considering both the chalk matrix and the interconnected fracture network. Major element concentrations and main chemical parameters calculated in groundwater and their evolution along flow lines are in fair agreement with field data. A relative homogeneity of the aquifer baseline chemistry is rapidly reached in terms of pH, alkalinity and Ca concentration since calcite equilibrium is achieved over the first metres of the vadose zone. However, incongruent chalk dissolution slowly releases Ba, Mg and Sr in groundwater. Introducing dilution effect by rainwater infiltration and a local occurrence of dolomite improves the agreement between modelling and field data. The dissolution of illite and opal-CT, controlling K and SiO2 concentrations in the model, can be approximately tackled by classical kinetic rate laws, but not the incongruent chalk dissolution. An apparent kinetic rate has therefore been fitted on field data by inverse modelling: 1.5 × 10- 5 molchalk L - 1water year - 1. Sensitivity analysis indicates that the CO2 partial pressure of the unsaturated zone is a critical parameter for modelling the baseline chemistry over the whole chalk aquifer.

Biosorption of Cd(II) from aqueous solution using xanthated nano banana cellulose: equilibrium and kinetic studies.

PubMed

Pillai, Saumya S; Deepa, B; Abraham, Eldho; Girija, N; Geetha, P; Jacob, Laly; Koshy, Mathew

2013-12-01

Present study explored the biosorption capacity of xanthated nano banana cellulose (XNBC) for Cd(II) from aqueous solution. The biosorbent containing sulfur-bearing groups have a high affinity for heavy metals. Sulfur can be considered as a soft ligand group having strong affinity for cadmium. In the present study, the influence of various important parameters such as pH, time, biosorbent dose and initial Cd(II) concentration on the biosorption capacity were investigated. The maximum biosorption capacity of XNBC for Cd(II) was found to be 154.26 mg g⁻¹ at 298 K. The Cd(II) sorption of XNBC was confirmed by SEM-EDS and XRF analysis. The isotherms such as Langmuir, Freundlich, Redlich-Peterson and Tempkin were studied. The Langmuir and the Redlich-Peterson isotherms had been well fitted the biosorption of Cd(II) with xanthated nano banana cellulose. The kinetics of Cd(II) removal using XNBC was well explained by second-order kinetic model. The thermodynamic parameters were also evaluated from the biosorption measurements. Among the various desorbing agents tested, the desorbing efficiency was found to be maximum with 0.1 mol L⁻¹ HCl. It was found that XNBC is also suitable to be used under column operation. © 2013 Elsevier Inc. All rights reserved.

Alterations of rings B and C of colchicine are cumulative in overall binding to tubulin but modify each kinetic step.

PubMed

Dumortier, C; Gorbunoff, M J; Andreu, J M; Engelborghs, Y

1996-12-10

The role of the elimination of ring B and/or the modification of ring C of colchicine in tubulin binding kinetics and thermodynamics has been characterized, using four different molecules. These ligands are colchicine (COL); 2-methoxy-5-(2',3',4'-trimethoxyphenyl)-2,4,6-cycloheptatrien-1-on e (MTC), in which the central ring B has been reduced to one bond; allocolchicine (ALLO), in which ring C has been replaced by a six-membered ring; and 2,3,4-trimethoxy-4'-carbomethoxy-1,1'-biphenyl (TCB), where the same two modifications are made simultaneously. This paper describes the kinetics of association of ALLO with tubulin. The binding is accompanied by a fluorescence increase with slow biphasic kinetics, indicating binding to fast and slow tubulin isotypes. Binding to each of these isotypes occurs in two steps: a fast initial binding followed by a slower isomerization step. The K1 and k2 values for ALLO at 25 degrees C are 14,000 +/- 2,000 and 25,000 +/- 6,000 M-1 (fast and slow isotypes) and 0.055 +/- 0.003 s-1 and 0.013 +/- 0.001 s-1 (fast and slow isotype), respectively. For ALLO the reaction standard enthalpy change of the initial binding is 68 +/- 5 kJ.mol-1 (fast isotype) and 45 +/- 33 kJ.mol-1 (slow isotype) and the activation energy for the second forward step is 58 +/- 14 kJ.mol-1 (fast isotype) and 81 +/- 17 kJ.mol-1 (slow isotype). Displacement kinetics of bound ALLO by podophyllotoxin was monoexponential. The activation energy for the isomerization in the off direction is 107 +/- 7 kJ.mol-1. Comparison of the thermodynamic parameters for all four compounds shows that the modifications of both rings are cumulative with respect to overall binding. For the intermediate state there is a mutual influence of both modifications, suggesting an alteration of the reaction pathway.

Thermodynamic properties of water in confined environments: a Monte Carlo study

NASA Astrophysics Data System (ADS)

Gladovic, Martin; Bren, Urban; Urbic, Tomaž

2018-05-01

Monte Carlo simulations of Mercedes-Benz water in a crowded environment were performed. The simulated systems are representative of both composite, porous or sintered materials and living cells with typical matrix packings. We studied the influence of overall temperature as well as the density and size of matrix particles on water density, particle distributions, hydrogen bond formation and thermodynamic quantities. Interestingly, temperature and space occupancy of matrix exhibit a similar effect on water properties following the competition between the kinetic and the potential energy of the system, whereby temperature increases the kinetic and matrix packing decreases the potential contribution. A novel thermodynamic decomposition approach was applied to gain insight into individual contributions of different types of inter-particle interactions. This decomposition proved to be useful and in good agreement with the total thermodynamic quantities especially at higher temperatures and matrix packings, where higher-order potential-energy mixing terms lose their importance.

Hydrogen storage properties of Mg xFe (x: 2, 3 and 15) compounds produced by reactive ball milling

NASA Astrophysics Data System (ADS)

Puszkiel, J. A.; Arneodo Larochette, P.; Gennari, F. C.

This work deals with the assessment of the thermo-kinetic properties of Mg-Fe based materials for hydrogen storage. Samples are prepared from Mg xFe (x: 2, 3 and 15) elemental powder mixtures via low energy ball milling under hydrogen atmosphere at room temperature. The highest yield is obtained with Mg 15Fe after 150 h of milling (90 wt% of MgH 2). The thermodynamic characterization carried out between 523 and 673 K shows that the obtained Mg-Fe-H hydride systems have similar thermodynamic parameters, i.e. enthalpy and entropy. However, in equilibrium conditions, Mg 15Fe has higher hydrogen capacity and small hysteresis. In dynamic conditions, Mg 15Fe also shows better hydrogen capacity (4.85 wt% at 623 K absorbed in less than 10 min and after 100 absorption/desorption cycles), reasonably good absorption/desorption times and cycling stability in comparison to the other studied compositions. From hydrogen uptake rate measurements performed at 573 and 623 K, the rate-limiting step of the hydrogen uptake reaction is determined by fitting particle kinetic models. According to our results, the hydrogen uptake is diffusion controlled, and this mechanism does not change with the Mg-Fe proportion and temperature.

Hydrolytic resolution of (R,S)-naproxen 2,2,2-trifluoroethyl thioester by Carica papaya lipase in water-saturated organic solvents.

PubMed

Ng, I-Son; Tsai, Shau-Wei

2005-01-05

For the first time, the Carica papaya lipase (CPL) stored in crude papain is explored as a potential enantioselective biocatalyst for obtaining chiral acids from their racemic thioesters. Hydrolytic resolution of (R,S)-naproxen 2,2,2-trifluoroethyl thioester in water-saturated organic solvents is employed as a model system for studying the effects of temperature and solvents on lipase activity and enantioselectivity. An optimal temperature of 60 degrees C, based on the initial rate of (S)-thioester and a high enantiomeric ratio (i.e., E-value defined as the ratio of initial rates for both substrates) of >100 at 45 degrees C in isooctane, is obtained. Kinetic analysis, considering product inhibition and enzyme deactivation, is also performed, showing agreement between the experimental and best-fit conversions for (S)-thioester. A comparison of the kinetic and thermodynamic behaviors of CPL and Candida rugosa lipase (CRL) in isooctane and cyclohexane indicates that both lipases are very similar in terms of thermodynamic parameters DeltaDeltaH and DeltaDeltaS, initial rate of (S)-substrate, and E-value when (R,S)-naproxen 2,2,2-trifluoroethyl thioester or ester is employed as substrate. (c) 2004 Wiley Periodicals, Inc.

Kinetic studies and thermodynamics of oil extraction and transesterification of Chlorella sp. for biodiesel production.

PubMed

Ahmad, A L; Yasin, N H Mat; Derek, C J C; Lim, J K

2014-01-01

In this work, a mixture of chloroform and methanol (1:1, v/v) was applied to oil extraction from Chlorella sp. at 30, 40, 50 and 60 degrees C for 150 min extraction times. Kinetic studies revealed that the values of n and the rate constants were found to depend strongly on temperature. The activation energy was Ea = 38.893 kJ/mol, and the activation thermodynamic parameters at 60 degrees C were ΔS≠ = -180.190 J/mol , ΔH≠ = 36.124k J/mol and ΔG≠ = 96.128k J/mol. Both ΔH and ΔS yielded positive values, whereas ΔG was negative at 60 degrees C, indicating that this process is endothermic, irreversible and spontaneous. The acidic transesterification process was also investigated by gas chromatographic analysis of the microalgae fatty acid methyl esters (biodiesel) at different temperatures and reaction times. The fatty acid profile indicated that the main components were palmitic, linoleic and linolenic acids. The concentration of linolenic acid increased and oleic acid decreased as the temperature increased. Two-hour transesterification is the best reaction time for biodiesel production because it produces the highest percentage of unsaturated fatty acids (74%). These results indicate the potential of Chlorella sp. to produce biodiesel of good quality.

Effects and mechanism of ultrasound pretreatment on rapeseed protein enzymolysis.

PubMed

Jin, Jian; Ma, Haile; Wang, Weiwei; Luo, Min; Wang, Bei; Qu, Wenjuan; He, Ronghai; Owusu, John; Li, Yunliang

2016-03-15

The disadvantages which stem from the use of traditional enzymolysis of protein has necessitated the need to employ sweeping frequency and pulsed ultrasound (SFPU) in the pretreatment of rapeseed protein prior to proteolysis in order to bring about improvement in enzymolysis efficiency. Further, in order to determine the mechanism of ultrasound-accelerated enzymolysis of RP, the effects of SFPU on the kinetics, thermodynamics, molecular conformation and microstructure of RP were investigated. Kinetic studies showed that SFPU pretreatment on RP improved enzymolysis by decreasing the apparent constant KM significantly (P < 0.05) by 32.8% and reducing the thermodynamic parameters Ea , ΔH and ΔS by 16.6%, 17.7% and 9.2% respectively. Fluorescence spectra revealed that SFPU pretreatment induced molecular unfolding, causing more hydrophobic groups and regions inside the molecules to be exposed to the outside. Circular dichroism analysis indicated that SFPU pretreatment decreased the α-helix content by 16.1% and increased the random coil content by 3.6%. In addition, scanning electron microscopy showed that SFPU pretreatment increased the specific surface area of RP. Ultrasound pretreatment is an efficient method in RP proteolysis to produce peptides through its impact on the molecular conformation and microstructure of proteins. © 2015 Society of Chemical Industry.

Kinetic and thermodynamic studies on the adsorption of heavy metals from aqueous solution by melanin nanopigment obtained from marine source: Pseudomonas stutzeri.

PubMed

Manirethan, Vishnu; Raval, Keyur; Rajan, Reju; Thaira, Harsha; Balakrishnan, Raj Mohan

2018-05-15

The difficulty in removal of heavy metals at concentrations below 10 mg/L has led to the exploration of efficient adsorbents for removal of heavy metals. The adsorption capacity of biosynthesized melanin for Mercury (Hg(II)), Chromium (Cr(VI)), Lead (Pb(II)) and Copper (Cu(II)) was investigated at different operating conditions like pH, time, initial concentration and temperature. The heavy metals adsorption process was well illustrated by the Lagergren's pseudo-second-order kinetic model and the equilibrium data fitted excellently to Langmuir isotherm. Maximum adsorption capacity obtained from Langmuir isotherm for Hg(II) was 82.4 mg/g, Cr(VI) was 126.9 mg/g, Pb(II) was 147.5 mg/g and Cu(II) was 167.8 mg/g. The thermodynamic parameters revealed that the adsorption of heavy metals on melanin is favorable, spontaneous and endothermic in nature. Binding of heavy metals on melanin surface was proved by Fourier Transform Infrared Spectroscopy (FT-IR) and X-ray Photoelectron Spectroscopy (XPS). Contemplating the results, biosynthesized melanin can be a potential adsorbent for efficient removal of Hg(II), Cr(VI), Pb(II) and Cu(II) ions from aqueous solution. Copyright © 2018 Elsevier Ltd. All rights reserved.

Stories to Make Thermodynamics and Related Subjects More Palatable

NASA Astrophysics Data System (ADS)

Bartell, Lawrence S.

2001-08-01

A collection of vignettes either recounting the personalities of some of the architects of thermodynamics or noting steps and missteps in the development of thermodynamics and the kinetic theory is combined with a set of stories illustrating thermodynamic principles. These offerings turned out to be much more easily remembered by students and were more effective in conveying certain points than a direct, unadorned exposition of thermodynamic laws and applications. For one thing, the stories kept the students awake and receptive to ideas. Students had invariably entered the class having heard horror stories about how tedious and impossibly difficult thermodynamics courses are.

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

Ji, Yanzhou; Heo, Tae Wook; Zhang, Fan

Here we present our theoretical assessment of the kinetic pathways during phase transformations of multi-component Ti alloys. Employing the graphical thermodynamic approach and an integrated free energy function based on the realistic thermodynamic database and assuming that a displacive structural transformation occurs much faster than long-range diffusional processes, we analyze the phase stabilities of Ti-6Al -4V (Ti-6wt.%Al -4wt.%V). Our systematic analyses predict a variety of possible kinetic pathways for β to (α + β) transformations leading to different types of microstructures under various heat treatment conditions. In addition, the possibility of unconventional kinetic pathways is discussed. Lastly, we also brieflymore » discuss the application of our approach to general multicomponent/multiphase alloy systems.« less

Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase.

PubMed

Topin, Jérémie; Rousset, Marc; Antonczak, Serge; Golebiowski, Jérôme

2012-03-01

We have investigated O₂ and H₂ transport across a NiFe hydrogenase at the atomic scale by means of computational methods. The Wild Type protein has been compared with the V74Q mutant. Two distinct methodologies have been applied to study the gas access to the active site. Temperature locally enhanced sampling simulations have emphasized the importance of protein dynamics on gas diffusion. The O₂ diffusion free energy profiles, obtained by umbrella sampling, are in agreement with the known kinetic data and show that in the V74Q mutant, the inhibition process is lowered from both a kinetic and a thermodynamic point of view. Copyright © 2011 Wiley Periodicals, Inc.

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

PubMed Central

Frank, Joachim; Gonzalez, Ruben L.

2015-01-01

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

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

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.

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

PubMed

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

2015-08-27

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

Bioenergy potential of Wolffia arrhiza appraised through pyrolysis, kinetics, thermodynamics parameters and TG-FTIR-MS study of the evolved gases.

PubMed

Ahmad, Muhammad Sajjad; Mehmood, Muhammad Aamer; Liu, Chen-Guang; Tawab, Abdul; Bai, Feng-Wu; Sakdaronnarong, Chularat; Xu, Jianren; Rahimuddin, Sawsan Abdulaziz; Gull, Munazza

2018-04-01

This study evaluated the bioenergy potential of Wolffia arrhiza via pyrolysis. The biomass was collected from the pond receiving city wastewater. Oven dried powdered biomass was exposed to thermal degradation at three heating rates (10, 30 and 50° C min -1 ) using Thermogravimetry-Differential Scanning Calorimetry analyzer in an inert environment. Data obtained were subjected to the isoconversional models of Kissenger-Akahira-Sunose (KSA) and Flynn-Wall-Ozawa (FWO) to elucidate the reaction chemistry. Kinetic parameters including, E a (136-172 kJmol -1 ) and Gibb's free energy (171 kJmol -1 ) showed the remarkable bioenergy potential of the biomass. The average enthalpies indicated that the product formation is favored during pyrolysis. Advanced coupled TG-FTIR-MS analyses showed the evolved gases to contain the compounds containing CO functional groups (aldehydes, ketones), aromatic and aliphatic hydrocarbons as major pyrolytic products. This low-cost abundant biomass may be used to produce energy and chemicals in a cost-efficient and environmentally friendly way. Copyright © 2018 Elsevier Ltd. All rights reserved.

Molecular Imprinted Polymer of Methacrylic Acid Functionalised β-Cyclodextrin for Selective Removal of 2,4-Dichlorophenol

PubMed Central

Surikumaran, Hemavathy; Mohamad, Sharifah; Sarih, Norazilawati Muhamad

2014-01-01

This work describes methacrylic acid functionalized β-cyclodextrin (MAA-βCD) as a novel functional monomer in the preparation of molecular imprinted polymer (MIP MAA-βCD) for the selective removal of 2,4-dichlorophenol (2,4-DCP). The polymer was characterized using Fourier Transform Infrared (FTIR) spectroscopy, Brunauer-Emmett-Teller (BET) and Field Emission Scanning Electron Microscopy (FESEM) techniques. The influence of parameters such as solution pH, contact time, temperature and initial concentrations towards removal of 2,4-DCP using MIP MAA-βCD have been evaluated. The imprinted material shows fast kinetics and the optimum pH for removal of 2,4-DCP is pH 7. Compared with the corresponding non-imprinted polymer (NIP MAA-βCD), the MIP MAA-βCD exhibited higher adsorption capacity and outstanding selectivity towards 2,4-DCP. Freundlich isotherm best fitted the adsorption equilibrium data of MIP MAA-βCD and the kinetics followed a pseudo-second-order model. The calculated thermodynamic parameters showed that adsorption of 2,4-DCP was spontaneous and exothermic under the examined conditions. PMID:24727378

Effect of temperature on Brettanomyces bruxellensis: metabolic and kinetic aspects.

PubMed

Brandam, Cédric; Castro-Martínez, Claudia; Délia, Marie-Line; Ramón-Portugal, Felipe; Strehaiano, Pierre

2008-01-01

The effect of temperatures ranging from 15 to 35 degrees C on a culture of Brettanomyces bruxellensis was investigated in regards to thermodynamics, metabolism, and kinetics. In this temperature range, we observed an increase in growth and production rates. The growth behavior was well represented using the Arrhenius model, and an apparent activation energy of 16.61 kcal/mol was estimated. A stuck fermentation was observed at 35 degrees C as represented by high cell death. The carbon balance established that temperature had no effect on repartition of the glucose consumption between biomass and products. Hence, the same biomass concentration was obtained for all temperatures, except at 35 degrees C. Moreover, using logistic and Luedeking-Piret models, we demonstrated that production rates of ethanol and acetic acid were partially growth associated. Parameters associated with growth (alpha eth and alpha aa) remained constant with changing temperature, whereas, parameters associated with the population (beta eth and beta aa) varied. Optimal values were obtained at 32 degrees C for ethanol and at 25 degrees C for acetic acid.

Kinetic studies of adsorption of thiocyanate onto ZnCl2 activated carbon from coir pith, an agricultural solid waste.

PubMed

Namasivayam, C; Sangeetha, D

2005-09-01

The adsorption of thiocyanate onto ZnCl2 activated carbon developed from coir pith was investigated to assess the possible use of this adsorbent. The influence of various parameters such as agitation time, thiocyanate concentration, adsorbent dose, pH and temperature has been studied. Adsorption followed second-order rate kinetics. Two theoretical adsorption isotherms, namely, Langmuir and Freundlich were used to describe the experimental results. The Langmuir adsorption capacity (Q0) was found to be 16.2 mg g(-1) of the adsorbent. The per cent adsorption was maximum in the pH range 3.0-7.0. pH effect and desorption studies showed that ion exchange and chemisorption mechanism are involved in the adsorption process. Thermodynamic parameters such as DeltaG0, DeltaH0 and DeltaS0 for the adsorption were evaluated. The negative values of DeltaH0 confirm the exothermic nature of adsorption. Effects of foreign ions on the adsorption of thiocyanate have been investigated. Removal of thiocyanate from ground water was also tested.

An integrated computational tool for precipitation simulation

NASA Astrophysics Data System (ADS)

Cao, W.; Zhang, F.; Chen, S.-L.; Zhang, C.; Chang, Y. A.

2011-07-01

Computer aided materials design is of increasing interest because the conventional approach solely relying on experimentation is no longer viable within the constraint of available resources. Modeling of microstructure and mechanical properties during precipitation plays a critical role in understanding the behavior of materials and thus accelerating the development of materials. Nevertheless, an integrated computational tool coupling reliable thermodynamic calculation, kinetic simulation, and property prediction of multi-component systems for industrial applications is rarely available. In this regard, we are developing a software package, PanPrecipitation, under the framework of integrated computational materials engineering to simulate precipitation kinetics. It is seamlessly integrated with the thermodynamic calculation engine, PanEngine, to obtain accurate thermodynamic properties and atomic mobility data necessary for precipitation simulation.

Metal Al produced by H2 plasma reduction of AlCl3: a thermodynamic and kinetic study on the plasma chemistry.

PubMed

Zheng, Jie; Sun, Bo; Yang, Rong; Song, Xubo; Li, Xingguo; Pu, Yikang

2008-10-09

In this paper we reported that low temperature plasma may reverse the direction of a chemical reaction. The thermodynamically forbidden reaction between H 2 and AlCl 3 was able to take place with the assistance of low temperature plasma, yielding metal Al. The plasma chemistry of the reaction was investigated by optical emission spectroscopy, which suggested that the dissociation of H 2 and AlCl 3 molecules by plasma led the reaction to a thermodynamically favorable one by creating reaction channels with low Gibbs free energy change. The addition of Ar promoted the reaction kinetics dramatically, which was attributed to the enhanced dissociation of AlCl 3 molecules by excited Ar species.

Theoretical Assessment on the Phase Transformation Kinetic Pathways of Multi-component Ti Alloys: Application to Ti-6Al- 4V

DOE PAGES

Ji, Yanzhou; Heo, Tae Wook; Zhang, Fan; ...

2015-12-21

Here we present our theoretical assessment of the kinetic pathways during phase transformations of multi-component Ti alloys. Employing the graphical thermodynamic approach and an integrated free energy function based on the realistic thermodynamic database and assuming that a displacive structural transformation occurs much faster than long-range diffusional processes, we analyze the phase stabilities of Ti-6Al -4V (Ti-6wt.%Al -4wt.%V). Our systematic analyses predict a variety of possible kinetic pathways for β to (α + β) transformations leading to different types of microstructures under various heat treatment conditions. In addition, the possibility of unconventional kinetic pathways is discussed. Lastly, we also brieflymore » discuss the application of our approach to general multicomponent/multiphase alloy systems.« less

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

Zhao, Donghui; Key Lab of Inorganic Coating Materials, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi, Changning, Shanghai 200050; Zhu, Yingchun, E-mail: yzhu@mail.sic.ac.cn

In this article, the polymorph selection of calcium carbonate has been successfully achieved in water-soluble carboxymethyl chitosan aqueous solution at different temperatures (25-95 {sup o}C). Vaterite is formed in carboxymethyl chitosan solution 25 {sup o}C accompanied with trace of calcite, whereas pure aragonite is obtained at 95 {sup o}C. Scanning electron microscopy and transmission electron microscopy analyses show that the products are formed from the recrystallization of nanometer crystallites. Thermodynamic and kinetic analyses reveal that the polymorph of calcium carbonate is controlled and selected by kinetics in various temperatures. As a heterogeneous nucleator and stabilizing agent, carboxymethyl chitosan changes themore » nucleation and growth of calcium carbonate from thermodynamic into kinetic control. Under kinetic limitation, the reaction rate of aragonite increases along with the elevating of temperature and surpasses the rate of vaterite above 327 K.« less

Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc01627a

PubMed Central

Wang, Yong; Martins, João Miguel

2017-01-01

The behaviour of biomolecular systems is governed by their thermodynamic and kinetic properties. It is thus important to be able to calculate, for example, both the affinity and rate of binding and dissociation of a protein–ligand complex, or the populations and exchange rates between distinct conformational states. Because these are typically rare events, calculating these properties from long molecular dynamics simulations remains extremely difficult. Instead, one often adopts a divide-and-conquer strategy in which equilibrium free-energy differences and the fastest state-to-state transition (e.g. ligand association or minor-to-major state conversion) are combined to estimate the slow rate (e.g. ligand dissociation) using a two-state assumption. Here we instead address these problems by using a previously developed method to calculate both the forward and backward rates directly from simulations. We then estimate the thermodynamics from the rates, and validate these values by independent means. We applied the approach to three systems of increasing complexity, including the association and dissociation of benzene to a fully buried cavity inside the L99A mutant variant of T4 lysozyme. In particular, we were able to determine both millisecond association and dissociation rates, and the affinity, of the protein–ligand system by directly observing dozens of rare events in atomic detail. Our approach both sheds light on the precision of methods for calculating kinetics and further provides a generally useful test for the internal consistency of kinetics and thermodynamics. We also expect our route to be useful for obtaining both the kinetics and thermodynamics at the same time in more challenging cases. PMID:29619200

Revisiting thermodynamics and kinetic diffusivities of uranium–niobium with Bayesian uncertainty analysis

DOE PAGES

Duong, Thien C.; Hackenberg, Robert E.; Landa, Alex; ...

2016-09-20

In this paper, thermodynamic and kinetic diffusivities of uranium–niobium (U–Nb) are re-assessed by means of the CALPHAD (CALculation of PHAse Diagram) methodology. In order to improve the consistency and reliability of the assessments, first-principles calculations are coupled with CALPHAD. In particular, heats of formation of γ -U–Nb are estimated and verified using various density-functional theory (DFT) approaches. These thermochemistry data are then used as constraints to guide the thermodynamic optimization process in such a way that the mutual-consistency between first-principles calculations and CALPHAD assessment is satisfactory. In addition, long-term aging experiments are conducted in order to generate new phase equilibriamore » data at the γ 2/α+γ 2 boundary. These data are meant to verify the thermodynamic model. Assessment results are generally in good agreement with experiments and previous calculations, without showing the artifacts that were observed in previous modeling. The mutual-consistent thermodynamic description is then used to evaluate atomic mobility and diffusivity of γ-U–Nb. Finally, Bayesian analysis is conducted to evaluate the uncertainty of the thermodynamic model and its impact on the system's phase stability.« less

Competitive adsorption from mixed hen egg-white lysozyme/surfactant solutions at the air-water interface studied by tensiometry, ellipsometry, and surface dilational rheology.

PubMed

Alahverdjieva, V S; Grigoriev, D O; Fainerman, V B; Aksenenko, E V; Miller, R; Möhwald, H

2008-02-21

The competitive adsorption at the air-water interface from mixed adsorption layers of hen egg-white lysozyme with a non-ionic surfactant (C10DMPO) was studied and compared to the mixture with an ionic surfactant (SDS) using bubble and drop shape analysis tensiometry, ellipsometry, and surface dilational rheology. The set of equilibrium and kinetic data of the mixed solutions is described by a thermodynamic model developed recently. The theoretical description of the mixed system is based on the model parameters for the individual components.

Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four vλ6 proteins

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

Wall, J.S.; Gupta, V.; Wilkerson, M.

2004-04-01

Primary (AL) amyloidosis results from the pathologic deposition of monoclonal light chains as amyloid fibrils. Studies of recombinant-derived variable region (V{sub L}) fragments of these proteins have shown an inverse relationship between thermodynamic stability and fibrillogenic potential. Further, ionic interactions within the V{sub L} domain were predicted to influence the kinetics of light chain fibrillogenicity, as evidenced from our analyses of a relatively stable V{sub {lambda}}6 protein (Jto) with a long range electrostatic interaction between Asp and Arg side chains at position 29 and 68, respectively, and an unstable, highly fibrillogenic V{sub {lambda}}6 protein (Wil) that had neutral amino acidsmore » at these locations. To test this hypothesis, we have generated two Jto-related mutants designed to disrupt the interaction between Asp 29 and Arg 68 (JtoD29A and JtoR68S). Although the thermodynamic stabilities of unfolding for these two molecules were identical, they exhibited very different kinetics of fibril formation: the rate of JtoD29A fibrillogenesis was slow and comparable to the parent molecule, whereas that of JtoR68S was significantly faster. High-resolution X-ray diffraction analyses of crystals prepared from the two mutants having the same space group and unit cell dimensions revealed no significant main-chain conformational changes. However, several notable side-chain alterations were observed in JtoR68S, as compared with JtoD29A, that resulted in the solvent exposure of a greater hydrophobic surface and modifications in the electrostatic potential surface. We posit that these differences contributed to the enhanced fibrillogenic potential of the Arg 68 mutant, since both Jto mutants lacked the intrachain ionic interaction and were equivalently unstable. The information gleaned from our studies has provided insight into structural parameters that in addition to overall thermodynamic stability, contribute to the fibril forming propensity of immunoglobulin light chains.« less

Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors.

PubMed

Lange, Jos H M; Venhorst, Jennifer; van Dongen, Maria J P; Frankena, Jurjen; Bassissi, Firas; de Bruin, Natasja M W J; den Besten, Cathaline; de Beer, Stephanie B A; Oostenbrink, Chris; Markova, Natalia; Kruse, Chris G

2011-10-01

Many early drug research efforts are too reductionist thereby not delivering key parameters such as kinetics and thermodynamics of target-ligand binding. A set of human D-Amino Acid Oxidase (DAAO) inhibitors 1-6 was applied to demonstrate the impact of key biophysical techniques and physicochemical methods in the differentiation of chemical entities that cannot be adequately distinguished on the basis of their normalized potency (ligand efficiency) values. The resulting biophysical and physicochemical data were related to relevant pharmacodynamic and pharmacokinetic properties. Surface Plasmon Resonance data indicated prolonged target-ligand residence times for 5 and 6 as compared to 1-4, based on the observed k(off) values. The Isothermal Titration Calorimetry-derived thermodynamic binding profiles of 1-6 to the DAAO enzyme revealed favorable contributions of both ΔH and ΔS to their ΔG values. Surprisingly, the thermodynamic binding profile of 3 elicited a substantially higher favorable contribution of ΔH to ΔG in comparison with the structurally closely related fused bicyclic acid 4. Molecular dynamics simulations and free energy calculations of 1, 3, and 4 led to novel insights into the thermodynamic properties of the binding process at an atomic level and in the different thermodynamic signatures of 3 and 4. The presented holistic approach is anticipated to facilitate the identification of compounds with best-in-class properties at an early research stage. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

NASA Astrophysics Data System (ADS)

Shapiro, B.; Jin, Q.

2015-12-01

Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

PubMed Central

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R.; Stedtfeld, Robert D.; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A.

2017-01-01

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131). PMID:28555058

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.

PubMed

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R; Stedtfeld, Robert D; Gulari, Erdogan; Tiedje, James M; Hashsham, Syed A

2017-05-29

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R² = 0.8131).

Nonlinear magnetoacoustic wave propagation with chemical reactions

NASA Astrophysics Data System (ADS)

Margulies, Timothy Scott

2002-11-01

The magnetoacoustic problem with an application to sound wave propagation through electrically conducting fluids such as the ocean in the Earth's magnetic field, liquid metals, or plasmas has been addressed taking into account several simultaneous chemical reactions. Using continuum balance equations for the total mass, linear momentum, energy; as well as Maxwell's electrodynamic equations, a nonlinear beam equation has been developed to generalize the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation for a fluid with linear viscosity but nonlinear and diffraction effects. Thermodynamic parameters are used and not tailored to only an adiabatic fluid case. The chemical kinetic equations build on a relaxing media approach presented, for example, by K. Naugolnukh and L. Ostrovsky [Nonlinear Wave Processes in Acoustics (Cambridge Univ. Press, Cambridge, 1998)] for a linearized single reaction and thermodynamic pressure equation of state. Approximations for large and small relaxation times and for magnetohydrodynamic parameters [Korsunskii, Sov. Phys. Acoust. 36 (1990)] are examined. Additionally, Cattaneo's equation for heat conduction and its generalization for a memory process rather than a Fourier's law are taken into account. It was introduced for the heat flux depends on the temperature gradient at an earlier time to generate heat pulses of finite speed.

Pd (II) complexes of bidentate chalcone ligands: Synthesis, spectral, thermal, antitumor, antioxidant, antimicrobial, DFT and SAR studies

NASA Astrophysics Data System (ADS)

Gaber, Mohamed; Awad, Mohamed K.; Atlam, Faten M.

2018-05-01

The ligation behavior of two chalcone ligands namely, (E)-3-(4-chlorophenyl)-1-(pyridin-2-yl)prop-2-en-1-one (L1) and (E)-3-(4-methoxyphenyl)-1-(pyridin-2-yl)prop-2-en-1-one (L2), towards the Pd(II) ion is determined. The structures of the complexes are elucidated by elemental analysis, spectral methods (IR, electronic and NMR spectra) as well as the conductance measurements and thermal analysis. The metal complexes exhibit a square planar geometrical arrangement. The kinetic and thermodynamic parameters for some selected decomposition steps have been calculated. The antimicrobial, antioxidant and anticancer activities of the chalcones and their Pd(II) complexes have been evaluated. Molecular orbital computations are performed using DFT at B3LYP level with 6-31 + G(d) and LANL2DZ basis sets to access reliable results to the experimental values. The calculations are performed to obtain the optimized molecular geometry, charge density distribution, extent of distortion from regular geometry. Thermodynamic parameters for the investigated compounds are also studied. The calculations confirm that the investigated complexes have square planner geometry, which is in a good agreement with the experimental observation.

Temperature and Voltage Offsets in High- ZT Thermoelectrics

NASA Astrophysics Data System (ADS)

Levy, George S.

2018-06-01

Thermodynamic temperature can take on different meanings. Kinetic temperature is an expectation value and a function of the kinetic energy distribution. Statistical temperature is a parameter of the distribution. Kinetic temperature and statistical temperature, identical in Maxwell-Boltzmann statistics, can differ in other statistics such as those of Fermi-Dirac or Bose-Einstein when a field is present. Thermal equilibrium corresponds to zero statistical temperature gradient, not zero kinetic temperature gradient. Since heat carriers in thermoelectrics are fermions, the difference between these two temperatures may explain voltage and temperature offsets observed during meticulous Seebeck measurements in which the temperature-voltage curve does not go through the origin. In conventional semiconductors, temperature offsets produced by fermionic electrical carriers are not observable because they are shorted by heat phonons in the lattice. In high- ZT materials, however, these offsets have been detected but attributed to faulty laboratory procedures. Additional supporting evidence for spontaneous voltages and temperature gradients includes data collected in epistatic experiments and in the plasma Q-machine. Device fabrication guidelines for testing the hypothesis are suggested including using unipolar junctions stacked in a superlattice, alternating n/ n + and p/ p + junctions, selecting appropriate dimensions, doping, and loading.

Understanding the oriented-attachment growth of nanocrystals from an energy point of view: a review

NASA Astrophysics Data System (ADS)

Lv, Weiqiang; He, Weidong; Wang, Xiaoning; Niu, Yinghua; Cao, Huanqi; Dickerson, James H.; Wang, Zhiguo

2014-02-01

Since Penn et al. first discovered the oriented attachment growth of crystals, the oriented attachment mechanism has now become a major research focus in the crystal field, and extensive efforts have been carried out over the past decade to systematically investigate the growth mechanism and the statistical kinetic models. However, most of the work mainly focuses on the experimental results on the oriented attachment growth. In contrast to the previous reviews, our review provides an overview of the recent theoretical advances in oriented attachment kinetics combined with experimental evidences. After a brief introduction to the van der Waals interaction and Coulombic interaction in a colloidal system, the correlation between the kinetic models of oriented attachment growth and the interactions is then our focus. The impact of in situ experimental observation techniques on the study of oriented attachment growth is examined with insightful examples. In addition, the advances in theoretical simulations mainly investigating the thermodynamic origin of these interactions at the atomic level are reviewed. This review seeks to understand the oriented attachment crystal growth from a kinetic point of view and provide a quantitative methodology to rationally design an oriented attachment system with pre-evaluated crystal growth parameters.

Temperature and Voltage Offsets in High-ZT Thermoelectrics

NASA Astrophysics Data System (ADS)

Levy, George S.

2017-10-01

Thermodynamic temperature can take on different meanings. Kinetic temperature is an expectation value and a function of the kinetic energy distribution. Statistical temperature is a parameter of the distribution. Kinetic temperature and statistical temperature, identical in Maxwell-Boltzmann statistics, can differ in other statistics such as those of Fermi-Dirac or Bose-Einstein when a field is present. Thermal equilibrium corresponds to zero statistical temperature gradient, not zero kinetic temperature gradient. Since heat carriers in thermoelectrics are fermions, the difference between these two temperatures may explain voltage and temperature offsets observed during meticulous Seebeck measurements in which the temperature-voltage curve does not go through the origin. In conventional semiconductors, temperature offsets produced by fermionic electrical carriers are not observable because they are shorted by heat phonons in the lattice. In high-ZT materials, however, these offsets have been detected but attributed to faulty laboratory procedures. Additional supporting evidence for spontaneous voltages and temperature gradients includes data collected in epistatic experiments and in the plasma Q-machine. Device fabrication guidelines for testing the hypothesis are suggested including using unipolar junctions stacked in a superlattice, alternating n/n + and p/p + junctions, selecting appropriate dimensions, doping, and loading.

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.

Effect of medium acidity on the thermodynamics and kinetics of the reaction of pyridoxal 5'-phosphate with isoniazid in an aqueous solution

NASA Astrophysics Data System (ADS)

Gamov, G. A.; Zavalishin, M. N.; Usacheva, T. R.; Sharnin, V. A.

2017-05-01

Thermodynamic characteristics of the formation of the Schiff base between isoniazid and pyridoxal 5'-phosphate in an aqueous solution at different pH values of a medium are determined by means of spectrophotometry and calorimetric titration. The process kinetics is studied spectrophotometrically, and the reaction rate constants for the formation of the imine at different acidities of a medium are determined. Biochemical aspects of the binding of pyridoxal 5'-phosphate into stable compounds are discussed.

Understanding materials behavior from atomistic simulations: Case study of al-containing high entropy alloys and thermally grown aluminum oxide

NASA Astrophysics Data System (ADS)

Yinkai Lei

Atomistic simulation refers to a set of simulation methods that model the materials on the atomistic scale. These simulation methods are faster and cheaper alternative approaches to investigate thermodynamics and kinetics of materials compared to experiments. In this dissertation, atomistic simulation methods have been used to study the thermodynamic and kinetic properties of two material systems, i.e. the entropy of Al-containing high entropy alloys (HEAs) and the vacancy migration energy of thermally grown aluminum oxide. (Abstract shortened by ProQuest.).

Course 1: Physics of Protein-DNA Interaction

NASA Astrophysics Data System (ADS)

Bruinsma, R. F.

1 Introduction 1.1 The central dogma and bacterial gene expression 1.2 Molecular structure 2 Thermodynamics and kinetics of repressor-DNA interaction 2.1 Thermodynamics and the lac repressor 2.2 Kinetics of repressor-DNA interaction 3 DNA deformability and protein-DNA interaction 3.1 Introduction 3.2 The worm-like chain 3.3 The RST model 4 Electrostatics in water and protein-DNA interaction 4.1 Macro-ions and aqueous electrostatics 4.2 The primitive model 4.3 Manning condensation 4.4 Counter-ion release and non-specific protein-DNA interaction

A general theory of kinetics and thermodynamics of steady-state copolymerization.

PubMed

Shu, Yao-Gen; Song, Yong-Shun; Ou-Yang, Zhong-Can; Li, Ming

2015-06-17

Kinetics of steady-state copolymerization has been investigated since the 1940s. Irreversible terminal and penultimate models were successfully applied to a number of comonomer systems, but failed for systems where depropagation is significant. Although a general mathematical treatment of the terminal model with depropagation was established in the 1980s, a penultimate model and higher-order terminal models with depropagation have not been systematically studied, since depropagation leads to hierarchically-coupled and unclosed kinetic equations which are hard to solve analytically. In this work, we propose a truncation method to solve the steady-state kinetic equations of any-order terminal models with depropagation in a unified way, by reducing them into closed steady-state equations which give the exact solution of the original kinetic equations. Based on the steady-state equations, we also derive a general thermodynamic equality in which the Shannon entropy of the copolymer sequence is explicitly introduced as part of the free energy dissipation of the whole copolymerization system.

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

Cantera and Cantera Electrolyte Thermodynamics Objects

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

John Hewson, Harry Moffat

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It is a multi-organizational effort to create and formulate high quality 0D and 1D constitutive modeling tools for reactive transport codes.Institutions involved with the effort include Sandia, MIT, Colorado School of Mines, U. Texas, NASA, and Oak Ridge National Labs. Specific to Sandia's contributions, the Cantera Electrolyte Thermo Objects (CETO) packages is comprised of add-on routines for Cantera that handle electrolyte thermochemistry and reactions within the overall Cantera package. Cantera is a C++ Cal Tech code that handles gas phase species transport, reaction,more » and thermodynamics. With this addition, Cantera can be extended to handle problems involving liquid phase reactions and transport in electrolyte systems, and phase equilibrium problemsinvolving concentrated electrolytes and gas/solid phases. A full treatment of molten salt thermodynamics and transport has also been implemented in CETO. The routines themselves consist of .cpp and .h files containing C++ objects that are derived from parent Cantera objects representing thermodynamic functions. They are linked unto the main Cantera libraries when requested by the user. As an addendum to the main thermodynamics objects, several utility applications are provided. The first is multiphase Gibbs free energy minimizer based on the vcs algorithm, called vcs_cantera. This code allows for the calculation of thermodynamic equilibrium in multiple phases at constant temperature and pressure. Note, a similar code capability exists already in Cantera. This version follows the same algorithm, but gas a different code-base starting point, and is used as a research tool for algorithm development. The second program, cttables, prints out tables of thermodynamic and kinetic information for thermodynamic and kinetic objects within Cantera. This program serves as a "Get the numbers out" utility for Cantera, and as such it is very useful as a verification tool. These add-on utilities are encapsulated into a directory structure named cantera_apps, whose installation uses autoconf and also utilizes Cantera's application environment (i.e., they utilize Cantera as a library).« less

First-principles thermodynamics and defect kinetics guidelines for engineering a tailored RRAM device

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

Clima, Sergiu, E-mail: clima@imec.be; Chen, Yang Yin; Goux, Ludovic

Resistive Random Access Memories are among the most promising candidates for the next generation of non-volatile memory. Transition metal oxides such as HfOx and TaOx attracted a lot of attention due to their CMOS compatibility. Furthermore, these materials do not require the inclusion of extrinsic conducting defects since their operation is based on intrinsic ones (oxygen vacancies). Using Density Functional Theory, we evaluated the thermodynamics of the defects formation and the kinetics of diffusion of the conducting species active in transition metal oxide RRAM materials. The gained insights based on the thermodynamics in the Top Electrode, Insulating Matrix and Bottommore » Electrode and at the interfaces are used to design a proper defect reservoir, which is needed for a low-energy reliable switching device. The defect reservoir has also a direct impact on the retention of the Low Resistance State due to the resulting thermodynamic driving forces. The kinetics of the diffusing conducting defects in the Insulating Matrix determine the switching dynamics and resistance retention. The interface at the Bottom Electrode has a significant impact on the low-current operation and long endurance of the memory cell. Our first-principles findings are confirmed by experimental measurements on fabricated RRAM devices.« less

Osmosis and thermodynamics explained by solute blocking.

PubMed

Nelson, Peter Hugo

2017-01-01

A solute-blocking model is presented that provides a kinetic explanation of osmosis and ideal solution thermodynamics. It validates a diffusive model of osmosis that is distinct from the traditional convective flow model of osmosis. Osmotic equilibrium occurs when the fraction of water molecules in solution matches the fraction of pure water molecules that have enough energy to overcome the pressure difference. Solute-blocking also provides a kinetic explanation for why Raoult's law and the other colligative properties depend on the mole fraction (but not the size) of the solute particles, resulting in a novel kinetic explanation for the entropy of mixing and chemical potential of ideal solutions. Some of its novel predictions have been confirmed; others can be tested experimentally or by simulation.

Osmosis and thermodynamics explained by solute blocking

PubMed Central

Nelson, Peter Hugo

2016-01-01

A solute-blocking model is presented that provides a kinetic explanation of osmosis and ideal solution thermodynamics. It validates a diffusive model of osmosis that is distinct from the traditional convective flow model of osmosis. Osmotic equilibrium occurs when the fraction of water molecules in solution matches the fraction of pure water molecules that have enough energy to overcome the pressure difference. Solute-blocking also provides a kinetic explanation for why Raoult’s law and the other colligative properties depend on the mole fraction (but not the size) of the solute particles, resulting in a novel kinetic explanation for the entropy of mixing and chemical potential of ideal solutions. Some of its novel predictions have been confirmed, others can be tested experimentally or by simulation. PMID:27225298

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

PubMed

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

2014-03-06

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

Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations.

PubMed

Gould, Ian R; Wosinska, Zofia M; Farid, Samir

2006-01-01

Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.

Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.

PubMed

Bello-Rivas, Juan M; Elber, Ron

2016-03-05

We investigated by computational means the kinetics and stationary behavior of stochastic dynamics on an ensemble of rough two-dimensional energy landscapes. There are no obvious separations of temporal scales in these systems, which constitute a simple model for the behavior of glasses and some biomaterials. Even though there are significant computational challenges present in these systems due to the large number of metastable states, the Milestoning method is able to compute their kinetic and thermodynamic properties exactly. We observe two clearly distinguished regimes in the overall kinetics: one in which diffusive behavior dominates and another that follows an Arrhenius law (despite the absence of a dominant barrier). We compare our results with those obtained with an exactly-solvable one-dimensional model, and with the results from the rough one-dimensional energy model introduced by Zwanzig. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

A new bioenergetic and thermodynamic approach to batch photoautotrophic growth of Arthrospira (Spirulina) platensis in different photobioreactors and under different light conditions.

PubMed

da Silva, Milena Fernandes; Casazza, Alessandro Alberto; Ferrari, Pier Francesco; Perego, Patrizia; Bezerra, Raquel Pedrosa; Converti, Attilio; Porto, Ana Lucia Figueiredo

2016-05-01

Photobioreactor configuration, mode of operation and light intensity are known to strongly impact on cyanobacteria growth. To shed light on these issues, kinetic, bioenergetic and thermodynamic parameters of batch Arthrospira platensis cultures were estimated along the time at photosynthetic photon flux density (PPFD) of 70μmolm(-2)s(-1) in different photobioreactors with different surface/volume ratio (S/V), namely open pond (0.25cm(-1)), shaken flask (0.48cm(-1)), horizontal photobioreactor (HoP) (1.94cm(-1)) and helicoidal photobioreactor (HeP) (3.88cm(-1)). Maximum biomass concentration and productivity remarkably increased with S/V up to 1.94cm(-1). HoP was shown to be the best-performing system throughout the whole runs, while HeP behaved better only at the start. Runs carried out in HoP increasing PPFD from 40 to 100μmolm(-2)s(-1) revealed a progressive enhancement of bioenergetics and thermodynamics likely because of favorable light distribution. HoP appeared to be a promising configuration to perform high-yield indoor cyanobacterial cultures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetic and thermodynamic parameters, and partial characterization of the crude extract of tannase produced by Saccharomyces cerevisiae CCMB 520.

PubMed

Lopes, Lúzia Morgana de Melo; Costa Batista, Larissa Hayannyelly; Gouveia, Marcos Juliano; Leite, Tonny Cley Campos; de Mello, Marcelo Rodrigues Figueira; de Assis, Sandra Aparecida; de Sena, Amanda Reges

2018-05-01

Tannase can be used in different industrial sectors such as in food (juices and wine) and pharmaceutical production (trimethoprim) because it catalyses the hydrolysis of hydrolysable tannins. The aim of the current study is to assess the tannase found in the crude extract of Saccharomyces cerevisiae CCMB 520, and to set its catalytic and thermodynamic properties. The enzyme was optimally active at pH 6.0 and temperature 30 °C. Tannase was activated by Na + , Ca 2+ , K + at 5 × 10 -3  mol/L. The half-life at 30 °C was 3465.7 min. The activation energy was 40.32 kJ/mol. The Gibbs free energy, enthalpy and entropy at 30 °C were 85.40, 48.10 and -0.12 kJ/mol K, respectively. Our results suggest that the tannase found in the crude extract of S. cerevisiae is an attractive enzyme for industrial applications, such as for beverage manufacturing and gallic acid production, due its catalytic and thermodynamic properties (heat-stable and resistant to metal ions).

Reaction kinetics in open reactors and serial transfers between closed reactors

NASA Astrophysics Data System (ADS)

Blokhuis, Alex; Lacoste, David; Gaspard, Pierre

2018-04-01

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with a finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.

The multispecies modeling of the premixed, laminar steady-state ozone flame

NASA Technical Reports Server (NTRS)

Heimerl, J. M.; Coffee, T. P.

1980-01-01

Species dependent kinetic, transport and thermodynamic coefficients were employed in a one dimensional model of the premixed, laminar, steady state ozone flame. Convenient expressions for these coefficients are reported. They are based on independent measurements, no arbitrary parameters are used. The governing equations are solved using a relaxation technique and the partial differential equation package, PDECOL. Species and temperature profiles and the burning velocities are found over the range of initial ozone mole fraction of 0.25 to 1.00. The computed burning velocities are no more than 30% greater than the measurements of Streng and Grosses. Comparison with the computed results of Warnatz shows agreement within + or - 12%, even though quite different expressions for some of the kinetic coefficients were used. These differences are most obvious in the atomic oxygen and temperature profiles at an initial ozone mole fraction of unity.

Kinetics and mechanism of degradation of some 2-sulfanilamidopyrimidine derivatives. Part VI. The use of Hammett equation for kinetic investigation of 2-sulfanilamidopyrimidine derivatives hydrolysis.

PubMed

Zajac, M

1977-01-01

General, k, and specific, k1 and k2, first-order rate constants for the parallel reaction of hydrolysis catalized by H+ ions were estimated for sulfadiazine (I), sulfamerazine (II), sulfadimidine (III), sulfaperine (IV) and sulfamethoxydiazine (V), hydrolyzed in 1 mole/dm3 HCl at 333, 343, 355 and 363 K. General first-order rate constants for the spontaneous hydrolysis of I--V in borate buffer pH 9.20 at 403, 411 and 418 K were also determined. Thermodynamic parameters of the reaction (delta Ha, deltaH not equal to, deltaS not equal to, deltaG not equal to and log A) were calculated. The effect of substituents in positions 4, 5 and 6 of the pyrimidine ring on the rate of hydrolysis was interpreted in terms of Hammett equation.

Adsorption of 2,4-Dichlorophenoxyacetic Acid from an Aqueous Solution on Fly Ash.

PubMed

Kuśmierek, Krzysztof; Świątkowski, Andrzej

2016-03-01

The adsorption of 2,4-dichlorophenoxyacetic acid (2,4-D) on fly ash was studied. The effects of adsorbent dose, contact time, pH, ionic strength, and temperature on the adsorption were investigated. Adsorption kinetic data were analyzed using pseudo-first and pseudo-second order models, and results showed that adsorption kinetics were better represented by the pseudo-second order model. Adsorption isotherms of 2,4-D on fly ash were analyzed using the Freundlich and Langmuir models. Thermodynamic parameters (ΔG°, ΔH°, and ΔS°) indicated that the adsorption process was spontaneous and endothermic. The negative values of ΔG° and the positive value of ΔH° indicate the spontaneous nature of 2,4-D adsorption on fly ash, and that the adsorption process was endothermic. Results showed that fly ash is an efficient, low-cost adsorbent for removal of 2,4-D from water.

Polypeptide Translocation Through the Mitochondrial TOM Channel: Temperature-Dependent Rates at the Single-Molecule Level.

PubMed

Mahendran, Kozhinjampara R; Lamichhane, Usha; Romero-Ruiz, Mercedes; Nussberger, Stephan; Winterhalter, Mathias

2013-01-03

The TOM protein complex facilitates the transfer of nearly all mitochondrial preproteins across outer mitochondrial membranes. Here we characterized the effect of temperature on facilitated translocation of a mitochondrial presequence peptide pF1β. Ion current fluctuations analysis through single TOM channels revealed thermodynamic and kinetic parameters of substrate binding and allowed determining the energy profile of peptide translocation. The activation energy for the on-rate and off-rate of the presequence peptide into the TOM complex was symmetric with respect to the electric field and estimated to be about 15 and 22 kT per peptide. These values are above that expected for free diffusion of ions in water (6 kT) and reflect the stronger interaction in the channel. Both values are in the range for typical enzyme kinetics and suggest one process without involving large conformational changes within the channel protein.

Theory of chemical kinetics and charge transfer based on nonequilibrium thermodynamics.

PubMed

Bazant, Martin Z

2013-05-21

Advances in the fields of catalysis and electrochemical energy conversion often involve nanoparticles, which can have kinetics surprisingly different from the bulk material. Classical theories of chemical kinetics assume independent reactions in dilute solutions, whose rates are determined by mean concentrations. In condensed matter, strong interactions alter chemical activities and create variations that can dramatically affect the reaction rate. The extreme case is that of a reaction coupled to a phase transformation, whose kinetics must depend not only on the order parameter but also on its gradients at phase boundaries. Reaction-driven phase transformations are common in electrochemistry, when charge transfer is accompanied by ion intercalation or deposition in a solid phase. Examples abound in Li-ion, metal-air, and lead-acid batteries, as well as metal electrodeposition-dissolution. Despite complex thermodynamics, however, the standard kinetic model is the Butler-Volmer equation, based on a dilute solution approximation. The Marcus theory of charge transfer likewise considers isolated reactants and neglects elastic stress, configurational entropy, and other nonidealities in condensed phases. The limitations of existing theories recently became apparent for the Li-ion battery material LixFePO4 (LFP). It has a strong tendency to separate into Li-rich and Li-poor solid phases, which scientists believe limits its performance. Chemists first modeled phase separation in LFP as an isotropic "shrinking core" within each particle, but experiments later revealed striped phase boundaries on the active crystal facet. This raised the question: What is the reaction rate at a surface undergoing a phase transformation? Meanwhile, dramatic rate enhancement was attained with LFP nanoparticles, and classical battery models could not predict the roles of phase separation and surface modification. In this Account, I present a general theory of chemical kinetics, developed over the past 7 years, which is capable of answering these questions. The reaction rate is a nonlinear function of the thermodynamic driving force, the free energy of reaction, expressed in terms of variational chemical potentials. The theory unifies and extends the Cahn-Hilliard and Allen-Cahn equations through a master equation for nonequilibrium chemical thermodynamics. For electrochemistry, I have also generalized both Marcus and Butler-Volmer kinetics for concentrated solutions and ionic solids. This new theory provides a quantitative description of LFP phase behavior. Concentration gradients and elastic coherency strain enhance the intercalation rate. At low currents, the charge-transfer rate is focused on exposed phase boundaries, which propagate as "intercalation waves", nucleated by surface wetting. Unexpectedly, homogeneous reactions are favored above a critical current and below a critical size, which helps to explain the rate capability of LFP nanoparticles. Contrary to other mechanisms, elevated temperatures and currents may enhance battery performance and lifetime by suppressing phase separation. The theory has also been extended to porous electrodes and could be used for battery engineering with multiphase active materials. More broadly, the theory describes nonequilibrium chemical systems at mesoscopic length and time scales, beyond the reach of molecular simulations and bulk continuum models. The reaction rate is consistently defined for inhomogeneous, nonequilibrium states, for example, with phase separation, large electric fields, or mechanical stresses. This research is also potentially applicable to fluid extraction from nanoporous solids, pattern formation in electrophoretic deposition, and electrochemical dynamics in biological cells.

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.

Removal of lead (II) ions from aqueous solutions onto activated carbon derived from waste biomass.

PubMed

Erdem, Murat; Ucar, Suat; Karagöz, Selhan; Tay, Turgay

2013-01-01

The removal of lead (II) ions from aqueous solutions was carried out using an activated carbon prepared from a waste biomass. The effects of various parameters such as pH, contact time, initial concentration of lead (II) ions, and temperature on the adsorption process were investigated. Energy Dispersive X-Ray Spectroscopy (EDS) analysis after adsorption reveals the accumulation of lead (II) ions onto activated carbon. The Langmuir and Freundlich isotherm models were applied to analyze equilibrium data. The maximum monolayer adsorption capacity of activated carbon was found to be 476.2 mg g⁻¹. The kinetic data were evaluated and the pseudo-second-order equation provided the best correlation. Thermodynamic parameters suggest that the adsorption process is endothermic and spontaneous.

Isotherm Modelling, Kinetic Study and Optimization of Batch Parameters Using Response Surface Methodology for Effective Removal of Cr(VI) Using Fungal Biomass

PubMed Central

Chidambaram, Ramalingam

2015-01-01

Biosorption is a promising alternative method to replace the existing conventional technique for Cr(VI) removal from the industrial effluent. In the present experimental design, the removal of Cr(VI) from the aqueous solution was studied by Aspergillus niger MSR4 under different environmental conditions in the batch systems. The optimum conditions of biosorption were determined by investigating pH (2.0) and temperature (27°C). The effects of parameters such as biomass dosage (g/L), initial Cr(VI) concentration (mg/L) and contact time (min) on Cr(VI) biosorption were analyzed using a three parameter Box–Behnken design (BBD). The experimental data well fitted to the Langmuir isotherm, in comparison to the other isotherm models tested. The results of the D-R isotherm model suggested that a chemical ion-exchange mechanism was involved in the biosorption process. The biosorption process followed the pseudo-second-order kinetic model, which indicates that the rate limiting step is chemisorption process. Fourier transform infrared (FT-IR) spectroscopic studies revealed the possible involvement of functional groups, such as hydroxyl, carboxyl, amino and carbonyl group in the biosorption process. The thermodynamic parameters for Cr(VI) biosorption were also calculated, and the negative ∆Gº values indicated the spontaneous nature of biosorption process. PMID:25786227

Coarse Grained Modeling of Block Copolymer Lithography: The Effects of Pattern Design on the Thermodynamics and Kinetics of the Directed Self Assembly of Block Copolymers

NASA Astrophysics Data System (ADS)

Garner, Grant Parker

The directed self assembly of block copolymers is an exciting complimentary technique for the fabrication of nanoscale structures for lithographic applications. Typically a directed self assembly process is driven through substrates with chemical (chemoepitaxy) or topographical (graphoepitaxy) guiding features. These patterning strategies have led to the ability to assemble structures with a high degree of perfection over large areas. However, a guiding pattern has not been created which assembles the desired features with a defect density that is commensurate with industrial standards of 1 defect/100cm 2. This work focuses on using molecular simulations on the Theoretically Informed Coarse Grained model to provide design rules for substrate patterns which drive the assembly of desired, device-oriented morphologies. Prior to the work presented in Chapter 2, the TICG model has been used in conjunction with a chemical pattern that is approximated as a hard-impenetrable surface. As many experimental systems use polymer brushes to help guide the polymer melt deposited on the substrate, this work analyzes the consequences of such an assumption by comparing a model where the polymer brush is explicitly implemented to the hard-wall substrate used in the past. Then, a methodology which utilizes a evolutionary optimization method is used to map the parameters of the more detailed model to the hard-surface model. This provides a qualitative understanding of how to interpret the model parameters used in previous works in the context of real experimental pattern designs. Chapter 3 discuss the concept of competitive assemblies in regards to defining a thermodynamic processing window in design space for assembling lines-and-spaces. The most competitive assembly to the desired orientation of the lamella is defined as a rotation of assembled lamella to the underlying pattern. Thermodynamic integration is used to calculate the free-energy difference between these assemblies over chemical patterns with varied design parameters. Local maximums in the free-energy difference are observed over pattern designs that are in qualitatively agreement with the pattern designs which produce the most perfect assemblies in experiments. The analysis is extended to study how choice of chemistry impacts this thermodynamic selection for the desired morphology. Finally, Chapter 4 provides insight into the kinetics of patterned directed self-assembly by investigating cylinder forming block copolymers within cylindrical confinements. Through the use of the string method, the minimum free-energy path between a defective state and the desired assembled morphology is calculated and clear transition states are highlighted. The effects of key parameters of the confinement design on the calculated minimum free energy path are calculated to identify design rules which should lead to a better understanding of optimal connement design for eliminating defects. In addition, a specific modification to existing cylindrical confinements is discussed as a possibility for tackling the problem of placement accuracy for a cylinder that is assembled within the confinement.

Effects of gold nanoparticles on the photophysical and photosynthetic parameters of leaves and chloroplasts.

PubMed

Torres, Rocio; Diz, Virginia E; Lagorio, M Gabriela

2018-04-18

Effects of gold nanoparticles (average diameter: 10-14 nm) on leaves and chloroplasts have been studied. Gold nanoparticles (AuNPs) quenched significantly chlorophyll fluorescence when introduced both in intact leaves and isolated chloroplasts. Additionally, the fluorescence spectra corrected for light re-absorption processes showed a net decrease in the fluorescence ratio calculated as the quotient between the maximum fluorescence at 680 and 735 nm. This fact gave evidence for a reduction in the fluorescence emission of the PSII relative to that of the PSI. Strikingly, the photosynthetic parameters derived from the analysis of the slow phase of Kautsky's kinetics, the rate of oxygen evolution and the rate of photo-reduction of 2,6-dichlorophenolindophenol were increased in the presence of AuNPs indicating an apparent greater photosynthetic capacity. The observed results were consistent with an electron transfer process from the excited PSII, which was thermodynamically possible, and which competed with both the electron transport process that initiated photosynthesis and the deactivation of the excited PSII by fluorescence emission. Additionally, it is here explained, in terms of a completely rational kinetic scheme and their corresponding algebraic expressions, why the photosynthetic parameters and the variable and non-variable fluorescence of chlorophyll are modified in a photosynthetic tissue containing gold nanoparticles.

Polymer Principles in the Undergraduate Physical Chemistry Course. Part 2.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1985

1985-01-01

Part l (SE 538 305) covered application of classical thermodynamics, polymer crystallinity, and phase diagrams to teaching physical chemistry. This part covers statistical thermodynamics, conformation, molecular weights, rubber elasticity and viscoelasticity, and kinetics of polymerization. Eight polymer-oriented, multiple-choice test questions…

Analysis of non-equilibrium phenomena in inductively coupled plasma generators

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

Zhang, W.; Panesi, M., E-mail: mpanesi@illinois.edu; Lani, A.

This work addresses the modeling of non-equilibrium phenomena in inductively coupled plasma discharges. In the proposed computational model, the electromagnetic induction equation is solved together with the set of Navier-Stokes equations in order to compute the electromagnetic and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles, with the method of Chapman and Enskog. Particle ambipolar diffusive fluxes are found by solving the Stefan-Maxwell equations with a simple iterative method. Two physico-mathematical formulations are used to model the chemical reaction processes: (1) Amore » Local Thermodynamics Equilibrium (LTE) formulation and (2) a thermo-chemical non-equilibrium (TCNEQ) formulation. In the TCNEQ model, thermal non-equilibrium between the translational energy mode of the gas and the vibrational energy mode of individual molecules is accounted for. The electronic states of the chemical species are assumed in equilibrium with the vibrational temperature, whereas the rotational energy mode is assumed to be equilibrated with translation. Three different physical models are used to account for the coupling of chemistry and energy transfer processes. Numerical simulations obtained with the LTE and TCNEQ formulations are used to characterize the extent of non-equilibrium of the flow inside the Plasmatron facility at the von Karman Institute. Each model was tested using different kinetic mechanisms to assess the sensitivity of the results to variations in the reaction parameters. A comparison of temperatures and composition profiles at the outlet of the torch demonstrates that the flow is in non-equilibrium for operating conditions characterized by pressures below 30 000 Pa, frequency 0.37 MHz, input power 80 kW, and mass flow 8 g/s.« less

Analysis of non-equilibrium phenomena in inductively coupled plasma generators

NASA Astrophysics Data System (ADS)

Zhang, W.; Lani, A.; Panesi, M.

2016-07-01

This work addresses the modeling of non-equilibrium phenomena in inductively coupled plasma discharges. In the proposed computational model, the electromagnetic induction equation is solved together with the set of Navier-Stokes equations in order to compute the electromagnetic and flow fields, accounting for their mutual interaction. Semi-classical statistical thermodynamics is used to determine the plasma thermodynamic properties, while transport properties are obtained from kinetic principles, with the method of Chapman and Enskog. Particle ambipolar diffusive fluxes are found by solving the Stefan-Maxwell equations with a simple iterative method. Two physico-mathematical formulations are used to model the chemical reaction processes: (1) A Local Thermodynamics Equilibrium (LTE) formulation and (2) a thermo-chemical non-equilibrium (TCNEQ) formulation. In the TCNEQ model, thermal non-equilibrium between the translational energy mode of the gas and the vibrational energy mode of individual molecules is accounted for. The electronic states of the chemical species are assumed in equilibrium with the vibrational temperature, whereas the rotational energy mode is assumed to be equilibrated with translation. Three different physical models are used to account for the coupling of chemistry and energy transfer processes. Numerical simulations obtained with the LTE and TCNEQ formulations are used to characterize the extent of non-equilibrium of the flow inside the Plasmatron facility at the von Karman Institute. Each model was tested using different kinetic mechanisms to assess the sensitivity of the results to variations in the reaction parameters. A comparison of temperatures and composition profiles at the outlet of the torch demonstrates that the flow is in non-equilibrium for operating conditions characterized by pressures below 30 000 Pa, frequency 0.37 MHz, input power 80 kW, and mass flow 8 g/s.

Heterocatalytic Fenton oxidation process for the treatment of tannery effluent: kinetic and thermodynamic studies.

PubMed

Karthikeyan, S; Ezhil Priya, M; Boopathy, R; Velan, M; Mandal, A B; Sekaran, G

2012-06-01

BACKGROUND, AIM, SCOPE: Treatment of wastewater has become significant with the declining water resources. The presence of recalcitrant organics is the major issue in meeting the pollution control board norms in India. The theme of the present investigation was on partial or complete removal of pollutants or their transformation into less toxic and more biodegradable products by heterogeneous Fenton oxidation process using mesoporous activated carbon (MAC) as the catalyst. Ferrous sulfate (FeSO(4)·7H(2)O), sulfuric acid (36 N, specific gravity 1.81, 98% purity), hydrogen peroxide (50% v/v) and all other chemicals used in this study were of analytical grade (Merck). Two reactors, each of height 50 cm and diameter 6 cm, were fabricated with PVC while one reactor was packed with MAC of mass 150 g and other without MAC served as control. The oxidation process was presented with kinetic and thermodynamic constants for the removal of COD, BOD, and TOC from the wastewater. The activation energy (Ea) for homogeneous and heterogeneous Fenton oxidation processes were 44.79 and 25.89 kJ/mol, respectively. The thermodynamic parameters ΔG, ΔH, and ΔS were calculated for the oxidation processes using Van't Hoff equation. Furthermore, the degradation of organics was confirmed through FTIR and UV-visible spectroscopy, and cyclic voltammetry. The heterocatalytic Fenton oxidation process efficiently increased the biodegradability index (BOD/COD) of the tannery effluent. The optimized conditions for the heterocatalytic Fenton oxidation of organics in tannery effluent were pH 3.5, reaction time-4 h, and H(2)O(2)/FeSO(4)·7H(2)O in the molar ratio of 2:1.

Thermodynamic and Kinetic Aspects Involved in the Development of Nanocarriers and Drug Delivery Systems Based on Cationic Biopolymers.

PubMed

Bianco, Ismael D; Alasino, Roxana V; Leonhard, Victoria; Beltramo, Dante M

2016-01-01

During the last years we have seen an increasing number of reports describing new properties and potential applications of cationic polymers and derived nanostructures. This review gives a summary of their applications in drug delivery, the preparation methods for nano and microstructures and will attempt to give a glimpse on how their structure, chemical composition and properties may be affected or modulated as to make them suitable for an intended application as drug delivery nanocarriers. The compositional complexity with the existence of several reacting groups makes cationic nanostructures critically sensitive to the contribution of thermodynamic and kinetic parameters in the determination of the type and stability of a particular structure and its ability to respond to changes in environmental conditions in the right time frame. Curiously, and contrarily to what could be expected, despite the fact that cationic polymers can form strong electrostatic interactions the contribution of the entropic component has been often found to be very important for their association with negatively charged supramolecular structures. Some general considerations indicate that when considering a complex multimolecular system like a nanocarrier containing an active ingredient it is frequently possible to find conditions under which enthalpic and entropic contributions are compensated leading to stable structures with a marginal thermodynamic stability (free energy change close to zero) which make them able to respond relatively fast to changes in the environmental conditions and therefore suitable for the design of smart drug delivery systems. Like with other nanocarriers, it should always be kept in mind that the properties of cationic nanocarriers will depend not only on their chemical composition but also on the properties of the structures formed by them.

Entropy in self-similar shock profiles

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

Margolin, Len G.; Reisner, Jon Michael; Jordan, Pedro M.

In this paper, we study the structure of a gaseous shock, and in particular the distribution of entropy within, in both a thermodynamics and a statistical mechanics context. The problem of shock structure has a long and distinguished history that we review. We employ the Navier–Stokes equations to construct a self–similar version of Becker’s solution for a shock assuming a particular (physically plausible) Prandtl number; that solution reproduces the well–known result of Morduchow & Libby that features a maximum of the equilibrium entropy inside the shock profile. We then construct an entropy profile, based on gas kinetic theory, that ismore » smooth and monotonically increasing. The extension of equilibrium thermodynamics to irreversible processes is based in part on the assumption of local thermodynamic equilibrium. We show that this assumption is not valid except for the weakest shocks. Finally, we conclude by hypothesizing a thermodynamic nonequilibrium entropy and demonstrating that it closely estimates the gas kinetic nonequilibrium entropy within a shock.« less

Entropy in self-similar shock profiles

DOE PAGES

Margolin, Len G.; Reisner, Jon Michael; Jordan, Pedro M.

2017-07-16

In this paper, we study the structure of a gaseous shock, and in particular the distribution of entropy within, in both a thermodynamics and a statistical mechanics context. The problem of shock structure has a long and distinguished history that we review. We employ the Navier–Stokes equations to construct a self–similar version of Becker’s solution for a shock assuming a particular (physically plausible) Prandtl number; that solution reproduces the well–known result of Morduchow & Libby that features a maximum of the equilibrium entropy inside the shock profile. We then construct an entropy profile, based on gas kinetic theory, that ismore » smooth and monotonically increasing. The extension of equilibrium thermodynamics to irreversible processes is based in part on the assumption of local thermodynamic equilibrium. We show that this assumption is not valid except for the weakest shocks. Finally, we conclude by hypothesizing a thermodynamic nonequilibrium entropy and demonstrating that it closely estimates the gas kinetic nonequilibrium entropy within a shock.« less

Determination of arrhenius and thermodynamic parameters for the aqueous reaction of the hydroxyl radical with lactic acid.

PubMed

Martin, Leigh R; Mezyk, Stephen P; Mincher, Bruce J

2009-01-08

Lactic acid is a major component of the TALSPEAK process planned for use in the separation of trivalent lanthanide and actinide elements. This acid acts both as a buffer and to protect the actinide complexant from radiolytic damage. However, there is little kinetic information on the reaction of water radiolysis species with lactic acid, particularly under the anticipated process conditions of aerated aqueous solution at pH approximately 3, where oxidizing reactions are expected to dominate. Here we have determined temperature-dependent reaction rate constants for the reactions of the hydroxyl radical with lactic acid and the lactate ion. For lactic acid this rate constant is given by the following equation: ln k(1) = (23.85 +/- 0.19) - (1120 +/- 54)/T, corresponding to an activation energy of 9.31 +/- 0.45 kJ mol(-1) and a room temperature reaction rate constant of (5.24 +/- 0.35) x 10(8) M(-1) s(-1) (24.0 degrees C). For the lactate ion, the temperature-dependent rate constant is given by ln k(2) = (24.83 +/- 0.14) - (1295 +/- 42)/T, for an activation energy of 10.76 +/- 0.35 kJ mol(-1) and a room temperature value of (7.77 +/- 0.50) x 10(8) M(-1) s(-1) (22.2 degrees C). These kinetic data have been combined with autotitration measurements to determine the temperature-dependent behavior of the lactic acid pK(a) value, allowing thermodynamic parameters for the acid dissociation to be calculated as DeltaH(o) = -10.75 +/- 1.77 kJ mol(-1), DeltaS(o) = -103.9 +/- 6.0 J K(-1) mol(-1) and DeltaG(o) = 20.24 +/- 2.52 kJ mol(-1) at low ionic strength.

Kinetic and thermodynamic parameters for thermal denaturation of ovine milk lactoferrin determined by its loss of immunoreactivity.

PubMed

Navarro, F; Harouna, S; Calvo, M; Pérez, M D; Sánchez, L

2015-07-01

Lactoferrin is a protein with important biological functions that can be obtained from milk and by-products derived from the dairy industry, such as whey. Although bovine lactoferrin has been extensively studied, ovine lactoferrin is not quite as well known. In the present study, the effect of several heat treatments in 3 different media, over a temperature range from 66 to 75°C, has been studied on lactoferrin isolated from sheep milk. Denaturation of lactoferrin was determined by measuring its immunoreactivity with specific polyclonal antibodies. Kinetic and thermodynamic parameters obtained indicate that lactoferrin denatures by heat more rapidly in whey than in phosphate buffer or milk. The value of activation energy found for the denaturation process of lactoferrin when treated in whey is higher (390kJ/mol) than that obtained in milk (194kJ/mol) or phosphate buffer (179kJ/mol). This indicates that a great amount of energy is necessary to start denaturation of ovine lactoferrin, probably due to the interaction of this protein with other whey proteins. The changes in the hydrophobicity of lactoferrin after heat treatments were determined by fluorescence measurement using acrylamide. The decrease in the hydrophobicity constant was very small for the treatments from 66 to 75°C, up to 20min, which indicates that lactoferrin conformation did not experienced a great change. The results obtained in this study permit the prediction of behavior of ovine lactoferrin under several heat treatments and show that high-temperature, short-time pasteurization (72°C, 15 s) does not cause loss of its immunoreactivity and, consequently, would not affect its conformation and biological activity. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Approach for discrimination and quantification of electroactive species: kinetics difference revealed by higher harmonics of Fourier transformed sinusoidal voltammetry.

PubMed

Fang, Yishan; Huang, Xinjian; Wang, Lishi

2015-01-06

Discrimination and quantification of electroactive species are traditionally realized by a potential difference which is mainly determined by thermodynamics. However, the resolution of this approach is limited to tens of millivolts. In this paper, we described an application of Fourier transformed sinusoidal voltammetry (FT-SV) that provides a new approach for discrimination and quantitative evaluation of electroactive species, especially thermodynamic similar ones. Numerical simulation indicates that electron transfer kinetics difference between electroactive species can be revealed by the phase angle of higher order harmonics of FT-SV, and the difference can be amplified order by order. Thus, even a very subtle kinetics difference can be amplified to be distinguishable at a certain order of harmonics. This method was verified with structurally similar ferrocene derivatives which were chosen as the model systems. Although these molecules have very close redox potential (<10 mV), discrimination and selective detection were achieved by as high as the thirteenth harmonics. The results demonstrated the feasibility and reliability of the method. It was also implied that the combination of the traditional thermodynamic method and this kinetics method can form a two-dimension resolved detection method, and it has the potential to extend the resolution of voltammetric techniques to a new level.

Characterization of bioimprinted tannase and its kinetic and thermodynamics properties in synthesis of propyl gallate by transesterification in anhydrous medium.

PubMed

Nie, Guangjun; Zheng, Zhiming; Gong, Guohong; Zhao, Genhai; Liu, Yan; Song, Junying; Dai, Jun

2012-08-01

Tannase has been extensively applied to synthesize gallic acid esters. Bioimprinting technique can evidently enhance transesterification-catalyzing performance of tannase. In order to promote the practical utilization of the modified tannase, a few enzymatic characteristics of the enzyme and its kinetic and thermodynamics properties in synthesis of propyl gallate by transesterification in anhydrous medium have been studied. The investigations of pH and temperature found that the imprinted tannase holds an optimum activity at pH 5.0 and 40 °C. On the other hand, the bioimprinting technique has a profound enhancing effect on the adapted tannase in substrate affinity and thermostability. The kinetic and thermodynamic analyses showed that the modified tannase has a longer half-time of 1,710 h at 40 °C; the kinetic constants, the activation energy of reversible thermal inactivation, and the activation energy of irreversible thermal inactivation, respectively, are 0.054 mM, 17.35 kJ mol(-1), and 85.54 kJ mol(-1) with tannic acid as a substrate at 40 °C; the free energy of Gibbs (ΔG) and enthalpy (ΔH) were found to be 97.1 and 82.9 kJ mol(-1) separately under the same conditions.

Synthesis of zeolite/nickel ferrite/sodium alginate bionanocomposite via a co-precipitation technique for efficient removal of water-soluble methylene blue dye.

PubMed

Bayat, Mahsa; Javanbakht, Vahid; Esmaili, Javad

2018-05-05

In this study, we sought to synthesize magnetic nanocomposite of zeolite/nickel ferrite through co-precipitation method and modify its surface by sodium alginate to enhance its methylene blue adsorption capacity and to prevent its oxidation. Nanocomposite characteristics were investigated by SEM, VSM, XRD and FTIR analyses. The results indicate that nanocomposite synthesis and modification has been completely successful. Adsorption thermodynamics, kinetics, and isotherms were examined and parameters were optimized by Minitab software using experimental design method, response surface methodology and Box-Behnken design. The highest capacity of methylene blue adsorption from the aqueous solution obtained at optimal pH of 5, the initial dye concentration of 10 mg/L and an adsorbent amount of 0.03 g was about 54.05 mg/g. Analyzing kinetic data of adsorption experiments confirmed that adsorption process complies with the pseudo-second-order kinetic model. Assessing equilibrium isotherm data at different temperatures showed that these data are in good agreement with Langmuir isotherm model. Copyright © 2018 Elsevier B.V. All rights reserved.

Adsorption of Zinc(II) on diatomite and manganese-oxide-modified diatomite: a kinetic and equilibrium study.

PubMed

Caliskan, Necla; Kul, Ali Riza; Alkan, Salih; Sogut, Eda Gokirmak; Alacabey, Ihsan

2011-10-15

The removal of Zn(II) ions from aqueous solution was studied using natural and MnO(2) modified diatomite samples at different temperatures. The linear Langmuir, Freundlich and Dubinin-Radushkevich (D-R) adsorption equations were applied to describe the equilibrium isotherms. From the D-R model, the mean adsorption energy was calculated as >8 kJ mol(-1), indicating that the adsorption of Zn(II) onto diatomite and Mn-diatomite was physically carried out. In addition, the pseudo-first-order, pseudo-second-order and intraparticle diffusion models were used to determine the kinetic data. The experimental data were well fitted by the pseudo-second-order kinetic model. Thermodynamic parameters such as the enthalpy (ΔH(0)), Gibbs' free energy (ΔG(0)) and entropy (ΔS(0)) were calculated for natural and MnO(2) modified diatomite. These values showed that the adsorption of Zn(II) ions onto diatomite samples was controlled by a physical mechanism and occurred spontaneously. Copyright © 2011 Elsevier B.V. All rights reserved.

Physiochemical properties and kinetics of glucoamylase produced from deoxy-d-glucose resistant mutant of Aspergillus niger for soluble starch hydrolysis.

PubMed

Riaz, Muhammad; Rashid, Muhammad Hamid; Sawyer, Lindsay; Akhtar, Saeed; Javed, Muhammad Rizwan; Nadeem, Habibullah; Wear, Martin

2012-01-01

Glucoamylases (GAs) from a wild and a deoxy-d-glucose-resistant mutant of a locally isolated Aspergillus niger were purified to apparent homogeneity. The subunit molecular mass estimated by SDS-PAGE was 93 kDa for both strains, while the molecular masses determined by MALDI-TOF for wild and mutant GAs were 72.876 and 72.063 kDa, respectively. The monomeric nature of the enzymes was confirmed through activity staining. Significant improvement was observed in the kinetic properties of the mutant GA relative to the wild type enzyme. Kinetic constants of starch hydrolysis for A. niger parent and mutant GAs calculated on the basis of molecular masses determined through MALDI-TOF were as follows: k cat = 343 and 727 s -1 , K m = 0.25 and 0.16 mg mL -1 , k cat / K m (specificity constant) = 1374 and 4510 mg mL -1 s -1 , respectively. Thermodynamic parameters for soluble starch hydrolysis also suggested that mutant GA was more efficient compared to the parent enzyme.

Enceladus' Plumes Reflectance. Particle-in-Cell Model Parametric Study

NASA Astrophysics Data System (ADS)

Kotlarz, J. P.; Zalewska, N. E.

2018-06-01

In our work we are using kinetic numerical model to describe plumes curtain forms as a result of kinetic and thermodynamic processes: a) in the ocean, b) inside Tiger Stripes icy forms and c) over moon's surface.

A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.

PubMed

Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G; Hellinga, Homme W

2011-04-01

Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics. Copyright © 2010 Wiley-Liss, Inc.

Computational Thermodynamics and Kinetics-Based ICME Framework for High-Temperature Shape Memory Alloys

NASA Astrophysics Data System (ADS)

Arróyave, Raymundo; Talapatra, Anjana; Johnson, Luke; Singh, Navdeep; Ma, Ji; Karaman, Ibrahim

2015-11-01

Over the last decade, considerable interest in the development of High-Temperature Shape Memory Alloys (HTSMAs) for solid-state actuation has increased dramatically as key applications in the aerospace and automotive industry demand actuation temperatures well above those of conventional SMAs. Most of the research to date has focused on establishing the (forward) connections between chemistry, processing, (micro)structure, properties, and performance. Much less work has been dedicated to the development of frameworks capable of addressing the inverse problem of establishing necessary chemistry and processing schedules to achieve specific performance goals. Integrated Computational Materials Engineering (ICME) has emerged as a powerful framework to address this problem, although it has yet to be applied to the development of HTSMAs. In this paper, the contributions of computational thermodynamics and kinetics to ICME of HTSMAs are described. Some representative examples of the use of computational thermodynamics and kinetics to understand the phase stability and microstructural evolution in HTSMAs are discussed. Some very recent efforts at combining both to assist in the design of HTSMAs and limitations to the full implementation of ICME frameworks for HTSMA development are presented.

OPAC (orange peel activated carbon) derived from waste orange peel for the adsorption of chlorophenoxyacetic acid herbicides from water: Adsorption isotherm, kinetic modelling and thermodynamic studies.

PubMed

Pandiarajan, Aarthi; Kamaraj, Ramakrishnan; Vasudevan, Sudharshan; Vasudevan, Subramanyan

2018-08-01

This study presents the orange peel activated carbon (OPAC), derived from biowaste precursor (orange peel) by single step pyrolysis method and its application for the adsorption of chlorophenoxyacetic acid herbicides from the water. The OPAC exhibited the surface area of 592.471 m 2  g -1 , pore volume and pore diameter of 0.242 cc g -1 and 1.301 nm respectively. The adsorption kinetics and thermodynamic equilibrium modelling for all chlorophenoxyacetic acid herbicides were investigated. The various parametric effects such as pH and temperature were evaluated. A pseudo-second-order kinetic model was well fitted for all the herbicides. The Langmuir isotherm was obeyed for all the herbicides and the maximum Langmuir capacity of 574.71 mg g -1 was achieved. The thermodynamic studies revealed that the adsorption increases with increase in temperature. The results shows that the orange peel derived carbon (OPAC) as effective and efficient adsorbent material for the removal of chlorophenoxyacid herbicides from the water. Copyright © 2018 Elsevier Ltd. All rights reserved.

Multiensemble Markov models of molecular thermodynamics and kinetics.

PubMed

Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank

2016-06-07

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model.

Multiensemble Markov models of molecular thermodynamics and kinetics

PubMed Central

Wu, Hao; Paul, Fabian; Noé, Frank

2016-01-01

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302

Quantitative correlations between collision induced dissociation mass spectrometry coupled with electrospray ionization or atmospheric pressure chemical ionization mass spectrometry - Experiment and theory

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2018-04-01

The problematic that we consider in this paper treats the quantitative correlation model equations between experimental kinetic and thermodynamic parameters of coupled electrospray ionization (ESI) mass spectrometry (MS) or atmospheric pressure chemical ionization (APCI) mass spectrometry with collision induced dissociation mass spectrometry, accounting for the fact that the physical phenomena and mechanisms of ESI- and APCI-ion formation are completely different. There are described forty two fragment reactions of three analytes under independent ESI- and APCI-measurements. The developed new quantitative models allow us to study correlatively the reaction kinetics and thermodynamics using the methods of mass spectrometry, which complementary application with the methods of the quantum chemistry provide 3D structural information of the analytes. Both static and dynamic quantum chemical computations are carried out. The object of analyses are [2,3-dimethyl-4-(4-methyl-benzoyl)-2,3-di-p-tolyl-cyclobutyl]-p-tolyl-methanone (1) and the polycyclic aromatic hydrocarbons derivatives of dibenzoperylen (2) and tetrabenzo [a,c,fg,op]naphthacene (3), respectively. As far as (1) is known to be a product of [2π+2π] cycloaddition reactions of chalcone (1,3-di-p-tolyl-propenone), however producing cyclic derivatives with different stereo selectivity, so that the study provide crucial data about the capability of mass spectrometry to provide determine the stereo selectivity of the analytes. This work also first provides quantitative treatment of the relations '3D molecular/electronic structures'-'quantum chemical diffusion coefficient'-'mass spectrometric diffusion coefficient', thus extending the capability of the mass spectrometry for determination of the exact 3D structure of the analytes using independent measurements and computations of the diffusion coefficients. The determination of the experimental diffusion parameters is carried out within the 'current monitoring method' evaluating the translation diffusion of charged analytes, while the theoretical modelling of MS ions and computations of theoretical diffusion coefficients are based on the Arrhenius type behavior of the charged species under ESI- and APCI-conditions. Although the study provide certain sound considerations for the quantitative relations between the reaction kinetic-thermodynamics and 3D structure of the analytes together with correlations between 3D molecular/electronic structures-quantum chemical diffusion coefficient-mass spectrometric diffusion coefficient, which contribute significantly to the structural analytical chemistry, the results have importance to other areas such as organic synthesis and catalysis as well.

Reactive transport modelling of groundwater chemistry in a chalk aquifer at the watershed scale.

PubMed

Mangeret, A; De Windt, L; Crançon, P

2012-09-01

This study investigates thermodynamics and kinetics of water-rock interactions in a carbonate aquifer at the watershed scale. A reactive transport model is applied to the unconfined chalk aquifer of the Champagne Mounts (France), by considering both the chalk matrix and the interconnected fracture network. Major element concentrations and main chemical parameters calculated in groundwater and their evolution along flow lines are in fair agreement with field data. A relative homogeneity of the aquifer baseline chemistry is rapidly reached in terms of pH, alkalinity and Ca concentration since calcite equilibrium is achieved over the first metres of the vadose zone. However, incongruent chalk dissolution slowly releases Ba, Mg and Sr in groundwater. Introducing dilution effect by rainwater infiltration and a local occurrence of dolomite improves the agreement between modelling and field data. The dissolution of illite and opal-CT, controlling K and SiO(2) concentrations in the model, can be approximately tackled by classical kinetic rate laws, but not the incongruent chalk dissolution. An apparent kinetic rate has therefore been fitted on field data by inverse modelling: 1.5×10(-5) mol(chalk)L (-1) water year (-1). Sensitivity analysis indicates that the CO(2) partial pressure of the unsaturated zone is a critical parameter for modelling the baseline chemistry over the whole chalk aquifer. Copyright © 2012 Elsevier B.V. All rights reserved.

Effects of bay substituents on the racemization barriers of perylene bisimides: resolution of atropo-enantiomers.

PubMed

Osswald, Peter; Würthner, Frank

2007-11-21

The activation parameters for the interconversion of atropisomers (P- and M-enantiomer) of core-twisted perylene bisimides have been determined by dynamic NMR spectroscopy (DNMR) and time- and temperature-dependent CD spectroscopy. By comparing the activation parameters of a series of perylene bisimides containing halogen or aryloxy substituents in the bay area (1,6,7,12-positions), a clear structure-property relationship has been found that demonstrates that the kinetic and thermodynamic parameters for the inversion of enantiomers are dependent on the apparent overlap parameter Sigmar* of the bay substituents. This study reveals a high stability (DeltaG(368 K) = 118 kJ/mol) for the atropo-enantiomers of tetrabromo-substituted perylene bisimide in solution. Accordingly, the enantiomers of this derivative could be resolved by HPLC on a chiral column. These enantiomers do not racemize in solution at room temperature and, thus, represent the first examples of enantiomerically pure core-twisted perylene bisimides.

Ab initio thermodynamics and kinetics for coalescence on nanoislands and nanopits on metal(100) surfaces

NASA Astrophysics Data System (ADS)

Evans, Jim; Han, Yong; Stoldt, Conrad; Thiel, Patricia

Coalescence or sintering of nanoscale features on metal(100) surfaces is mediated by periphery or edge diffusion. These processes are highly sensitive to the multiple diffusion barriers for various local edge environments. We provide an optimal strategy to determine both thermodynamics and kinetics for these systems at the ab initio level. The former requires assessing conventional interactions between adatoms at adsorption sites. The latter requires assessing unconventional interactions between the hopping atom at a bridge site transition state and other nearby atoms. KMC simulation reveals that this formulation recovers observed sintering times for Ag nanoislands on Ag(100), including a novel size dependence. The formulation also applies for nanopits where there are additional challenges to capture kinetics. Work supported by NSF Grant CHE-1507223.

Disulphide bond exchange inhibited by air - kinetic and thermodynamic products in a library of macrocyclic cysteine derivatives.

PubMed

Cholewiak, Agnieszka; Dobrzycki, Łukasz; Jurczak, Janusz; Ulatowski, Filip

2018-04-04

In this paper we present the synthesis and reactivity of dithiols comprising of two cysteine moieties attached to a dipicolinic acid core. Oxidation of these thiols provides oligomeric macrocycles. Monomers with 13-membered rings are kinetic products which are, however, strained and readily transform into higher oligomers under basic conditions or elevated temperature via a disulphide exchange reaction. Dimers, which are the most stable thermodynamic products, equilibrate only under inert conditions with thiolate as a catalyst. Under aerobic conditions, the thiols are oxidised before the equilibrium is reached.

Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

DOEpatents

Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

2010-05-04

A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

Nonequilibrium steady state of biochemical cycle kinetics under non-isothermal conditions

NASA Astrophysics Data System (ADS)

Jin, Xiao; Ge, Hao

2018-04-01

The nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but that under non-isothermal conditions has been much less extensively investigated. When the heat exchange between subsystems is slow, the isothermal assumption of the whole system breaks down, as is true for many types of living organisms. Here, starting with a four-state model of molecular transporter across the cell membrane, we generalize the nonequilibrium steady-state theory of isothermal biochemical cycle kinetics to the circumstances with non-uniform temperatures of subsystems in terms of general master equation models. We obtain a new thermodynamic relationship between the chemical reaction rates and thermodynamic potentials in non-isothermal circumstances, based on the overdamped dynamics along the continuous reaction coordinate. We show that the entropy production can vary up to 3% in real cells, even when the temperature difference across the cell membrane is only approximately 1 K. We then decompose the total thermodynamic driving force into its thermal and chemical components and predict that the net flux of molecules transported by the molecular transporter can potentially go against the temperature gradient in the absence of a chemical driving force. Furthermore, we demonstrate that the simple application of the isothermal transition-state rate formula for each chemical reaction in terms of only the reactant’ temperature is not thermodynamically consistent. Therefore, we mathematically derive several revised reaction rate formulas that are not only consistent with the new thermodynamic relationship but also approximate the exact reaction rate better than Kramers’ rate formula under isothermal conditions.

Application of Taguchi L32 orthogonal array design to optimize copper biosorption by using Spaghnum moss.

PubMed

Ozdemir, Utkan; Ozbay, Bilge; Ozbay, Ismail; Veli, Sevil

2014-09-01

In this work, Taguchi L32 experimental design was applied to optimize biosorption of Cu(2+) ions by an easily available biosorbent, Spaghnum moss. With this aim, batch biosorption tests were performed to achieve targeted experimental design with five factors (concentration, pH, biosorbent dosage, temperature and agitation time) at two different levels. Optimal experimental conditions were determined by calculated signal-to-noise ratios. "Higher is better" approach was followed to calculate signal-to-noise ratios as it was aimed to obtain high metal removal efficiencies. The impact ratios of factors were determined by the model. Within the study, Cu(2+) biosorption efficiencies were also predicted by using Taguchi method. Results of the model showed that experimental and predicted values were close to each other demonstrating the success of Taguchi approach. Furthermore, thermodynamic, isotherm and kinetic studies were performed to explain the biosorption mechanism. Calculated thermodynamic parameters were in good accordance with the results of Taguchi model. Copyright © 2014 Elsevier Inc. All rights reserved.

Hydrogen interactions with metals

NASA Technical Reports Server (NTRS)

Mclellan, R. B.; Harkins, C. G.

1975-01-01

Review of the literature on the nature and extent of hydrogen interactions with metals and the role of hydrogen in metal failure. The classification of hydrogen-containing systems is discussed, including such categories as covalent hydrides, volatile hydrides, polymeric hydrides, and transition metal hydride complexes. The use of electronegativity as a correlating parameter in determining hydride type is evaluated. A detailed study is made of the thermodynamics of metal-hydrogen systems, touching upon such aspects as hydrogen solubility, the positions occupied by hydrogen atoms within the solvent metal lattice, the derivation of thermodynamic functions of solid solutions from solubility data, and the construction of statistical models for hydrogen-metal solutions. A number of theories of hydrogen-metal bonding are reviewed, including the rigid-band model, the screened-proton model, and an approach employing the augmented plane wave method to solve the one-electron energy band problem. Finally, the mechanism of hydrogen embrittlement is investigated on the basis of literature data concerning stress effects and the kinetics of hydrogen transport to critical sites.

Ultrasound assisted two-stage biodiesel synthesis from non-edible Schleichera triguga oil using heterogeneous catalyst: Kinetics and thermodynamic analysis.

PubMed

Sarve, Antaram N; Varma, Mahesh N; Sonawane, Shriram S

2016-03-01

Present work deals with the ultrasound-assisted biodiesel production from low cost, substantial acid value kusum (Schleichera triguga) oil using a two-step method of esterification in presence of acid (H2SO4) catalyst followed by transesterification using a basic heterogeneous barium hydroxide (Ba(OH)2) catalyst. The initial acid value of kusum oil was reduced from 21.65 to 0.84 mg of KOH/g of oil, by acid catalyzed esterification with 4:1 methanol to oil molar ratio, catalyst concentration 1% (v/v), ultrasonic irradiation time 20 min at 40 °C. Then, Ba(OH)2 concentration of 3% (w/w), methanol to oil molar ratio of 9:1, ultrasonic irradiation time of 80 min, and temperature of 50 °C was found to be the optimum conditions for transesterification step and triglyceride conversion of 96.8% (wt) was achieved. This paper also examined the kinetics as well as the evaluation of thermodynamic parameters for both esterification and transesterification reactions. The lower value of activation energy and higher values of kinetic constants indicated a fast rate of reaction, which could be attributed to the physical effect of emulsification, in which the microturbulence generated due to radial motion of bubbles, creates an intimate mixing of the immiscible reactants causing the increase in the interfacial area, giving faster reaction kinetics. The positive values of Gibbs-free energy (ΔG), enthalpy (ΔH) and negative value of entropy (ΔS) revealed that both the esterification and transesterification were non-spontaneous, endothermic and endergonic reactions. Therefore, the present work has not only established the escalation obtained due to ultrasonication but also exemplified the two-step approach for synthesis of biodiesel from non-edible kusum oil based on the use of heterogeneous catalyst for the transesterification step. Copyright © 2015 Elsevier B.V. All rights reserved.

Teaching Thermodynamics with Physlets[R] in Introductory Physics

ERIC Educational Resources Information Center

Cox, Anne J.; Belloni, Mario; Dancy, Melissa; Christian, Wolfgang

2003-01-01

This paper describes the use of interactive, Physlet[R]-based curricular material designed to help students learn concepts of thermodynamics with a particular focus on the use of kinetic theory models. These exercises help students visualize ideal gas particle dynamics and engine cycles, make concrete connections between mechanics and…

Estimation of parameters in rational reaction rates of molecular biological systems via weighted least squares

NASA Astrophysics Data System (ADS)

Wu, Fang-Xiang; Mu, Lei; Shi, Zhong-Ke

2010-01-01

The models of gene regulatory networks are often derived from statistical thermodynamics principle or Michaelis-Menten kinetics equation. As a result, the models contain rational reaction rates which are nonlinear in both parameters and states. It is challenging to estimate parameters nonlinear in a model although there have been many traditional nonlinear parameter estimation methods such as Gauss-Newton iteration method and its variants. In this article, we develop a two-step method to estimate the parameters in rational reaction rates of gene regulatory networks via weighted linear least squares. This method takes the special structure of rational reaction rates into consideration. That is, in the rational reaction rates, the numerator and the denominator are linear in parameters. By designing a special weight matrix for the linear least squares, parameters in the numerator and the denominator can be estimated by solving two linear least squares problems. The main advantage of the developed method is that it can produce the analytical solutions to the estimation of parameters in rational reaction rates which originally is nonlinear parameter estimation problem. The developed method is applied to a couple of gene regulatory networks. The simulation results show the superior performance over Gauss-Newton method.

Kinetics of degradation of enalapril maleate in dosage forms.

PubMed

Stanisz, Beata

2004-01-01

The effect of humidity and temperature on the stability of enalapril maleate (ENA) in tablets have been studied. Tablets with ENA were stored in final packs (blisters) and without final packs in the atmosphere of increased humidity (76.4 % RH) and in the temperature range from 313 K to 333 K (forced degradation test). Degradation of ENA in tablets stored in final packs and without final packs followed the first order reaction model. During this study, the product of hydrolysis of the ester group and intramolecular cyclization have been observed. Thermodynamic parameters (activation energies, enthalpy and entropy) for the decomposition of ENA in tablets were calculated.

Equilibrium high entropy alloy phase stability from experiments and thermodynamic modeling

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

Saal, James E.; Berglund, Ida S.; Sebastian, Jason T.

Long-term stability of high entropy alloys (HEAs) is a critical consideration for the design and practical application of HEAs. It has long been assumed that many HEAs are a kinetically-stabilized metastable structure, and recent experiments have confirmed this hypothesis by observing HEA ecomposition after long-termequilibration. In the presentwork,we demonstrate the use of the CALculation of PHAse Diagrams (CALPHAD) approach to predict HEA stability and processing parameters, comparing experimental long-term annealing observations to CALPHAD phase diagrams from a commercially-available HEA database. As a result, we find good agreement between single- and multi-phase predictions and experiments.

Equilibrium high entropy alloy phase stability from experiments and thermodynamic modeling

DOE PAGES

Saal, James E.; Berglund, Ida S.; Sebastian, Jason T.; ...

2017-10-29

Long-term stability of high entropy alloys (HEAs) is a critical consideration for the design and practical application of HEAs. It has long been assumed that many HEAs are a kinetically-stabilized metastable structure, and recent experiments have confirmed this hypothesis by observing HEA ecomposition after long-termequilibration. In the presentwork,we demonstrate the use of the CALculation of PHAse Diagrams (CALPHAD) approach to predict HEA stability and processing parameters, comparing experimental long-term annealing observations to CALPHAD phase diagrams from a commercially-available HEA database. As a result, we find good agreement between single- and multi-phase predictions and experiments.

Adsorptive removal of dissolved organic matter (DOM) in landfill leachate by iron oxide nanoparticles (FeONPs)

NASA Astrophysics Data System (ADS)

Ghani, Zaidi Ab; Yusoff, Mohd Suffian; Zaman, Nastaein Qamaruz; Andas, Jeyashelly; Aziz, Hamidi Abdul

2017-10-01

A study was conducted to investigate the efficiency of iron oxide nanoparticle (FeONPs) adsorption for removing of DOM in landfill leachate. FeONPs was directly prepared via sodium borohydride (KBH4) reduction method. Adsorption kinetics, isotherm and thermodynamic studies were developed to design the model for DOM removal. Pseudo first-order and pseudo second-order model have been studied to fit the experimental data. The regression results showed that the adsorption kinetics were more accurately represented by a pseudo second-order model. The Weber-Morris intraparticle diffusion model was used to analyze the adsorption kinetics data. The plot of qt versus t1/2 represents multi linearity, which showed that the adsorption processes occurred in more than one step. Adsorption isotherms were analyzed by Langmuir, Freundlich, Tempkin and Dubinin-Radushkevich, isotherms model. Equilibrium data were well fitted to the Dubinin- Radushkevich isotherm model. Maximum monolayer adsorption based on Langmuir was calculated to be 21.74 mg/g. Thermodynamic parameters such as free energy changes (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) were evaluated between temperatures of 25 °C and 40 °C. The ΔG° was noticed progressively decrease from -9.620 -9.820 -10.021, and -10.222 kJ/mol as the temperature increase. The ΔH° and ΔS° values were found to be 2.350 kJ/mol and 40.165 J/mol.K respectively. The results showed that the overall adsorption process was endothermic and spontaneous. The results from this study suggested that FeNPs could be a viable adsorbent in managing higher DOM problems associated with landfill leachate.

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo.

PubMed

Ruminski, Dana J; Watson, Peter Y; Mahen, Elisabeth M; Fedor, Martha J

2016-03-01

RNAs must assemble into specific structures in order to carry out their biological functions, but in vitro RNA folding reactions produce multiple misfolded structures that fail to exchange with functional structures on biological time scales. We used carefully designed self-cleaving mRNAs that assemble through well-defined folding pathways to identify factors that differentiate intracellular and in vitro folding reactions. Our previous work showed that simple base-paired RNA helices form and dissociate with the same rate and equilibrium constants in vivo and in vitro. However, exchange between adjacent secondary structures occurs much faster in vivo, enabling RNAs to quickly adopt structures with the lowest free energy. We have now used this approach to probe the effects of an extensively characterized DEAD-box RNA helicase, Mss116p, on a series of well-defined RNA folding steps in yeast. Mss116p overexpression had no detectable effect on helix formation or dissociation kinetics or on the stability of interdomain tertiary interactions, consistent with previous evidence that intracellular factors do not affect these folding parameters. However, Mss116p overexpression did accelerate exchange between adjacent helices. The nonprocessive nature of RNA duplex unwinding by DEAD-box RNA helicases is consistent with a branch migration mechanism in which Mss116p lowers barriers to exchange between otherwise stable helices by the melting and annealing of one or two base pairs at interhelical junctions. These results suggest that the helicase activity of DEAD-box proteins like Mss116p distinguish intracellular RNA folding pathways from nonproductive RNA folding reactions in vitro and allow RNA structures to overcome kinetic barriers to thermodynamic equilibration in vivo. © 2016 Ruminski et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Sorption characteristics and separation of tellurium ions from aqueous solutions using nano-TiO2.

PubMed

Zhang, Lei; Zhang, Min; Guo, Xingjia; Liu, Xueyan; Kang, Pingli; Chen, Xia

2010-12-15

Titanium dioxide nanoparticles (nano-TiO(2)) were employed for the sorption of Te(IV) ions from aqueous solution. A detailed study of the process was performed by varying the sorption time, pH, and temperature. The sorption was found to be fast, equilibrium was reached within 8 min. When the concentration of Te(IV) was below 40 mg L(-1), at least 97% of tellurium was adsorbed by nano-TiO(2) in the pH range of 1-2 and 8-9. The sorbed Te(IV) ions were desorbed with 2.0 mL of 0.5 mol L(-1) NaOH. The sorption data could be well interpreted by the Langmuir model with the maximum adsorption capacity of 32.75 mg g(-1) (20 ± 0.1 °C) of Te(IV) on nano-TiO(2). The kinetics and thermodynamics of the sorption of Te(IV) onto nano-TiO(2) were also studied. The kinetic experimental data properly correlated with the second-order kinetic model (k(2)=0.0368 g mg(-1)min(-1), 293 K). The overall rate process appeared to be influenced by both boundary layer diffusion and intra-particle diffusion. The mean energy of adsorption was calculated to be 17.41 kJ mol(-1) from the Dubinin-Radushkevich (D-R) adsorption isotherm at room temperature. Moreover, the thermodynamic parameters for the sorption were estimated, and the ΔH(0) and ΔG(0) values indicated the exothermic and spontaneous nature of the sorption process, respectively. Finally, Nano-TiO(2) as sorbent was successfully applied to the separation of Te(IV) from the environmental samples with satisfactory results (recoveries >95%, relative standard deviations was 2.0%). Copyright © 2010 Elsevier B.V. All rights reserved.

Adsorption of fluoride to UiO-66-NH2 in water: Stability, kinetic, isotherm and thermodynamic studies.

PubMed

Lin, Kun-Yi Andrew; Liu, Yu-Ting; Chen, Shen-Yi

2016-01-01

To provide safe drinking water, fluoride in water must be removed and adsorption processes appear to be the most widely used method. Metal organic frameworks (MOFs) represent a new class of adsorbents that have been used in various adsorption applications. To study the adsorption mechanism of fluoride to MOFs in water and obtain related adsorption parameters, we synthesized a zirconium-based MOF with a primary amine group on its ligand, named UiO-66-NH2. The kinetics, adsorption isotherm and thermodynamics of fluoride adsorption to UiO-66-NH2 were investigated. The crystalline structure of UiO-66-NH2 remained intact and the local structure of zirconium in UiO-66-NH2 did not change significantly after being exposed to fluoride. The kinetics of the fluoride adsorption in UiO-66-NH2 could be well represented by the pseudo second order rate law. The enthalpy of the adsorption indicates that the F(-) adsorption to UiO-66-NH2 was classified as a physical adsorption. However, the comparison between the adsorption capacities of UiO-66-NH2 and UiO-66 suggests that the fluoride adsorption to UiO-66-NH2 might primarily involve a strong interaction between F(-) and the metal site. The fluoride adsorption capacity of UiO-66-NH2 was found to decrease when pH>7. While the presence of chloride/bromide ions did not noticeably change the adsorption capacity of UiO-66-NH2, the ionic surfactants slightly affected the adsorption capacity of UiO-66-NH2. These findings provide insights to further optimize the adsorption process for removal of fluoride using zirconium-based MOFs. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantitative collision induced mass spectrometry of substituted piperazines - A correlative analysis between theory and experiment

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2017-12-01

The present paper deals with quantitative kinetics and thermodynamics of collision induced dissociation (CID) reactions of piperazines under different experimental conditions together with a systematic description of effect of counter-ions on common MS fragment reactions of piperazines; and intra-molecular effect of quaternary cyclization of substituted piperazines yielding to quaternary salts. There are discussed quantitative model equations of rate constants as well as free Gibbs energies of series of m-independent CID fragment processes in GP, which have been evidenced experimentally. Both kinetic and thermodynamic parameters are also predicted by computational density functional theory (DFT) and ab initio both static and dynamic methods. The paper examines validity of Maxwell-Boltzmann distribution to non-Boltzmann CID processes in quantitatively as well. The experiments conducted within the latter framework yield to an excellent correspondence with theoretical quantum chemical modeling. The important property of presented model equations of reaction kinetics is the applicability in predicting unknown and assigning of known mass spectrometric (MS) patterns. The nature of "GP" continuum of CID-MS coupled scheme of measurements with electrospray ionization (ESI) source is discussed, performing parallel computations in gas-phase (GP) and polar continuum at different temperatures and ionic strengths. The effect of pressure is presented. The study contributes significantly to methodological and phenomenological developments of CID-MS and its analytical implementations for quantitative and structural analyses. It also demonstrates great prospective of a complementary application of experimental CID-MS and computational quantum chemistry studying chemical reactivity, among others. To a considerable extend this work underlies the place of computational quantum chemistry to the field of experimental analytical chemistry in particular highlighting the structural analysis.

Alternative bases in the RNA world: the prebiotic synthesis of urazole and its ribosides

NASA Technical Reports Server (NTRS)

Kolb, V. M.; Dworkin, J. P.; Miller, S. L.

1994-01-01

Urazole is a five-membered heterocyclic compound which is isosteric with uracil's hydrogen-bonding segment. Urazole reacts spontaneoulsy with ribose (and other aldoses) to give a mixture of four ribosides: alpha and beta pyranosides and furanosides. This reaction occurs in aqueous solution at mild temperatures. Thermodynamic and kinetic parameters for the reaction of urazole with ribose were determined. In contrast, uracil is completely unreactive with ribose under these conditions. Urazole's unusual reactivity is ascribed to the hydrazine portion of the molecule. Urazole can be synthesized from biuret and hydrazine under prebiotic conditions. The prebiotic synthesis of guanazole, which is isosteric in part to diaminopyrimidine and cytosine, is accomplished from dicyandiamide and hydrazine. Kinetic parameters for both prebiotic reactions were measured. Urazole and guanazole are transparent in the UV, which would be a favorable property in the absence of an ozone layer on the early Earth. Urazole makes hydrogen bonds with adenine in DMSO similar to those of uracil, as established by H NMR. All of these properties make urazole an attractive potential precursor to uracil and guanazole a potential precursor to cytosine in the RNA or pre-RNA world.

Thermodynamic controls on the kinetics of microbial low-pH Fe(II) oxidation.

PubMed

Larson, Lance N; Sánchez-España, Javier; Kaley, Bradley; Sheng, Yizhi; Bibby, Kyle; Burgos, William D

2014-08-19

Acid mine drainage (AMD) is a major worldwide environmental threat to surface and groundwater quality. Microbial low-pH Fe(II) oxidation could be exploited for cost-effective AMD treatment; however, its use is limited because of uncertainties associated with its rate and ability to remove Fe from solution. We developed a thermodynamic-based framework to evaluate the kinetics of low-pH Fe(II) oxidation. We measured the kinetics of low-pH Fe(II) oxidation at five sites in the Appalachian Coal Basin in the US and three sites in the Iberian Pyrite Belt in Spain and found that the fastest rates of Fe(II) oxidation occurred at the sites with the lowest pH values. Thermodynamic calculations showed that the Gibbs free energy of Fe(II) oxidation (ΔG(oxidation)) was also most negative at the sites with the lowest pH values. We then conducted two series of microbial Fe(II) oxidation experiments in laboratory-scale chemostatic bioreactors operated through a series of pH values (2.1-4.2) and found the same relationships between Fe(II) oxidation kinetics, ΔG(oxidation), and pH. Conditions that favored the fastest rates of Fe(II) oxidation coincided with higher Fe(III) solubility. The solubility of Fe(III) minerals, thus plays an important role on Fe(II) oxidation kinetics. Methods to incorporate microbial low-pH Fe(II) oxidation into active and passive AMD treatment systems are discussed in the context of these findings. This study presents a simplified model that describes the relationship between free energy and microbial kinetics and should be broadly applicable to many biogeochemical systems.

High resolution approach to the native state ensemble kinetics and thermodynamics.

PubMed

Wu, Sangwook; Zhuravlev, Pavel I; Papoian, Garegin A

2008-12-15

Many biologically interesting functions such as allosteric switching or protein-ligand binding are determined by the kinetics and mechanisms of transitions between various conformational substates of the native basin of globular proteins. To advance our understanding of these processes, we constructed a two-dimensional free energy surface (FES) of the native basin of a small globular protein, Trp-cage. The corresponding order parameters were defined using two native substructures of Trp-cage. These calculations were based on extensive explicit water all-atom molecular dynamics simulations. Using the obtained two-dimensional FES, we studied the transition kinetics between two Trp-cage conformations, finding that switching process shows a borderline behavior between diffusive and weakly-activated dynamics. The transition is well-characterized kinetically as a biexponential process. We also introduced a new one-dimensional reaction coordinate for the conformational transition, finding reasonable qualitative agreement with the two-dimensional kinetics results. We investigated the distribution of all the 38 native nuclear magnetic resonance structures on the obtained FES, analyzing interactions that stabilize specific low-energy conformations. Finally, we constructed a FES for the same system but with simple dielectric model of water instead of explicit water, finding that the results were surprisingly similar in a small region centered on the native conformations. The dissimilarities between the explicit and implicit model on the larger-scale point to the important role of water in mediating interactions between amino acid residues.

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.

ZMOTTO- MODELING THE INTERNAL COMBUSTION ENGINE

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.

1994-01-01

The ZMOTTO program was developed to model mathematically a spark-ignited internal combustion engine. ZMOTTO is a large, general purpose program whose calculations can be established at five levels of sophistication. These five models range from an ideal cycle requiring only thermodynamic properties, to a very complex representation demanding full combustion kinetics, transport properties, and poppet valve flow characteristics. ZMOTTO is a flexible and computationally economical program based on a system of ordinary differential equations for cylinder-averaged properties. The calculations assume that heat transfer is expressed in terms of a heat transfer coefficient and that the cylinder average of kinetic plus potential energies remains constant. During combustion, the pressures of burned and unburned gases are assumed equal and their heat transfer areas are assumed proportional to their respective mass fractions. Even the simplest ZMOTTO model provides for residual gas effects, spark advance, exhaust gas recirculation, supercharging, and throttling. In the more complex models, 1) finite rate chemistry replaces equilibrium chemistry in descriptions of both the flame and the burned gases, 2) poppet valve formulas represent fluid flow instead of a zero pressure drop flow, and 3) flame propagation is modeled by mass burning equations instead of as an instantaneous process. Input to ZMOTTO is determined by the model chosen. Thermodynamic data is required for all models. Transport properties and chemical kinetics data are required only as the model complexity grows. Other input includes engine geometry, working fluid composition, operating characteristics, and intake/exhaust data. ZMOTTO accommodates a broad spectrum of reactants. The program will calculate many Otto cycle performance parameters for a number of consecutive cycles (a cycle being an interval of 720 crankangle degrees). A typical case will have a number of initial ideal cycles and progress through levels of nonideal cycles. ZMOTTO has restart capabilities and permits multicycle calculations with parameters varying from cycle to cycle. ZMOTTO is written in FORTRAN IV (IBM Level H) but has also been compiled with IBM VSFORTRAN (1977 standard). It was developed on an IBM 3033 under the TSS operating system and has also been implemented under MVS. Approximately 412K of 8 bit bytes of central memory are required in a nonpaging environment. ZMOTTO was developed in 1985.

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

NASA Astrophysics Data System (ADS)

Shalashilin, Dmitrii V.; Beddard, Godfrey S.; Paci, Emanuele; Glowacki, David R.

2012-10-01

Molecular dynamics (MD) methods are increasingly widespread, but simulation of rare events in complex molecular systems remains a challenge. We recently introduced the boxed molecular dynamics (BXD) method, which accelerates rare events, and simultaneously provides both kinetic and thermodynamic information. We illustrate how the BXD method may be used to obtain high-resolution kinetic data from explicit MD simulations, spanning picoseconds to microseconds. The method is applied to investigate the loop formation dynamics and kinetics of cyclisation for a range of polypeptides, and recovers a power law dependence of the instantaneous rate coefficient over six orders of magnitude in time, in good agreement with experimental observations. Analysis of our BXD results shows that this power law behaviour arises when there is a broad and nearly uniform spectrum of reaction rate coefficients. For the systems investigated in this work, where the free energy surfaces have relatively small barriers, the kinetics is very sensitive to the initial conditions: strongly non-equilibrium conditions give rise to power law kinetics, while equilibrium initial conditions result in a rate coefficient with only a weak dependence on time. These results suggest that BXD may offer us a powerful and general algorithm for describing kinetics and thermodynamics in chemical and biochemical systems.

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.

Torque-coupled thermodynamic model for FoF1 -ATPase

NASA Astrophysics Data System (ADS)

Ai, Guangkuo; Liu, Pengfei; Ge, Hao

2017-05-01

FoF1 -ATPase is a motor protein complex that utilizes transmembrane ion flow to drive the synthesis of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) and phosphate (Pi). While many theoretical models have been proposed to account for its rotary activity, most of them focus on the Fo or F1 portions separately rather than the complex as a whole. Here, we propose a simple but new torque-coupled thermodynamic model of FoF1 -ATPase. Solving this model at steady state, we find that the monotonic variation of each portion's efficiency becomes much more robust over a wide range of parameters when the Fo and F1 portions are coupled together, as compared to cases when they are considered separately. Furthermore, the coupled model predicts the dependence of each portion's kinetic behavior on the parameters of the other. Specifically, the power and efficiency of the F1 portion are quite sensitive to the proton gradient across the membrane, while those of the Fo portion as well as the related Michaelis constants for proton concentrations respond insensitively to concentration changes in the reactants of ATP synthesis. The physiological proton gradient across the membrane in the Fo portion is also shown to be optimal for the Michaelis constants of ADP and phosphate in the F1 portion during ATP synthesis. Together, our coupled model is able to predict key dynamic and thermodynamic features of the FoF1 -ATPase in vivo semiquantitatively, and suggests that such coupling approach could be further applied to other biophysical systems.

Nonlinear Dynamics and Nucleation Kinetics in Near-Critical Liquids

NASA Technical Reports Server (NTRS)

Patashinski, Alexander Z.; Ratner, Mark A.; Pines, Vladimir

1996-01-01

The objective of our study is to model the nonlinear behavior of a near-critical liquid following a rapid change of the temperature and/or other thermodynamic parameters (pressure, external electric or gravitational field). The thermodynamic critical point is manifested by large, strongly correlated fluctuations of the order parameter (particle density in liquid-gas systems, concentration in binary solutions) in the critical range of scales. The largest critical length scale is the correlation radius r(sub c). According to the scaling theory, r(sub c) increases as r(sub c) = r(sub 0)epsilon(exp -alpha) when the nondimensional distance epsilon = (T - T(sub c))/T(sub c) to the critical point decreases. The normal gravity alters the nature of correlated long-range fluctuations when one reaches epsilon approximately equal to 10(exp -5), and correspondingly the relaxation time, tau(r(sub c)), is approximately equal to 10(exp -3) seconds; this time is short when compared to the typical experimental time. Close to the critical point, a rapid, relatively small temperature change may perturb the thermodynamic equilibrium on many scales. The critical fluctuations have a hierarchical structure, and the relaxation involves many length and time scales. Above the critical point, in the one-phase region, we consider the relaxation of the liquid following a sudden temperature change that simultaneously violates the equilibrium on many scales. Below T(sub c), a non-equilibrium state may include a distribution of small scale phase droplets; we consider the relaxation of such a droplet following a temperature change that has made the phase of the matrix stable.

Structural characterization, catalytic, kinetic and thermodynamic properties of Aspergillus oryzae tannase.

PubMed

Abdel-Naby, Mohamed A; El-Tanash, Arafat Bedier; Sherief, Abdel Daium A

2016-11-01

Tannase (EC.3.1.1.20) from Aspergillus oryzae was purified using ammonium sulphate precipitation (75%), gel filtration chromatography through Sephadex G-100, and G-200. The purified enzyme was monomeric protein with a molecular mass of 106kDa. The activation energy for tannic acid hydrolysis was 32.6kJmol -1 and its temperature quotient (Q 10 ) was 1.0. The pK a1 and pK a2 values of acidic and basic limbs of the active site residues were 4.6 and 6.4. The calculated values of thermodynamic parameters for tannic acid hydrolysis, were as follows: ΔH*=30.02kJmol -1 , ΔG*=59.75kJmol -1 ΔS*=-95.90Jmol -1 K -1 , (ΔG* E-S )=3.66kJmol -1 and ΔG* E-T -12.61kJmol -1 . The pure enzyme exhibited K m , V max and k cat of 4.13mM, 3507Umgprotein -1 and 551.4s -1 . The calculated half-life time at 40, 45, 50, 55, 60, and 70°C was 955.15, 142.0, 30.28, 17.88, 8.23 and 2.95min, respectively. The thermodynamic parameters for irreversible thermal inactivation at different temperatures (40-70°C) were determined. The enzyme was activated by Ca 2+ , and Mg 2+ while Hg 2+ , Fe 2+ , and Cu 2+ strongly inhibited it. Hydrolysis of tannic acid by the pure enzyme indicated that gallic acid was the end-product. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Anggita, R. K. Wardani, E-mail: anggita14@mhs.chem.its.ac.id; Yuniar, V. T. P., E-mail: yuniar11@mhs.chem.its.ac.id; Aini, W. T., E-mail: aini11@mhs.chem.its.ac.id

In this study, the influence of hydrothermal temperature and time at zeolite X supported on glasswool were investigated. The results of characterization using XRD showed that a single phase zeolite X with highest crystallinity was obtained when hydrothermal temperature and time at 100°C during 24 hours (ZXF100-24H). The CO{sub 2} adsorption capacity of ZXF100-24H has reached up to 10.15 wt. %. Kinetics of CO{sub 2} adsorption onto zeolite X supported on glasswool was investigated using pseudo-first-order, pseudo-second-order and intra-particle diffusion kinetic models. After evaluating three kinetic models for CO{sub 2} adsorption at adsorption temperatures of 30°C, 40°C and 50°C, itmore » was found that intra-particle diffusion kinetic model provided the best fitting for the adsorption data. Furthermore, the thermodynamic parameters of CO{sub 2} adsorption were obtained as follows, Gibbs free energy change (ΔG°) are −0.409 kJ/mol at 30°C, −0.274 kJ/mol at 40°C and −0.138 kJ/mol at 50 °C, whereas the enthalpy change (ΔH°) is −4.53 kJ/mol and the entropy change (ΔS°) is −0.0135 kJ/(mol K).« less

Limits to Dihydrogen Incorporation into Electron Sinks Alternative to Methanogenesis in Ruminal Fermentation

PubMed Central

Ungerfeld, Emilio M.

2015-01-01

Research is being conducted with the objective of decreasing methane (CH4) production in the rumen, as methane emissions from ruminants are environmentally damaging and a loss of digestible energy to ruminants. Inhibiting ruminal methanogenesis generally results in accumulation of dihydrogen (H2), which is energetically inefficient and can inhibit fermentation. It would be nutritionally beneficial to incorporate accumulated H2 into propionate or butyrate production, or reductive acetogenesis. The objective of this analysis was to examine three possible physicochemical limitations to the incorporation of accumulated H2 into propionate and butyrate production, and reductive acetogenesis, in methanogenesis-inhibited ruminal batch and continuous cultures: (i) Thermodynamics; (ii) Enzyme kinetics; (iii) Substrate kinetics. Batch (N = 109) and continuous (N = 43) culture databases of experiments with at least 50% inhibition in CH4 production were used in this meta-analysis. Incorporation of accumulated H2 into propionate production and reductive acetogenesis seemed to be thermodynamically feasible but quite close to equilibrium, whereas this was less clear for butyrate. With regard to enzyme kinetics, it was speculated that hydrogenases of ruminal microorganisms may have evolved toward high-affinity and low maximal velocity to compete for traces of H2, rather than for high pressure accumulated H2. Responses so far obtained to the addition of propionate production intermediates do not allow distinguishing between thermodynamic and substrate kinetics control. PMID:26635743

Methods for Kinetic and Thermodynamic Analysis of Aminoacyl-tRNA Synthetases

PubMed Central

Francklyn, Christopher S.; First, Eric A.; Perona, John J.; Hou, Ya-Ming

2008-01-01

The accuracy of protein synthesis relies on the ability of aminoacyl-tRNA synthetases (aaRSs) to discriminate among true and near cognate substrates. To date, analysis of aaRSs function, including identification of residues of aaRS participating in amino acid and tRNA discrimination, has largely relied on the steady state kinetic pyrophosphate exchange and aminoacylation assays. Pre-steady state kinetic studies investigating a more limited set of aaRS systems have also been undertaken to assess the energetic contributions of individual enzyme-substrate interactions, particularly in the adenylation half reaction. More recently, a renewed interest in the use of rapid kinetics approaches for aaRSs has led to their application to several new aaRS systems, resulting in the identification of mechanistic differences that distinguish the two structurally distinct aaRS classes. Here, we review the techniques for thermodynamic and kinetic analysis of aaRS function. Following a brief survey of methods for the preparation of materials and for steady state kinetic analysis, this review will describe pre-steady state kinetic methods employing rapid quench and stopped-flow fluorescence for analysis of the activation and aminoacyl transfer reactions. Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion. PMID:18241792

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.

Uranium biosorption by Padina sp. algae biomass: kinetics and thermodynamics.

PubMed

Khani, Mohammad Hassan

2011-11-01

Kinetic, thermodynamic, and equilibrium isotherms of the biosorption of uranium ions onto Padina sp., a brown algae biomass, in a batch system have been studied. The kinetic data were found to follow the pseudo-second-order model. Intraparticle diffusion is not the sole rate-controlling factor. The equilibrium experimental results were analyzed in terms of Langmuir isotherm depending with temperature. Equilibrium data fitted very well to the Langmuir model. The maximum uptakes estimated by using the Langmuir model were 434.8, 416.7, 400.0, and 370.4 mg/g at 10°C, 20°C, 30°C, and 40°C, respectively. Gibbs free energy was spontaneous for all interactions, and the adsorption process exhibited exothermic enthalpy values. Padina sp. algae were shown to be a favorable biosorbent for uranium removal from aqueous solutions.

Dependence of intramolecular electron-transfer rates on driving force, pH, and temperature in ammineruthenium-modified ferrocytochromes c

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

Wishart, J.F.; Sun, J.; Su, C.

1997-01-23

Several ruthenium ammine complexes were used to modify horse-heart cytochrome c at histidine-33, creating a series of (NH{sub 3}){sub 4}(L)Ru-Cyt c derivatives (L = H{sub 2}O/OH{sup -}, ammonia, 4-ethylpyridine, 3,5-lutidine, pyridine, isonicotinamide, N-methylpyrazinium) with a wide range of driving forces for Fe-to-Ru electron transfer (-{Delta}G{degree} = -0.125 to +0.46 eV). Electron-transfer rates and activation parameters were measured by pulse radiolysis using azide or carbonate radicals. The driving-force dependence of electron-transfer rates between redox centers of the same charge types obeys Marcus-Hush theory. The activationless rate limit for all of the ruthenium derivatives except the N-methylpyrazinium complex is 3.9x10{sup 5} s{supmore » -1}. Thermodynamic parameters obtained from nonisothermal differential pulse voltammetry show that the electron-transfer reactions are entropy-driven. The thermodynamic and kinetic effects of phosphate ion binding to the ruthenium center are examined. The rate of intramolecular electron transfer in (NH{sub 3}){sub 4}(isn)Ru{sup III}-Cyt c{sup II} decreases at high pH, with a midpoint at pH 9.1. 28 refs., 4 figs., 3 tabs.« less

Characterization of tannery sludge activated carbon and its utilization in the removal of azo reactive dye.

PubMed

Geethakarthi, A; Phanikumar, B R

2012-03-01

The removal of azo Reactive Red 31(RR31) from synthetic dye solution using tannery sludge-developed activated carbon (TSC) was investigated. TSC was prepared from a combination of physical and chemical activation. The developed TSC was characterized by FT-IR, SEM, TG-DTA, specific surface area and zero point charge of pH (pH(zpc)). The isotherm models, kinetic models and thermodynamic parameters were also analysed to describe the adsorptive behaviour of TSC. The effect of contact time, initial dye concentration, carbon dosage, agitation speed, initial pH and temperature were carried out for batch adsorption studies. The isotherm plot of the dye RR31 on TSC fitted better with the Langmuir adsorption isotherm than the Freundlich model. The maximum monolayer adsorption capacity of TSC in the removal of RR31 ranged from 23.15 to 39.37 mg/g. The thermodynamic parameters showed the endothermic and physical nature of the Reactive Red 31 adsorption on TSC. The entropy and enthalpy values were 181.515 J/Kmol and 5.285 kJ/mol, respectively. The developed cationic tannery sludge carbon was found to be an effective adsorbent in the removal of the anionic azo reactive dye RR31.

Relationship between thermodynamic parameter and thermodynamic scaling parameter for orientational relaxation time for flip-flop motion of nematic liquid crystals.

PubMed

Satoh, Katsuhiko

2013-03-07

Thermodynamic parameter Γ and thermodynamic scaling parameter γ for low-frequency relaxation time, which characterize flip-flop motion in a nematic phase, were verified by molecular dynamics simulation with a simple potential based on the Maier-Saupe theory. The parameter Γ, which is the slope of the logarithm for temperature and volume, was evaluated under various conditions at a wide range of temperatures, pressures, and volumes. To simulate thermodynamic scaling so that experimental data at isobaric, isothermal, and isochoric conditions can be rescaled onto a master curve with the parameters for some liquid crystal (LC) compounds, the relaxation time was evaluated from the first-rank orientational correlation function in the simulations, and thermodynamic scaling was verified with the simple potential representing small clusters. A possibility of an equivalence relationship between Γ and γ determined from the relaxation time in the simulation was assessed with available data from the experiments and simulations. In addition, an argument was proposed for the discrepancy between Γ and γ for some LCs in experiments: the discrepancy arises from disagreement of the value of the order parameter P2 rather than the constancy of relaxation time τ1(*) on pressure.

Prediction of precipitate evolution and martensite transformation in Ti-Ni-Cu shape memory alloys by computational thermodynamics

NASA Astrophysics Data System (ADS)

Povoden-Karadeniz, A.; Cirstea, D. C.; Kozeschnik, E.

2016-04-01

Ti-50Ni to Ti-55Ni (at.%) can be termed as the pioneer of shape memory alloys (SMA). Intermetallic precipitates play an important role for strengthening. Their influence on the start temperature of the martensitic transformation is a crucial property for the shape memory effect. Efforts for increasing the martensite start temperature include replacement of a part of Ni atoms by Cu. The influence of Cu-addition to Ti-Ni SMA on T0- temperatures and the character of the austenite-martensite transformation is evaluated using a new thermodynamic database for the Ti-Ni-system extended by Cu. Trends of precipitation of intermetallic phases are simulated by combining the assessed thermodynamics of the Ti-Ni-Cu system with assessed diffusion mobility data and kinetic models, as implemented in the solid-state transformation software MatCalc and are presented in the form of time-temperature-precipitation diagrams. Thermodynamic equilibrium considerations, complemented by predictive thermo-kinetic precipitation simulation, facilitates SMA alloy design and definition of optimized aging conditions.

Thermodynamics of information processing based on enzyme kinetics: An exactly solvable model of an information pump.

PubMed

Cao, Yuansheng; Gong, Zongping; Quan, H T

2015-06-01

Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA 109, 11641 (2012)] and the information refrigerator [Phys. Rev. Lett. 111, 030602 (2013)], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device can either pump molecules against the chemical potential gradient by consuming the information to be encoded in the bit stream or (partially) erase the information initially encoded in the bit stream by consuming the Gibbs free energy. The dynamics of this model is solved exactly, and the "phase diagram" of the operation regimes is determined. The efficiency and the power of the information machine is analyzed. The validity of the second law of thermodynamics within our model is clarified. Our model offers a simple paradigm for the investigating of the thermodynamics of information processing involving the chemical potential in small systems.

Thermodynamic Investigation of the Reduction-Distillation Process for Rare Earth Metals Production

NASA Astrophysics Data System (ADS)

Judge, W. D.; Azimi, G.

2017-10-01

Owing to their high vapor pressure, the four rare earth metals samarium, europium, thulium, and ytterbium are produced by reduction-distillation whereby their oxides are reduced with metallic lanthanum in vacuo, and the produced metal is subsequently vaporized off. Here, we performed a thorough thermodynamic investigation to establish a fundamental understanding of the reduction-distillation process. Thermodynamic functions including vapor pressures, Gibbs free energies, and enthalpies of reaction were calculated and compared with available experimental data. Furthermore, the kinetics of the process was explored and theoretical evaporation rates were calculated from thermodynamic data. The thermodynamic model developed in this work can help optimize processing conditions to maximize the yield and improve the overall process.

Peptide hydrogelation triggered by enzymatic induced pH switch

NASA Astrophysics Data System (ADS)

Cheng, Wei; Li, Ying

2016-07-01

It remains challenging to develop methods that can precisely control the self-assembling kinetics and thermodynamics of peptide hydrogelators to achieve hydrogels with optimal properties. Here we report the hydrogelation of peptide hydrogelators by an enzymatically induced pH switch, which involves the combination of glucose oxidase and catalase with D-glucose as the substrate, in which both the gelation kinetics and thermodynamics can be controlled by the concentrations of D-glucose. This novel hydrogelation method could result in hydrogels with higher mechanical stability and lower hydrogelation concentrations. We further illustrate the application of this hydrogelation method to differentiate different D-glucose levels.

Thermodynamics and kinetics of pack aluminide coating formation on IN-100

NASA Technical Reports Server (NTRS)

Levine, S. R.; Caves, R. M.

1973-01-01

An investigation of the effects of pack variables on the formation of aluminide coatings on nickel-base superalloy IN-100 was conducted. Also, the thermodynamics and kinetics of coating formation were analyzed. Observed coating weights were in good agreement with predictions made from the analysis. Pack temperature rather than pack aluminum activity controls the principal coating phase formed. In 1 weight percent aluminum packs, aluminum weight gains were related to the halide pack activator. Solid-state nickel diffusion controlled coating formation from sodium fluoride and chloride and ammonium fluoride activated packs. In other ammonium and sodium halide activated 1 weight percent aluminum packs, gaseous diffusion controlled coating formation.

First-principles study on influence of molybdenum on acicular ferrite formation on TiC particles in microallyed steels

NASA Astrophysics Data System (ADS)

Hua, Guomin; Li, Changsheng; Cheng, Xiaonong; Zhao, Xinluo; Feng, Quan; Li, Zhijie; Li, Dongyang; Szpunar, Jerzy A.

2018-01-01

In this study, influences of molybdenum on acicular ferrite formation on precipitated TiC particles are investigated from thermodynamic and kinetic respects. In thermodynamics, Segregation of Mo towards austenite/TiC interface releases the interfacial energy and induces phase transformation from austenite to acicular ferrite on the precipitated TiC particles. The Phase transformation can be achieved by displacive deformation along uniaxial Bain path. In addition, the segregation of Mo atom will also lead to the enhanced stability of ferrite in comparison with austenite no matter at low temperature or at high temperature. In kinetics, the Mo solute in acicular ferrite can effectively suppress the diffusion of carbon atoms, which ensures that orientation relationship between acicular ferrite and austenitized matrix can be satisfied during the diffusionless phase transformation. In contrast to ineffectiveness of TiC particles, the alloying Mo element can facilitate the formation of acicular ferrite on precipitated TiC particles, which is attributed to the above thermodynamic and kinetic reasons. Furthermore, Interfacial toughness and ductility of as-formed acicular ferrite/TiC interface can be improved simultaneously by segregation of Mo atom.

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

PubMed Central

Wang, Jin; Oliveira, Ronaldo J.; Chu, Xiakun; Whitford, Paul C.; Chahine, Jorge; Han, Wei; Wang, Erkang; Onuchic, José N.; Leite, Vitor B.P.

2012-01-01

The energy landscape approach has played a fundamental role in advancing our understanding of protein folding. Here, we quantify protein folding energy landscapes by exploring the underlying density of states. We identify three quantities essential for characterizing landscape topography: the stabilizing energy gap between the native and nonnative ensembles δE, the energetic roughness ΔE, and the scale of landscape measured by the entropy S. We show that the dimensionless ratio between the gap, roughness, and entropy of the system accurately predicts the thermodynamics, as well as the kinetics of folding. Large Λ implies that the energy gap (or landscape slope towards the native state) is dominant, leading to more funneled landscapes. We investigate the role of topological and energetic roughness for proteins of different sizes and for proteins of the same size, but with different structural topologies. The landscape topography ratio Λ is shown to be monotonically correlated with the thermodynamic stability against trapping, as characterized by the ratio of folding temperature versus trapping temperature. Furthermore, Λ also monotonically correlates with the folding kinetic rates. These results provide the quantitative bridge between the landscape topography and experimental folding measurements. PMID:23019359

Consistent Estimation of Gibbs Energy Using Component Contributions

PubMed Central

Milo, Ron; Fleming, Ronan M. T.

2013-01-01

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism. PMID:23874165

Mechanical properties of protein adsorption layers at the air/water and oil/water interface: a comparison in light of the thermodynamical stability of proteins.

PubMed

Mitropoulos, Varvara; Mütze, Annekathrin; Fischer, Peter

2014-04-01

Over the last decades numerous studies on the interfacial rheological response of protein adsorption layers have been published. The comparison of these studies and the retrieval of a common parameter to compare protein interfacial activity are hampered by the fact that different boundary conditions (e.g. physico-chemical, instrumental, interfacial) were used. In the present work we review previous studies and attempt a unifying approach for the comparison between bulk protein properties and their adsorption films. Among many common food grade proteins we chose bovine serum albumin, β-lactoglobulin and lysozyme for their difference in thermodynamic stability and studied their adsorption at the air/water and limonene/water interface. In order to achieve this we have i) systematically analyzed protein adsorption kinetics in terms of surface pressure rise using a drop profile analysis tensiometer and ii) we addressed the interfacial layer properties under shear stress using an interfacial shear rheometer under the same experimental conditions. We could show that thermodynamically less stable proteins adsorb generally faster and yield films with higher shear rheological properties at air/water interface. The same proteins showed an analog behavior when adsorbing at the limonene/water interface but at slower rates. Copyright © 2013 Elsevier B.V. All rights reserved.

NOx Direct Decomposition: Potentially Enhanced Thermodynamics and Kinetics on Chemically Modified Ferroelectric Surfaces

NASA Astrophysics Data System (ADS)

Kakekhani, Arvin; Ismail-Beigi, Sohrab

2014-03-01

NOx are regulated pollutants produced during automotive combustion. As part of an effort to design catalysts for NOx decomposition that operate in oxygen rich environment and permit greater fuel efficiency, we study chemistry of NOx on (001) ferroelectric surfaces. Changing the polarization at such surfaces modifies electronic properties and leads to switchable surface chemistry. Using first principles theory, our previous work has shown that addition of catalytic RuO2 monolayer on ferroelectric PbTiO3 surface makes direct decomposition of NO thermodynamically favorable for one polarization. Furthermore, the usual problem of blockage of catalytic sites by strong oxygen binding is overcome by flipping polarization that helps desorb the oxygen. We describe a thermodynamic cycle for direct NO decomposition followed by desorption of N2 and O2. We provide energy barriers and transition states for key steps of the cycle as well as describing their dependence on polarization direction. We end by pointing out how a switchable order parameter of substrate,in this case ferroelectric polarization, allows us to break away from some standard compromises for catalyst design(e.g. the Sabatier principle). This enlarges the set of potentially catalytic metals. Primary support from Toyota Motor Engineering and Manufacturing, North America, Inc.

The rheology and phase separation kinetics of mixed-matrix membrane dopes

NASA Astrophysics Data System (ADS)

Olanrewaju, Kayode Olaseni

Mixed-matrix hollow fiber membranes are being developed to offer more efficient gas separations applications than what the current technologies allow. Mixed-matrix membranes (MMMs) are membranes in which molecular sieves incorporated in a polymer matrix enhance separation of gas mixtures based on the molecular size difference and/or adsorption properties of the component gases in the molecular sieve. The major challenges encountered in the efficient development of MMMs are associated with some of the paradigm shifts involved in their processing, as compared to pure polymer membranes. For instance, mixed-matrix hollow fiber membranes are prepared by a dry-wet jet spinning method. Efficient large scale processing of hollow fibers by this method requires knowledge of two key process variables: the rheology and kinetics of phase separation of the MMM dopes. Predicting the rheological properties of MMM dopes is not trivial; the presence of particles significantly affects neat polymer membrane dopes. Therefore, the need exists to characterize and develop predictive capabilities for the rheology of MMM dopes. Furthermore, the kinetics of phase separation of polymer solutions is not well understood. In the case of MMM dopes, the kinetics of phase separation are further complicated by the presence of porous particles in a polymer solution. Thus, studies on the phase separation kinetics of polymer solutions and suspensions of zeolite particles in polymer solutions are essential. Therefore, this research thesis aims to study the rheology and phase separation kinetics of mixed-matrix membrane dopes. In our research efforts to develop predictive models for the shear rheology of suspensions of zeolite particles in polymer solutions, it was found that MFI zeolite suspensions have relative viscosities that dramatically exceed the Krieger-Dougherty predictions for hard sphere suspensions. Our investigations showed that the major origin of this discrepancy is the selective absorption of solvent molecules from the suspending polymer solution into the zeolite pores. Consequently, both the viscosity of the polymer solution and the particle contribution to the suspension viscosity are greatly increased. A predictive model for the viscosity of porous zeolite suspensions incorporating a solvent absorption parameter, alpha, into the Krieger-Dougherty model was developed. We experimentally determined the solvent absorption parameter and our results are in good agreement with the theoretical pore volume of MFI particles. In addition, fundamental studies were conducted with spherical nonporous silica suspensions to elucidate the role of colloidal and hydrodynamic forces on the rheology of mixed-matrix membrane dopes. Also in this thesis, details of a novel microfluidic device for measuring the phase separation kinetics of membrane dopes are presented. We have used this device to quantify the phase separation kinetics (PSK) of polymer solutions and MMM dopes upon contact with an array of relevant nonsolvent. For the polymer solution, we found that PSK is governed by the micro-rheological and thermodynamic properties of the polymer solution and nonsolvent. For the MMM dopes, we found that the PSK may increase with increase in particles surface area due to surface diffusion enhancement. In addition, it was found that the dispersed particles alter the thermodynamic properties of the dope based on the hydrophilicity and porosity of the particle.

Steepest entropy ascent model for far-nonequilibrium thermodynamics: Unified implementation of the maximum entropy production principle

NASA Astrophysics Data System (ADS)

Beretta, Gian Paolo

2014-10-01

By suitable reformulations, we cast the mathematical frameworks of several well-known different approaches to the description of nonequilibrium dynamics into a unified formulation valid in all these contexts, which extends to such frameworks the concept of steepest entropy ascent (SEA) dynamics introduced by the present author in previous works on quantum thermodynamics. Actually, the present formulation constitutes a generalization also for the quantum thermodynamics framework. The analysis emphasizes that in the SEA modeling principle a key role is played by the geometrical metric with respect to which to measure the length of a trajectory in state space. In the near-thermodynamic-equilibrium limit, the metric tensor is directly related to the Onsager's generalized resistivity tensor. Therefore, through the identification of a suitable metric field which generalizes the Onsager generalized resistance to the arbitrarily far-nonequilibrium domain, most of the existing theories of nonequilibrium thermodynamics can be cast in such a way that the state exhibits the spontaneous tendency to evolve in state space along the path of SEA compatible with the conservation constraints and the boundary conditions. The resulting unified family of SEA dynamical models is intrinsically and strongly consistent with the second law of thermodynamics. The non-negativity of the entropy production is a general and readily proved feature of SEA dynamics. In several of the different approaches to nonequilibrium description we consider here, the SEA concept has not been investigated before. We believe it defines the precise meaning and the domain of general validity of the so-called maximum entropy production principle. Therefore, it is hoped that the present unifying approach may prove useful in providing a fresh basis for effective, thermodynamically consistent, numerical models and theoretical treatments of irreversible conservative relaxation towards equilibrium from far nonequilibrium states. The mathematical frameworks we consider are the following: (A) statistical or information-theoretic models of relaxation; (B) small-scale and rarefied gas dynamics (i.e., kinetic models for the Boltzmann equation); (C) rational extended thermodynamics, macroscopic nonequilibrium thermodynamics, and chemical kinetics; (D) mesoscopic nonequilibrium thermodynamics, continuum mechanics with fluctuations; and (E) quantum statistical mechanics, quantum thermodynamics, mesoscopic nonequilibrium quantum thermodynamics, and intrinsic quantum thermodynamics.

Kinetics of the Multistep Rupture of Fibrin ‘A-a’ Polymerization Interactions Measured Using Atomic Force Microscopy

PubMed Central

Averett, Laurel E.; Schoenfisch, Mark H.; Akhremitchev, Boris B.; Gorkun, Oleg V.

2009-01-01

Abstract Fibrin, the structural scaffold of blood clots, spontaneously polymerizes through the formation of ‘A-a’ knob-hole bonds. When subjected to external force, the dissociation of this bond is accompanied by two to four abrupt changes in molecular dimension observable as rupture events in a force curve. Herein, the configuration, molecular extension, and kinetic parameters of each rupture event are examined. The increases in contour length indicate that the D region of fibrinogen can lengthen by ∼50% of the length of a fibrin monomer before rupture of the ‘A-a’ interaction. The dependence of the dissociation rate on applied force was obtained using probability distributions of rupture forces collected at different pull-off velocities. These distributions were fit using a model in which the effects of the shape of the binding potential are used to quantify the kinetic parameters of forced dissociation. We found that the weak initial rupture (i.e., event 1) was not well approximated by these models. The ruptured bonds comprising the strongest ruptures, events 2 and 3, had kinetic parameters similar to those commonly found for the mechanical unfolding of globular proteins. The bonds ruptured in event 4 were well described by these analyses, but were more loosely bound than the bonds in events 2 and 3. We propose that the first event represents the rupture of an unknown interaction parallel to the ‘A-a’ bond, events 2 and 3 represent unfolding of structures in the D region of fibrinogen, and event 4 is the rupture of the ‘A-a’ knob-hole bond weakened by prior structural unfolding. Comparison of the activation energy obtained via force spectroscopy measurements with the thermodynamic free energy of ‘A-a’ bond dissociation indicates that the ‘A-a’ bond may be more resistant to rupture by applied force than to rupture by thermal dissociation. PMID:19917237

HIGH-AFFINITY T CELL RECEPTOR DIFFERENTIATES COGNATE PEPTIDE-MHC AND ALTERED PEPTIDE LIGANDS WITH DISTINCT KINETICS AND THERMODYNAMICS

PubMed Central

Persaud, Stephen P.; Donermeyer, David L.; Weber, K. Scott; Kranz, David M.; Allen, Paul M.

2010-01-01

Interactions between the T cell receptor and cognate peptide-MHC are crucial initiating events in the adaptive immune response. These binding events are highly specific yet occur with micromolar affinity. Even weaker interactions between TCR and self-pMHC complexes play critical regulatory roles in T cell development, maintenance and coagonist activity. Due to their low affinity, the kinetics and thermodynamics of such weak interactions are difficult to study. In this work, we used M15, a high-affinity TCR engineered from the 3.L2 TCR system, to study the binding properties, thermodynamics, and specificity of two altered peptide ligands (APLs). Our affinity measurements of the high-affinity TCR support the view that the wild type TCR binds these APLs in the millimolar affinity range, and hence very low affinities can still elicit biological functions. Finally, single methylene differences among the APLs gave rise to strikingly different binding thermodynamics. These minor changes in the pMHC antigen were associated with significant and unpredictable changes in both the entropy and enthalpy of the reaction. As the identical TCR was analyzed with several structurally similar ligands, the distinct thermodynamic binding profiles provide a mechanistic perspective on how exquisite antigen specificity is achieved by the T cell receptor. PMID:20334923

Effect of temperature on the protonation of N-(2-hydroxyethyl)ethylenediamine-N,N',N'-triacetic acid in aqueous solutions: Potentiometric and calorimetric studies

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

Li, Xingliang; Zhang, Zhicheng; Endrizzi, Francesco

2015-06-01

The TALSPEAK process (Trivalent Actinide Lanthanide Separations by Phosphorus-reagent Extraction from Aqueous Komplexes) has been demonstrated in several pilot-scale operations to be effective at separating trivalent actinides (An 3+) from trivalent lanthanides (Ln 3+). However, fundamental studies have revealed undesired aspects of TALSPEAK, such as the significant partitioning of Na +, lactic acid, and water into the organic phase, thermodynamically unpredictable pH dependence, and the slow extraction kinetics. In the modified TALSPEAK process, the combination of the aqueous holdback complexant HEDTA (N-(2-hydroxyethyl)ethylenediamine-N,N',N'-triacetic acid) with the extractant HEH[EHP] (2-ethyl(hexyl) phosphonic acid mono-2-ethylhexyl ester) in the organic phase has been found tomore » exhibit a nearly flat pH dependence between 2.5 and 4.5 and more rapid phase transfer kinetics for the heavier lanthanides. To help understand the speciation of Ln 3+ and An 3+ in the modified TALSPEAK, systematic studies are underway on the thermodynamics of major reactions in the HEDTA system under conditions relevant to the process (e.g., higher temperatures). Thermodynamics of the protonation and complexation of HEDTA with Ln 3+ were studied at variable temperatures. Equilibrium constants and enthalpies were determined by a combination of techniques including potentiometry and calorimetry. This paper presents the protonation constants of HEDTA at T = (25 to 70) °C. The potentiometric titrations have demonstrated that, stepwise, the first two protonation constants decrease and the third one slightly increases with the increase of temperature. This trend is in good agreement with the enthalpy of protonation directly determined by calorimetry. The results of NMR analysis further confirm that the first two protonation reactions occur on the diamine nitrogen atoms, while the third protonation reaction occurs on the oxygen of a carboxylate group. These data, in conjunction with the thermodynamic parameters of Ln 3+/An 3+ complexes with HEDTA at different temperatures, will help to predict the speciation and temperature-dependent behavior of Ln 3+/An 3+ in the modified TALSPEAK process.« less

Mechanics, Waves and Thermodynamics

NASA Astrophysics Data System (ADS)

Ranjan Jain, Sudhir

2016-05-01

Figures; Preface; Acknowledgement; 1. Energy, mass, momentum; 2. Kinematics, Newton's laws of motion; 3. Circular motion; 4. The principle of least action; 5. Work and energy; 6. Mechanics of a system of particles; 7. Friction; 8. Impulse and collisions; 9. Central forces; 10. Dimensional analysis; 11. Oscillations; 12. Waves; 13. Sound of music; 14. Fluid mechanics; 15. Water waves; 16. The kinetic theory of gases; 17. Concepts and laws of thermodynamics; 18. Some applications of thermodynamics; 19. Basic ideas of statistical mechanics; Bibliography; Index.

On the definition of a Monte Carlo model for binary crystal growth.

PubMed

Los, J H; van Enckevort, W J P; Meekes, H; Vlieg, E

2007-02-01

We show that consistency of the transition probabilities in a lattice Monte Carlo (MC) model for binary crystal growth with the thermodynamic properties of a system does not guarantee the MC simulations near equilibrium to be in agreement with the thermodynamic equilibrium phase diagram for that system. The deviations remain small for systems with small bond energies, but they can increase significantly for systems with large melting entropy, typical for molecular systems. These deviations are attributed to the surface kinetics, which is responsible for a metastable zone below the liquidus line where no growth occurs, even in the absence of a 2D nucleation barrier. Here we propose an extension of the MC model that introduces a freedom of choice in the transition probabilities while staying within the thermodynamic constraints. This freedom can be used to eliminate the discrepancy between the MC simulations and the thermodynamic equilibrium phase diagram. Agreement is achieved for that choice of the transition probabilities yielding the fastest decrease of the free energy (i.e., largest growth rate) of the system at a temperature slightly below the equilibrium temperature. An analytical model is developed, which reproduces quite well the MC results, enabling a straightforward determination of the optimal set of transition probabilities. Application of both the MC and analytical model to conditions well away from equilibrium, giving rise to kinetic phase diagrams, shows that the effect of kinetics on segregation is even stronger than that predicted by previous models.

Modeling of dielectric properties of aqueous salt solutions with an equation of state.

PubMed

Maribo-Mogensen, Bjørn; Kontogeorgis, Georgios M; Thomsen, Kaj

2013-09-12

The static permittivity is the most important physical property for thermodynamic models that account for the electrostatic interactions between ions. The measured static permittivity in mixtures containing electrolytes is reduced due to kinetic depolarization and reorientation of the dipoles in the electrical field surrounding ions. Kinetic depolarization may explain 25-75% of the observed decrease in the permittivity of solutions containing salts, but since this is a dynamic property, this effect should not be included in the thermodynamic modeling of electrolytes. Kinetic depolarization has, however, been ignored in relation to thermodynamic modeling, and authors have either neglected the effect of salts on permittivity or used empirical correlations fitted to the measured static permittivity, leading to an overestimation of the reduction in the thermodynamic static permittivity. We present a new methodology for obtaining the static permittivity over wide ranges of temperatures, pressures, and compositions for use within an equation of state for mixed solvents containing salts. The static permittivity is calculated from a new extension of the framework developed by Onsager, Kirkwood, and Fröhlich to associating mixtures. Wertheim's association model as formulated in the statistical associating fluid theory is used to account for hydrogen-bonding molecules and ion-solvent association. Finally, we compare the Debye-Hückel Helmholtz energy obtained using an empirical model with the new physical model and show that the empirical models may introduce unphysical behavior in the equation of state.

Nonisothermal Analysis of Solution Kinetics by Spreadsheet Simulation

ERIC Educational Resources Information Center

de Levie, Robert

2012-01-01

A fast and generally applicable alternative solution to the problem of determining the useful shelf life of medicinal solutions is described. It illustrates the power and convenience of the combination of numerical simulation and nonlinear least squares with a practical pharmaceutical application of chemical kinetics and thermodynamics, validated…

Glycosidation of Methanol with Ribose: An Interdisciplinary Undergraduate Laboratory Experiment

ERIC Educational Resources Information Center

Simon, Erin; Cook, Katie; Pritchard, Meredith R.; Stripe, Wayne; Bruch, Martha; Bendinskas, Kestutis

2010-01-01

This exercise provides students hands-on experience with the topics of glycosidation, hemiacetal and acetal formation, proton nuclear magnetic resonance ([superscript 1]H NMR) spectroscopy, and kinetic and thermodynamic product formation. In this laboratory experiment, the methyl acetal of ribose is synthesized, and the kinetic and thermodynamic…

The Roles of Biofilm Conductivity and Donor Substrate Kinetics in a Mixed-Culture Biofilm Anod

EPA Science Inventory

We experimentally assessed kinetics and thermodynamics of electron transfer (ET) from the donor substrate (acetate) to the anode for a mixed-culture biofilm anode. We interpreted the results with a modified biofilm-conduction model consisting of three ET steps: (1) intracellular...

Integrated computational model of the bioenergetics of isolated lung mitochondria

PubMed Central

Zhang, Xiao; Jacobs, Elizabeth R.; Camara, Amadou K. S.; Clough, Anne V.

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria. PMID:29889855

Integrated computational model of the bioenergetics of isolated lung mitochondria.

PubMed

Zhang, Xiao; Dash, Ranjan K; Jacobs, Elizabeth R; Camara, Amadou K S; Clough, Anne V; Audi, Said H

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria.

Enhancing the Effectiveness of Carbon Dioxide Flooding by Managing Asphaltene Precipitation

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

Deo, Milind D.

2002-02-21

This project was undertaken to understand fundamental aspects of carbon dioxide (CO2) induced asphaltene precipitation. Oil and asphaltene samples from the Rangely field in Colorado were used for most of the project. The project consisted of pure component and high-pressure, thermodynamic experiments, thermodynamic modeling, kinetic experiments and modeling, targeted corefloods and compositional modeling.

Thermodynamics of a Block Sliding across a Frictional Surface

ERIC Educational Resources Information Center

Mungan, Carl E.

2007-01-01

The following idealized problem is intended to illustrate some basic thermodynamic concepts involved in kinetic friction. A block of mass m is sliding on top of a frictional, flat-topped table of mass M. The table is magnetically levitated, so that it can move without thermal contact and friction across a horizontal floor. The table is initially…

Photophysical behavior of polyatomic molecules

NASA Astrophysics Data System (ADS)

Ware, W. R.

1980-10-01

Part one of this report deals with attempts over the past several years to devise a more sophisticated theory of diffusion controlled reactions than that presented by Collins and Kimball. In particular, the investigators were interested in a more realistic formulation of the problem of high concentration quenching where quenches in the vicinity of the molecular to be quenched must be considered. It was desired however, to obtain a formalism which was tractable mathematically and which contained parameters which would be related to experiment. Part two deals with the photophysics of systems exhibiting molecular association both in the ground and excited states has been studied. The emphasis has been on kinetic models, the measurement of rate constants associated with these models, and the determination of activation parameters and equilibrium thermodynamic parameters associated with the exciplex formation and disappearance. Studies of solvent effects and steric effects on the behavior of exciplex systems have been carried out. The case of rapid equilibrium where the monomer and exciplex decay with the same rate constant has also been examined.

Hindered rotor models with variable kinetic functions for accurate thermodynamic and kinetic predictions

NASA Astrophysics Data System (ADS)

Reinisch, Guillaume; Leyssale, Jean-Marc; Vignoles, Gérard L.

2010-10-01

We present an extension of some popular hindered rotor (HR) models, namely, the one-dimensional HR (1DHR) and the degenerated two-dimensional HR (d2DHR) models, allowing for a simple and accurate treatment of internal rotations. This extension, based on the use of a variable kinetic function in the Hamiltonian instead of a constant reduced moment of inertia, is extremely suitable in the case of rocking/wagging motions involved in dissociation or atom transfer reactions. The variable kinetic function is first introduced in the framework of a classical 1DHR model. Then, an effective temperature and potential dependent constant is proposed in the cases of quantum 1DHR and classical d2DHR models. These methods are finally applied to the atom transfer reaction SiCl3+BCl3→SiCl4+BCl2. We show, for this particular case, that a proper accounting of internal rotations greatly improves the accuracy of thermodynamic and kinetic predictions. Moreover, our results confirm (i) that using a suitably defined kinetic function appears to be very adapted to such problems; (ii) that the separability assumption of independent rotations seems justified; and (iii) that a quantum mechanical treatment is not a substantial improvement with respect to a classical one.

On the biophysics and kinetics of toehold-mediated DNA strand displacement

PubMed Central

Srinivas, Niranjan; Ouldridge, Thomas E.; Šulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, Erik

2013-01-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. PMID:24019238

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

PubMed

Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

2013-12-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

Adsorption of Azo-Dye Orange II from Aqueous Solutions Using a Metal-Organic Framework Material: Iron- Benzenetricarboxylate

PubMed Central

Rojas García, Elizabeth; López Medina, Ricardo; May Lozano, Marcos; Hernández Pérez, Isaías; Valero, Maria J.; Maubert Franco, Ana M.

2014-01-01

A Metal-Organic Framework (MOF), iron-benzenetricarboxylate (Fe(BTC)), has been studied for the adsorptive removal of azo-dye Orange II from aqueous solutions, where the effect of various parameters was tested and isotherm and kinetic models were suggested. The adsorption capacities of Fe(BTC) were much higher than those of an activated carbon. The experimental data can be best described by the Langmuir isotherm model (R2 > 0.997) and revealed the ability of Fe(BTC) to adsorb 435 mg of Orange II per gram of adsorbent at the optimal conditions. The kinetics of Orange II adsorption followed a pseudo-second-order kinetic model, indicating the coexistence of physisorption and chemisorption, with intra-particle diffusion being the rate controlling step. The thermodynamic study revealed that the adsorption of Orange II was feasible, spontaneous and exothermic process (−25.53 kJ·mol−1). The high recovery of the dye showed that Fe(BTC) can be employed as an effective and reusable adsorbent for the removal of Orange II from aqueous solutions and showed the economic interest of this adsorbent material for environmental purposes. PMID:28788289

Cadmium telluride nanoparticles loaded on activated carbon as adsorbent for removal of sunset yellow

NASA Astrophysics Data System (ADS)

Ghaedi, M.; Hekmati Jah, A.; Khodadoust, S.; Sahraei, R.; Daneshfar, A.; Mihandoost, A.; Purkait, M. K.

2012-05-01

Adsorption is a promising technique for decolorization of effluents of textile dyeing industries but its application is limited due to requirement of high amounts of adsorbent required. The objective of this study was to assess the potential of cadmium telluride nanoparticles loaded onto activated carbon (CdTN-AC) for the removal of sunset yellow (SY) dye from aqueous solution. Adsorption studies were conducted in a batch mode varying solution pH, contact time, initial dye concentration, CdTN-AC dose, and temperature. In order to investigate the efficiency of SY adsorption on CdTN-AC, pseudo-first-order, pseudo-second-order, Elovich, and intra-particle diffusion kinetic models were studied. It was observed that the pseudo-second-order kinetic model fits better than other kinetic models with good correlation coefficient. Equilibrium data were fitted to the Langmuir model. Thermodynamic parameters such as enthalpy, entropy, activation energy, and sticking probability were also calculated. It was found that the sorption of SY onto CdTN-AC was spontaneous and endothermic in nature. The proposed adsorbent is applicable for SY removal from waste of real effluents including pea-shooter, orange drink and jelly banana with efficiency more than 97%.

Adsorption isotherm, kinetic and mechanism of expanded graphite for sulfadiazine antibiotics removal from aqueous solutions.

PubMed

Zhang, Ling; Wang, Yong; Jin, SuWan; Lu, QunZan; Ji, Jiang

2017-10-01

The adsorption of sulfadiazine from water by expanded graphite (EG), a low cost and environmental-friendly adsorbent, was investigated. Several adsorption parameters (including the initial sulfadiazine concentration, contact time, pH of solution, ionic strength and temperature) were studied. Results of equilibrium experiments indicated that adsorption of sulfadiazine onto EG were better described by the Langmuir and Tempkin models than by the Freundlich model. The maximum adsorption capacity is calculated to be 16.586 mg/g at 298 K. The kinetic data were analyzed by pseudo-first-order, pseudo-second-order and intraparticle models. The results indicated that the adsorption process followed pseudo-second-order kinetics and may be controlled by two steps. Moreover, the pH significantly influenced the adsorption process, with the relatively high adsorption capacity at pH 2-10. The electrostatic and hydrophobic interactions are manifested to be two main mechanisms for sulfadiazine adsorption of EG. Meanwhile, the ionic concentration of Cl - slightly impacted the removal of sulfadiazine. Results of thermodynamics analysis showed spontaneous and exothermic nature of sulfadiazine adsorption on EG. In addition, regeneration experiments imply that the saturated EG could be reused for sulfadiazine removal by immersing sodium hydroxide.

Nucleation kinetics of MgCl2-ethanol adduct for the supported Ziegler-Natta catalysts with a thermodynamic approach

NASA Astrophysics Data System (ADS)

Ansari, Ziaul Haque; Zeng, Yan; Demopoulos, George P.; Li, Zhibao

2018-07-01

MgCl2-ethanol adducts play a key role in the synthesis of supported Ziegler-Natta catalysts. The morphology of the MgCl2-ethanol adducts, which is controlled by their crystallization process, can determine the structure and thus the property of the polyolefin products. Here we study the nucleation kinetics of MgCl2-ethanol adducts by measuring the metastable zone width (MSZW) and induction time at different temperatures. Supersaturation ratios used in induction time measurements were predicted by the Mixed Solvent Electrolyte (MSE) model embedded in OLI System. Nývlt‧s approach was applied to determine MSZW. By the induction time measurement, the effect of temperature, and supersaturation were studied. It was found that induction time decreases as either temperature or supersaturation increases. The measured MSZW and induction time are used to estimate the nucleation kinetics of the system, and thereby distinguishing between the homogeneous and heterogeneous mechanisms. The interfacial tension and other related nucleation parameters were calculated from the induction time data. XRD and TGA indicate that the MgCl2-ethanol adduct has the stoichiometry of MgCl2·6C2H5OH.

Adsorption characteristics of (-)-epigallocatechin gallate and caffeine in the extract of waste tea on macroporous adsorption resins functionalized with chloromethyl, amino, and phenylamino groups.

PubMed

Liu, Yongfeng; Bai, Qingqing; Lou, Song; Di, Duolong; Li, Jintian; Guo, Mei

2012-02-15

According to the Friedel-Crafts and amination reaction, a series of macroporous adsorption resins (MARs) with novel structures were synthesized and identified by the Brunauer-Emmett-Teller (BET) method and Fourier transform infrared (FTIR) spectra, and corresponding adsorption behaviors for (-)-epigallocatechin gallate (EGCG) and caffeine (CAF) extracted from waste tea were systemically investigated. Based on evaluation of adsorption kinetics, the kinetic data were well fitted by pseudo-second-order kinetics. Langmuir, Freundlich, Temkin-Pyzhev, and Dubinin-Radushkevich isotherms were selected to illustrate the adsorption process of EGCG and CAF on the MARs. Thermodynamic parameters were adopted to explain in-depth information of inherent energetic changes associated with the adsorption process. The effect of temperature on EGCG and CAF adsorption by D101-3 was further expounded. Van der Waals force, hydrogen bonding, and electrostatic interaction were the main driving forces for the adsorption of EGCG and CAF on the MARs. This study might provide a scientific reference point to aid the industrial large-scale separation and enrichment of EGCG from the extracts of waste tea using modified MARs.

Full kinetics investigation of the formation reaction of phosphonate esters in the gas-phase: a theoretical study.

PubMed

Kazemian, Mohammad Amin; Habibi-Khorassani, Sayyed Mostafa; Maghsoodlu, Malek Taher; Ebrahimi, Ali

2014-04-01

In the present work, the proposed multiple-mechanisms have been investigated theoretically for the reaction between triphenyl phosphite and dimethyl acetylenedicarboxylate in the presence of N-H acid such as aniline for generation of phosphonate esters using ab initio molecular orbital theory in gas phase. The profile of the potential energy surface was constructed at the HF/6-311G(d,p) level of theory. The kinetics of the gas phase reaction was studied by evaluating the reaction path of various mechanisms. Between 12 speculative proposed mechanisms {step₁, step₂ (with four possibilities), step₃ (with three possibilities), and step₄} only the third speculative mechanism was recognized as a desirable mechanism. Theoretical kinetics data involving k and E(a), activation (ΔG(‡), ΔS(‡) and ΔH(‡)), and thermodynamic parameters (ΔG°, ΔS° and ΔH°) were calculated for each step of the various mechanisms. Step₁ of the desirable mechanism was identified as the rate determining step. Comparison of the theoretical desirable mechanism with the rate law that has been previously obtained by UV spectrophotometry experiments indicated that the results are in good agreement.

Nitrate decontamination through functionalized chitosan in brackish water.

PubMed

Appunni, Sowmya; Rajesh, Mathur P; Prabhakar, Sivaraman

2016-08-20

N, N, N-Triethyl ammonium functionalized cross-linked chitosan beads (TEACCB) was prepared by alkylation of glutaraldehyde cross-linked chitosan beads to remove nitrate from brackish water. Physico-chemical characteristics of TEACCB were analyzed using FTIR, SEM, EDAX, TGA, DTA, BET surface area, swelling ratio and pHzpc. The maximum nitrate removal capacity of TEACCB was 2.26meq/g and is higher than other reported chitosan based adsorbents. Nitrate removal ratio in the presence and absence of common anions like chloride and sulphate demonstrated the selectively of TEACCB towards nitrate. The kinetic data of nitrate removal fitted well with the pseudo-second-order kinetic model. The thermodynamic parameters indicated that nitrate removal could be spontaneous and exothermic in nature. TEACCB was reused with 100% efficiency after regenerating with 0.05N HCl. Column study was carried out to remove nitrate from brackish water. These results are very significant to develop TEACCB based nitrate removal technology with great efficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

DOE PAGES

Dangkulwanich, Manchuta; Ishibashi, Toyotaka; Liu, Shixin; ...

2013-09-24

During transcription elongation, RNA polymerase has been assumed to attain equilibrium between pre- and post-translocated states rapidly relative to the subsequent catalysis. Under this assumption, recent single-molecule studies proposed a branched Brownian ratchet mechanism that necessitates a putative secondary nucleotide binding site on the enzyme. By challenging individual yeast RNA polymerase II with a nucleosomal barrier, we separately measured the forward and reverse translocation rates. Surprisingly, we found that the forward translocation rate is comparable to the catalysis rate. This finding reveals a linear, non-branched ratchet mechanism for the nucleotide addition cycle in which translocation is one of the rate-limitingmore » steps. We further determined all the major on- and off-pathway kinetic parameters in the elongation cycle. The resulting translocation energy landscape shows that the off-pathway states are favored thermodynamically but not kinetically over the on-pathway states, conferring the enzyme its propensity to pause and furnishing the physical basis for transcriptional regulation.« less

Modeling the internal combustion engine

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.; Mcbride, B. J.

1985-01-01

A flexible and computationally economical model of the internal combustion engine was developed for use on large digital computer systems. It is based on a system of ordinary differential equations for cylinder-averaged properties. The computer program is capable of multicycle calculations, with some parameters varying from cycle to cycle, and has restart capabilities. It can accommodate a broad spectrum of reactants, permits changes in physical properties, and offers a wide selection of alternative modeling functions without any reprogramming. It readily adapts to the amount of information available in a particular case because the model is in fact a hierarchy of five models. The models range from a simple model requiring only thermodynamic properties to a complex model demanding full combustion kinetics, transport properties, and poppet valve flow characteristics. Among its many features the model includes heat transfer, valve timing, supercharging, motoring, finite burning rates, cycle-to-cycle variations in air-fuel ratio, humid air, residual and recirculated exhaust gas, and full combustion kinetics.

The potential use of activated carbon prepared from Ziziphus species for removing dyes from waste waters

NASA Astrophysics Data System (ADS)

Regti, Abdelmajid; Laamari, My Rachid; Stiriba, Salah-Eddine; El Haddad, Mohammadine

2017-11-01

In this study, the adsorption potential of activated carbon prepared from Ziziphus mauritiana nuts for the removal of methylene blue (MB) from aqueous solution has been investigated using batch mode experiments. The effects of some operating parameters on the removal dye such as, initial pH (2-12), temperature (298-328 K), initial MB concentration (20-100 mg L-1), and contact time (5-70 min) were investigated. Adsorption kinetic showed that the rate adsorption followed the pseudo-second-order kinetic model. Four adsorption isotherms models were applied to experimental equilibrium data (Langmuir, Freundlich, Redlich-Peterson, and Fritz-Schlunder) and the different constants were calculated using non-linear equations models. Fritz-Schlunder model was found the best one to describe the adsorption process which suggests that the adsorption of MB onto activated carbon derived from Ziziphus mauritiana is heterogeneous with a multilayer. Thermodynamic adsorption showed that the process was endothermic and spontaneous in nature.

Adsorption of Ag (I) from aqueous solution by waste yeast: kinetic, equilibrium and mechanism studies.

PubMed

Zhao, Yufeng; Wang, Dongfang; Xie, Hezhen; Won, Sung Wook; Cui, Longzhe; Wu, Guiping

2015-01-01

One type of biosorbents, brewer fermentation industry waste yeast, was developed to adsorb the Ag (I) in aqueous solution. The result of FTIR analysis of waste yeast indicated that the ion exchange, chelating and reduction were the main binding mechanisms between the silver ions and the binding sites on the surface of the biomass. Furthermore, TEM, XRD and XPS results suggested that Ag(0) nanoparticles were deposited on the surface of yeast. The kinetic experiments revealed that sorption equilibrium could reach within 60 min, and the removal efficiency of Ag (I) could be still over 93 % when the initial concentration of Ag (I) was below 100 mg/L. Thermodynamic parameters of the adsorption process (ΔG, ΔH and ΔS) identified that the adsorption was a spontaneous and exothermic process. The waste yeast, playing a significant role in the adsorption of the silver ions, is useful to fast adsorb Ag (I) from low concentration.

Functionalization of multiwalled carbon nanotubes by microwave irradiation for lysozyme attachment: comparison of covalent and adsorption methods by kinetics of thermal inactivation

NASA Astrophysics Data System (ADS)

Puentes-Camacho, Daniel; Velázquez, Enrique F.; Rodríguez-Félix, Dora E.; Castillo-Ortega, Mónica; Sotelo-Mundo, Rogerio R.; del Castillo-Castro, Teresa

2017-12-01

Proteins suffer changes in their tertiary structure when they are immobilized, and enzymatic activity is affected due to the low biocompatibility of some supporting materials. In this work immobilization of lysozyme on carbon nanotubes previously functionalized by microwave irradiation was studied. The effectiveness of the microwave-assisted acid treatment of carbon nanotubes was evaluated by XPS, TEM, Raman and FTIR spectroscopy. The carboxylic modification of nanotube surfaces by this fast, simple and feasible method allowed the physical adsorption and covalent linking of active lysozyme onto the carbonaceous material. Thermal inactivation kinetics, thermodynamic parameters and storage stability were studied for adsorbed and covalent enzyme complexes. A major stability was found for lysozyme immobilized by the covalent method, the activation energy for inactivation of the enzyme was higher for the covalent method and it was stable after 50 d of storage at 4 °C. The current study highlights the effect of protein immobilization method on the biotechnological potential of nanostructured biocatalysts.

Application of Glycyrrhiza glabra Root as a Novel Adsorbent in the Removal of Toluene Vapors: Equilibrium, Kinetic, and Thermodynamic Study

PubMed Central

Mohammadi-Moghadam, Fazel; Amin, Mohammad Mehdi; Khiadani (Hajian), Mehdi; Momenbeik, Fariborz; Nourmoradi, Heshmatollah; Hatamipour, Mohammad Sadegh

2013-01-01

The aim of this paper is to investigate the removal of toluene from gaseous solution through Glycyrrhiza glabra root (GGR) as a waste material. The batch adsorption experiments were conducted at various conditions including contact time, adsorbate concentration, humidity, and temperature. The adsorption capacity was increased by raising the sorbent humidity up to 50 percent. The adsorption of toluene was also increased over contact time by 12 h when the sorbent was saturated. The pseudo-second-order kinetic model and Freundlich model fitted the adsorption data better than other kinetic and isotherm models, respectively. The Dubinin-Radushkevich (D-R) isotherm also showed that the sorption by GGR was physical in nature. The results of the thermodynamic analysis illustrated that the adsorption process is exothermic. GGR as a novel adsorbent has not previously been used for the adsorption of pollutants. PMID:23554821

Exploring ultrastability in nanostructured glassy polymer films by fast-scanning calorimetry.

NASA Astrophysics Data System (ADS)

Chowdhury, Mithun; Wang, Yucheng; Jeong, Hyuncheol; Cangialosi, Daniele; Priestley, Rodney

A decade ago ultra-stable small molecule glass formers were discovered. Since then a significant amount of research has been devoted to traverse down the energy landscape of such glass formers via physical vapor deposition (PVD). Matrix assisted pulsed laser evaporation (MAPLE) has the known ability to produce vapour deposited nanostructured polymer glass with exceptional kinetic stability. We explored the role of deposition temperature/ growth rate on thermodynamic and kinetic stabilities of poly (methyl methacrylate) (PMMA) films, deposited over a fast-scanning calorimetry sensor. We found in general any MAPLE deposited glass is kinetically more stable than bulk polymer and its spin-coated film. Moreover slow growth rate and optimum temperature during MAPLE deposition can additionally lead to thermodynamically stable (low-energy) glass. The role of interfaces formed through dramatic nanostructuring and packing of nanoglobules (removal of void space) may have additional role on such ultrastability. NSF-MRSEC through PCCM (Grant: DMR-1420541).

Nonlinear machine learning and design of reconfigurable digital colloids.

PubMed

Long, Andrew W; Phillips, Carolyn L; Jankowksi, Eric; Ferguson, Andrew L

2016-09-14

Digital colloids, a cluster of freely rotating "halo" particles tethered to the surface of a central particle, were recently proposed as ultra-high density memory elements for information storage. Rational design of these digital colloids for memory storage applications requires a quantitative understanding of the thermodynamic and kinetic stability of the configurational states within which information is stored. We apply nonlinear machine learning to Brownian dynamics simulations of these digital colloids to extract the low-dimensional intrinsic manifold governing digital colloid morphology, thermodynamics, and kinetics. By modulating the relative size ratio between halo particles and central particles, we investigate the size-dependent configurational stability and transition kinetics for the 2-state tetrahedral (N = 4) and 30-state octahedral (N = 6) digital colloids. We demonstrate the use of this framework to guide the rational design of a memory storage element to hold a block of text that trades off the competing design criteria of memory addressability and volatility.

Simulations of the thermodynamics and kinetics of NH3 at the RuO2 (110) surface

NASA Astrophysics Data System (ADS)

Erdtman, Edvin; Andersson, Mike; Lloyd Spetz, Anita; Ojamäe, Lars

2017-02-01

Ruthenium(IV)oxide (RuO2) is a material used for various purposes. It acts as a catalytic agent in several reactions, for example oxidation of carbon monoxide. Furthermore, it is used as gate material in gas sensors. In this work theoretical and computational studies were made on adsorbed molecules on RuO2 (110) surface, in order to follow the chemistry on the molecular level. Density functional theory calculations of the reactions on the surface have been performed. The calculated reaction and activation energies have been used as input for thermodynamic and kinetics calculations. A surface phase diagram was calculated, presenting the equilibrium composition of the surface at different temperature and gas compositions. The kinetics results are in line with the experimental studies of gas sensors, where water has been produced on the surface, and hydrogen is found at the surface which is responsible for the sensor response.

Equilibrium isotherms, kinetics, and thermodynamics studies for congo red adsorption using calcium alginate beads impregnated with nano-goethite.

PubMed

Munagapati, Venkata Subbaiah; Kim, Dong-Su

2017-07-01

The present study is concerned with the batch adsorption of congo red (CR) from an aqueous solution using calcium alginate beads impregnated with nano-goethite (CABI nano-goethite) as an adsorbent. The optimum conditions for CR removal were determined by studying operational variables viz. pH, adsorbent dose, contact time, initial dye ion concentration and temperature. The CABI nano-goethite was characterized by Fourier transform infrared spectroscopy (FTIR), X- ray diffraction (XRD) and Scanning electron microscopy/energy dispersive spectroscopy (SEM/EDS) analysis. The CR sorption data onto CABI nano-goethite were described using Langmuir, Freundlich, Dubinin-Radushkevich and Temkin isotherm models. The results show that the best fit was achieved with the Langmuir isotherm model. The maximum adsorption capacity (181.1mg/g) of CR was occurred at pH 3.0. Kinetic studies showed that the adsorption followed a pseudo-second-order model. Desorption experiments were carried out to explore the feasibility of regenerating the adsorbent and the adsorbed CR from CABI nano-goethite. The best desorbing agent was 0.1M NaOH with an efficiency of 94% recovery. The thermodynamic parameters ΔG°, ΔH°, and ΔS° for the CR adsorption were determined by using adsorption capacities at five different temperatures (293, 303, 313, 323 and 303K). Results show that the adsorption process was endothermic and favoured at high temperature. Copyright © 2017 Elsevier Inc. All rights reserved.

Biosorption of Cd+2 by green plant biomass, Araucaria heterophylla: characterization, kinetic, isotherm and thermodynamic studies

NASA Astrophysics Data System (ADS)

Sarada, B.; Krishna Prasad, M.; Kishore Kumar, K.; Murthy, Ch V. R.

2017-11-01

The present study attempted to analyze the biosorption behavior of novel biosorbent, Araucaria heterophylla (green plant) biomass, to remove Cd+2 from solutions against various parameters, i.e., initial metal ion concentration, pH, temperature, sorbent dosage and biomass particle size. The maximum biosorption was found to be 90.02% at pH 5.5 and biosorption capacity ( q e) of Cd+2 is 9.2506 mg g-1. The Langmuir and Freundlich equilibrium adsorption isotherms were studied and it was observed that Freundlich model is the best fit than the Langmuir model with correlation co-efficient of 0.999. Kinetic studies indicated that the biosorption process of Cd+2 well followed the pseudo-second-order model with R 2 0.999. Thermodynamic studies observed that the process is exothermic (Δ H ° negative). Free energy change (Δ G °) with negative sign reflected the feasibility and spontaneous nature of the process. The chemical functional -OH groups, CH2 stretching vibrations, C=O carbonyl group of alcohol, C=O carbonyl group of amide, P=O stretching vibrations and -CH groups were involved in the biosorption process. The XRD pattern of the A. heterophylla was found to be mostly amorphous in nature. The SEM studies showed Cd+2 biosorption on selective grains of the biosorbent. It was concluded that A. heterophylla leaf powder can be used as an effective, low-cost, and environmentally friendly biosorbent for the removal of Cd+2 from aqueous solution.

Adsorption Properties of Tetracycline onto Graphene Oxide: Equilibrium, Kinetic and Thermodynamic Studies

PubMed Central

Ghadim, Ehsan Ezzatpour; Manouchehri, Firouzeh; Soleimani, Gholamreza; Hosseini, Hadi; Kimiagar, Salimeh; Nafisi, Shohreh

2013-01-01

Graphene oxide (GO) nanoparticle is a high potential effective absorbent. Tetracycline (TC) is a broad-spectrum antibiotic produced, indicated for use against many bacterial infections. In the present research, a systematic study of the adsorption and release process of tetracycline on GO was performed by varying pH, sorption time and temperature. The results of our studies showed that tetracycline strongly loads on the GO surface via π–π interaction and cation–π bonding. Investigation of TC adsorption kinetics showed that the equilibrium was reached within 15 min following the pseudo-second-order model with observed rate constants of k2 = 0.2742–0.5362 g/mg min (at different temperatures). The sorption data has interpreted by the Langmuir model with the maximum adsorption of 323 mg/g (298 K). The mean energy of adsorption was determined 1.83 kJ/mol (298 K) based on the Dubinin–Radushkevich (D–R) adsorption isotherm. Moreover, the thermodynamic parameters such as ΔH°, ΔS° and ΔG° values for the adsorption were estimated which indicated the endothermic and spontaneous nature of the sorption process. The electrochemistry approved an ideal reaction for the adsorption under electrodic process. Simulation of GO and TC was done by LAMMPS. Force studies in z direction showed that tetracycline comes close to GO sheet by C8 direction. Then it goes far and turns and again comes close from amine group to the GO sheet. PMID:24302989

Adsorption properties of tetracycline onto graphene oxide: equilibrium, kinetic and thermodynamic studies.

PubMed

Ghadim, Ehsan Ezzatpour; Manouchehri, Firouzeh; Soleimani, Gholamreza; Hosseini, Hadi; Kimiagar, Salimeh; Nafisi, Shohreh

2013-01-01

Graphene oxide (GO) nanoparticle is a high potential effective absorbent. Tetracycline (TC) is a broad-spectrum antibiotic produced, indicated for use against many bacterial infections. In the present research, a systematic study of the adsorption and release process of tetracycline on GO was performed by varying pH, sorption time and temperature. The results of our studies showed that tetracycline strongly loads on the GO surface via π-π interaction and cation-π bonding. Investigation of TC adsorption kinetics showed that the equilibrium was reached within 15 min following the pseudo-second-order model with observed rate constants of k2 = 0.2742-0.5362 g/mg min (at different temperatures). The sorption data has interpreted by the Langmuir model with the maximum adsorption of 323 mg/g (298 K). The mean energy of adsorption was determined 1.83 kJ/mol (298 K) based on the Dubinin-Radushkevich (D-R) adsorption isotherm. Moreover, the thermodynamic parameters such as ΔH°, ΔS° and ΔG° values for the adsorption were estimated which indicated the endothermic and spontaneous nature of the sorption process. The electrochemistry approved an ideal reaction for the adsorption under electrodic process. Simulation of GO and TC was done by LAMMPS. Force studies in z direction showed that tetracycline comes close to GO sheet by C8 direction. Then it goes far and turns and again comes close from amine group to the GO sheet.

Microbial diversity arising from thermodynamic constraints

PubMed Central

Großkopf, Tobias; Soyer, Orkun S

2016-01-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

Study on the interaction mechanism between aromatic amino acids and quercetin

NASA Astrophysics Data System (ADS)

Gou, Xingxing; Pu, Xiaohua; Li, Zongxiao

2017-11-01

In this paper, we selected quercetin and aromatic amino acids (tryptophan, tyrosine, phenylalanine) as the research objects to investigate the change rules in the reaction process. The thermodynamic functions (Ka, Δ G, and Δ S) of the interactions between quercetin and aromatic amino acids (tryptophan, tyrosine, phenylalanine) were measured by isothermal titration calorimetry. The values of binding constant (Ka) reached maximum at 25°C; the entropies and Gibbs free energies were both negative at different temperatures. The kinetic parameters of quercetin and amino acids in the interaction process was determined by microcalorimetry. The results inferred that the driving force of the reaction was hydrogen bond or van der Waals force.

Thermodynamics and statistical mechanics. [thermodynamic properties of gases

NASA Technical Reports Server (NTRS)

1976-01-01

The basic thermodynamic properties of gases are reviewed and the relations between them are derived from the first and second laws. The elements of statistical mechanics are then formulated and the partition function is derived. The classical form of the partition function is used to obtain the Maxwell-Boltzmann distribution of kinetic energies in the gas phase and the equipartition of energy theorem is given in its most general form. The thermodynamic properties are all derived as functions of the partition function. Quantum statistics are reviewed briefly and the differences between the Boltzmann distribution function for classical particles and the Fermi-Dirac and Bose-Einstein distributions for quantum particles are discussed.

Thermodynamic behavior of glassy state of structurally related compounds.

PubMed

Kaushal, Aditya Mohan; Bansal, Arvind Kumar

2008-08-01

Thermodynamic properties of amorphous pharmaceutical forms are responsible for enhanced solubility as well as poor physical stability. The present study was designed to investigate the differences in thermodynamic parameters arising out of disparate molecular structures and associations for four structurally related pharmaceutical compounds--celecoxib, valdecoxib, rofecoxib, and etoricoxib. Conventional and modulated temperature differential scanning calorimetry were employed to study glass forming ability and thermodynamic behavior of the glassy state of model compounds. Glass transition temperature of four glassy compounds was in a close range of 327.6-331.8 K, however, other thermodynamic parameters varied considerably. Kauzmann temperature, strength parameter and fragility parameter showed rofecoxib glass to be most fragile of the four compounds. Glass forming ability of the compounds fared similar in the critical cooling rate experiments, suggesting that different factors were determining the glass forming ability and subsequent behavior of the compounds in glassy state. A comprehensive understanding of such thermodynamic facets of amorphous form would help in rationalizing the approaches towards development of stable glassy pharmaceuticals.

Modeling biosorption of Cr(VI) onto Ulva compressa L. from aqueous solutions.

PubMed

Aid, Asma; Amokrane, Samira; Nibou, Djamel; Mekatel, Elhadj; Trari, Mohamed; Hulea, Vasile

2018-01-01

The marine biomass Ulva compressa L. (ECL) was used as a low-cost biosorbent for the removal of Cr(VI) from contaminated aqueous solutions. The operating variables were optimized: pH ∼ 2, initial concentration of 25 mg/L, solid/liquid ratio of 6 g/L and a temperature of 50 °C, leading to an uptake elimination of 96%. A full factorial experimental design technique enabled us to obtain a mathematical model describing the Cr(VI) biosorption and to study the main effects and interactions among operational parameters. The equilibrium isotherm was analyzed by the Langmuir, Freundlich and Dubinin-Radushkevich (D-R) models; it has been found that the adsorption process follows well the Langmuir model. Kinetic studies showed that the pseudo-second order model describes suitably the experimental data. The thermodynamic parameters indicated an endothermic heat and a spontaneity of the Cr(VI) biosorption onto ECL.

Kinetics of calcium oxalate crystal formation in urine.

PubMed

Laube, Norbert; Klein, Florian; Bernsmann, Falk

2017-04-01

It is routinely observed that persons with increased urinary stone risk factors do not necessarily form uroliths. Furthermore, stone formers can present with urinalyses that do not reflect the clinical picture. We explain this discrepancy by differences in crystallization kinetics. In 1162 urines, crystallization of Ca-oxalate was induced according to the BONN-Risk-Index (BRI) method. The urine's relative light transmissivity (RLT) was recorded from 100 % at start of titration to 95 % due to nuclei formation and crystal growth. From the RLT changes, a measure of the thermodynamic inhibition threshold of crystal formation (BRI) and of crystal growth kinetics is derived ("turbidity slope" after crystallization onset). On average, subjects presenting with a low inhibition threshold, i.e., high BRI, also present significantly higher crystal growth rates compared with subjects in lower BRI classes. Only subjects in the highest BRI class show a lower growth rate than expected, probably due to a depletion of supersaturation by massive initial nucleation. With increasing thermodynamic risk of crystal formation (i.e., increasing BRI) due to an imbalance between inhibitors and promoters of crystal formation, an increase in the imbalance between inhibitors and promoters of crystal growth (i.e., increasing growth rate) is observed. Both lead to an increased urolith formation risk. Healthy subjects with increased BRI are an exception to this trend: their urine is thermodynamically prone to form stones, but they show a kinetic inhibition preventing nuclei from significant growth.

[Progress in Raman spectroscopic measurement of methane hydrate].

PubMed

Xu, Feng; Zhu, Li-hua; Wu, Qiang; Xu, Long-jun

2009-09-01

Complex thermodynamics and kinetics problems are involved in the methane hydrate formation and decomposition, and these problems are crucial to understanding the mechanisms of hydrate formation and hydrate decomposition. However, it was difficult to accurately obtain such information due to the difficulty of measurement since methane hydrate is only stable under low temperature and high pressure condition, and until recent years, methane hydrate has been measured in situ using Raman spectroscopy. Raman spectroscopy, a non-destructive and non-invasive technique, is used to study vibrational modes of molecules. Studies of methane hydrate using Raman spectroscopy have been developed over the last decade. The Raman spectra of CH4 in vapor phase and in hydrate phase are presented in this paper. The progress in the research on methane hydrate formation thermodynamics, formation kinetics, decomposition kinetics and decomposition mechanism based on Raman spectroscopic measurements in the laboratory and deep sea are reviewed. Formation thermodynamic studies, including in situ observation of formation condition of methane hydrate, analysis of structure, and determination of hydrate cage occupancy and hydration numbers by using Raman spectroscopy, are emphasized. In the aspect of formation kinetics, research on variation in hydrate cage amount and methane concentration in water during the growth of hydrate using Raman spectroscopy is also introduced. For the methane hydrate decomposition, the investigation associated with decomposition mechanism, the mutative law of cage occupancy ratio and the formulation of decomposition rate in porous media are described. The important aspects for future hydrate research based on Raman spectroscopy are discussed.

Equation of State of Detonation Products for TNT by Aquarium Technique

NASA Astrophysics Data System (ADS)

Han, Yong

2017-06-01

During explosive detonation, the detonation pressure (P) and temperature (T) will decay quickly with the expansion of detonation products, and the damage effect is determined by the thermodynamic state of detonation products under high pressure. The traditional and important method for calibrating the parameters of thermodynamic state is cylinder test, but the results showed that when the cylinder expanded to a certain distance, the cylinder wall would break up and the detonation products would jet out, which would affect the accuracy of the calibration parameters of thermodynamic state. In this paper, the aquarium technique was used to study the detonation product thermodynamic state of TNT explosive, obtaining the shock wave track under the water and the trace of the interface between water and detonation products in the specific position with the high speed rotating mirror camera. By thermodynamic calculation program BKW and VHL, the parameters of equation of state were obtained. Using the parameters and the dynamic software LS-DYNA, the underwater explosion of TNT was simulated. Comparison with experimental results shows that the thermodynamic state parameters which is calculated by VHL is more accurate than that of BKW. It is concluded that the aquarium test is a more effective method to calibrate the thermodynamic state than cylinder test.

Modeling brine-rock interactions in an enhanced geothermal systemdeep fractured reservoir at Soultz-Sous-Forets (France): a joint approachusing two geochemical codes: frachem and toughreact

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

Andre, Laurent; Spycher, Nicolas; Xu, Tianfu

The modeling of coupled thermal, hydrological, and chemical (THC) processes in geothermal systems is complicated by reservoir conditions such as high temperatures, elevated pressures and sometimes the high salinity of the formation fluid. Coupled THC models have been developed and applied to the study of enhanced geothermal systems (EGS) to forecast the long-term evolution of reservoir properties and to determine how fluid circulation within a fractured reservoir can modify its rock properties. In this study, two simulators, FRACHEM and TOUGHREACT, specifically developed to investigate EGS, were applied to model the same geothermal reservoir and to forecast reservoir evolution using theirmore » respective thermodynamic and kinetic input data. First, we report the specifics of each of these two codes regarding the calculation of activity coefficients, equilibrium constants and mineral reaction rates. Comparisons of simulation results are then made for a Soultz-type geothermal fluid (ionic strength {approx}1.8 molal), with a recent (unreleased) version of TOUGHREACT using either an extended Debye-Hueckel or Pitzer model for calculating activity coefficients, and FRACHEM using the Pitzer model as well. Despite somewhat different calculation approaches and methodologies, we observe a reasonably good agreement for most of the investigated factors. Differences in the calculation schemes typically produce less difference in model outputs than differences in input thermodynamic and kinetic data, with model results being particularly sensitive to differences in ion-interaction parameters for activity coefficient models. Differences in input thermodynamic equilibrium constants, activity coefficients, and kinetics data yield differences in calculated pH and in predicted mineral precipitation behavior and reservoir-porosity evolution. When numerically cooling a Soultz-type geothermal fluid from 200 C (initially equilibrated with calcite at pH 4.9) to 20 C and suppressing mineral precipitation, pH values calculated with FRACHEM and TOUGHREACT/Debye-Hueckel decrease by up to half a pH unit, whereas pH values calculated with TOUGHREACT/Pitzer increase by a similar amount. As a result of these differences, calcite solubilities computed using the Pitzer formalism (the more accurate approach) are up to about 1.5 orders of magnitude lower. Because of differences in Pitzer ion-interaction parameters, the calcite solubility computed with TOUGHREACT/Pitzer is also typically about 0.5 orders of magnitude lower than that computed with FRACHEM, with the latter expected to be most accurate. In a second part of this investigation, both models were applied to model the evolution of a Soultz-type geothermal reservoir under high pressure and temperature conditions. By specifying initial conditions reflecting a reservoir fluid saturated with respect to calcite (a reasonable assumption based on field data), we found that THC reservoir simulations with the three models yield similar results, including similar trends and amounts of reservoir porosity decrease over time, thus pointing to the importance of model conceptualization. This study also highlights the critical effect of input thermodynamic data on the results of reactive transport simulations, most particularly for systems involving brines.« less

Nonequilibrium thermodynamics and energy efficiency in weight loss diets.

PubMed

Feinman, Richard D; Fine, Eugene J

2007-07-30

Carbohydrate restriction as a strategy for control of obesity is based on two effects: a behavioral effect, spontaneous reduction in caloric intake and a metabolic effect, an apparent reduction in energy efficiency, greater weight loss per calorie consumed. Variable energy efficiency is established in many contexts (hormonal imbalance, weight regain and knock-out experiments in animal models), but in the area of the effect of macronutrient composition on weight loss, controversy remains. Resistance to the idea comes from a perception that variable weight loss on isocaloric diets would somehow violate the laws of thermodynamics, that is, only caloric intake is important ("a calorie is a calorie"). Previous explanations of how the phenomenon occurs, based on equilibrium thermodynamics, emphasized the inefficiencies introduced by substrate cycling and requirements for increased gluconeogenesis. Living systems, however, are maintained far from equilibrium, and metabolism is controlled by the regulation of the rates of enzymatic reactions. The principles of nonequilibrium thermodynamics which emphasize kinetic fluxes as well as thermodynamic forces should therefore also be considered. Here we review the principles of nonequilibrium thermodynamics and provide an approach to the problem of maintenance and change in body mass by recasting the problem of TAG accumulation and breakdown in the adipocyte in the language of nonequilibrium thermodynamics. We describe adipocyte physiology in terms of cycling between an efficient storage mode and a dissipative mode. Experimentally, this is measured in the rate of fatty acid flux and fatty acid oxidation. Hormonal levels controlled by changes in dietary carbohydrate regulate the relative contributions of the efficient and dissipative parts of the cycle. While no experiment exists that measures all relevant variables, the model is supported by evidence in the literature that 1) dietary carbohydrate, via its effect on hormone levels controls fatty acid flux and oxidation, 2) the rate of lipolysis is a primary target of insulin, postprandial, and 3) chronic carbohydrate-restricted diets reduce the levels of plasma TAG in response to a single meal. In summary, we propose that, in isocaloric diets of different macronutrient composition, there is variable flux of stored TAG controlled by the kinetic effects of insulin and other hormones. Because the fatty acid-TAG cycle never comes to equilibrium, net gain or loss is possible. The greater weight loss on carbohydrate restricted diets, popularly referred to as metabolic advantage can thus be understood in terms of the principles of nonequilibrium thermodynamics and is a consequence of the dynamic nature of bioenergetics where it is important to consider kinetic as well as thermodynamic variables.

Nonequilibrium thermodynamics and energy efficiency in weight loss diets

PubMed Central

Feinman, Richard D; Fine, Eugene J

2007-01-01

Carbohydrate restriction as a strategy for control of obesity is based on two effects: a behavioral effect, spontaneous reduction in caloric intake and a metabolic effect, an apparent reduction in energy efficiency, greater weight loss per calorie consumed. Variable energy efficiency is established in many contexts (hormonal imbalance, weight regain and knock-out experiments in animal models), but in the area of the effect of macronutrient composition on weight loss, controversy remains. Resistance to the idea comes from a perception that variable weight loss on isocaloric diets would somehow violate the laws of thermodynamics, that is, only caloric intake is important ("a calorie is a calorie"). Previous explanations of how the phenomenon occurs, based on equilibrium thermodynamics, emphasized the inefficiencies introduced by substrate cycling and requirements for increased gluconeogenesis. Living systems, however, are maintained far from equilibrium, and metabolism is controlled by the regulation of the rates of enzymatic reactions. The principles of nonequilibrium thermodynamics which emphasize kinetic fluxes as well as thermodynamic forces should therefore also be considered. Here we review the principles of nonequilibrium thermodynamics and provide an approach to the problem of maintenance and change in body mass by recasting the problem of TAG accumulation and breakdown in the adipocyte in the language of nonequilibrium thermodynamics. We describe adipocyte physiology in terms of cycling between an efficient storage mode and a dissipative mode. Experimentally, this is measured in the rate of fatty acid flux and fatty acid oxidation. Hormonal levels controlled by changes in dietary carbohydrate regulate the relative contributions of the efficient and dissipative parts of the cycle. While no experiment exists that measures all relevant variables, the model is supported by evidence in the literature that 1) dietary carbohydrate, via its effect on hormone levels controls fatty acid flux and oxidation, 2) the rate of lipolysis is a primary target of insulin, postprandial, and 3) chronic carbohydrate-restricted diets reduce the levels of plasma TAG in response to a single meal. In summary, we propose that, in isocaloric diets of different macronutrient composition, there is variable flux of stored TAG controlled by the kinetic effects of insulin and other hormones. Because the fatty acid-TAG cycle never comes to equilibrium, net gain or loss is possible. The greater weight loss on carbohydrate restricted diets, popularly referred to as metabolic advantage can thus be understood in terms of the principles of nonequilibrium thermodynamics and is a consequence of the dynamic nature of bioenergetics where it is important to consider kinetic as well as thermodynamic variables. PMID:17663761

Classical Example of Total Kinetic and Thermodynamic Control: The Diels-Alder Reaction between DMAD and Bis-furyl Dienes.

PubMed

Borisova, Kseniya K; Kvyatkovskaya, Elizaveta A; Nikitina, Eugeniya V; Aysin, Rinat R; Novikov, Roman A; Zubkov, Fedor I

2018-04-20

A rare example of chemospecificity in the tandem Diels-Alder reaction of activated alkynes and bis-dienes has been revealed. The reaction between bis-furyl dienes and DMAD occurs at 25-80 °C and leads to kinetically controlled "pincer" adducts, 4a,8a-disubstituted 1,4:5,8-diepoxynaphthalenes. On the contrary, only thermodynamically controlled "domino" adducts (2,3-disubstituted 1,4:5,8-diepoxynaphthalenes) are formed in the same reaction at 140 °C. The "pincer" adducts can be transformed to the "domino" adducts at heating. The rate constants for reactions of both types were calculated using dynamic 1 H NMR spectroscopy.

Origin of fatty acid synthesis - Thermodynamics and kinetics of reaction pathways

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

1991-01-01

The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, an alternative pathway of primitive fatty acid synthesis is proposed that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy. Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.