Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

Science.gov (United States)

Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

2011-06-09

Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

Kinetics of current formation in molecular diode

International Nuclear Information System (INIS)

Petrov, Eh.G.; Leonov, V.A.; Shevchenko, E.V.

2012-01-01

Based on the kinetic theory of election transfer in low-dimensional molecular systems, the formation of transient and stationary currents in a system 'electrode l-molecule-electrode 2' (molecular diode) is studied for different regimes of charge transmission. In the framework of the HOMO-LUMO molecular model, a situation is considered where the current formation is initiated either by molecule photoexcitation or by change of interelectrode voltage bias. It is found that the distant (tunnel) inelastic electron transfer plays a crucial role in changing molecular electronic states and, as a result, in generating transmission channels for hopping (sequential) and distant (direct) current components. The effect of inelastic tunneling is especially pronounced in the condition of resonant electron transmission.

Active mechanics in living oocytes reveal molecular-scale force kinetics

Science.gov (United States)

Ahmed, Wylie; Fodor, Etienne; Almonacid, Maria; Bussonnier, Matthias; Verlhac, Marie-Helene; Gov, Nir; Visco, Paolo; van Wijland, Frederic; Betz, Timo

Unlike traditional materials, living cells actively generate forces at the molecular scale that change their structure and mechanical properties. This nonequilibrium activity is essential for cellular function, and drives processes such as cell division. Single molecule studies have uncovered the detailed force kinetics of isolated motor proteins in-vitro, however their behavior in-vivo has been elusive due to the complex environment inside the cell. Here, we quantify active forces and intracellular mechanics in living oocytes using in-vivo optical trapping and laser interferometry of endogenous vesicles. We integrate an experimental and theoretical framework to connect mesoscopic measurements of nonequilibrium properties to the underlying molecular- scale force kinetics. Our results show that force generation by myosin-V drives the cytoplasmic-skeleton out-of-equilibrium (at frequencies below 300 Hz) and actively softens the environment. In vivo myosin-V activity generates a force of F ~ 0 . 4 pN, with a power-stroke of length Δx ~ 20 nm and duration τ ~ 300 μs, that drives vesicle motion at vv ~ 320 nm/s. This framework is widely applicable to characterize living cells and other soft active materials.

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

Science.gov (United States)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-02-01

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

Kinetic methods for measuring the temperature of clusters and nanoparticles in molecular beams

International Nuclear Information System (INIS)

Makarov, Grigorii N

2011-01-01

The temperature (internal energy) of clusters and nanoparticles is an important physical parameter which affects many of their properties and the character of processes they are involved in. At the same time, determining the temperature of free clusters and nanoparticles in molecular beams is a rather complicated problem because the temperature of small particles depends on their size. In this paper, recently developed kinetic methods for measuring the temperature of clusters and nanoparticles in molecular beams are reviewed. The definition of temperature in the present context is given, and how the temperature affects the properties of and the processes involving the particles is discussed. The temperature behavior of clusters and nanoparticles near a phase transition point is analyzed. Early methods for measuring the temperature of large clusters are briefly described. It is shown that, compared to other methods, new kinetic methods are more universal and applicable for determining the temperature of clusters and nanoparticles of practically any size and composition. The future development and applications of these methods are outlined. (reviews of topical problems)

Molecular processes in cellular arsenic metabolism

International Nuclear Information System (INIS)

Thomas, David J.

2007-01-01

Elucidating molecular processes that underlie accumulation, metabolism and binding of iAs and its methylated metabolites provides a basis for understanding the modes of action by which iAs acts as a toxin and a carcinogen. One approach to this problem is to construct a conceptual model that incorporates available information on molecular processes involved in the influx, metabolism, binding and efflux of arsenicals in cells. This conceptual model is initially conceived as a non-quantitative representation of critical molecular processes that can be used as a framework for experimental design and prediction. However, with refinement and incorporation of additional data, the conceptual model can be expressed in mathematical terms and should be useful for quantitative estimates of the kinetic and dynamic behavior of iAs and its methylated metabolites in cells. Development of a quantitative model will be facilitated by the availability of tools and techniques to manipulate molecular processes underlying transport of arsenicals across cell membranes or expression and activity of enzymes involved in methylation of arsenicals. This model of cellular metabolism might be integrated into more complex pharmacokinetic models for systemic metabolism of iAs and its methylated metabolites. It may also be useful in development of biologically based dose-response models describing the toxic and carcinogenic actions of arsenicals

A Similarity Search Using Molecular Topological Graphs

Directory of Open Access Journals (Sweden)

Yoshifumi Fukunishi

2009-01-01

Full Text Available A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

Science.gov (United States)

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermodynamics and kinetics of vesicles formation processes.

Science.gov (United States)

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.

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

Science.gov (United States)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-02-15

Large scale of steam flaked corn has been used in dairy ration to maintain high milk production level. This study aimed to determine effects of steam flaking on processing-induced intrinsic molecular structure changes that were associated with rumen degradation kinetics and nutrients supply. The advanced vibrational molecular spectroscopy was applied to reveal the processing-induced intrinsic structure changes on a molecular basis. The rumen degradation kinetics and nutrient supply were determined using in situ approach in ruminant livestock system. Raw corn grain (RC) and steam flaked corn grain (SFC) were obtained from two different processing plants. The results showed that (1) Compared to RC, SFC had greater truly digestible non-fiber carbohydrate [tdNFC: 86.8 versus 78.0% dry matter (DM)], but lower truly digestible crude protein [tdCP: 7.7 versus 9.0% DM]. (2) The steam flaking increased (PMolecular absorbance intensities of most carbohydrate biopolymers were greater in SFC (Pmolecular spectral intensities were lower (Pmolecular structure and nutrient interactive study showed that carbohydrate spectral intensities were positively (Pmolecular structure changes had an interactive relationship with rumen degradation kinetics. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

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Kai-Jun Yuan

2015-01-01

Full Text Available We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented.

Molecular alignment dependent electron interference in attosecond ultraviolet photoionization

Science.gov (United States)

Yuan, Kai-Jun; Bandrauk, André D.

2015-01-01

We present molecular photoionization processes by intense attosecond ultraviolet laser pulses from numerical solutions of time-dependent Schrödinger equations. Simulations preformed on a single electron diatomic H2+ show minima in molecular photoelectron energy spectra resulting from two center interference effects which depend strongly on molecular alignment. We attribute such sensitivity to the spatial orientation asymmetry of the photoionization process from the two nuclei. A similar influence on photoelectron kinetic energies is also presented. PMID:26798785

Effects of molecular confinement and crowding on horseradish peroxidase kinetics using a nanofluidic gradient mixer.

Science.gov (United States)

Wichert, William R A; Han, Donghoon; Bohn, Paul W

2016-03-07

The effects of molecular confinement and crowding on enzyme kinetics were studied at length scales and under conditions similar to those found in biological cells. These experiments were carried out using a nanofluidic network of channels constituting a nanofluidic gradient mixer, providing the basis for measuring multiple experimental conditions simultaneously. The 100 nm × 40 μm nanochannels were wet etched directly into borosilicate glass, then annealed and characterized with fluorescein emission prior to kinetic measurements. The nanofluidic gradient mixer was then used to measure the kinetics of the conversion of the horseradish peroxidase (HRP)-catalyzed conversion of non-fluorescent Amplex Red (AR) to the fluorescent product resorufin in the presence of hydrogen peroxide (H2O2). The design of the gradient mixer allows reaction kinetics to be studied under multiple (five) unique solution compositions in a single experiment. To characterize the efficiency of the device the effects of confinement on HRP-catalyzed AR conversion kinetics were studied by varying the starting ratio of AR : H2O2. Equimolar concentrations of Amplex Red and H2O2 yielded the highest reaction rates followed by 2 : 1, 1 : 2, 5 : 1, and finally 1 : 5 [AR] : [H2O2]. Under all conditions, initial reaction velocities were decreased by excess H2O2. Crowding effects on kinetics were studied by increasing solution viscosity in the nanochannels in the range 1.0-1.6 cP with sucrose. Increasing the solution viscosities in these confined geometries decreases the initial reaction velocity at the highest concentration from 3.79 μM min(-1) at 1.00 cP to 0.192 μM min(-1) at 1.59 cP. Variations in reaction velocity are interpreted in the context of models for HRP catalysis and for molecular crowding.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

Science.gov (United States)

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Development of the kinetic molecular theory of gases concept inventory: Preliminary results on university students’ misconceptions

Directory of Open Access Journals (Sweden)

Nataša Erceg

2016-11-01

Full Text Available In this study, we investigated students’ understanding of concepts related to the microscopic model of gas. We thoroughly reviewed the relevant literature and conducted think alouds with students by asking them to answer open-ended questions about the kinetic molecular theory of gases. Thereafter, we transformed the open-ended questions into multiple-choice questions, whereby distractors were based on the results of the think alouds. Thus, we obtained a set of 22 questions, which constitutes our current version of the kinetic molecular theory of gases concept inventory. The inventory has been administered to 250 students from different universities in Croatia, and its content validity has been investigated trough physics teacher surveys. The results of our study not only corroborate the existence of some already known student misconceptions, but also reveal new insights about a great spectrum of students’ misconceptions that had not been reported in earlier research (e.g., misconceptions about intermolecular potential energy and molecular velocity distribution. Moreover, we identified similar distribution of students’ responses across the surveyed student groups, despite the fact that they had been enrolled in different curricular environments.

Molecularly Imprinted Polymers: Thermodynamic and Kinetic Considerations on the Specific Sorption and Molecular Recognition

Directory of Open Access Journals (Sweden)

Kejun Tong

2008-04-01

Full Text Available This article presents a work aiming at thermodynamically and kinetically interpreting the specific sorption and recognition by a molecularly imprinted polymer. Using Boc-L-Phe-OH as a template, the imprinted material was prepared. The result indicates that the prepared polymer can well discriminate the imprint species from its analogue (Boc-D-Phe-OH, so as to adsorb more for the former but less for the latter. Kinetic analysis indicates that this specific sorption, in nature, can be a result of a preferential promotion. The imprint within the polymer causes a larger adsorption rate for the template than for the analogue. Thermodynamic study also implies that the molecular induction from the specific imprint to the template is larger than to the analogue, which thus makes the polymer capable of preferentially alluring the template to bind.

Kinetic study of solid-state processes

International Nuclear Information System (INIS)

Malek, Jiri; Mitsuhashi, Takefumi

2003-01-01

A simple method for kinetic analysis of solid-state processes has been developed and the criteria capable of classifying different processes are explored. They provide a useful tool for the determination of the most suitable kinetic model. The method has been applied to the analysis of calorimetric data corresponding to the crystallization processes in amorphous ZrO 2 . It is found that the crystallization kinetics of amorphous powder sample exhibits a complex behavior under non-isothermal conditions. A two-parameter model provides a satisfactory description of the crystallization process for isothermal and non-isothermal conditions. This enables better control of crystallization extent in fine ZrO 2 powders that is important for preparation of zirconia ceramics with defined properties. (author)

PECULIARITIES OF GENERALIZATION OF SIMILAR PHENOMENA IN THE PROCESS OF FISH HEAT TREATMENT

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V. A. Pokhol’chenko

2015-01-01

Full Text Available The theoretical presuppositions for the possibility of generalizing and similarity founding in dehydration and wet materials heating processes are studieded in this article. It is offered to carry out the given processes generalization by using dimensionless numbers of similarity. At the detailed analyzing of regularities of heat treatment processes of fish in different modes a significant amount of experienced material was successfully generalized on the basis of dimensionless simplex (similarity numbers. Using the dimensionless simplex allowed to detect a number of simple mathematical models for the studied phenomena. The generalized kinetic models of fish dehydration, the generalized dynamic models (changing moisture diffusion coefficients, the generalized kinetic models of fish heating (the temperature field changing in the products thickness, average volume and center were founded. These generalized mathematical models showed also relationship of dehydration and heating at the processes of fish semi-hot, hot smoking (drying and frying. The relationship of the results from the physical nature of the dehydration process, including a change in the binding energy of the moisture with the material to the extent of the process and the shrinkage impact on the rate of the product moisture removal is given in the article. The factors influencing the internal structure and properties of the raw material changing and retarding the dehydration processes are described there. There was a heating rate dependence of fish products on the chemical composition the geometric dimensions of the object of heating and on the coolant regime parameters. A unique opportunity is opened by using the generalized models, combined with empirically derived equations and the technique of engineering calculation of these processes, to design a rational modes of heat treatment of raw materials and to optimize the performance of thermal equipment.

Detectable states, cycle fluxes, and motility scaling of molecular motor kinesin: An integrative kinetic graph theory analysis

Science.gov (United States)

Ren, Jie

2017-12-01

The process by which a kinesin motor couples its ATPase activity with concerted mechanical hand-over-hand steps is a foremost topic of molecular motor physics. Two major routes toward elucidating kinesin mechanisms are the motility performance characterization of velocity and run length, and single-molecular state detection experiments. However, these two sets of experimental approaches are largely uncoupled to date. Here, we introduce an integrative motility state analysis based on a theorized kinetic graph theory for kinesin, which, on one hand, is validated by a wealth of accumulated motility data, and, on the other hand, allows for rigorous quantification of state occurrences and chemomechanical cycling probabilities. An interesting linear scaling for kinesin motility performance across species is discussed as well. An integrative kinetic graph theory analysis provides a powerful tool to bridge motility and state characterization experiments, so as to forge a unified effort for the elucidation of the working mechanisms of molecular motors.

New Methods for Processing and Quantifying VO2 Kinetics to Steady State: VO2 Onset Kinetics

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Craig R. McNulty

2017-09-01

Full Text Available Current methods of oxygen uptake (VO2 kinetics data handling may be too simplistic for the complex physiology involved in the underlying physiological processes. Therefore, the aim of this study was to quantify the VO2 kinetics to steady state across the full range of sub-ventilatory threshold work rates, with a particular focus on the VO2 onset kinetics. Ten healthy, moderately trained males participated in five bouts of cycling. Each bout involved 10 min at a percentage of the subject's ventilation threshold (30, 45, 60, 75, 90% from unloaded cycling. The VO2 kinetics was quantified using the conventional mono-exponential time constant (tau, τ, as well as the new methods for VO2 onset kinetics. Compared to linear modeling, non-linear modeling caused a deterioration of goodness of fit (main effect, p < 0.001 across all exercise intensities. Remainder kinetics were also improved using a modified application of the mono-exponential model (main effect, p < 0.001. Interestingly, the slope from the linear regression of the onset kinetics data is similar across all subjects and absolute exercise intensities, and thereby independent of subject fitness and τ. This could indicate that there are no functional limitations between subjects during this onset phase, with limitations occurring for the latter transition to steady state. Finally, the continuing use of mono-exponential modeling could mask important underlying physiology of more instantaneous VO2 responses to steady state. Consequently, further research should be conducted on this new approach to VO2 onset kinetics.

Isoconversional kinetics of thermally stimulated processes

CERN Document Server

Vyazovkin, Sergey

2015-01-01

The use of isoconversional kinetic methods for analysis of thermogravimetric and calorimetric data on thermally stimulated processes is quickly growing in popularity. The purpose of this book is to create the first comprehensive resource on the theory and applications of isoconversional methodology. The book introduces the reader to the kinetics of physical and chemical condensed phase processes that occur as a result of changing temperature and discusses how isoconversional analysis can provide important kinetic insights into them. The book will help the readers to develop a better understanding of the methodology, and promote its efficient usage and successful development.

Molecular modeling of the microstructure evolution during carbon fiber processing

Science.gov (United States)

Desai, Saaketh; Li, Chunyu; Shen, Tongtong; Strachan, Alejandro

2017-12-01

The rational design of carbon fibers with desired properties requires quantitative relationships between the processing conditions, microstructure, and resulting properties. We developed a molecular model that combines kinetic Monte Carlo and molecular dynamics techniques to predict the microstructure evolution during the processes of carbonization and graphitization of polyacrylonitrile (PAN)-based carbon fibers. The model accurately predicts the cross-sectional microstructure of the fibers with the molecular structure of the stabilized PAN fibers and physics-based chemical reaction rates as the only inputs. The resulting structures exhibit key features observed in electron microcopy studies such as curved graphitic sheets and hairpin structures. In addition, computed X-ray diffraction patterns are in good agreement with experiments. We predict the transverse moduli of the resulting fibers between 1 GPa and 5 GPa, in good agreement with experimental results for high modulus fibers and slightly lower than those of high-strength fibers. The transverse modulus is governed by sliding between graphitic sheets, and the relatively low value for the predicted microstructures can be attributed to their perfect longitudinal texture. Finally, the simulations provide insight into the relationships between chemical kinetics and the final microstructure; we observe that high reaction rates result in porous structures with lower moduli.

Kinetics and Thermodynamics of Flexographic-plate Polymer Interaction With Low-molecular Liquids

Directory of Open Access Journals (Sweden)

Akaky Dzhvarsheyshvili

2007-11-01

Full Text Available Flexographic printing plates contact solvents in the process of their production and operation: washing solvents and printing paint components. As a results of such contact plates swell. Swelling changes polymers’ elastic properties of which the plate is made, changes the scan point sizes that, in the final analysis, affects the printing product quality. The kinetics of swelling flexographic plate polymer interaction with low-molecular liquids used in the process of plate production and operation was studied. Constants of speed, parameters Flory - Huggins, diffusion coefficient D for each solvent was determined. The changes of the basic thermodynamic functions ΔG, ΔS, ΔH of swelling, are calculated. The received data allow to choose the optimum solvents for processes of polygraphic technology.

Textual and chemical information processing: different domains but similar algorithms

Directory of Open Access Journals (Sweden)

Peter Willett

2000-01-01

Full Text Available This paper discusses the extent to which algorithms developed for the processing of textual databases are also applicable to the processing of chemical structure databases, and vice versa. Applications discussed include: an algorithm for distribution sorting that has been applied to the design of screening systems for rapid chemical substructure searching; the use of measures of inter-molecular structural similarity for the analysis of hypertext graphs; a genetic algorithm for calculating term weights for relevance feedback searching for determining whether a molecule is likely to exhibit biological activity; and the use of data fusion to combine the results of different chemical similarity searches.

Transient processes in cell proliferation kinetics

CERN Document Server

Yakovlev, Andrej Yu

1989-01-01

A mathematician who has taken the romantic decision to devote himself to biology will doubtlessly look upon cell kinetics as the most simple and natural field of application for his knowledge and skills. Indeed, the thesaurus he is to master is not so complicated as, say, in molecular biology, the structural elements of the system, i. e. ceils, have been segregated by Nature itself, simple considerations of balance may be used for deducing basic equations, and numerous analogies in other areas of science also superficial add to one"s confidence. Generally speaking, this number of impression is correct, as evidenced by the very great theoretical studies on population kinetics, unmatched in other branches of mathematical biology. This, however, does not mean that mathematical theory of cell systems has traversed in its development a pathway free of difficulties or errors. The seeming ease of formalizing the phenomena of cell kinetics not infrequently led to the appearance of mathematical models lacking in adequ...

Chemical kinetics and oil shale process design

Energy Technology Data Exchange (ETDEWEB)

Burnham, A.K.

1993-07-01

Oil shale processes are reviewed with the goal of showing how chemical kinetics influences the design and operation of different processes for different types of oil shale. Reaction kinetics are presented for organic pyrolysis, carbon combustion, carbonate decomposition, and sulfur and nitrogen reactions.

A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

Science.gov (United States)

Simon, Sílvia; Duran, Miquel

1997-08-01

Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.

Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

Science.gov (United States)

Zhao, Lei; Cheng, Jiangtao

2017-09-07

In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

The interaction of C60 on Si(111 7x7 studied by Supersonic Molecular Beams: interplay between precursor kinetic energy and substrate temperature in surface activated processes.

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Lucrezia eAversa

2015-06-01

Full Text Available Buckminsterfullerene (C60 is a molecule fully formed of carbon that can be used, owing to its electronic and mechanical properties, as clean precursor for the growth of carbon-based materials, ranging from -conjugated systems (graphenes to synthesized species, e.g. carbides such as silicon carbide (SiC. To this goal, C60 cage rupture is the main physical process that triggers material growth. Cage breaking can be obtained either thermally by heating up the substrate to high temperatures (630°C, after C60 physisorption, or kinetically by using Supersonic Molecular Beam Epitaxy (SuMBE techniques. In this work, aiming at demonstrating the growth of SiC thin films by C60 supersonic beams, we present the experimental investigation of C60 impacts on Si(111 7x7 kept at 500°C for translational kinetic energies ranging from 18 to 30 eV. The attained kinetically activated synthesis of SiC submonolayer films is probed by in-situ surface electron spectroscopies (XPS and UPS. Furthermore, in these experimental conditions the C60-Si(111 7×7 collision has been studied by computer simulations based on a tight-binding approximation to Density Functional Theory, DFT. Our theoretical and experimental findings point towards a kinetically driven growth of SiC on Si, where C60 precursor kinetic energy plays a crucial role, while temperature is relevant only after cage rupture to enhance Si and carbon reactivity. In particular, we observe a counterintuitive effect in which for low kinetic energy (below 22 eV, C60 bounces back without breaking more effectively at high temperature due to energy transfer from excited phonons. At higher kinetic energy (22 < K < 30 eV, for which cage rupture occurs, temperature enhances reactivity without playing a major role in the cage break. These results are in good agreement with ab-initio molecular dynamics simulations. SuMBE is thus a technique able to drive materials growth at low temperature regime.

Kinetics and mechanism of the biodegradation of PLA/clay nanocomposites during thermophilic phase of composting process.

Science.gov (United States)

Stloukal, Petr; Pekařová, Silvie; Kalendova, Alena; Mattausch, Hannelore; Laske, Stephan; Holzer, Clemens; Chitu, Livia; Bodner, Sabine; Maier, Guenther; Slouf, Miroslav; Koutny, Marek

2015-08-01

The degradation mechanism and kinetics of polylactic acid (PLA) nanocomposite films, containing various commercially available native or organo-modified montmorillonites (MMT) prepared by melt blending, were studied under composting conditions in thermophilic phase of process and during abiotic hydrolysis and compared to the pure polymer. Described first order kinetic models were applied on the data from individual experiments by using non-linear regression procedures to calculate parameters characterizing aerobic composting and abiotic hydrolysis, such as carbon mineralization, hydrolysis rate constants and the length of lag phase. The study showed that the addition of nanoclay enhanced the biodegradation of PLA nanocomposites under composting conditions, when compared with pure PLA, particularly by shortening the lag phase at the beginning of the process. Whereas the lag phase of pure PLA was observed within 27days, the onset of CO2 evolution for PLA with native MMT was detected after just 20days, and from 13 to 16days for PLA with organo-modified MMT. Similarly, the hydrolysis rate constants determined tended to be higher for PLA with organo-modified MMT, particularly for the sample PLA-10A with fastest degradation, in comparison with pure PLA. The acceleration of chain scission in PLA with nanoclays was confirmed by determining the resultant rate constants for the hydrolytical chain scission. The critical molecular weight for the hydrolysis of PLA was observed to be higher than the critical molecular weight for onset of PLA mineralization, suggesting that PLA chains must be further shortened so as to be assimilated by microorganisms. In conclusion, MMT fillers do not represent an obstacle to acceptance of the investigated materials in composting facilities. Copyright © 2015 Elsevier Ltd. All rights reserved.

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

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Fabrizio Marinelli

2009-08-01

Full Text Available Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

Kinetics of molecular transformations in connective tissue hyaluronic acid

International Nuclear Information System (INIS)

Phillips, G.O.

1990-01-01

When exposed to ionizing radiations or inflammatory disease, the glycosaminolycan component of connective tissue is preferentially degraded, probably by a free-radical mediate pathway. The resulting changes in molecular structure adversely change the properties of the matrix. Rooster comb hyaluronic acid of high molecular weight was used to investigate the mechanisms of these structural changes at macro and molecular level. Intrinsic viscosity and gel permeation chromatography measurements are suitable for demonstrating that random chain session occurs. Fast kinetic techniques are necessary to identify the mechanisms of single strand breaks. Pulse conductivity and low-angle laser light scattering pulse radiolysis can quantify the rate and yield of strand breaks. Competitive radical scavenging methods have also allowed the quantification of the rate of spontaneous and alkali-catalyzed hydrolysis of a-hydroxy radicals on polysaccharide chains, which control molecular structure changes

Kinetics of FeII-polyaminocarboxylate oxidation by molecular oxygen

Science.gov (United States)

Wilson, Jessica M.; Farley, Kevin J.; Carbonaro, Richard F.

2018-03-01

Complexation of iron by naturally-occurring and synthetic organic ligands has a large effect on iron oxidation and reduction rates which in turn affect the aqueous geochemistry of many other chemical constituents. In this study, the kinetics of FeII oxidation in the presence of the polyaminocarboxylate synthetic chelating agents ethylene glycol tetraacetic acid (EGTA) and trimethylenediamine-N,N,N‧,N‧-tetraacetic acid (TMDTA) was investigated over the pH range 5.50-8.53. Batch oxidation experiments in the presence of molecular oxygen were conducted using a 2:1 M concentration ratio of polyaminocarboxylate (ligand, L) to FeII. The experimental data resembled first order kinetics for the oxidation of FeII-L to FeIII-L and observed rate constants at pH 6.0 were comparable to rate constants for the oxidation of inorganic FeII. Similar to other structurally-similar FeII-polyaminocarboxylate complexes, oxidation rates of FeII-EGTA and FeII-TMDTA decrease with increasing pH, which is the opposite trend for the oxidation of FeII complexed with inorganic ligands. However, the oxidation rates of FeII complexed with EGTA and TMDTA were considerably lower (4-5 orders of magnitude) than FeII complexed to ethylenediaminetetraacetic acid (EDTA). The distinguishing feature of the slower-reacting complexes is that they have a longer backbone between diamine functional groups. An analytical equilibrium model was developed to determine the contributions of the species FeIIL2- and FeII(H)L- to the overall oxidation rate of FeII-L. Application of this model indicated that the protonated FeII(H)L species are more than three orders of magnitude more reactive than FeIIL2-. These rate constants were used in a coupled kinetic equilibrium numerical model where the ligand to iron ratio (TOTL:TOTFe) and pH were varied to evaluate the effect on the FeII oxidation rate. Overall, increasing TOTL:TOTFe for EGTA and TMDTA enhances FeII oxidation rates at lower pH and inhibits FeII oxidation

THE SURFACE-MEDIATED UNFOLDING KINETICS OF GLOBULAR PROTEINS IS DEPENDENT ON MOLECULAR WEIGHT AND TEMPERATURE

Energy Technology Data Exchange (ETDEWEB)

Patananan, A.N.; Goheen, S.C.

2008-01-01

The adsorption and unfolding pathways of proteins on rigid surfaces are essential in numerous complex processes associated with biomedical engineering, nanotechnology, and chromatography. It is now well accepted that the kinetics of unfolding are characterized by chemical and physical interactions dependent on protein deformability and structure, as well as environmental pH, temperature, and surface chemistry. Although this fundamental process has broad implications in medicine and industry, little is known about the mechanism because of the atomic lengths and rapid time scales involved. Therefore, the unfolding kinetics of myoglobin, β-glucosidase, and ovalbumin were investigated by adsorbing the globular proteins to non-porous cationic polymer beads. The protein fractions were adsorbed at different residence times (0, 9, 10, 20, and 30 min) at near-physiological conditions using a gradient elution system similar to that in high-performance liquid chromatography. The elution profi les and retention times were obtained by ultraviolet/visible spectrophotometry. A decrease in recovery was observed with time for almost all proteins and was attributed to irreversible protein unfolding on the non-porous surfaces. These data, and those of previous studies, fi t a positively increasing linear trend between percent unfolding after a fi xed (9 min) residence time (71.8%, 31.1%, and 32.1% of myoglobin, β-glucosidase, and ovalbumin, respectively) and molecular weight. Of all the proteins examined so far, only myoglobin deviated from this trend with higher than predicted unfolding rates. Myoglobin also exhibited an increase in retention time over a wide temperature range (0°C and 55°C, 4.39 min and 5.74 min, respectively) whereas ovalbumin and β-glucosidase did not. Further studies using a larger set of proteins are required to better understand the physiological and physiochemical implications of protein unfolding kinetics. This study confi rms that surface

Kinetic models for irreversible processes on a lattice

Energy Technology Data Exchange (ETDEWEB)

Wolf, N.O.

1979-04-01

The development and application of kinetic lattice models are considered. For the most part, the discussions are restricted to lattices in one-dimension. In Chapter 1, a brief overview of kinetic lattice model formalisms and an extensive literature survey are presented. A review of the kinetic models for non-cooperative lattice events is presented in Chapter 2. The development of cooperative lattice models and solution of the resulting kinetic equations for an infinite and a semi-infinite lattice are thoroughly discussed in Chapters 3 and 4. The cooperative models are then applied to the problem of theoretically dtermining the sticking coefficient for molecular chemisorption in Chapter 5. In Chapter 6, other possible applications of these models and several model generalizations are considered. Finally, in Chapter 7, an experimental study directed toward elucidating the mechanistic factors influencing the chemisorption of methane on single crystal tungsten is reported. In this it differs from the rest of the thesis which deals with the statistical distributions resulting from a given mechanism.

Kinetic models for irreversible processes on a lattice

International Nuclear Information System (INIS)

Wolf, N.O.

1979-04-01

The development and application of kinetic lattice models are considered. For the most part, the discussions are restricted to lattices in one-dimension. In Chapter 1, a brief overview of kinetic lattice model formalisms and an extensive literature survey are presented. A review of the kinetic models for non-cooperative lattice events is presented in Chapter 2. The development of cooperative lattice models and solution of the resulting kinetic equations for an infinite and a semi-infinite lattice are thoroughly discussed in Chapters 3 and 4. The cooperative models are then applied to the problem of theoretically dtermining the sticking coefficient for molecular chemisorption in Chapter 5. In Chapter 6, other possible applications of these models and several model generalizations are considered. Finally, in Chapter 7, an experimental study directed toward elucidating the mechanistic factors influencing the chemisorption of methane on single crystal tungsten is reported. In this it differs from the rest of the thesis which deals with the statistical distributions resulting from a given mechanism

Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

Science.gov (United States)

Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

2017-01-25

This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

Dynamic similarity in erosional processes

Science.gov (United States)

Scheidegger, A.E.

1963-01-01

A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

Comparison of molecular dynamics and kinetic modeling of gas-surface interactions

NARCIS (Netherlands)

Frezzotti, A.; Gaastra - Nedea, S.V.; Markvoort, A.J.; Spijker, P.; Gibelli, L.

2008-01-01

The interaction of a dilute monatomic gas with a solid surface is studied byMolecular Dynamics (MD) simulations and by numerical solutions of a recently proposed kinetic model. Following previous investigations, the heat transport between parallel walls and Couette flow have been adopted as test

Probing Interactions in Complex Molecular Systems through Ordered Assembly

International Nuclear Information System (INIS)

De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

2002-01-01

Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

Processes of Similarity Judgment

Science.gov (United States)

Larkey, Levi B.; Markman, Arthur B.

2005-01-01

Similarity underlies fundamental cognitive capabilities such as memory, categorization, decision making, problem solving, and reasoning. Although recent approaches to similarity appreciate the structure of mental representations, they differ in the processes posited to operate over these representations. We present an experiment that…

Modeling the kinetics of hydrates formation using phase field method under similar conditions of petroleum pipelines; Modelagem da cinetica de formacao de hidratos utilizando o Modelo do Campo de Fase em condicoes similares a dutos de petroleo

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Mabelle Biancardi; Castro, Jose Adilson de; Silva, Alexandre Jose da [Universidade Federal Fluminense (UFF), Volta Redonda, RJ (Brazil). Programa de Pos-Graduacao em Engenharia Metalurgica], e-mails: mabelle@metal.eeimvr.uff.br; adilson@metal.eeimvr.uff.br; ajs@metal.eeimvr.uff.br

2008-10-15

Natural hydrates are crystalline compounds that are ice-like formed under oil extraction transportation and processing. This paper deals with the kinetics of hydrate formation by using the phase field approach coupled with the transport equation of energy. The kinetic parameters of the hydrate formation were obtained by adjusting the proposed model to experimental results in similar conditions of oil extraction. The effect of thermal and nucleation conditions were investigated while the rate of formation and morphology were obtained by numerical computation. Model results of kinetics growth and morphology presented good agreement with the experimental ones. Simulation results indicated that super-cooling and pressure were decisive parameters for hydrates growth, morphology and interface thickness. (author)

AND PI (π) FROM THE KINETIC MOLECULAR THEORY OF MATTER

African Journals Online (AJOL)

DJFLEX

This paper considers the possible physical origins of the important natural constants epsilon (e = 2.7182 ) and pi (π = 3.1415 ). They are suggested to originate from the kinetic molecular nature of matter. Epsilon (e) is suggested to be the ratio of the driving force on a randomly moving particle accelerated with a quantum of ...

Generic Schemes for Single-Molecule Kinetics. 3: Self-Consistent Pathway Solutions for Nonrenewal Processes.

Science.gov (United States)

Piephoff, D Evan; Cao, Jianshu

2018-04-23

We recently developed a pathway analysis framework (paper 1) for describing single-molecule kinetics for renewal (i.e., memoryless) processes based on the decomposition of a kinetic scheme into generic structures. In our approach, waiting time distribution functions corresponding to such structures are expressed in terms of self-consistent pathway solutions and concatenated to form measurable probability distribution functions (PDFs), affording a simple way to decompose and recombine a network. Here, we extend this framework to nonrenewal processes, which involve correlations between events, and employ it to formulate waiting time PDFs, including the first-passage time PDF, for a general kinetic network model. Our technique does not require the assumption of Poissonian kinetics, permitting a more general kinetic description than the usual rate approach, with minimal topological restrictiveness. To demonstrate the usefulness of this technique, we provide explicit calculations for our general model, which we adapt to two generic schemes for single-enzyme turnover with conformational interconversion. For each generic scheme, wherein the intermediate state(s) need not undergo Poissonian decay, the functional dependence of the mean first-passage time on the concentration of an external substrate is analyzed. When conformational detailed balance is satisfied, the enzyme turnover rate (related to the mean first-passage time) reduces to the celebrated Michaelis-Menten functional form, consistent with our previous work involving a similar scheme with all rate processes, thereby establishing further generality to this intriguing result. Our framework affords a general and intuitive approach for evaluating measurable waiting time PDFs and their moments, making it a potentially useful kinetic tool for a wide variety of single-molecule processes.

Kinetic synergistic transitions in the Ostwald ripening processes

Science.gov (United States)

Sachkov, I. N.; Turygina, V. F.; Dolganov, A. N.

2018-01-01

There is proposed approach to mathematical description of the kinetic transitions in Ostwald ripening processes of volatile substance in nonuniformly heated porous materials. It is based upon the finite element method. There are implemented computer software. The main feature of the software is to calculate evaporation and condensation fluxes on the walls of a nonuniformly heated cylindrical capillary. Kinetic transitions are detected for three modes of volatile substances migration which are different by condensation zones location. There are controlling dimensionless parameters of the kinetic transition which are revealed during research. There is phase diagram of the Ostwald ripening process modes realization.

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

Science.gov (United States)

Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

2011-09-01

Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

Uniqueness of thermodynamic projector and kinetic basis of molecular individualism

Science.gov (United States)

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.

Molecular basis of structural makeup of hulless barley in relation to rumen degradation kinetics and intestinal availability in dairy cattle: A novel approach.

Science.gov (United States)

Damiran, D; Yu, P

2011-10-01

To date, no study has been done of molecular structures in relation to nutrient degradation kinetics and intestinal availability in dairy cattle. The objectives of this study were to (1) reveal molecular structures of hulless barley affected by structural alteration using molecular spectroscopy (diffuse reflectance infrared Fourier transform) as a novel approach, and (2) quantify structure features on a molecular basis in relation to digestive kinetics and nutritive value in the rumen and intestine in cattle. The modeled feeds in this study were 4 types of hulless barley (HB) cultivars modified in starch traits: (a) normal starch cultivar, (b) zero-amylose waxy, (c) waxy, and (d) high-amylose. The molecular structural features were determined using diffuse reflectance infrared Fourier transform spectroscopy in the mid-infrared region (ca. 4,000-800 cm(-1)) of the electromagnetic spectrum. The items assessed included infrared intensity attributed to protein amide I (ca. 1,715-1,575 cm(-1)), amide II (ca. 1,575-1,490 cm(-1)), α-helix (ca. 1,648-1,660 cm(-1)), β-sheet (ca. 1,625-1,640 cm(-1)), and their ratio, β-glucan (ca. 1,445-1,400 cm(-1)), total carbohydrates (CHO; ca. 1,188-820 cm(-1)) and their 3 major peaks, structural carbohydrates (ca. 1,277-1,190 cm(-1)), and ratios of amide I to II and amide I to CHO. The results show that (1) the zero-amylose waxy was the greatest in amide I and II peak areas, as well as in the ratio of protein amide I to CHO among HB; (2) α-helix-to-β-sheet ratio differed among HB: the high-amylose was the greatest, the zero-amylose waxy and waxy were the intermediate, and the normal starch was the lowest; (3) HB were similar in β-glucan and CHO molecular structural makeup; (4) altered starch HB cultivars were similar to each other, but were different from the normal starch cultivar in protein molecular makeup; and (5) the rate and extent of rumen degradation of starch and protein were highly related to the molecular structural

First principle chemical kinetics in zeolites: the methanol-to-olefin process as a case study.

Science.gov (United States)

Van Speybroeck, Veronique; De Wispelaere, Kristof; Van der Mynsbrugge, Jeroen; Vandichel, Matthias; Hemelsoet, Karen; Waroquier, Michel

2014-11-07

To optimally design next generation catalysts a thorough understanding of the chemical phenomena at the molecular scale is a prerequisite. Apart from qualitative knowledge on the reaction mechanism, it is also essential to be able to predict accurate rate constants. Molecular modeling has become a ubiquitous tool within the field of heterogeneous catalysis. Herein, we review current computational procedures to determine chemical kinetics from first principles, thus by using no experimental input and by modeling the catalyst and reacting species at the molecular level. Therefore, we use the methanol-to-olefin (MTO) process as a case study to illustrate the various theoretical concepts. This process is a showcase example where rational design of the catalyst was for a long time performed on the basis of trial and error, due to insufficient knowledge of the mechanism. For theoreticians the MTO process is particularly challenging as the catalyst has an inherent supramolecular nature, for which not only the Brønsted acidic site is important but also organic species, trapped in the zeolite pores, must be essentially present during active catalyst operation. All these aspects give rise to specific challenges for theoretical modeling. It is shown that present computational techniques have matured to a level where accurate enthalpy barriers and rate constants can be predicted for reactions occurring at a single active site. The comparison with experimental data such as apparent kinetic data for well-defined elementary reactions has become feasible as current computational techniques also allow predicting adsorption enthalpies with reasonable accuracy. Real catalysts are truly heterogeneous in a space- and time-like manner. Future theory developments should focus on extending our view towards phenomena occurring at longer length and time scales and integrating information from various scales towards a unified understanding of the catalyst. Within this respect molecular

Recent developments in thermoluminescence kinetics: applications to other thermally stimulated processes

International Nuclear Information System (INIS)

Levy, P.W.

1985-01-01

Recent thermoluminescence (TL) studies indicate that many kinetic properties are not in accord with the well known 1st and 2nd order TL kinetic equations. For example, the usual equations do not describe: (1) the shape of certain single glow peaks. (2) The shape of glow peaks in many glow curves containing more than one glow peak. (3) The dependence of the peak temperature, the FWHM, the shape, and other properties on the pre-measurement dose. However, the properties of some single glow peaks are precisely described, or closely approximated by, the more general basic equation from which the usual 1st and 2nd order equations are obtained as special cases. Furthermore, glow curves containing more than one glow peak are described by a system of equations that includes interactions between different types of traps and is a straightforward extension of the general one peak equation. This system - called Interactive Kinetics - accounts for most properties, and explains many anomalies, associated with glow curves containing more than one glow peak. It is particularly convenient for computerized analysis procedures. Lastly, it is suggested that other thermally stimulated processes depend on analogous interactions and are describable by similar sets of kinetic equations that are convenient for computer analysis. 11 refs., 2 figs

Similar kinetics of chromatid aberrations in X-irradiated xrs 5 and wild-type Chinese hamster ovary cells

International Nuclear Information System (INIS)

MacLeod, R.A.F.; Bryant, P.E.

1990-01-01

We have studied the kinetics of chromatid aberrations in cells of the Chinese hamster ovary (CHO-K1) derived, X-ray sensitive cell line xrs 5 irradiated in the G 2 phase at 37 0 C, as well as during a cell cycle extended by transient hypothermia at 33 0 C. While a given X-ray dose was estimated to produce about 4 times as many chromatid break and twice the frequency of exchanges in xrs 5 cells as in the parent line, there was no difference between the lines in the rates of disappearance of chromatid breaks during G 2 at either temperature; and similar patterns of chromatid exchange kinetics were observed in the two lines. Both the frequencies and distributions of chromatid breaks at different times after irradiation are consistent with the view that the disappearance of these during incubation represents a repair process. These results imply that the G 2 chromosomal radiosensitivity of the xrs 5 mutant resides at the level of initial chromatid damage. (author)

Process Simulation for the Design and Scale Up of Heterogeneous Catalytic Process: Kinetic Modelling Issues

Directory of Open Access Journals (Sweden)

Antonio Tripodi

2017-05-01

Full Text Available Process simulation represents an important tool for plant design and optimization, either applied to well established or to newly developed processes. Suitable thermodynamic packages should be selected in order to properly describe the behavior of reactors and unit operations and to precisely define phase equilibria. Moreover, a detailed and representative kinetic scheme should be available to predict correctly the dependence of the process on its main variables. This review points out some models and methods for kinetic analysis specifically applied to the simulation of catalytic processes, as a basis for process design and optimization. Attention is paid also to microkinetic modelling and to the methods based on first principles, to elucidate mechanisms and independently calculate thermodynamic and kinetic parameters. Different case studies support the discussion. At first, we have selected two basic examples from the industrial chemistry practice, e.g., ammonia and methanol synthesis, which may be described through a relatively simple reaction pathway and the relative available kinetic scheme. Then, a more complex reaction network is deeply discussed to define the conversion of bioethanol into syngas/hydrogen or into building blocks, such as ethylene. In this case, lumped kinetic schemes completely fail the description of process behavior. Thus, in this case, more detailed—e.g., microkinetic—schemes should be available to implement into the simulator. However, the correct definition of all the kinetic data when complex microkinetic mechanisms are used, often leads to unreliable, highly correlated parameters. In such cases, greater effort to independently estimate some relevant kinetic/thermodynamic data through Density Functional Theory (DFT/ab initio methods may be helpful to improve process description.

Generalized Ornstein-Uhlenbeck processes and associated self-similar processes

CERN Document Server

Lim, S C

2003-01-01

We consider three types of generalized Ornstein-Uhlenbeck processes: the stationary process obtained from the Lamperti transformation of fractional Brownian motion, the process with stretched exponential covariance and the process obtained from the solution of the fractional Langevin equation. These stationary Gaussian processes have many common properties, such as the fact that their local covariances share a similar structure and they exhibit identical spectral densities at large frequency limit. In addition, the generalized Ornstein-Uhlenbeck processes can be shown to be local stationary representations of fractional Brownian motion. Two new self-similar Gaussian processes, in addition to fractional Brownian motion, are obtained by applying the (inverse) Lamperti transformation to the generalized Ornstein-Uhlenbeck processes. We study some of the properties of these self-similar processes such as the long-range dependence. We give a simulation of their sample paths based on numerical Karhunan-Loeve expansi...

Generalized Ornstein-Uhlenbeck processes and associated self-similar processes

International Nuclear Information System (INIS)

Lim, S C; Muniandy, S V

2003-01-01

We consider three types of generalized Ornstein-Uhlenbeck processes: the stationary process obtained from the Lamperti transformation of fractional Brownian motion, the process with stretched exponential covariance and the process obtained from the solution of the fractional Langevin equation. These stationary Gaussian processes have many common properties, such as the fact that their local covariances share a similar structure and they exhibit identical spectral densities at large frequency limit. In addition, the generalized Ornstein-Uhlenbeck processes can be shown to be local stationary representations of fractional Brownian motion. Two new self-similar Gaussian processes, in addition to fractional Brownian motion, are obtained by applying the (inverse) Lamperti transformation to the generalized Ornstein-Uhlenbeck processes. We study some of the properties of these self-similar processes such as the long-range dependence. We give a simulation of their sample paths based on numerical Karhunan-Loeve expansion

Wetting kinetics of water nano-droplet containing non-surfactant nanoparticles: A molecular dynamics study

International Nuclear Information System (INIS)

Lu, Gui; Hu, Han; Sun, Ying; Duan, Yuanyuan

2013-01-01

In this Letter, dynamic wetting of water nano-droplets containing non-surfactant gold nanoparticles on a gold substrate is examined via molecular dynamics simulations. The results show that the addition of non-surfactant nanoparticles hinders the nano-second droplet wetting process, attributed to the increases in both surface tension of the nanofluid and friction between nanofluid and substrate. The droplet wetting kinetics decreases with increasing nanoparticle loading and water-particle interaction energy. The observed wetting suppression and the absence of nanoparticle ordering near the contact line of nano-sized droplets differ from the wetting behaviors reported from nanofluid droplets of micron size or larger

Out-of-order event processing in kinetic data structures

DEFF Research Database (Denmark)

Abam, Mohammad; de Berg, Mark; Agrawal, Pankaj

2011-01-01

’s for the maintenance of several fundamental structures such as kinetic sorting and kinetic tournament trees, which overcome the difficulty by employing a refined event scheduling and processing technique. We prove that the new event scheduling mechanism leads to a KDS that is correct except for finitely many short......We study the problem of designing kinetic data structures (KDS’s for short) when event times cannot be computed exactly and events may be processed in a wrong order. In traditional KDS’s this can lead to major inconsistencies from which the KDS cannot recover. We present more robust KDS...

An overview of atomic and molecular processes in critical velocity ionization

International Nuclear Information System (INIS)

Lai, S.T.; Murad, E.; McNeil, W.J.

1989-01-01

Alfven's critical ionization velocity (CIV) is a multistep process involving plasma physics and plasma chemistry. The authors present an overview of the time development of some atomic and molecular processes in CIV. In the pre-onset stage, metastable states play an important role: They provide an energy pooling mechanism allowing low energy electrons to participate in the ionization processes; they may explain the low energy threshold as well as the fast time scale in the onset of CIV. For a sustaining CIV to occur, Townsend's criterion has to be satisfied. The kinetic energies of the neutrals are transformed to plasma wave energies via beam-plasma instabilities, and the plasma waves that heat the electrons result in a tail formation. Excitation of neutrals with subsequent radiation is an important energy loss mechanism. Finite beam size also limits the instability growth rate. In the propagation of CIV, ion-molecule reactions and molecular dissociative recombination are important. Ion-molecule reactions change the temporal chemical composition in a CIV process and help explain some results in CIV experiments. Molecular dissociative recombination reduces the plasma density, lowers the effective neutral mass, and loses energy via excitation and radiation; it tends to quench the propagation of CIV. Depending on various parameters, oscillatory behavior of CIV may occur

Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

Energy Technology Data Exchange (ETDEWEB)

Yoon, Hong Min [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Kondaraju, Sasidhar [Department of Mechanical Science, Indian Institute of Technology Bhubaneswar, Bhubaneswar, Odisha 751013 (India); Lee, Jung Shin [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Suh, Youngho; Lee, Joonho H. [Samsung Electronics, Mechatronics R& D Center, Hwaseong-si, Gyeonggi-do 445-330 (Korea, Republic of); Lee, Joon Sang, E-mail: joonlee@yonsei.ac.kr [Department of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of)

2017-07-01

Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

Molecular dynamics study of the nanosized droplet spreading: The effect of the contact line forces on the kinetic energy dissipation

International Nuclear Information System (INIS)

Yoon, Hong Min; Kondaraju, Sasidhar; Lee, Jung Shin; Suh, Youngho; Lee, Joonho H.; Lee, Joon Sang

2017-01-01

Highlights: • Contact line forces, including friction and spreading forces are directly calculated. • Overall trends of variations in contact line forces during droplet spreading process show characteristics of contact line forces. • Detail relations of contact line forces and atomic kinetics in the contact line provide a clear evidence of the possible energy dissipation mechanism in droplet spreading process. - Abstract: Recent studies have revealed that contact line forces play an important role in the droplet spreading process. Despite their significance, the physics related to them has been studied only indirectly and the effect of contact line forces is still being disputed. We performed a molecular dynamics simulation and mimicked the droplet spreading process at the nanoscale. Based on the results of the simulation, the contact line forces were directly calculated. We found that the forces acting on the bulk and the contact line region showed different trends. Distinct positive and negative forces, contact line spreading, and friction forces were observed near the contact line. We also observed a strong dependency of the atomic kinetics in the contact line region on the variations in the contact line forces. The atoms of the liquid in the contact line region lost their kinetic energy due to the contact line friction force and became partially immobile on the solid surface. The results of the current study will be useful for understanding the role of the contact line forces on the kinetic energy dissipation in the contact line region.

Monte Carlo simulation on kinetics of batch and semi-batch free radical polymerization

KAUST Repository

Shao, Jing

2015-10-27

Based on Monte Carlo simulation technology, we proposed a hybrid routine which combines reaction mechanism together with coarse-grained molecular simulation to study the kinetics of free radical polymerization. By comparing with previous experimental and simulation studies, we showed the capability of our Monte Carlo scheme on representing polymerization kinetics in batch and semi-batch processes. Various kinetics information, such as instant monomer conversion, molecular weight, and polydispersity etc. are readily calculated from Monte Carlo simulation. The kinetic constants such as polymerization rate k p is determined in the simulation without of “steady-state” hypothesis. We explored the mechanism for the variation of polymerization kinetics those observed in previous studies, as well as polymerization-induced phase separation. Our Monte Carlo simulation scheme is versatile on studying polymerization kinetics in batch and semi-batch processes.

From an equilibrium based MOF adsorbent to a kinetic selective carbon molecular sieve for paraffin/iso-paraffin separation

KAUST Repository

Li, Baiyan

2016-11-04

We unveil a unique kinetic driven separation material for selectively removing linear paraffins from iso-paraffins via a molecular sieving mechanism. Subsequent carbonization and thermal treatment of CD-MOF-2, the cyclodextrin metal-organic framework, afforded a carbon molecular sieve with a uniform and reduced pore size of ca. 5.0 Å, and it exhibited highly selective kinetic separation of n-butane and n-pentane from iso-butane and iso-pentane, respectively. © The Royal Society of Chemistry.

Kinetics and mechanism of synthetic CoS oxidation process

Directory of Open Access Journals (Sweden)

Štrbac N.

2006-01-01

Full Text Available The results of investigation of kinetics and mechanism for synthetic a-CoS oxidation process are presented in this paper. Based on experimental data obtained using DTA and XRD analysis and constructed PSD diagrams for Co-S-O system, mechanism of synthetic a-CoS oxidation process is suggested. Characteristic kinetic parameters were obtained for experimental isothermal investigations of desulfurization degree using Sharp method.

Molecular-Level Processes Governing the Interaction of Contaminants with Iron and Manganese Oxides - Final Report; FINAL

International Nuclear Information System (INIS)

Brown, G. E. Jr.; Chambers, S. A.

1999-01-01

Many of the inorganic and organic contaminants present in sediments at DOE sites can be altered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on structurally and compositionally well-defined mineral surfaces will lead to: (i) improved models of contaminant fate and transport in geochemical systems, and (ii) optimized manipulation of these processes for remediation purposes. To contribute to this understanding, we will study, both experimentally and theoretically, redox processes involving three important contaminants - chromate ion, carbon tetrachloride, and trichloroethene TCE, on the following iron and manganese oxides - hematite, magnetite, maghemite, and pyrolusite. These oxides and their hydroxylated analogs commonly occur as coatings on minerals or as interfaces in the subsurface environment. Single-crystal surfaces of these oxides will be synthesized in carefully controlled fashion by molecular beam epitaxy. These surfaces, as well as high surface are powdered samples of these oxides, will be used in spectroscopic and kinetic experiments in both aqueous and gas phases. Our goal is to identify products and to determine the kinetics and mechanisms of surface-catalyzed redox reaction of Cr(VI) and CR(III), and the reductive dechlorination of carbon tetrachloride and TCE. The combination of theory and experiment will provide the base information needed to scale from the molecular level to the microscopic grain level minerals

Transient currents in a molecular photo-diode

OpenAIRE

Petrov, E. G.; Leonov, V. O.; May, V.; Hänggi, P.

2012-01-01

Light-induced charge transmission through a molecular junction (molecular diode) is studied in the framework of a HOMO-LUMO model and in using a kinetic description. Expressions are presented for the sequential (hopping) and direct (tunneling) transient current components together with kinetic equations governing the time-dependent populations of the neutral and charged molecular states which participate in the current formation. Resonant and off-resonant charge transmission processes are ana...

Fast business process similarity search

NARCIS (Netherlands)

Yan, Z.; Dijkman, R.M.; Grefen, P.W.P.J.

2012-01-01

Nowadays, it is common for organizations to maintain collections of hundreds or even thousands of business processes. Techniques exist to search through such a collection, for business process models that are similar to a given query model. However, those techniques compare the query model to each

Effect of processing on carbon molecular sieve structure and performance

KAUST Repository

Das, Mita; Perry, John D.; Koros, William J.

2010-01-01

Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

Effect of processing on carbon molecular sieve structure and performance

KAUST Repository

Das, Mita

2010-11-01

Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

Processes of aggression described by kinetic method

Science.gov (United States)

Aristov, V. V.; Ilyin, O.

2014-12-01

In the last decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France and USSR based on the kinetic theory. We model this process with the Cauchy boundary problem for the two-element kinetic equations with spatial initial conditions. The solution of the problem is given in the form of traveling wave. The propagation velocity of a frontline depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the frontline velocities are complied with the historical data.

Processes of aggression described by kinetic method

International Nuclear Information System (INIS)

Aristov, V. V.; Ilyin, O.

2014-01-01

In the last decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France and USSR based on the kinetic theory. We model this process with the Cauchy boundary problem for the two-element kinetic equations with spatial initial conditions. The solution of the problem is given in the form of traveling wave. The propagation velocity of a frontline depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the frontline velocities are complied with the historical data

Processes of aggression described by kinetic method

Energy Technology Data Exchange (ETDEWEB)

Aristov, V. V.; Ilyin, O. [Dorodnicyn Computing Centre of Russian Academy of Sciences, Vavilova str. 40, Moscow, 119333 (Russian Federation)

2014-12-09

In the last decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France and USSR based on the kinetic theory. We model this process with the Cauchy boundary problem for the two-element kinetic equations with spatial initial conditions. The solution of the problem is given in the form of traveling wave. The propagation velocity of a frontline depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the frontline velocities are complied with the historical data.

Bioleaching of spent hydro-processing catalyst using acidophilic bacteria and its kinetics aspect

International Nuclear Information System (INIS)

Mishra, Debaraj; Kim, Dong J.; Ralph, David E.; Ahn, Jong G.; Rhee, Young H.

2008-01-01

Bioleaching of metals from hazardous spent hydro-processing catalysts was attempted in the second stage after growing the bacteria with sulfur in the first stage. The first stage involved transformation of elemental sulfur particles to sulfuric acid through an oxidation process by acidophilic bacteria. In the second stage, the acidic medium was utilized for the leaching process. Nickel, vanadium and molybdenum contained within spent catalyst were leached from the solid materials to liquid medium by the action of sulfuric acid that was produced by acidophilic leaching bacteria. Experiments were conducted varying the reaction time, amount of spent catalysts, amount of elemental sulfur and temperature. At 50 g/L spent catalyst concentration and 20 g/L elemental sulfur, 88.3% Ni, 46.3% Mo, and 94.8% V were recovered after 7 days. Chemical leaching with commercial sulfuric acid of the similar amount that produced by bacteria was compared. Thermodynamic parameters were calculated and the nature of reaction was found to be exothermic. Leaching kinetics of the metals was represented by different reaction kinetic equations, however, only diffusion controlled model showed the best correlation here. During the whole process Mo showed low dissolution because of substantiate precipitation with leach residues as MoO 3 . Bioleach residues were characterized by EDX and XRD

Bioleaching of spent hydro-processing catalyst using acidophilic bacteria and its kinetics aspect

Energy Technology Data Exchange (ETDEWEB)

Mishra, Debaraj [Mineral and Material Processing Division, Korea Institute of Geosciences and Mineral Resources, Daejeon 305-350 (Korea, Republic of); Department of Microbiology, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Kim, Dong J. [Mineral and Material Processing Division, Korea Institute of Geosciences and Mineral Resources, Daejeon 305-350 (Korea, Republic of)], E-mail: djkim@kigam.re.kr; Ralph, David E. [AJ Parker CRC for Hydrometallurgy, Murdoch University, South Street Murdoch, Perth 6153 (Australia); Ahn, Jong G. [Mineral and Material Processing Division, Korea Institute of Geosciences and Mineral Resources, Daejeon 305-350 (Korea, Republic of); Rhee, Young H. [Department of Microbiology, Chungnam National University, Daejeon 305-764 (Korea, Republic of)

2008-04-15

Bioleaching of metals from hazardous spent hydro-processing catalysts was attempted in the second stage after growing the bacteria with sulfur in the first stage. The first stage involved transformation of elemental sulfur particles to sulfuric acid through an oxidation process by acidophilic bacteria. In the second stage, the acidic medium was utilized for the leaching process. Nickel, vanadium and molybdenum contained within spent catalyst were leached from the solid materials to liquid medium by the action of sulfuric acid that was produced by acidophilic leaching bacteria. Experiments were conducted varying the reaction time, amount of spent catalysts, amount of elemental sulfur and temperature. At 50 g/L spent catalyst concentration and 20 g/L elemental sulfur, 88.3% Ni, 46.3% Mo, and 94.8% V were recovered after 7 days. Chemical leaching with commercial sulfuric acid of the similar amount that produced by bacteria was compared. Thermodynamic parameters were calculated and the nature of reaction was found to be exothermic. Leaching kinetics of the metals was represented by different reaction kinetic equations, however, only diffusion controlled model showed the best correlation here. During the whole process Mo showed low dissolution because of substantiate precipitation with leach residues as MoO{sub 3}. Bioleach residues were characterized by EDX and XRD.

Thermodynamics versus Kinetics Dichotomy in the Linear Self-Assembly of Mixed Nanoblocks.

Science.gov (United States)

Ruiz, L; Keten, S

2014-06-05

We report classical and replica exchange molecular dynamics simulations that establish the mechanisms underpinning the growth kinetics of a binary mix of nanorings that form striped nanotubes via self-assembly. A step-growth coalescence model captures the growth process of the nanotubes, which suggests that high aspect ratio nanostructures can grow by obeying the universal laws of self-similar coarsening, contrary to systems that grow through nucleation and elongation. Notably, striped patterns do not depend on specific growth mechanisms, but are governed by tempering conditions that control the likelihood of depropagation and fragmentation.

Optimization and kinetic modeling of cadmium desorption from citrus peels: A process for biosorbent regeneration

International Nuclear Information System (INIS)

Njikam, Eloh; Schiewer, Silke

2012-01-01

Graphical abstract: Cadmium was completely and quickly desorbed from grapefruit peels using 0.01 M HNO 3 . The kinetics followed a novel 1st or 2nd order kinetic model, related to the remaining metal bound as the rate-determining reactant concentration. For 0.001 M HNO 3 , desorption was incomplete and the model fit less perfect. Highlights: ► Metal desorption was over 90% complete within 50 min for most desorbents. ► Models for biosorbent desorption kinetics were developed. ► Desorption kinetics best fit a novel first-order model related to remaining metal bound. ► Cd uptake after desorption by HNO 3 was similar to the original uptake. ► The optimal desorbent was 0.1 or 0.01 M acid, being fast, efficient and cheap. - Abstract: Citrus peel biosorbents are efficient in removing heavy metals from wastewater. Heavy metal recovery and sorbent regeneration are important for the financial competitiveness of biosorption with other processes. The desorbing agents HNO 3 , NaNO 3 , Ca(NO 3 ) 2 , EDTA, S, S-EDDS, and Na-Citrate were studied at different concentrations to optimize cadmium elution from orange or grapefruit peels. In most cases, desorption was fast, being over 90% complete within 50 min. However sodium nitrate and 0.001 M nitric acid were less efficient. Several new models for desorption kinetics were developed. While zero-, first- and second-order kinetics are commonly applied for modeling adsorption kinetics, the present study adapts these models to describe desorption kinetics. The proposed models relate to the number of metal-filled binding sites as the rate-determining reactant concentration. A model based on first order kinetics with respect to the remaining metal bound performed best. Cd bound in subsequent adsorption after desorption was similar to the original amount bound for desorption by nitric acid, but considerably lower for calcium nitrate as the desorbent. While complexing agents were effective desorbents, their cost is higher than that

Molecular basis sets - a general similarity-based approach for representing chemical spaces.

Science.gov (United States)

Raghavendra, Akshay S; Maggiora, Gerald M

2007-01-01

A new method, based on generalized Fourier analysis, is described that utilizes the concept of "molecular basis sets" to represent chemical space within an abstract vector space. The basis vectors in this space are abstract molecular vectors. Inner products among the basis vectors are determined using an ansatz that associates molecular similarities between pairs of molecules with their corresponding inner products. Moreover, the fact that similarities between pairs of molecules are, in essentially all cases, nonzero implies that the abstract molecular basis vectors are nonorthogonal, but since the similarity of a molecule with itself is unity, the molecular vectors are normalized to unity. A symmetric orthogonalization procedure, which optimally preserves the character of the original set of molecular basis vectors, is used to construct appropriate orthonormal basis sets. Molecules can then be represented, in general, by sets of orthonormal "molecule-like" basis vectors within a proper Euclidean vector space. However, the dimension of the space can become quite large. Thus, the work presented here assesses the effect of basis set size on a number of properties including the average squared error and average norm of molecular vectors represented in the space-the results clearly show the expected reduction in average squared error and increase in average norm as the basis set size is increased. Several distance-based statistics are also considered. These include the distribution of distances and their differences with respect to basis sets of differing size and several comparative distance measures such as Spearman rank correlation and Kruscal stress. All of the measures show that, even though the dimension can be high, the chemical spaces they represent, nonetheless, behave in a well-controlled and reasonable manner. Other abstract vector spaces analogous to that described here can also be constructed providing that the appropriate inner products can be directly

Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

International Nuclear Information System (INIS)

Yu, P.

2007-01-01

The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

Monte Carlo simulation on kinetics of batch and semi-batch free radical polymerization

KAUST Repository

Shao, Jing; Tang, Wei; Xia, Ru; Feng, Xiaoshuang; Chen, Peng; Qian, Jiasheng; Song, Changjiang

2015-01-01

experimental and simulation studies, we showed the capability of our Monte Carlo scheme on representing polymerization kinetics in batch and semi-batch processes. Various kinetics information, such as instant monomer conversion, molecular weight

Kinetic Simulations of Type II Radio Burst Emission Processes

Science.gov (United States)

Ganse, U.; Spanier, F. A.; Vainio, R. O.

2011-12-01

The fundamental emission process of Type II Radio Bursts has been under discussion for many decades. While analytic deliberations point to three wave interaction as the source for fundamental and harmonic radio emissions, sparse in-situ observational data and high computational demands for kinetic simulations have not allowed for a definite conclusion to be reached. A popular model puts the radio emission into the foreshock region of a coronal mass ejection's shock front, where shock drift acceleration can create eletrcon beam populations in the otherwise quiescent foreshock plasma. Beam-driven instabilities are then assumed to create waves, forming the starting point of three wave interaction processes. Using our kinetic particle-in-cell code, we have studied a number of emission scenarios based on electron beam populations in a CME foreshock, with focus on wave-interaction microphysics on kinetic scales. The self-consistent, fully kinetic simulations with completely physical mass-ratio show fundamental and harmonic emission of transverse electromagnetic waves and allow for detailled statistical analysis of all contributing wavemodes and their couplings.

Self-similar analysis of the spherical implosion process

International Nuclear Information System (INIS)

Ishiguro, Yukio; Katsuragi, Satoru.

1976-07-01

The implosion processes caused by laser-heating ablation has been studied by self-similarity analysis. Attention is paid to the possibility of existence of the self-similar solution which reproduces the implosion process of high compression. Details of the self-similar analysis are reproduced and conclusions are drawn quantitatively on the gas compression by a single shock. The compression process by a sequence of shocks is discussed in self-similarity. The gas motion followed by a homogeneous isentropic compression is represented by a self-similar motion. (auth.)

Kinetics of pulp mill effluent treatment by ozone-based processes

International Nuclear Information System (INIS)

Ko, Chun-Han; Hsieh, Po-Hung; Chang, Meng-Wen; Chern, Jia-Ming; Chiang, Shih-Min; Tzeng, Chewn-Jeng

2009-01-01

The wastewaters generated from wood pulping and paper production processes are traditionally treated by biological and physicochemical processes. In order to reduce chemical oxygen demand (COD) and color to meet increasingly strict discharge standards, advanced oxidation processes (AOPs) are being adapted as polishing treatment units. Various ozone-based processes were used in this study to treat simulated wastewaters prepared from black liquor from a hardwood Kraft pulp mill in Taiwan. The experimental results showed that the COD and color were primarily removed by direct ozone oxidation and activated carbon adsorption. While the addition of activated carbon could enhance the COD and color removal during ozonation, the addition of hydrogen peroxide improved the color removal only. For the various ozone-based treatment processes, kinetic models were developed to satisfactorily predict the COD and color removal rates. According to the kinetic parameters obtained from the various ozone-based processes, the enhanced COD and color removal of ozonation in the presence of activated carbon was attributed to the regeneration of the activated carbon by ozonation. These kinetic models can be used for reactor design and process design to treat pulping wastewater using ozone-based processes.

Thermodynamics, kinetics and process control of nitriding

DEFF Research Database (Denmark)

Mittemeijer, Eric J.; Somers, Marcel A. J.

1999-01-01

As a prerequisite for predictability of properties obtained by a nitriding treatment of iron-based workpieces, the relation between the process parameters and the composition and structure of the surface layer produced must be known. At present (even) the description of thermodynamic equilibrium...... of pure iron-nitrogen phases has not been achieved fully. It has been shown that taking into account ordering of nitrogen in the epsilon and gamma' iron-nitride phases, leads to an improved understanding of the Fe-N phase diagram. Although thermodynamics indicate the state the system strives for......, the nitriding result is determined largely by the kinetics of the process. The nitriding kinetics have been shown to be characterised by the occurring local near-equilibria and stationary states at surfaces and interfaces, and the diffusion coefficient of nitrogen in the various phases, for which new data have...

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

Science.gov (United States)

Otero, Toribio F

2017-01-18

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

Watching Nanoscale Self-Assembly Kinetics of Gold Prisms in Liquids

Science.gov (United States)

Kim, Juyeong; Ou, Zihao; Jones, Matthew R.; Chen, Qian

We use liquid-phase transmission electron microscopy to watch self-assembly of gold triangular prisms into polymer-like structures. The in situ dynamics monitoring enabled by liquid-phase transmission electron microscopy, single nanoparticle tracking, and the marked conceptual similarity between molecular reactions and nanoparticle self-assembly combined elucidate the following mechanistic understanding: a step-growth polymerization based assembly statistics, kinetic pathways sampling particle curvature dependent energy minima and their interconversions, and directed assembly into polymorphs (linear or cyclic chains) through in situ modulation of the prism bonding geometry. Our study bridges the constituent kinetics on the molecular and nanoparticle length scales, which enriches the design rules in directed self-assembly of anisotropic nanoparticles.

Effective potential kinetic theory for strongly coupled plasmas

Science.gov (United States)

Baalrud, Scott D.; Daligault, Jérôme

2016-11-01

The effective potential theory (EPT) is a recently proposed method for extending traditional plasma kinetic and transport theory into the strongly coupled regime. Validation from experiments and molecular dynamics simulations have shown it to be accurate up to the onset of liquid-like correlation parameters (corresponding to Γ ≃ 10-50 for the one-component plasma, depending on the process of interest). Here, this theory is briefly reviewed along with comparisons between the theory and molecular dynamics simulations for self-diffusivity and viscosity of the one-component plasma. A number of new results are also provided, including calculations of friction coefficients, energy exchange rates, stopping power, and mobility. The theory is also cast in the Landau and Fokker-Planck kinetic forms, which may prove useful for enabling efficient kinetic computations.

Some fundamental questions concerning the kinetic theory of electrons in molecular gases and the e H2 vibrational cross section controversy

Science.gov (United States)

Robson, R. E.; White, R. D.; Morrison, Michael A.

2003-10-01

We commence a fundamental re-examination of the kinetic theory of charged particle swarms in molecular gases, focusing on collisional excitation of molecular rotational and ro-vibrational states by electrons. Modern day analysis of electron swarms has been based upon the kinetic equation of Wang-Chang et al, which simply treats all processes as scalar energy excitations, and ignores angular momentum conservation and the vector dynamics associated with rotational excitation. It is pointed out that there is no alternative, more exact kinetic equation readily available for electrons which enables one to directly ascertain the degree of error introduced by this approximation. Thus in this preliminary study, we approach the problem indirectly, from the standpoint of the neutral molecules, using the Waldmann-Snider quantum kinetic equation, and insist that an electron-molecule collision must look the same from the perspective of both electron and molecule. We give a formula for quantitatively assessing the importance of scalar versus vectorial treatments of rotational excitation by looking at the post-collisional 'echo' produced by an electron swarm as it passes through the gas. It is then pointed out that in order to remedy any deficiency, it will be necessary to introduce a kinetic collisional operator non-local in space to properly account for angular momentum conservation, as has long been established in the literature. This is a major exercise and given the preliminary nature of this study, we consider the inclusion of such effects from a formal point of view only. In particular we show how non-local effects lead to a spatially dependent 'source' term in the equation of continuity, and hence to corrections for both drift velocity and diffusion coefficients. The magnitude of these corrections has yet to be established.

Some fundamental questions concerning the kinetic theory of electrons in molecular gases and the e-H2 vibrational cross section controversy

International Nuclear Information System (INIS)

Robson, R E; White, R D; Morrison, Michael A

2003-01-01

We commence a fundamental re-examination of the kinetic theory of charged particle swarms in molecular gases, focusing on collisional excitation of molecular rotational and ro-vibrational states by electrons. Modern day analysis of electron swarms has been based upon the kinetic equation of Wang-Chang et al, which simply treats all processes as scalar energy excitations, and ignores angular momentum conservation and the vector dynamics associated with rotational excitation. It is pointed out that there is no alternative, more exact kinetic equation readily available for electrons which enables one to directly ascertain the degree of error introduced by this approximation. Thus in this preliminary study, we approach the problem indirectly, from the standpoint of the neutral molecules, using the Waldmann-Snider quantum kinetic equation, and insist that an electron-molecule collision must look the same from the perspective of both electron and molecule. We give a formula for quantitatively assessing the importance of scalar versus vectorial treatments of rotational excitation by looking at the post-collisional 'echo' produced by an electron swarm as it passes through the gas. It is then pointed out that in order to remedy any deficiency, it will be necessary to introduce a kinetic collisional operator non-local in space to properly account for angular momentum conservation, as has long been established in the literature. This is a major exercise and given the preliminary nature of this study, we consider the inclusion of such effects from a formal point of view only. In particular we show how non-local effects lead to a spatially dependent 'source' term in the equation of continuity, and hence to corrections for both drift velocity and diffusion coefficients. The magnitude of these corrections has yet to be established

Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.

Science.gov (United States)

Michaels, Thomas C T; Šarić, Anđela; Habchi, Johnny; Chia, Sean; Meisl, Georg; Vendruscolo, Michele; Dobson, Christopher M; Knowles, Tuomas P J

2018-04-20

Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.

Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation

Science.gov (United States)

Michaels, Thomas C. T.; Šarić, Anđela; Habchi, Johnny; Chia, Sean; Meisl, Georg; Vendruscolo, Michele; Dobson, Christopher M.; Knowles, Tuomas P. J.

2018-04-01

Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.

Anaerobic digestion of buffalo dung: simulation of process kinetics

International Nuclear Information System (INIS)

Sahito, A.R.

2015-01-01

Assessment of kinetic of AD (Anaerobic Digestion) is a beneficial practice to forecast the performance of the process. It is helpful in the design of AD vessels, substrate feeding and digestate exit systems. The aim of this work was to assess the kinetics of anaerobically digested buffalo dung at different quantities of water added. It comprises the assessment of the specific methane production on the basis of VS (Volatile Solids) added in each reactor by using three first order models, i.e. the modified Gompertz model, the Cone model and the Exponential Curve Factor model. The analysis was tested by using the three statistical parameters, i.e. the coefficient of multiple determinations, the standard deviation of residuals and the Akaike's Information Criteria. The result reveals that the Exponential Curve Factor model was the best model that described the experimental data well. Moreover, there was not a direct or indirect relation between the kinetic coefficients of the AD process with the varying total or volatile solid content. (author)

Molecular weight kinetics and chain scission models for dextran polymers during ultrasonic degradation.

Science.gov (United States)

Pu, Yuanyuan; Zou, Qingsong; Hou, Dianzhi; Zhang, Yiping; Chen, Shan

2017-01-20

Ultrasonic degradation of six dextran samples with different initial molecular weights (IMW) has been performed to investigate the degradation behavior and chain scission mechanism of dextrans. The weight-average molecular weight (Mw) and polydispersity index (D value) were monitored by High Performance Gel Permeation Chromatography (HPGPC). Results showed that Mw and D value decreased with increasing ultrasonic time, resulting in a more homologous dextran solution with lower molecular weight. A significant degradation occurred in dextrans with higher IMW, particularly at the initial stage of the ultrasonic treatment. The Malhotra model was found to well describe the molecular weight kinetics for all dextran samples. Experimental data was fitted into two chain scission models to study dextran chain scission mechanism and the model performance was compared. Results indicated that the midpoint scission model agreed well with experimental results, with a linear regression factor of R 2 >0.99. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetics of fragmentation-annihilation processes

OpenAIRE

Filipe, JAN; Rodgers, GJ

1996-01-01

We investigate the kinetics of systems in which particles of one species undergo binary fragmentation and pair annihilation. In the latter, nonlinear process, fragments react at collision to produce an inert species, causing loss of mass. We analyze these systems in the reaction-limited regime by solving a continuous model within the mean-field approximation. The rate of fragmentation for a particle of mass x to break into fragments of masses y and x-y has the form x(lambda-1) (lambda > 0), a...

Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity

Science.gov (United States)

Huang, Bing; von Lilienfeld, O. Anatole

2016-10-01

The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. Inspired by the postulates of quantum mechanics, we introduce a hierarchy of representations which meet uniqueness and target similarity criteria. To systematically control target similarity, we simply rely on interatomic many body expansions, as implemented in universal force-fields, including Bonding, Angular (BA), and higher order terms. Addition of higher order contributions systematically increases similarity to the true potential energy and predictive accuracy of the resulting ML models. We report numerical evidence for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heat capacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After training, BAML predicts energies or electronic properties of out-of-sample molecules with unprecedented accuracy and speed.

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

Science.gov (United States)

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

2017-04-01

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

Kinetics and

Directory of Open Access Journals (Sweden)

Mojtaba Ahmadi

2016-11-01

Full Text Available The aqueous degradation of Reactive Yellow 84 (RY84 by potassium peroxydisulfate (K2S2O8 has been studied in laboratory scale experiments. The effect of the initial concentrations of potassium peroxydisulfate and RY84, pH and temperature on RY84 degradation were also examined. Experimental data were analyzed using first and second-order kinetics. The degradation kinetics of RY84 of the potassium peroxydisulfate process followed the second-order reaction kinetics. These rate constants have an extreme values similar to of 9.493 mM−1min−1 at a peroxydisulfate dose of 4 mmol/L. Thermodynamic parameters such as activation (Ea and Gibbs free energy (ΔG° were also evaluated. The negative value of ΔGo and Ea shows the spontaneous reaction natural conditions and exothermic nature.

Mechanistic and kinetic aspects of microbial inactivation in food irradiation processes

International Nuclear Information System (INIS)

Tukenmez, I.

2004-01-01

Full text: A proper reaction mechanism was searched by analyzing the inactivation processes of microorganisms during food irradiation by ionizing radiation. By employing transition-state theory, it was assumed that the overall inactivation process involves a reversible sub-lethal stress and repair reactions to form reversibly injured cell or sensitized cell, which then undergoes irreversible injury leading to dead cell. A shoulder in low dose range in survival kinetics was associated with the repair process. Depending on the postulated mechanism, kinetic model equations were derived. The kinetics of cell inactivation by irradiation was expressed as depending on irradiation dose. By using experimental data in the developed model the inactivation parameters including threshold dose, radiation yield, decimal reduction dose and minimum sterilization dose were evaluated and microbial inactivation by irradiation was simulated by using the numerical values of the parameters. Developed model and model parameters may be used for the process control and the assessment of product quality in radiation preservation of food

Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

Science.gov (United States)

Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

2016-08-11

Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times.

Roles of kinetics and energetics in the growth of AlN by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Im, I. H.; Minegishi, T.; Hanada, T.; Lee, S. W.; Cho, M. W.; Yao, T.; Oh, D. C.; Chang, J. H.

2006-01-01

The roles of kinetics and energetics in the growth processes of AlN on c-sapphire by plasma assisted molecular beam epitaxy are investigated by varying the growth rate from 1 to 31 A/min and the substrate temperature from 800 to 1000 .deg. C. The energetics is found to govern the growth of AlN in the low-growth rate region even at a low substrate temperature of 800 .deg. C owing to the enhanced residence time of adatoms, thereby increasing the surface migration length. As the growth rate increases, the growth tends to be governed by kinetics because of a reduction in the residence time of adatoms. Consequently, the surface roughness and crystal quality are greatly improved for the low-growth-rate case. In addition, the lattice strain relaxation is completed from the beginning of epitaxy for energetics-limiting growth while lattice strain relaxation is retarded for kinetics-limiting growth because of pre-existing partial strain relaxation. Energetics becomes more favorable as the substrate temperature is raised because of an increase in the surface diffusion length owing to an enhanced diffusion coefficient. Consequently high-crystal-quality AlN layers are grown under the energetics-limiting growth condition with a screw dislocation density of 7.4 x 10 8 cm -2 even for a thin 42-nm thick film.

On the measurements of molecular similarity: a connection between quantum chemistry and artificial intelligence

International Nuclear Information System (INIS)

Carbo, R.; Calabuig, B.

1988-01-01

Molecular similarity measures within the quantum concept of density functions are described and analyzed. It is intended to show how artificial intelligence techniques can be used within the framework of quantum theory, in order to study and classify the molecular structures and their properties. (A.C.A.S) [pt

Spray Drying Processing: granules production and drying kinetics of droplets

International Nuclear Information System (INIS)

Mondragon, R.; Julia, J. E.; Barba, A.; Jarque, J. C.

2013-01-01

Spray drying is a unit operation very common in many industrial processes. For each particular application, the resulting granulated material must possess determined properties that depend on the conditions in which the spray drying processing has been carried out, and whose dependence must be known in order to optimize the quality of the material obtained. The large number of variables that influence on the processes of matter and energy transfer and on the formation of granular material has required a detailed analysis of the drying process. Over the years there have been many studies on the spray drying processing of all kind of materials and the influence of process variables on the drying kinetics of the granulated material properties obtained. This article lists the most important works published for both the spray drying processing and the drying of individual droplets, as well as studies aimed at modeling the drying kinetics of drops. (Author)

Two-time temperature Green functions in kinetic theory and molecular hydrodynamics. 3. Account of interactions of hydrodynamic fluctuations

International Nuclear Information System (INIS)

Tserkovnikov, Yu.A.

2001-01-01

The regular method for deriving the equations for the Green functions in the tasks on the molecular hydrodynamics and kinetics, making it possible to account consequently the contribution into the generalized kinetics coefficients, conditioned by interaction of two, three and more hydrodynamic modes. In contrast to the general theory of perturbations by the interaction constant the consequent approximations are accomplished by the degree of accounting for the higher correlations, described by the irreducible functions [ru

The unified description of kinetic and hydrodynamic processes in gases and plasmas

International Nuclear Information System (INIS)

Klimontovich, Yu.L.

1992-01-01

The unified description of kinetic and hydrodynamic processes in gases and plasmas for all values of the Knudsen number is proposed. The generalized kinetic equation consists of the additional dissipative term and is defined by the diffusion of the distribution function in the coordinate space. This equation is used for the description of nonequilibrium processes in passive and active media. (orig.)

Determination of the crystal-melt interface kinetic coefficient from molecular dynamics simulations

International Nuclear Information System (INIS)

Monk, J; Mendelev, M I; Yang, Y; Asta, M; Hoyt, J J; Sun, D Y

2010-01-01

The generation and dissipation of latent heat at the moving solid–liquid boundary during non-equilibrium molecular dynamics (MD) simulations of crystallization can lead to significant underestimations of the interface mobility. In this work we examine the heat flow problem in detail for an embedded atom description of pure Ni and offer strategies to obtain an accurate value of the kinetic coefficient, μ. For free-solidification simulations in which the entire system is thermostated using a Nose–Hoover or velocity rescaling algorithm a non-uniform temperature profile is observed and a peak in the temperature is found at the interface position. It is shown that if the actual interface temperature, rather than the thermostat set point temperature, is used to compute the kinetic coefficient then μ is approximately a factor of 2 larger than previous estimates. In addition, we introduce a layered thermostat method in which several sub-regions, aligned normal to the crystallization direction, are indepently thermostated to a desired undercooling. We show that as the number of thermostats increases (i.e., as the width of each independently thermostated layer decreases) the kinetic coefficient converges to a value consistent with that obtained using a single thermostat and the calculated interface temperature. Also, the kinetic coefficient was determined from an analysis of the equilibrium fluctuations of the solid–liquid interface position. We demonstrate that the kinetic coefficient obtained from the relaxation times of the fluctuation spectrum is equivalent to the two values obtained from free-solidification simulations provided a simple correction is made for the contribution of heat flow controlled interface motion. Finally, a one-dimensional phase field model that captures the effect of thermostats has been developed. The mesoscale model reproduces qualitatively the results from MD simulations and thus allows for an a priori estimate of the accuracy of a

A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects.

Directory of Open Access Journals (Sweden)

Jeanette Prinz

2016-09-01

Full Text Available The molecular mechanisms that translate drug treatment into beneficial and unwanted effects are largely unknown. We present here a novel approach to detect gene-drug and gene-side effect associations based on the phenotypic similarity of drugs and single gene perturbations in mice that account for the polypharmacological property of drugs. We scored the phenotypic similarity of human side effect profiles of 1,667 small molecules and biologicals to profiles of phenotypic traits of 5,384 mouse genes. The benchmarking with known relationships revealed a strong enrichment of physical and indirect drug-target connections, causative drug target-side effect links as well as gene-drug links involved in pharmacogenetic associations among phenotypically similar gene-drug pairs. The validation by in vitro assays and the experimental verification of an unknown connection between oxandrolone and prokineticin receptor 2 reinforces the ability of this method to provide new molecular insights underlying drug treatment. Thus, this approach may aid in the proposal of novel and personalized treatments.

Effect of environmental factors on the kinetics of insulin fibril formation: elucidation of the molecular mechanism.

Science.gov (United States)

Nielsen, L; Khurana, R; Coats, A; Frokjaer, S; Brange, J; Vyas, S; Uversky, V N; Fink, A L

2001-05-22

In the search for the molecular mechanism of insulin fibrillation, the kinetics of insulin fibril formation were studied under different conditions using the fluorescent dye thioflavin T (ThT). The effect of insulin concentration, agitation, pH, ionic strength, anions, seeding, and addition of 1-anilinonaphthalene-8-sulfonic acid (ANS), urea, TMAO, sucrose, and ThT on the kinetics of fibrillation was investigated. The kinetics of the fibrillation process could be described by the lag time for formation of stable nuclei (nucleation) and the apparent rate constant for the growth of fibrils (elongation). The addition of seeds eliminated the lag phase. An increase in insulin concentration resulted in shorter lag times and faster growth of fibrils. Shorter lag times and faster growth of fibrils were seen at acidic pH versus neutral pH, whereas an increase in ionic strength resulted in shorter lag times and slower growth of fibrils. There was no clear correlation between the rate of fibril elongation and ionic strength. Agitation during fibril formation attenuated the effects of insulin concentration and ionic strength on both lag times and fibril growth. The addition of ANS increased the lag time and decreased the apparent growth rate for insulin fibril formation. The ANS-induced inhibition appears to reflect the formation of amorphous aggregates. The denaturant, urea, decreased the lag time, whereas the stabilizers, trimethylamine N-oxide dihydrate (TMAO) and sucrose, increased the lag times. The results indicated that both nucleation and fibril growth were controlled by hydrophobic and electrostatic interactions. A kinetic model, involving the association of monomeric partially folded intermediates, whose concentration is stimulated by the air-water interface, leading to formation of the critical nucleus and thence fibrils, is proposed.

A Study on the Kinetic Characteristics of Transmutation Process Reactor

Energy Technology Data Exchange (ETDEWEB)

Chung, Chang Hyun; You, Young Woo; Cho, Jae seon; Huh, Chang Wook; Kim, Doh Hyung [Seoul National University, Seoul (Korea, Republic of)

1997-07-01

The purpose of this study is to examine the transient heat transfer characteristics of liquid mental as the coolant used in accelerator-driven transmutation process reactor which is related the disposal of high-level radioactive nuclide. At current stage, the accelerator-driven transmutation process is investigated as the most appropriate method among many transmutation process methods. In this study, previous research works are investigated especially about the thermal hydraulics and kinetic behavior of coolant material including heat transfer of coolant in transmutation process reactor. A study on the heat transfer characteristics of liquid metal is performed based on the thermal hydraulic kinetic characteristics of liquid metal reactor which uses liquid metal coolant. Based on this study, the most appropriate material for the coolant of transmutation reactor will be recommended. 53 refs., 15 tabs., 33 figs. (author)

Degradation kinetics of seven organophosphorus pesticides in milk during yoghurt processing

Directory of Open Access Journals (Sweden)

LI-YING BO

2011-03-01

Full Text Available Bovine milk spiked with seven organophosphorus pesticides, i.e., dimethoate, fenthion, malathion, methyl parathion, monocrotophos, phorate and trichlorphon, was fermented at 42 °C with commercial directed vat set (DVS starters to investigate the degradation kinetics of the pesticides during yoghurt processing. The spiked pesticides were extracted from the prepared samples with an organic solvent and analyzed by gas chromatography after purification. Based on published results that the degradation kinetics of pesticides is first order, the rate constant of degradation and the half live period of the pesticides were calculated. The results indicated that degradation of the pesticides in milk during yoghurt processing were enhanced by one or both starters, except for malathion, and the two commercial DVS starters had different influences on the degradation kinetics of the pesticides.

A global resource allocation strategy governs growth transition kinetics of Escherichia coli.

Science.gov (United States)

Erickson, David W; Schink, Severin J; Patsalo, Vadim; Williamson, James R; Gerland, Ulrich; Hwa, Terence

2017-11-02

A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms and they remain a topic of active investigation. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions.

Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

Science.gov (United States)

Cernusca, S.; Winter, HP.; Aumayr, F.; Díez Muiño, R.; Juaristi, J. I.

2003-04-01

Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to "projectile molecular effects" (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials.

Molecular size evolution of oligomers in organic aerosols collected in urban atmospheres and generated in a smog chamber.

Science.gov (United States)

Kalberer, Markus; Sax, Mirjam; Samburova, Vera

2006-10-01

Only a minor fraction of the total organic aerosol mass can be resolved on a molecular level. High molecular weight compounds in organic aerosols have recently gained much attention because this class of compound potentially explains a major fraction of the unexplained organic aerosol mass. These compounds have been identified with different mass spectrometric methods, and compounds with molecular masses up to 1000 Da are found in secondary organic aerosols (SOA) generated from aromatic and terpene precursors in smog chamber experiments. Here, we apply matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to SOA particles from two biogenic precursors, alpha-pinene and isoprene. Similar oligomer patterns are found in these two SOA systems, but also in SOA from trimethylbenzene, an anthropogenic SOA precursor. However, different maxima molecular sizes were measured for these three SOA systems. While oligomers in alpha-pinene and isoprene have sizes mostly below 600-700 Da, they grow up to about 1000 Da in trimethylbenzene-SOA. The final molecular size of the oligomers is reached early during the particle aging process, whereas other particle properties related to aging, such as the overall acid concentration or the oligomer concentration, increase continuously over a much longer time scale. This kinetic behavior of the oligomer molecular size growth can be explained by a chain growth kinetic regime. Similar oligomer mass patterns were measured in aqueous extracts of ambient aerosol samples (measured with the same technique). Distinct differences between summer and winter were observed. In summer a few single mass peaks were measured with much higher intensity than in winter, pointing to a possible difference in the formation processes of these compounds in winter and summer.

Kinetics and mechanism of azo dye destruction in advanced oxidation processes

International Nuclear Information System (INIS)

Wojnarovits, L.; Palfi, T.; Takacs, E.

2007-01-01

The kinetics and mechanism of dye destruction in advanced oxidation processes is discussed on the example of Apollofix Red (Ar-28) radiolysis in aqueous solution. When the reactive intermediate reacts with the color bearing part of the molecule causing with nearly 100% efficiency destruction of the conjugation, the dose dependence, or time dependence of color disappearance is linear. In this case, spectrophotometry can be used to follow-up dye decomposition. Linear dependence was observed when hydrated electrons or hydrogen atoms reacted with the dye. In hydroxyl radical reactions some colored products form with spectra similar to those of the starting dye molecules. For that reason, spectrophotometry gives false result about the intact dye molecule concentration. Analysis by the HPLC reveals logarithmic time dependence in agreement with a theoretical model developed

Fluctuation kinetics of fluorescence hopping quenching in the Nd3+:Y2O3 spherical nanoparticles

International Nuclear Information System (INIS)

Orlovskii, Yu.V.; Popov, A.V.; Platonov, V.V.; Fedorenko, S.G.; Sildos, I.; Osipov, V.V.

2013-01-01

We study the peculiarities of energy transfer kinetics from the 4 F 3/2 laser level in the Nd 3+ doped Y 2 O 3 spherical nanoparticles of monoclinic phase synthesized by laser ablation of solid targets with subsequent recondensation in flow of air at atmospheric pressure comparing to the similar bulk crystal. We show that the fluorescence quenching in the nanoparticles is determined by two processes depending on Nd 3+ concentration and the degree of dehydration. At concentrations less than 1% the fluorescence quenching is mainly determined by direct (static) quenching by vibrations of OH − molecular groups associated with oxygen vacancies. At concentrations greater than 1 at % quenching is due to energy migration over neodymium ions, followed by the Nd 3+ –OH − quenching. In the latter case, the first time in a solid-state impurity laser medium we observe non-stationary kinetics on the entire length of a time-dependent luminescence quenching, starting from static decay and ending with fluctuation kinetics of fluorescence hopping quenching. -- Highlights: ► We prepare monoclinic Nd 3+ :Y 2 O 3 spherical NPs of mean D=12 nm by laser ablation of solid targets. ► We detect the fluorescence quenching of Nd 3+ the 4 F 3/2 level by vibrations of OH – molecular groups. ► We find that at 0.1% of Nd 3+ the process of static quenching by vibrations of OH – dominates. ► We find that Nd 3+ –Nd 3+ energy migration accelerates the Nd 3+ –OH − quenching at 1% of Nd 3+ . ► We detect non-stationary quenching kinetics ending with fluctuation stage of hopping quenching

Extraction Kinetics and Molecular Size Fractionation of Humic Substances From Two Brazilian Soils

Directory of Open Access Journals (Sweden)

Dick Deborah Pinheiro

1999-01-01

Full Text Available In the present study, the extraction behaviour of humic substances (HS from an Oxisol and a Mollisol from South Brazil, by using 0.1 and 0.5 mol L-1 NaOH and 0.15 mol L-1 neutral pyrophosphate solutions, respectively, was systematically studied. The kinetics and efficiency of HS extraction were evaluated by means of UV/Vis spectroscopy. The isolated humic acids (HA and fulvic acids (FA were size-classified by multistage ultrafiltration (six fractions in the molecular weight range of 1 to 100 kDa. The obtained data show that the HS extraction yield depended not only on the extractant, but also on the soil type. Within 3 h approximately 90% of the soluble HS could be extracted following complex extraction kinetics by both methods and none or little structural modification was verified as observed from their stable extinction ratio E350/E550. In the Mollisol the pyrophosphate extraction was more effective, suggesting that a great part of HS occurred as macromolecules bonded to clay minerals and aggregated between themselves through cationic bridges. In the Oxisol a higher HS yield was verified with the alkaline method, presumably due to HS fixation onto the oxide surface by H-bonds and/or surface complexation reactions. In general, HS extracted by the pyrophosphate procedure showed higher molecular weights than those extracted by NaOH.

A Motion Planning Approach to Studying Molecular Motions

KAUST Repository

Amato, Nancy M.

2010-01-01

While structurally very different, protein and RNA molecules share an important attribute. The motions they undergo are strongly related to the function they perform. For example, many diseases such as Mad Cow disease or Alzheimer\\'s disease are associated with protein misfolding and aggregation. Similarly, RNA folding velocity may regulate the plasmid copy number, and RNA folding kinetics can regulate gene expression at the translational level. Knowledge of the stability, folding, kinetics and detailed mechanics of the folding process may help provide insight into how proteins and RNAs fold. In this paper, we present an overview of our work with a computational method we have adapted from robotic motion planning to study molecular motions. We have validated against experimental data and have demonstrated that our method can capture biological results such as stochastic folding pathways, population kinetics of various conformations, and relative folding rates. Thus, our method provides both a detailed view (e.g., individual pathways) and a global view (e.g., population kinetics, relative folding rates, and reaction coordinates) of energy landscapes of both proteins and RNAs. We have validated these techniques by showing that we observe the same relative folding rates as shown in experiments for structurally similar protein molecules that exhibit different folding behaviors. Our analysis has also been able to predict the same relative gene expression rate for wild-type MS2 phage RNA and three of its mutants.

Kinetics of low temperature polyester dyeing with high molecular weight disperse dyes by solvent microemulsion and agrosourced auxiliaries

OpenAIRE

Radei, Shahram; Carrión-Fité, Francisco Javier; Ardanuy Raso, Mònica; Canal Arias, José Ma

2018-01-01

This work focused on the evaluation of the kinetics of dyeing polyester fabrics with high molecular weight disperse dyes, at low temperature by solvent microemulsion. This study also compared the effect of two non-toxic agro-sourced auxiliaries (o-vanillin and coumarin) using a non-toxic organic solvent. A dyeing bath consisting of a micro-emulsion system involving a small proportion of n-butyl acetate was used, and the kinetics of dyeing were analysed at four temperatures (83, 90, 95 and 100...

The freezing process of small lipid vesicles at molecular resolution

NARCIS (Netherlands)

Risselada, H. Jelger; Marrink, Siewert J.

2009-01-01

At present very little is known about the kinetic barriers which a small vesicle will face during the transformation from the liquid-crystalline to the gel phase, and what the structure of frozen vesicles looks like at the molecular level. The formation of gel domains in the strongly curved bilayer

Molecular dynamics simulation of carbon molecular sieve preparation for air separation

International Nuclear Information System (INIS)

Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh; Shariaty-Niassar, Mojtaba

2015-01-01

Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments

Molecular dynamics simulation of carbon molecular sieve preparation for air separation

Energy Technology Data Exchange (ETDEWEB)

Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh [Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Shariaty-Niassar, Mojtaba [University of Tehran, Tehran(Iran, Islamic Republic of)

2015-03-15

Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments.

Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron

International Nuclear Information System (INIS)

Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.

2010-01-01

Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.

Decarboxylation of Δ 9-tetrahydrocannabinol: Kinetics and molecular modeling

Science.gov (United States)

Perrotin-Brunel, Helene; Buijs, Wim; van Spronsen, Jaap; van Roosmalen, Maaike J. E.; Peters, Cor J.; Verpoorte, Rob; Witkamp, Geert-Jan

2011-02-01

Efficient tetrahydrocannabinol (Δ 9-THC) production from cannabis is important for its medical application and as basis for the development of production routes of other drugs from plants. This work presents one of the steps of Δ 9-THC production from cannabis plant material, the decarboxylation reaction, transforming the Δ 9-THC-acid naturally present in the plant into the psychoactive Δ 9-THC. Results of experiments showed pseudo-first order reaction kinetics, with an activation barrier of 85 kJ mol -1 and a pre-exponential factor of 3.7 × 10 8 s -1. Using molecular modeling, two options were identified for an acid catalyzed β-keto acid type mechanism for the decarboxylation of Δ 9-THC-acid. Each of these mechanisms might play a role, depending on the actual process conditions. Formic acid proved to be a good model for a catalyst of such a reaction. Also, the computational idea of catalysis by water to catalysis by an acid, put forward by Li and Brill, and Churchev and Belbruno was extended, and a new direct keto-enol route was found. A direct keto-enol mechanism catalyzed by formic acid seems to be the best explanation for the observed activation barrier and the pre-exponential factor of the decarboxylation of Δ 9-THC-acid. Evidence for this was found by performing an extraction experiment with Cannabis Flos. It revealed the presence of short chain carboxylic acids supporting this hypothesis. The presented approach is important for the development of a sustainable production of Δ 9-THC from the plant.

Calculation the kinetics of the baking biscuit process

Directory of Open Access Journals (Sweden)

S. T. Antipov

2013-01-01

Full Text Available Based on the input values of the equivalent values of thermophysical units and the heat transfer coefficient were calculated: values that reflect the kinetics of the process of baking; values allowing to determine the relationship duration baking temperature in the baking chamber; the voltage of the active area of the hearth.

Similarity search processing. Paralelization and indexing technologies.

Directory of Open Access Journals (Sweden)

Eder Dos Santos

2015-08-01

The next Scientific-Technical Report addresses the similarity search and the implementation of metric structures on parallel environments. It also presents the state of the art related to similarity search on metric structures and parallelism technologies. Comparative analysis are also proposed, seeking to identify the behavior of a set of metric spaces and metric structures over processing platforms multicore-based and GPU-based.

Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics

Science.gov (United States)

Dai, Hai-Lung

2002-03-01

Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

Kinetic studies on the degradation of crystal violet by the Fenton oxidation process.

Science.gov (United States)

Wu, H; Fan, M M; Li, C F; Peng, M; Sheng, L J; Pan, Q; Song, G W

2010-01-01

The degradation of dye crystal violet (CV) by Fenton oxidation process was investigated. The UV-Vis spectrogram has shown that CV can be degraded effectively by Fenton oxidation process. Different system variables namely initial H(2)O(2) concentration, initial Fe(2 + ) concentration and reaction temperature, which have effect on the degradation of CV by Fenton oxidation process, have been studied systematically. The degradation kinetics of CV was also elucidated based on the experimental data. The degradation of CV obeys the first-order reaction kinetics. The kinetic model can be described as k=1.5 exp(-(7.5)/(RT))[H(2)O(2)](0)(0.8718)[Fe(2+)](0)(0.5062). According to the IR spectrogram, it is concluded that the benzene ring of crystal violet has been destroyed by Fenton oxidation. The result will be useful in treating dyeing wastewater containing CV by Fenton oxidation process.

Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics.

Science.gov (United States)

Lee, Sangyun; Kim, Ji-Hyun; Lee, Sangyoub

2012-02-14

Acetylcholinesterase is an enzyme with a very high turnover rate; it quenches the neurotransmitter, acetylcholine, at the synapse. We have investigated the kinetics of the enzyme reaction by calculating the diffusion rate of the substrate molecule along an active site channel inside the enzyme from atomic-level molecular dynamics simulations. In contrast to the previous works, we have found that the internal substrate diffusion is the determinant of the acetylcholinesterase kinetics in the low substrate concentration limit. Our estimate of the overall bimolecular reaction rate constant for the enzyme is in good agreement with the experimental data. In addition, the present calculation provides a reasonable explanation for the effects of the ionic strength of solution and the mutation of surface residues of the enzyme. The study suggests that internal diffusion of the substrate could be a key factor in understanding the kinetics of enzymes of similar characteristics.

Kinetic models for historical processes of fast invasion and aggression

Science.gov (United States)

Aristov, Vladimir V.; Ilyin, Oleg V.

2015-04-01

In the last few decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological, and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France, and the USSR based on kinetic theory. We simulate this process with the Cauchy boundary problem for two-element kinetic equations. The solution of the problem is given in the form of a traveling wave. The propagation velocity of a front line depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the front-line velocities agree with the historical data.

Kinetics of Low Temperature Polyester Dyeing with High Molecular Weight Disperse Dyes by Solvent Microemulsion and AgroSourced Auxiliaries

OpenAIRE

Shahram Radei; F. Javier Carrión-Fité; Mònica Ardanuy; José María Canal

2018-01-01

This work focused on the evaluation of the kinetics of dyeing polyester fabrics with high molecular weight disperse dyes, at low temperature by solvent microemulsion. This study also compared the effect of two non-toxic agro-sourced auxiliaries (o-vanillin and coumarin) using a non-toxic organic solvent. A dyeing bath consisting of a micro-emulsion system involving a small proportion of n-butyl acetate was used, and the kinetics of dyeing were analysed at four temperatures (83, 90, 95 and 100...

Dynamical processes in atomic and molecular physics

CERN Document Server

Ogurtsov, Gennadi

2012-01-01

Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

Wetting kinetics of nanodroplets on lyophilic nanopillar-arrayed surfaces: A molecular dynamics study

Science.gov (United States)

Zong, Diyuan; Yang, Zhen; Duan, Yuanyuan

2017-10-01

Wetting kinetics of water droplets on substrates with lyophilic nanopillars was investigated using molecular dynamics simulations. Early spreading of the droplet is hindered by the nanopillars because of the penetration of the liquid which induce an extra dissipation in the droplet. Droplet spreading is mainly controlled by liquid viscosity and surface tension and not dependent on solid wettability. Propagation of the fringe film is hindered by the enhanced solid wettability because of the energy barrier introduced by the interaction between water molecules and nanopillars which increase with solid wettability.

Molecular moment similarity between several nucleoside analogs of thymidine and thymidine. sil@watson.ibm.com.

Science.gov (United States)

Silverman, B D; Pitman, M C; Platt, D E

1999-06-01

Molecular moment descriptors of the shape and charge distributions of twenty five nucleoside structures have been examined. The structures include thymidine as well as the difluorotoluene nucleoside analog which has been found to pair efficiently with adenine by polymerase catalysis. The remaining twenty three structures have been chosen to be as structurally similar to thymidine and to the difluorotoluene nucleoside analog as possible. The moment descriptors which include a description of the relationship of molecular charge to shape show the difluorotoluene nucleoside to be one of the most proximate molecules to thymidine in the space of the molecular moments. The calculations, therefore, suggest that polymerase specificity might be not only a consequence of molecular steric features alone but also of the molecular electrostatic environment and its registration with molecular shape.

Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

International Nuclear Information System (INIS)

Cernusca, S.; Winter, H.P.; Aumayr, F.; Diez Muino, R.; Juaristi, J.I.

2003-01-01

Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy <10 keV) on atomically clean surfaces of carbon-fiber inforced graphite used as first-wall armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to 'projectile molecular effects' (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials

Molecular projectile effects for kinetic electron emission from carbon- and metal-surfaces bombarded by slow hydrogen ions

CERN Document Server

Cernusca, S; Aumayr, F; Diez-Muino, R; Juaristi, J I

2003-01-01

Total yields for kinetic electron emission (KE) have been determined for impact of hydrogen monomer-, dimer- and trimer-ions (impact energy <10 keV) on atomically clean surfaces of carbon-fiber inforced graphite used as first-wall armour in magnetic fusion devices. The data are compared with KE yields for impact of same projectile ions on atomically clean highly oriented pyrolytic graphite and polycrystalline gold. We discuss KE yields for the different targets if bombarded by equally fast molecular and atomic ions in view to 'projectile molecular effects' (different yields per proton for equally fast atomic and molecular ions), which are expected from calculated electronic projectile energy losses in these target materials.

Kinetic Theory and Simulation of Single-Channel Water Transport

Science.gov (United States)

Tajkhorshid, Emad; Zhu, Fangqiang; Schulten, Klaus

Water translocation between various compartments of a system is a fundamental process in biology of all living cells and in a wide variety of technological problems. The process is of interest in different fields of physiology, physical chemistry, and physics, and many scientists have tried to describe the process through physical models. Owing to advances in computer simulation of molecular processes at an atomic level, water transport has been studied in a variety of molecular systems ranging from biological water channels to artificial nanotubes. While simulations have successfully described various kinetic aspects of water transport, offering a simple, unified model to describe trans-channel translocation of water turned out to be a nontrivial task.

Modeling texture kinetics during thermal processing of potato products.

Science.gov (United States)

Moyano, P C; Troncoso, E; Pedreschi, F

2007-03-01

A kinetic model based on 2 irreversible serial chemical reactions has been proposed to fit experimental data of texture changes during thermal processing of potato products. The model links dimensionless maximum force F*(MAX) with processing time. Experimental texture changes were obtained during frying of French fries and potato chips at different temperatures, while literature data for blanching/cooking of potato cubes have been considered. A satisfactory agreement between experimental and predicted values was observed, with root mean square values (RMSs) in the range of 4.7% to 16.4% for French fries and 16.7% to 29.3% for potato chips. In the case of blanching/cooking, the proposed model gave RMSs in the range of 1.2% to 17.6%, much better than the 6.2% to 44.0% obtained with the traditional 1st-order kinetics. The model is able to predict likewise the transition from softening to hardening of the tissue during frying.

Molecular theory of mass transfer kinetics and dynamics at gas-water interface

International Nuclear Information System (INIS)

Morita, Akihiro; Garrett, Bruce C

2008-01-01

The mass transfer mechanism across gas-water interface is studied with molecular dynamics (MD) simulation. The MD results provide a robust and qualitatively consistent picture to previous studies about microscopic aspects of mass transfer, including interface structure, free energy profiles for the uptake, scattering dynamics and energy relaxation of impinging molecules. These MD results are quantitatively compared with experimental uptake measurements, and we find that the apparent inconsistency between MD and experiment could be partly resolved by precise decomposition of the observed kinetics into elemental steps. Remaining issues and future perspectives toward constructing a comprehensive multi-scale description of interfacial mass transfer are summarized.

Dosimetric features and kinetic analysis of thermoluminescence from ultra-high molecular weight polyethylene

Science.gov (United States)

Chithambo, M. L.

2012-08-01

Thermoluminescence (TL) from beta irradiated ultra-high molecular weight polyethylene has been studied for measurements between 30 and 200 °C. An aliquot studied in this work produced TL glow curves consisting of two peaks, the main peak at 88 °C and a weaker intensity peak at 148 °C for heating at 1 °C s-1 following an excitation dose of 215 Gy. The position of the main peak is poorly reproducible for heating rates of 0.2 and 0.6 °C s-1 investigated with the peak position decreasing when the sample is freshly irradiated and the TL re-measured. The said change in peak position is however less of an effect for measurements made at 1 °C s-1 with the peak position being fairly reproducible in this case. Further measurements of the dosimetric properties of ultra-high molecular weight polyethylene showed that its dose response is linear from 26 Gy to about 161 Gy but exhibits slower growth in intensity with dose from about 860 Gy after regions of sub- and supra-linearity in between. If the TL is not measured immediately after irradiation, the signal fades with the delay approximately exponentially. In addition, a number of tests including phosphorescence analysis showed the possibility that the order of kinetics might not be unique but sensitive to several factors including measurement temperature. Thus for instance, the dependence of the peak position on the stop temperature in the partial heating procedure Tm - Tstop implied first-order kinetics but analysis of the geometrical factor μg for the same set of data gave μg = 0.46 ± 0.03 a value corresponding to characteristics somewhat intermediate between first and second order. In comparison, the results of analysis of the phosphorescence recorded at several temperatures on the rising edge of the main peak were only in agreement for measurements at 40 °C with general-order analysis suggesting second-order kinetics apply as did TL-like transformation of the monotonic phosphorescence decay. Both results were

Variations in calcite growth kinetics with surface topography: molecular dynamics simulations and process-based growth kinetics modelling

NARCIS (Netherlands)

Wolthers, M.; Di Tommaso, D.; Du, Zhimei; de Leeuw, Nora H.

2013-01-01

It is generally accepted that cation dehydration is the rate-limiting step to crystal growth from aqueous solution. Here we employ classical molecular dynamics simulations to show that the water exchange frequency at structurally distinct calcium sites in the calcite surface varies by about two

A first principles study of the oxidation energetics and kinetics of realgar

Science.gov (United States)

Renock, Devon; Becker, Udo

2010-08-01

Quantum-mechanical calculations allow resolving and quantifying in detail important aspects of reaction mechanisms such as spin transitions and oxygen dissociation that can be the major rate-limiting steps in redox processes on sulfide and oxide surfaces. In addition, this knowledge can help experimentalists in setting up the framework of rate equations that can be used to describe the kinetics of, e.g., oxidation processes. The unique molecular crystal structure of realgar, As 4S 4 clusters held together by van der Waals bonds, allows for a convenient quantum-mechanical (q.m.) cluster approach to investigate the thermodynamics and kinetic pathways of oxidation. The interaction of As 4S 4 clusters with oxygen and co-adsorbed ions provides a model system for understanding the molecular-scale processes that underpin empirically-derived rate expressions, and provides clues to the oxidation mechanisms of other sulfides and oxides. Two activated processes are shown to dominate the kinetics of oxidation by molecular oxygen: (i) a paramagnetic 3O to diamagnetic 1O spin transition and (ii) oxygen dissociation on the surface, in that order. The activation energies for the spin transition and O 2 dissociation step were determined to be 1.1 eV (106 kJ/mol) and 0.9 eV (87 kJ/mol), respectively, if molecular oxygen is the only reactant on the surface. In the case of As 4S 4, q.m. calculations reveal that 3O transfers its spin to the cluster and forms a low-spin, peroxo intermediate on the surface before dissociating. The adsorption of a hydroxide ion on the surface proximate to the 3O adsorption site changes the adsorption mechanism by lowering the activation energy barriers for both the spin transition (0.30 eV/29 kJ/mol) and the O 2 dissociation step (0.72 eV/69 kJ/mol). Thus, while spin transition is rate limiting for oxidation with O 2 alone, dissociation becomes the rate-limiting step for oxidation with co-adsorption of OH -. First-principles, periodic calculations of the

Monin-Obukhov Similarity Functions of the Structure Parameter of Temperature and Turbulent Kinetic Energy Dissipation Rate in the Stable Boundary Layer

NARCIS (Netherlands)

Hartogensis, O.K.; Debruin, H.A.R.

2005-01-01

The Monin-Obukhov similarity theory (MOST) functions fepsi; and fT, of the dissipation rate of turbulent kinetic energy (TKE), ¿, and the structure parameter of temperature, CT2, were determined for the stable atmospheric surface layer using data gathered in the context of CASES-99. These data cover

A new study of the kinetics of curd production in the process of cheese manufacture.

Science.gov (United States)

Muñoz, Susana Vargas; Torres, Maykel González; Guerrero, Francisco Quintanilla; Talavera, Rogelio Rodríguez

2017-11-01

We studied the role played by temperature and rennet concentration in the coagulation process for cheese manufacture and the evaluation of their kinetics. We concluded that temperature is the main factor that determines the kinetics. The rennet concentration was unimportant probably due to the fast action of the enzyme chymosin. The Dynamic light scattering technique allowed measuring the aggregate's size and their formation kinetics. The volume fraction of solids was determined from viscosity measurements, showing profiles that are in agreement with the size profiles. The results indicate that the formation of the aggregates for rennet cheese is strongly dependent on temperature and rennet concentration. The results revealed that at 35·5 °C the volume fraction of solids has the maximum slope, indicating that at this temperature the curd is formed rapidly. The optimal temperature throughout the process was established. Second-order kinetics were obtained for the process. We observed a quadratic dependence between the rennet volume and the volume fraction of solids (curd), thereby indicating that the kinetics of the curd production should be of order two.

Probing specific molecular processes and intermediates by time-resolved Fourier transform infrared spectroscopy: application to the bacteriorhodopsin photocycle.

Science.gov (United States)

Lórenz-Fonfría, Víctor A; Kandori, Hideki; Padrós, Esteve

2011-06-23

We present a general approach for probing the kinetics of specific molecular processes in proteins by time-resolved Fourier transform infrared (IR) spectroscopy. Using bacteriorhodopsin (bR) as a model we demonstrate that by appropriately monitoring some selected IR bands it is possible obtaining the kinetics of the most important events occurring in the photocycle, namely changes in the chromophore and the protein backbone conformation, and changes in the protonation state of the key residues implicated in the proton transfers. Besides confirming widely accepted views of the bR photocycle, our analysis also sheds light into some disputed issues: the degree of retinal torsion in the L intermediate to respect the ground state; the possibility of a proton transfer from Asp85 to Asp212; the relationship between the protonation/deprotonation of Asp85 and the proton release complex; and the timing of the protein backbone dynamics. By providing a direct way to estimate the kinetics of photocycle intermediates the present approach opens new prospects for a robust quantitative kinetic analysis of the bR photocycle, which could also benefit the study of other proteins involved in photosynthesis, in phototaxis, or in respiratory chains.

Dose dependent oxidation kinetics of lipids in fish during irradiation processing

International Nuclear Information System (INIS)

Tukenmez, I.; Ersen, M.S.; Bakioglu, A.T.; Bicer, A.; Pamuk, V.

1997-01-01

Kinetic aspects of the development of lipid oxidation in complex foods as fish in the course of irradiation were analyzed with respect to the associated formation of malonaldehyde (MA) through the reactions modified so as to be consistent with those in complex foods as fish. Air-packed anchovy (Engraulis encrasicholus) samples in polyethylene pouches were irradiated at the doses of 1, 2, 5, 10, 15,20 and 25 kGy at 20 o C in a Cs-137 gamma irradiator of 1.806 kGy/h dose rate. Immediately after each irradiation, MA contents of irradiated and unirradiated samples were determined by thiobarbituric acid test. Based on the MA formation, a kinetic model to simulate the apparent oxidation of lipid in fish as a function of irradiation dose was derived from the rate equations consistent with modified reactions. Kinetic parameters and simulation were related to conditions of lipid oxidation, and associated rancidity state of fish with respect to the doses applied in different irradiation-preservation processes. Numerical values of kinetic parameters based on the MA formation were found as a threshold dose of 0.375 kGy, an apparent yield of 1.871 μmol/kg kGy, and a maximum attainable concentration of 15.853 μmol/kg which may be used for process control and dosimetry. (author)

An analysis of the kinetics of molecular response during the first trimester of treatment with nilotinib in newly diagnosed chronic myeloid leukemia patients in chronic phase.

Science.gov (United States)

Steegmann, Juan Luis; Colomer, Dolors; Gómez-Casares, Maria-Teresa; García-Gutiérrez, Valentín; Ortí, Guillermo; Ramírez-Payer, Angel; Olavarria, Eduardo; Vall-Llovera, Ferrán; Giraldo, Pilar; Conde, Eulogio; Vallansot, Rolando; López-Lorenzo, Jose Luis; Palomera, Luis; Álvarez-Larrán, Alberto; Conesa, Venancio; Bautista, Guiomar; Casas, Laura; Giles, Frank; Hochhaus, Andreas; Casado-Montero, Luis Felipe

2017-10-01

This study was aimed to analyze the association of very early molecular response to nilotinib with the achievement of deep molecular response (MR4) at 18 months. We hypothesized that the BCR-ABL1 levels during the first 3 months of therapy, and the kinetics of their descent in this period, could be predictive of deep molecular response thereafter. This substudy of the ENEST1st trial included 60 patients with chronic myeloid leukemia in chronic phase treated with front-line nilotinib, and BCR-ABL1IS levels were measured using GUS as the control gene. The analysis included seven time points during the first trimester of treatment (baseline and fortnightly thereafter). The rates of MMR at 12 months, and of MR4 at 18 months (primary variable of the study), were 70 and 41%, respectively, similar to those obtained in the core study. BCR-ABL1IS ≤10% was achieved at 1, 1.5, 2 and 3 months in 50, 70, 83 and 93% of the patients, respectively. The observed shape of the BCR-ABL1IS descent was biphasic, with a faster slope during the first trimester and a median halving time (HT) of 11 days, the shortest reported in the literature. An HT ≤13 days was predictive of MMR at 12 months and MR4 at 18 months. The association of a shorter HT with response provides a rationale for exploring very early kinetics patterns in all patients treated with potent TKIs such as nilotinib.

Validation of kinetics similarity in qPCR

Czech Academy of Sciences Publication Activity Database

Bar, T.; Kubista, Mikael; Tichopád, Aleš

2012-01-01

Roč. 40, č. 4 (2012), s. 1395-1406 ISSN 0305-1048 R&D Projects: GA ČR GAP303/10/1338; GA ČR GA301/09/1752 Institutional research plan: CEZ:AV0Z50520701 Keywords : REAL-TIME PCR * POLYMERASE-CHAIN-REACTION * SYBR-GREEN-I Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.278, year: 2012

Stable non-Gaussian self-similar processes with stationary increments

CERN Document Server

Pipiras, Vladas

2017-01-01

This book provides a self-contained presentation on the structure of a large class of stable processes, known as self-similar mixed moving averages. The authors present a way to describe and classify these processes by relating them to so-called deterministic flows. The first sections in the book review random variables, stochastic processes, and integrals, moving on to rigidity and flows, and finally ending with mixed moving averages and self-similarity. In-depth appendices are also included. This book is aimed at graduate students and researchers working in probability theory and statistics.

The Characterization of Cognitive Processes Involved in Chemical Kinetics Using a Blended Processing Framework

Science.gov (United States)

Bain, Kinsey; Rodriguez, Jon-Marc G.; Moon, Alena; Towns, Marcy H.

2018-01-01

Chemical kinetics is a highly quantitative content area that involves the use of multiple mathematical representations to model processes and is a context that is under-investigated in the literature. This qualitative study explored undergraduate student integration of chemistry and mathematics during problem solving in the context of chemical…

Homeostasis-altering molecular processes as mechanisms of inflammasome activation.

Science.gov (United States)

Liston, Adrian; Masters, Seth L

2017-03-01

The innate immune system uses a distinct set of germline-encoded pattern recognition receptors (PRRs) to initiate downstream inflammatory cascades. This recognition system is in stark contrast to the adaptive immune system, which relies on highly variable, randomly generated antigen receptors. A key limitation of the innate immune system's reliance on fixed PRRs is its inflexibility in responding to rapidly evolving pathogens. Recent advances in our understanding of inflammasome activation suggest that the innate immune system also has sophisticated mechanisms for responding to pathogens for which there is no fixed PRR. This includes the recognition of debris from dying cells, known as danger-associated molecular patterns (DAMPs), which can directly activate PRRs in a similar manner to pathogen-associated molecular patterns (PAMPs). Distinct from this, emerging data for the inflammasome components NLRP3 (NOD-, LRR- and pyrin domain-containing 3) and pyrin suggest that they do not directly detect molecular patterns, but instead act as signal integrators that are capable of detecting perturbations in cytoplasmic homeostasis, for example, as initiated by infection. Monitoring these perturbations, which we term 'homeostasis-altering molecular processes' (HAMPs), provides potent flexibility in the capacity of the innate immune system to detect evolutionarily novel infections; however, HAMP sensing may also underlie the sterile inflammation that drives chronic inflammatory diseases.

Kinetics parameters of a slurry remediation process in rotating drum bioreactors

International Nuclear Information System (INIS)

Esquivel-Rios, I.; Rodriguez-Meza, M. A.; Barrera-Cortes, J.

2009-01-01

The knowledge of biotransformation pollution dynamics in any systems is important for design and optimization purposes of biochemical processes involved. this is focus to the determination of kinetics parameters such as the maximum specific growth rate (μMAX), saturation constant (Ks), biomass yield (YX/S; X: biomass, S: substrate) and oxygen consumption (YO 2 /S; O 2 : oxygen). Several approximations, based on Monod equation, have been developed for estimating kinetics parameters in terms of concentration and type of substrate, bioprocess type and microflora available. (Author)

On kinetic description of electromagnetic processes in a quantum plasma

International Nuclear Information System (INIS)

Tyshetskiy, Yu.; Vladimirov, S. V.; Kompaneets, R.

2011-01-01

A nonlinear kinetic equation for nonrelativistic quantum plasma with electromagnetic interaction of particles is obtained in the Hartree's mean-field approximation. It is cast in a convenient form of Vlasov-Boltzmann-type equation with ''quantum interference integral'', which allows for relatively straightforward modification of existing classical Vlasov codes to incorporate quantum effects (quantum statistics and quantum interference of overlapping particles wave functions), without changing the bulk of the codes. Such modification (upgrade) of existing Vlasov codes may provide a direct and effective path to numerical simulations of nonlinear electrostatic and electromagnetic phenomena in quantum plasmas, especially of processes where kinetic effects are important (e.g., modulational interactions and stimulated scattering phenomena involving plasma modes at short wavelengths or high-order kinetic modes, dynamical screening and interaction of charges in quantum plasma, etc.) Moreover, numerical approaches involving such modified Vlasov codes would provide a useful basis for theoretical analyses of quantum plasmas, as quantum and classical effects can be easily separated there.

Kinetic temperature of massive star-forming molecular clumps measured with formaldehyde. III. The Orion molecular cloud 1

Science.gov (United States)

Tang, X. D.; Henkel, C.; Menten, K. M.; Wyrowski, F.; Brinkmann, N.; Zheng, X. W.; Gong, Y.; Lin, Y. X.; Esimbek, J.; Zhou, J. J.; Yuan, Y.; Li, D. L.; He, Y. X.

2018-01-01

We mapped the kinetic temperature structure of the Orion molecular cloud 1 (OMC-1) with para-H2CO (JKaKc = 303-202, 322-221, and 321-220) using the APEX 12 m telescope. This is compared with the temperatures derived from the ratio of the NH3 (2, 2)/(1, 1) inversion lines and the dust emission. Using the RADEX non-LTE model, we derive the gas kinetic temperature modeling the measured averaged line ratios of para-H2CO 322-221/303-202 and 321-220/303-202. The gas kinetic temperatures derived from the para-H2CO line ratios are warm, ranging from 30 to >200 K with an average of 62 ± 2 K at a spatial density of 105 cm-3. These temperatures are higher than those obtained from NH3 (2, 2)/(1, 1) and CH3CCH (6-5) in the OMC-1 region. The gas kinetic temperatures derived from para-H2CO agree with those obtained from warm dust components measured in the mid infrared (MIR), which indicates that the para-H2CO (3-2) ratios trace dense and warm gas. The cold dust components measured in the far infrared (FIR) are consistent with those measured with NH3 (2, 2)/(1, 1) and the CH3CCH (6-5) line series. With dust at MIR wavelengths and para-H2CO (3-2) on one side, and dust at FIR wavelengths, NH3 (2, 2)/(1, 1), and CH3CCH (6-5) on the other, dust and gas temperatures appear to be equivalent in the dense gas (n(H2) ≳ 104 cm-3) of the OMC-1 region, but provide a bimodal distribution, one more directly related to star formation than the other. The non-thermal velocity dispersions of para-H2CO are positively correlated with the gas kinetic temperatures in regions of strong non-thermal motion (Mach number ≳ 2.5) of the OMC-1, implying that the higher temperature traced by para-H2CO is related to turbulence on a 0.06 pc scale. Combining the temperature measurements with para-H2CO and NH3 (2, 2)/(1, 1) line ratios, we find direct evidence for the dense gas along the northern part of the OMC-1 10 km s-1 filament heated by radiation from the central Orion nebula. The reduced datacubes are

Effect of the molecular structure of lignin-based polyoxyethylene ether on enzymatic hydrolysis efficiency and kinetics of lignocelluloses.

Science.gov (United States)

Lin, Xuliang; Qiu, Xueqing; Zhu, Duming; Li, Zihao; Zhan, Ningxin; Zheng, Jieyi; Lou, Hongming; Zhou, Mingsong; Yang, Dongjie

2015-10-01

Effect of the molecular structure of lignin-based polyoxyethylene ether (EHL-PEG) on enzymatic hydrolysis of Avicel and corn stover was investigated. With the increase of PEG contents and molecular weight of EHL-PEG, glucose yield of corn stover increased. EHL-PEG enhanced enzymatic hydrolysis of corn stover significantly at buffer pH 4.8-5.5. Glucose yield of corn stover at 20% solid content increased from 32.8% to 63.8% by adding EHL-PEG, while that with PEG4600 was 54.2%. Effect of EHL-PEG on enzymatic hydrolysis kinetics of cellulose film was studied by quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). An enhancing mechanism of EHL-PEG on enzymatic hydrolysis kinetics of cellulose was proposed. Cellulase aggregates dispersed by EHL-PEG excavated extensive cavities into the surface of cellulose film, making the film become more loose and exposed. After the maximum enzymatic hydrolysis rate, the film was mainly peeled off layer by layer until equilibrium. Copyright © 2015 Elsevier Ltd. All rights reserved.

Recrystallization kinetics of nanostructured copper processed by dynamic plastic deformation

DEFF Research Database (Denmark)

Lin, Fengxiang; Zhang, Yubin; Pantleon, Wolfgang

2012-01-01

The recrystallization kinetics of nanostructured copper samples processed by dynamic plastic deformation was investigated by electron backscatter diffraction. It was found that the evolution of the recrystallized volume fraction as a function of annealing time has a very low slope (n=0.37) when...

Co-pyrolysis characteristics and kinetics of coal and plastic blends

International Nuclear Information System (INIS)

Zhou Limin; Luo Taian; Huang Qunwu

2009-01-01

Co-pyrolysis behaviors of different plastics (high density polyethylene, low density polyethylene and polypropylene), low volatile coal (LVC) and their mixtures were investigated by TGA. Experiments were conducted under N 2 atmosphere at heating rate of 20 deg. C/min from room temperature to 750 deg. C. The results showed that the thermal degradation temperature range of plastic was 438-521 deg. C, while that of coal (LVC) was 174-710 deg. C. Plastics showed similar pyrolysis characteristics due to similar chemical bonds in their molecular structures. The overlapping degradation temperature interval between coal and plastic provide an opportunity for free radicals from coal pyrolysis to participate in the reactions of plastic decomposition. The difference of weight loss percent (ΔW) between experimental and theoretical ones, calculated as an algebraic sum of those from each separated component, ΔW is 2.0-2.7% at the pyrolysis temperature higher than 530 deg. C, which indicates that the synergistic effect during pyrolysis occurs mainly in the high temperature region. The kinetic studies were performed according to Coats and Redfern method for first-order reaction. It was found that for plastics (HDPE, LDPE and PP), the pyrolysis process can be described by one first-order reaction. However, for LVC and LVC/plastic blends, this process can be described by three and four consecutive first-order reactions, respectively. The estimated kinetic parameters viz., activation energies and pre-exponential factors for coal, plastic and their blends, were found to be in the range of 35.7-572.8 kJ/mol and 27-1.7 x 10 38 min -1 , respectively

Simulation of kinetic processes in the nuclear-excited helium non-ideal dusty plasma

International Nuclear Information System (INIS)

Budnik, A.P.; Kosarev, V.A.; Rykov, V.A.; Fortov, V.E.; Vladimirov, V.I.; Deputatova, L.V.

2009-01-01

The paper is devoted to the studying of kinetic processes in the nuclear-excited plasma of the helium gas with the fine uranium (or its chemical compounds) particles admixture. A new theoretical model for the mathematical simulation of the kinetic processes in dusty plasma of helium gas was developed. The main goal of this investigation is to determine possibilities of a creation of non-ideal dusty plasma, containing nano- and micro-particles, and excited by fission fragments (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

The influence of molecular weight in radiotracers of inflamators processes

International Nuclear Information System (INIS)

Mesa Duennas, N.; Zayas Crespo, F.; Piedra Mazorra, J.; Diaz Barreto, M; Rodriguez Alfonso, M.E.; Perez Fuentes, A.

2004-01-01

Four 99mTc-radiopharmaceuticals (RPs) were compared as a radiotracers of inflammatory process. The RPs were divided in two groups according to their molecular weights and nature. One group included the human IgG and the ior t3 MoAb (anti-CD3), another included the Ciprofloxacine and the DMSA. The RPs were studied by different quality controls, and a biodistribution study in an aseptic inflammatory model made by steril Carragenin. The results obtained in the reduction of the immunoglobulins with 2-mercaptoethanol and sodium metabisulphite demonstrated that both reducing agents were equivalent, because the radiochemical purity obtained were similar and independent of the immunoglobulins. The biodistribution demonstrated a higher incorporation for the radiopharmaceuticals of high molecular weight, and the highest values were obtained with the 2-mercaptoethanol

Effects of different per translational kinetics on the dynamics of a core circadian clock model.

Science.gov (United States)

Nieto, Paula S; Revelli, Jorge A; Garbarino-Pico, Eduardo; Condat, Carlos A; Guido, Mario E; Tamarit, Francisco A

2015-01-01

Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

Science.gov (United States)

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.

Molecular processes of transgenerational acclimation to a warming ocean

KAUST Repository

Veilleux, Heather D.; Ryu, Tae Woo; Donelson, Jennifer M.; van Herwerden, Lynne; Seridi, Loqmane; Ghosheh, Yanal; Berumen, Michael L.; Leggat, William; Ravasi, Timothy; Munday, Philip L.

2015-01-01

Some animals have the remarkable capacity to acclimate across generations to projected future climate change1, 2, 3, 4; however, the underlying molecular processes are unknown. We sequenced and assembled de novo transcriptomes of adult tropical reef fish exposed developmentally or transgenerationally to projected future ocean temperatures and correlated the resulting expression profiles with acclimated metabolic traits from the same fish. We identified 69 contigs representing 53 key genes involved in thermal acclimation of aerobic capacity. Metabolic genes were among the most upregulated transgenerationally, suggesting shifts in energy production for maintaining performance at elevated temperatures. Furthermore, immune- and stress-responsive genes were upregulated transgenerationally, indicating a new complement of genes allowing the second generation of fish to better cope with elevated temperatures. Other differentially expressed genes were involved with tissue development and transcriptional regulation. Overall, we found a similar suite of differentially expressed genes among developmental and transgenerational treatments. Heat-shock protein genes were surprisingly unresponsive, indicating that short-term heat-stress responses may not be a good indicator of long-term acclimation capacity. Our results are the first to reveal the molecular processes that may enable marine fishes to adjust to a future warmer environment over multiple generations.

Molecular processes of transgenerational acclimation to a warming ocean

KAUST Repository

Veilleux, Heather D.

2015-07-20

Some animals have the remarkable capacity to acclimate across generations to projected future climate change1, 2, 3, 4; however, the underlying molecular processes are unknown. We sequenced and assembled de novo transcriptomes of adult tropical reef fish exposed developmentally or transgenerationally to projected future ocean temperatures and correlated the resulting expression profiles with acclimated metabolic traits from the same fish. We identified 69 contigs representing 53 key genes involved in thermal acclimation of aerobic capacity. Metabolic genes were among the most upregulated transgenerationally, suggesting shifts in energy production for maintaining performance at elevated temperatures. Furthermore, immune- and stress-responsive genes were upregulated transgenerationally, indicating a new complement of genes allowing the second generation of fish to better cope with elevated temperatures. Other differentially expressed genes were involved with tissue development and transcriptional regulation. Overall, we found a similar suite of differentially expressed genes among developmental and transgenerational treatments. Heat-shock protein genes were surprisingly unresponsive, indicating that short-term heat-stress responses may not be a good indicator of long-term acclimation capacity. Our results are the first to reveal the molecular processes that may enable marine fishes to adjust to a future warmer environment over multiple generations.

Fluorescence based molecular in vivo imaging

International Nuclear Information System (INIS)

Ebert, Bernd

2008-01-01

Molecular imaging represents a modern research area that allows the in vivo study of molecular biological process kinetics using appropriate probes and visualization methods. This methodology may be defined- apart from the contrast media injection - as non-abrasive. In order to reach an in vivo molecular process imaging as accurate as possible the effects of the used probes on the biological should not be too large. The contrast media as important part of the molecular imaging can significantly contribute to the understanding of molecular processes and to the development of tailored diagnostics and therapy. Since more than 15 years PTB is developing optic imaging systems that may be used for fluorescence based visualization of tissue phantoms, small animal models and the localization of tumors and their predecessors, and for the early recognition of inflammatory processes in clinical trials. Cellular changes occur during many diseases, thus the molecular imaging might be of importance for the early diagnosis of chronic inflammatory diseases. Fluorescent dyes can be used as unspecific or also as specific contrast media, which allow enhanced detection sensitivity

The simulation of molecular clouds formation in the Milky Way

Science.gov (United States)

Khoperskov, S. A.; Vasiliev, E. O.; Sobolev, A. M.; Khoperskov, A. V.

2013-01-01

Using 3D hydrodynamic calculations we simulate formation of molecular clouds in the Galaxy. The simulations take into account molecular hydrogen chemical kinetics, cooling and heating processes. Comprehensive gravitational potential accounts for contributions from the stellar bulge, two- and four-armed spiral structure, stellar disc, dark halo and takes into account self-gravitation of the gaseous component. Gas clouds in our model form in the spiral arms due to shear and wiggle instabilities and turn into molecular clouds after t ≳ 100 Myr. At the times t ˜ 100-300 Myr the clouds form hierarchical structures and agglomerations with the sizes of 100 pc and greater. We analyse physical properties of the simulated clouds and find that synthetic statistical distributions like mass spectrum, `mass-size' relation and velocity dispersion are close to those observed in the Galaxy. The synthetic l-v (galactic longitude-radial velocity) diagram of the simulated molecular gas distribution resembles observed one and displays a structure with appearance similar to molecular ring of the Galaxy. Existence of this structure in our modelling can be explained by superposition of emission from the galactic bar and the spiral arms at ˜3-4 kpc.

Photo-assisted Fenton type processes for the degradation of phenol: A kinetic study

International Nuclear Information System (INIS)

Kusic, Hrvoje; Koprivanac, Natalija; Bozic, Ana Loncaric; Selanec, Iva

2006-01-01

In this study the application of advanced oxidation processes (AOPs), dark Fenton and photo-assisted Fenton type processes; Fe 2+ /H 2 O 2 , Fe 3+ /H 2 O 2 , Fe 0 /H 2 O 2 , UV/Fe 2+ /H 2 O 2 , UV/Fe 3+ /H 2 O 2 and UV/Fe 0 /H 2 O 2 , for degradation of phenol as a model organic pollutant in the wastewater was investigated. A detail kinetic modeling which describes the degradation of phenol was performed. Mathematical models which predict phenol decomposition and formation of primary oxidation by-products: catechol, hydroquinone and benzoquinone, by applied processes were developed. The study also consist the modeling of mineralization kinetic of the phenol solution by applied AOPs. This part, besides well known reactions of Fenton and photo-Fenton chemistry, involves additional reactions which describe removal of iron from catalytic cycle through formation of ferric complexes and its regeneration induced by UV radiation. Phenol decomposition kinetic was monitored by HPLC analysis and total organic carbon content measurements (TOC). Complete phenol removal was obtained by all applied processes. Residual TOC by applied Fenton type processes ranged between 60.2 and 44.7%, while the efficiency of those processes was significantly enhanced in the presence of UV light, where residual TOC ranged between 15.2 and 2.4%

Masked-Volume-Wise PCA and "reference Logan" illustrate similar regional differences in kinetic behavior in human brain PET study using [11C]-PIB

Directory of Open Access Journals (Sweden)

Engler Henry

2009-01-01

Full Text Available Abstract Background Kinetic modeling using reference Logan is commonly used to analyze data obtained from dynamic Positron Emission Tomography (PET studies on patients with Alzheimer's disease (AD and healthy volunteers (HVs using amyloid imaging agent N-methyl [11C]2-(4'-methylaminophenyl-6-hydroxy-benzothiazole, [11C]-PIB. The aim of the present study was to explore whether results obtained using the newly introduced method, Masked Volume Wise Principal Component Analysis, MVW-PCA, were similar to the results obtained using reference Logan. Methods MVW-PCA and reference Logan were performed on dynamic PET images obtained from four Alzheimer's disease (AD patients on two occasions (baseline and follow-up and on four healthy volunteers (HVs. Regions of interest (ROIs of similar sizes were positioned in different parts of the brain in both AD patients and HVs where the difference between AD patients and HVs is largest. Signal-to-noise ratio (SNR and discrimination power (DP were calculated for images generated by the different methods and the results were compared both qualitatively and quantitatively. Results MVW-PCA generated images that illustrated similar regional binding patterns compared to reference Logan images and with slightly higher quality, enhanced contrast, improved SNR and DP, without being based on modeling assumptions. MVW-PCA also generated additional MVW-PC images by using the whole dataset, which illustrated regions with different and uncorrelated kinetic behaviors of the administered tracer. This additional information might improve the understanding of kinetic behavior of the administered tracer. Conclusion MVW-PCA is a potential multivariate method that without modeling assumptions generates high quality images, which illustrated similar regional changes compared to modeling methods such as reference Logan. In addition, MVW-PCA could be used as a new technique, applicable not only on dynamic human brain studies but also on

Focuss algorithm application in kinetic compartment modeling for PET tracer

International Nuclear Information System (INIS)

Huang Xinrui; Bao Shanglian

2004-01-01

Molecular imaging is in the process of becoming. Its application mostly depends on the molecular discovery process of imaging probes and drugs, from the mouse to the patient, from research to clinical practice. Positron emission tomography (PET) can non-invasively monitor . pharmacokinetic and functional processes of drugs in intact organisms at tracer concentrations by kinetic modeling. It has been known that for all biological systems, linear or nonlinear, if the system is injected by a tracer in a steady state, the distribution of the tracer follows the kinetics of a linear compartmental system, which has sums of exponential solutions. Based on the general compartmental description of the tracer's fate in vivo, we presented a novel kinetic modeling approach for the quantification of in vivo tracer studies with dynamic positron emission tomography (PET), which can determine a parsimonious model consisting with the measured data. This kinetic modeling technique allows for estimation of parametric images from a voxel based analysis and requires no a priori decision about the tracer's fate in vivo, instead determining the most appropriate model from the information contained within the kinetic data. Choosing a set of exponential functions, convolved with the plasma input function, as basis functions, the time activity curve of a region or a pixel can be written as a linear combination of the basis functions with corresponding coefficients. The number of non-zero coefficients returned corresponds to the model order which is related to the number of tissue compartments. The system macro parameters are simply determined using the focal underdetermined system solver (FOCUSS) algorithm. The FOCUSS algorithm is a nonparametric algorithm for finding localized energy solutions from limited data and is a recursive linear estimation procedure. FOCUSS algorithm usually converges very fast, so demands a few iterations. The effectiveness is verified by simulation and clinical

A conservative scheme of drift kinetic electrons for gyrokinetic simulation of kinetic-MHD processes in toroidal plasmas

Science.gov (United States)

Bao, J.; Liu, D.; Lin, Z.

2017-10-01

A conservative scheme of drift kinetic electrons for gyrokinetic simulations of kinetic-magnetohydrodynamic processes in toroidal plasmas has been formulated and verified. Both vector potential and electron perturbed distribution function are decomposed into adiabatic part with analytic solution and non-adiabatic part solved numerically. The adiabatic parallel electric field is solved directly from the electron adiabatic response, resulting in a high degree of accuracy. The consistency between electrostatic potential and parallel vector potential is enforced by using the electron continuity equation. Since particles are only used to calculate the non-adiabatic response, which is used to calculate the non-adiabatic vector potential through Ohm's law, the conservative scheme minimizes the electron particle noise and mitigates the cancellation problem. Linear dispersion relations of the kinetic Alfvén wave and the collisionless tearing mode in cylindrical geometry have been verified in gyrokinetic toroidal code simulations, which show that the perpendicular grid size can be larger than the electron collisionless skin depth when the mode wavelength is longer than the electron skin depth.

KINETICS PROCESSES OF DEHYDRATION AND HEATING FISH DURING FRYING, DURING SEMI HOT AND HOT SMOKING

Directory of Open Access Journals (Sweden)

V. A. Pokholchenko

2014-01-01

Full Text Available Summary. Calculated methods of graphing of curves for kinetics of dehydration and fish heating during the processes of frying, semi hot smoking and hot smoking have been developed. The offered methods of calculating are based on the basic regularities of heat and mass exchanges of these processes. Based on the research of the regularities of dehydration on the kinetic curves, critical points were identified, that characterize the transition from the moisture removal with lower energy of its bond with material to the removal of one with higher energy bond, also the influence of the product shrinkage on the velocity of the moisture removal. These points are characteristic for the temperature curves as well. It’s suggested for the temperature curve to be replaced by broken line that consists of three straight lines that are crossing in points, corresponded with the critical moistures and critical temperatures. Significant amount of the experimental material of the research of the kinetics of dehydration and fish heating under different modes is shown by authors in the form of generalized dependencies. The method allows modeling the processes of heating and dehydrating of fish and choosing the most rational modes based on the calculated data. The proposed technique makes it possible to construct the curves of the kinetics of heating and dehydration kinetics in processes of roasting, semi hot and hot smoked fish, which allows to optimize a particular process, design more efficient in terms of consumption of raw materials and energy technology, as well as to create better machines or upgrade existing equipment into account the relationship of heat and mass transfer processes.

Splenic B cells and antigen-specific B cells process anti-Ig in a similar manner

International Nuclear Information System (INIS)

Myers, C.D.; Vitetta, E.S.

1989-01-01

B lymphocytes can process and present antigen to T cells. However, the fate of native antigen after its binding to specific B cells, i.e., the intracellular events involved in the processing and recycling of the antigenic fragments to the cell surface for antigen presentation, are not well understood. In the present study, we demonstrate that murine B cells degrade anti-Ig molecules bound to their surface and release acid soluble fragments into the supernatant. We also demonstrate that the kinetics of this process are identical for anti-mu, anti-delta, and anti-light chain antibodies, indicating that both surface IgM and surface IgD are equally effective in binding antigen and directing its processing. We also describe the effects of azide, chloroquine, and irradiation on this process. To extend these studies to the processing of specifically bound antigen, we demonstrate that highly purified trinitrophenyl antigen-binding cells degrade anti-Ig molecules with the same kinetics as unpurified splenic B cells. Thus, this purified population provides a suitable model system for the analysis of antigen degradation by antigen-specific cells

Chemical kinetics and transport processes in supercritical fluid extraction of coal. Final report, August 10, 1990--December 30, 1992

Energy Technology Data Exchange (ETDEWEB)

McCoy, B.J.; Smith, J.M.; Wang, M.; Zhang, C.J.

1993-02-01

The overall objective of this project was to study the supercritical fluid extraction of hydrocarbons from coal. Beyond the practical concern of deriving products from coal, the research has provided insights into the structure, properties, and reactivities of coal. Information on engineering fundamentals of coal thermolysis and extraction, including physical and chemical processes, is presented in this final report. To accomplish the goals of the project we developed continuous-flow experiments for fixed-bed samples of coal that allow two types of analysis of the extract: continuous spectrophotometric absorbance measurements of the lumped concentration of extract, and chromatographic determinations of molecular-weight distributions as a function of time. Thermolysis of coal yields a complex mixture of many extract products whose molecular-weight distribution (MWD) varies with time for continuous-flow, semibatch experiments. The flow reactor with a differential, fixed bed of coal particles contacted by supercritical t-butanol was employed to provide dynamic MWD data by means of HPLC gel permeation chromatography of the extract. The experimental results, time-dependent MWDs of extract molecules, were interpreted by a novel mathematical model based on continuous-mixture kinetics for thermal cleavage of chemical bonds in the coal network. The parameters for the MWDs of extractable groups in the coal and the rate constants for one- and two-fragment reaction are determined from the experimental data. The significant effect of temperature on the kinetics of the extraction was explained in terms of one- and two-fragment reactions in the coal.

Structural insights into cholinesterases inhibition by harmane β-carbolinium derivatives: a kinetics-molecular modeling approach.

Science.gov (United States)

Torres, Juliana M; Lira, Aline F; Silva, Daniel R; Guzzo, Lucas M; Sant'Anna, Carlos M R; Kümmerle, Arthur E; Rumjanek, Victor M

2012-09-01

The natural indole alkaloids, the β-carbolines, are often associated with cholinesterase inhibition, especially their quaternary salts, which frequently have higher activity than the free bases. Due to lack of information explaining this fact in the literature, the cholinesterase inhibition by the natural product harmane and its two β-carbolinium synthetic derivative salts (N-methyl and N-ethyl) was explored, together with a combination of kinetics and a molecular modeling approach. The results, mainly for the β-carbolinium salts, demonstrated a noncompetitive inhibition profile, ruling out previous findings which associated cholinesterase inhibition by β-carbolinium salts to a possible mimicking of the choline moiety of the natural substrate, acetylcholine. Molecular modeling studies corroborate this kind of inhibition through analyses of inhibitor/enzyme and inhibitor/substrate/enzyme complexes of both enzymes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Demonstration of Functional Similarity of Proposed Biosimilar ABP 501 to Adalimumab.

Science.gov (United States)

Velayudhan, Jyoti; Chen, Yuh-Feng; Rohrbach, Amanda; Pastula, Christina; Maher, Gwen; Thomas, Heather; Brown, Ryan; Born, Teresa L

2016-08-01

Due to the complex molecular structure and proprietary manufacturing processes of monoclonal antibodies (mAbs), differences in structure and function may be expected during development of biosimilar mAbs. Important regulatory requirements for approval of biosimilar products involve comprehensive assessments of any potential differences between proposed biosimilars and reference mAbs, including differences in all known mechanisms of action, using sensitive and relevant methods. Any identified structural differences should not result in differences in biofunctional or clinical activity. A comprehensive assessment comparing the Amgen biosimilar candidate ABP 501 with FDA-licensed adalimumab (adalimumab [US]) and EU-authorized adalimumab (adalimumab [EU]) was conducted to demonstrate similarity in biofunctional activity. The functional similarity assessment included testing of binding kinetics to soluble tumor necrosis factor α (TNFα) and relative binding to transmembrane TNFα. The neutralization of TNFα-induced caspase activation, TNFα- and lymphotoxin-α (LTα)-induced chemokine production, and cytotoxicity was also tested. Binding to Fc-gamma receptors FcγRIa, FcγRIIa (131H), FcγRIIIa (158V and 158F), and neonatal Fc receptor (FcRn) was compared with the reference mAbs, as was antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. The data demonstrate that ABP 501 is similar to both adalimumab (US) and adalimumab (EU) with respect to evaluated biofunctional activities. Similarity in biofunctional activity is a critical component of the totality of evidence required for demonstration of biosimilarity. The functional similarity demonstrated for ABP 501 comprehensively assesses the known mechanisms of action of adalimumab, supporting the conclusion that ABP 501, adalimumab (US), and adalimumab (EU) are likely to be clinically similar.

How Monte Carlo heuristics aid to identify the physical processes of drug release kinetics.

Science.gov (United States)

Lecca, Paola

2018-01-01

We implement a Monte Carlo heuristic algorithm to model drug release from a solid dosage form. We show that with Monte Carlo simulations it is possible to identify and explain the causes of the unsatisfactory predictive power of current drug release models. It is well known that the power-law, the exponential models, as well as those derived from or inspired by them accurately reproduce only the first 60% of the release curve of a drug from a dosage form. In this study, by using Monte Carlo simulation approaches, we show that these models fit quite accurately almost the entire release profile when the release kinetics is not governed by the coexistence of different physico-chemical mechanisms. We show that the accuracy of the traditional models are comparable with those of Monte Carlo heuristics when these heuristics approximate and oversimply the phenomenology of drug release. This observation suggests to develop and use novel Monte Carlo simulation heuristics able to describe the complexity of the release kinetics, and consequently to generate data more similar to those observed in real experiments. Implementing Monte Carlo simulation heuristics of the drug release phenomenology may be much straightforward and efficient than hypothesizing and implementing from scratch complex mathematical models of the physical processes involved in drug release. Identifying and understanding through simulation heuristics what processes of this phenomenology reproduce the observed data and then formalize them in mathematics may allow avoiding time-consuming, trial-error based regression procedures. Three bullet points, highlighting the customization of the procedure. •An efficient heuristics based on Monte Carlo methods for simulating drug release from solid dosage form encodes is presented. It specifies the model of the physical process in a simple but accurate way in the formula of the Monte Carlo Micro Step (MCS) time interval.•Given the experimentally observed curve of

Kinetics of CO2 diffusion in human carbonic anhydrase: a study using molecular dynamics simulations and the Markov-state model.

Science.gov (United States)

Chen, Gong; Kong, Xian; Lu, Diannan; Wu, Jianzhong; Liu, Zheng

2017-05-10

Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO 2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO 2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO 2 diffusion in hCA-II is a rate-limiting step in the CO 2 diffusion-binding-reaction process. The equilibrium distribution of CO 2 shows its preferential accumulation within a hydrophobic domain in the protein core region. An analysis of the committors and reactive fluxes indicates that the main pathway for CO 2 diffusion into the active site of hCA-II is through a binding pocket where residue Gln 136 contributes to the maximal flux. The simulation results offer a new perspective on the CO 2 hydration kinetics and useful insights toward the development of novel biochemical processes for more efficient CO 2 sequestration and utilization.

Models for discrete-time self-similar vector processes with application to network traffic

Science.gov (United States)

Lee, Seungsin; Rao, Raghuveer M.; Narasimha, Rajesh

2003-07-01

The paper defines self-similarity for vector processes by employing the discrete-time continuous-dilation operation which has successfully been used previously by the authors to define 1-D discrete-time stochastic self-similar processes. To define self-similarity of vector processes, it is required to consider the cross-correlation functions between different 1-D processes as well as the autocorrelation function of each constituent 1-D process in it. System models to synthesize self-similar vector processes are constructed based on the definition. With these systems, it is possible to generate self-similar vector processes from white noise inputs. An important aspect of the proposed models is that they can be used to synthesize various types of self-similar vector processes by choosing proper parameters. Additionally, the paper presents evidence of vector self-similarity in two-channel wireless LAN data and applies the aforementioned systems to simulate the corresponding network traffic traces.

Molecular Theory of the Living Cell Concepts, Molecular Mechanisms, and Biomedical Applications

CERN Document Server

Ji, Sungchul

2012-01-01

This book presents a comprehensive molecular theory of the living cell based on over thirty concepts, principles and laws imported from thermodynamics, statistical mechanics, quantum mechanics, chemical kinetics, informatics, computer science, linguistics, semiotics, and philosophy. The author formulates physically, chemically and enzymologically realistic molecular mechanisms to account for the basic living processes such as ligand-receptor interactions, protein folding, single-molecule enzymic catalysis, force-generating mechanisms in molecular motors, signal transduction, regulation of the genome-wide RNA metabolism, morphogenesis, the micro-macro coupling in coordination dynamics, the origin of life, and the mechanisms of biological evolution itself. Possible solutions to basic and practical problems facing contemporary biology and biomedical sciences have been suggested, including pharmacotheragnostics and personalized medicine.

Modeling of subtle kinetic processes in plasma simulation

International Nuclear Information System (INIS)

Sydora, R.D.; Decyk, V.K.; Dawson, J.M.

1988-01-01

A new diagnostic method for plasma simulation models is presented which enables one to probe the subtle dielectric properties of the plasma medium. The procedure involves the removal of the background plasma response in order to isolate the effects of small perturbing influences which are externally added. We have found the technique accurately describes fundamental kinetic plasma behavior such as the shielding of individual test charges and currents. Wave emission studies and drag of test particles has been carried out in explicit particle algorithms as well as large time step implicit and gyrokinetic models. Accurate plasma behavior is produced and it is possible to investigate in detail, processes which can be compared with plasma kinetic theory. The technique of subtraction is not only limited to particle simulation models but also can be used in MHD or fluid models where resolution is difficult due to the intensity of the background response relative to the phenomena one is interested in measuring, such as a weakly grouwing instability or nonlinear mode coupling effect. (author)

Combined TGA-MS kinetic analysis of multistep processes. Thermal decomposition and ceramification of polysilazane and polysiloxane preceramic polymers.

Science.gov (United States)

García-Garrido, C; Sánchez-Jiménez, P E; Pérez-Maqueda, L A; Perejón, A; Criado, José M

2016-10-26

The polymer-to-ceramic transformation kinetics of two widely employed ceramic precursors, 1,3,5,7-tetramethyl-1,3,5,7-tetravinylcyclotetrasiloxane (TTCS) and polyureamethylvinylsilazane (CERASET), have been investigated using coupled thermogravimetry and mass spectrometry (TG-MS), Raman, XRD and FTIR. The thermally induced decomposition of the pre-ceramic polymer is the critical step in the synthesis of polymer derived ceramics (PDCs) and accurate kinetic modeling is key to attaining a complete understanding of the underlying process and to attempt any behavior predictions. However, obtaining a precise kinetic description of processes of such complexity, consisting of several largely overlapping physico-chemical processes comprising the cleavage of the starting polymeric network and the release of organic moieties, is extremely difficult. Here, by using the evolved gases detected by MS as a guide it has been possible to determine the number of steps that compose the overall process, which was subsequently resolved using a semiempirical deconvolution method based on the Frasier-Suzuki function. Such a function is more appropriate that the more usual Gaussian or Lorentzian functions since it takes into account the intrinsic asymmetry of kinetic curves. Then, the kinetic parameters of each constituent step were independently determined using both model-free and model-fitting procedures, and it was found that the processes obey mostly diffusion models which can be attributed to the diffusion of the released gases through the solid matrix. The validity of the obtained kinetic parameters was tested not only by the successful reconstruction of the original experimental curves, but also by predicting the kinetic curves of the overall processes yielded by different thermal schedules and by a mixed TTCS-CERASET precursor.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

Science.gov (United States)

Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

2017-08-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

On-the-Fly Kinetic Monte Carlo Simulation of Aqueous Phase Advanced Oxidation Processes.

Science.gov (United States)

Guo, Xin; Minakata, Daisuke; Crittenden, John

2015-08-04

We have developed an on-the-fly kinetic Monte Carlo (KMC) model to predict the degradation mechanisms and fates of intermediates and byproducts that are produced during aqueous-phase advanced oxidation processes (AOPs). The on-the-fly KMC model is composed of a reaction pathway generator, a reaction rate constant estimator, a mechanistic reduction module, and a KMC solver. The novelty of this work is that we develop the pathway as we march forward in time rather than developing the pathway before we use the KMC method to solve the equations. As a result, we have fewer reactions to consider, and we have greater computational efficiency. We have verified this on-the-fly KMC model for the degradation of polyacrylamide (PAM) using UV light and titanium dioxide (i.e., UV/TiO2). Using the on-the-fly KMC model, we were able to predict the time-dependent profiles of the average molecular weight for PAM. The model provided detailed and quantitative insights into the time evolution of the molecular weight distribution and reaction mechanism. We also verified our on-the-fly KMC model for the destruction of (1) acetone, (2) trichloroethylene (TCE), and (3) polyethylene glycol (PEG) for the ultraviolet light and hydrogen peroxide AOP. We demonstrated that the on-the-fly KMC model can achieve the same accuracy as the computer-based first-principles KMC (CF-KMC) model, which has already been validated in our earlier work. The on-the-fly KMC is particularly suitable for molecules with large molecular weights (e.g., polymers) because the degradation mechanisms for large molecules can result in hundreds of thousands to even millions of reactions. The ordinary differential equations (ODEs) that describe the degradation pathways cannot be solved using traditional numerical methods, but the KMC can solve these equations.

Detailed Modelling of Kinetic Biodegradation Processes in a Laboratory Mmicrocosm

Science.gov (United States)

Watson, I.; Oswald, S.; Banwart, S.; Mayer, U.

2003-04-01

Biodegradation of organic contaminants in soil and groundwater usually takes places via different redox processes happening sequentially as well as simultaneously. We used numerical modelling of a long-term lab microcosm experiment to simulate the dynamic behaviour of fermentation and respiration in the aqueous phase in contact with the sandstone material, and to develop a conceptual model describing these processes. Aqueous speciation, surface complexation, mineral dissolution and precipitation were taken into account also. Fermentation can be the first step of the degradation process producing intermediate species, which are subsequently consumed by TEAPs. Microbial growth and substrate utilisation kinetics are coupled via a formulation that also includes aqueous speciation and other geochemical reactions including surface complexation, mineral dissolution and precipitation. Competitive exclusion between TEAPs is integral to the conceptual model of the simulation, and the results indicate that exclusion is not complete, but some overlap is found between TEAPs. The model was used to test approaches like the partial equilibrium approach that currently make use of hydrogen levels to diagnose prevalent TEAPs in groundwater. The observed pattern of hydrogen and acetate concentrations were reproduced well by the simulations, and the results show the relevance of kinetics, lag times and inhibition, and especially that intermediate products play a key role.

Kinetic Modeling of a Silicon Refining Process in a Moist Hydrogen Atmosphere

Science.gov (United States)

Chen, Zhiyuan; Morita, Kazuki

2018-06-01

We developed a kinetic model that considers both silicon loss and boron removal in a metallurgical grade silicon refining process. This model was based on the hypotheses of reversible reactions. The reaction rate coefficient kept the same form but error of terminal boron concentration could be introduced when relating irreversible reactions. Experimental data from published studies were used to develop a model that fit the existing data. At 1500 °C, our kinetic analysis suggested that refining silicon in a moist hydrogen atmosphere generates several primary volatile species, including SiO, SiH, HBO, and HBO2. Using the experimental data and the kinetic analysis of volatile species, we developed a model that predicts a linear relationship between the reaction rate coefficient k and both the quadratic function of p(H2O) and the square root of p(H2). Moreover, the model predicted the partial pressure values for the predominant volatile species and the prediction was confirmed by the thermodynamic calculations, indicating the reliability of the model. We believe this model provides a foundation for designing a silicon refining process with a fast boron removal rate and low silicon loss.

A kinetic model for chemical neurotransmission

Science.gov (United States)

Ramirez-Santiago, Guillermo; Martinez-Valencia, Alejandro; Fernandez de Miguel, Francisco

Recent experimental observations in presynaptic terminals at the neuromuscular junction indicate that there are stereotyped patterns of cooperativeness in the fusion of adjacent vesicles. That is, a vesicle in hemifusion process appears on the side of a fused vesicle and which is followed by another vesicle in a priming state while the next one is in a docking state. In this talk we present a kinetic model for this morphological pattern in which each vesicle state previous to the exocytosis is represented by a kinetic state. This chain states kinetic model can be analyzed by means of a Master equation whose solution is simulated with the stochastic Gillespie algorithm. With this approach we have reproduced the responses to the basal release in the absence of stimulation evoked by the electrical activity and the phenomena of facilitation and depression of neuromuscular synapses. This model offers new perspectives to understand the underlying phenomena in chemical neurotransmission based on molecular interactions that result in the cooperativity between vesicles during neurotransmitter release. DGAPA Grants IN118410 and IN200914 and Conacyt Grant 130031.

Experimental evidence of the role of viscosity in the molecular kinetic theory of dynamic wetting.

Science.gov (United States)

Duvivier, D; Seveno, D; Rioboo, R; Blake, T D; De Coninck, J

2011-11-01

We report an experimental study of the dynamics of spontaneous spreading of aqueous glycerol drops on glass. For a range of glycerol concentrations, we follow the evolution of the radius and contact angle over several decades of time and investigate the influence of solution viscosity. The application of the molecular kinetic theory to the resulting data allows us to extract the coefficient of contact-line friction ζ, the molecular jump frequency κ(0), and the jump length λ for each solution. Our results show that the modified theory, which explicitly accounts for the effect of viscosity, can successfully be applied to droplet spreading. The viscosity affects the jump frequency but not the jump length. In combining these data, we confirm that the contact-line friction of the solution/air interface against the glass is proportional to the viscosity and exponentially dependent on the work of adhesion.

Spectral analysis of multi-dimensional self-similar Markov processes

International Nuclear Information System (INIS)

Modarresi, N; Rezakhah, S

2010-01-01

In this paper we consider a discrete scale invariant (DSI) process {X(t), t in R + } with scale l > 1. We consider a fixed number of observations in every scale, say T, and acquire our samples at discrete points α k , k in W, where α is obtained by the equality l = α T and W = {0, 1, ...}. We thus provide a discrete time scale invariant (DT-SI) process X(.) with the parameter space {α k , k in W}. We find the spectral representation of the covariance function of such a DT-SI process. By providing the harmonic-like representation of multi-dimensional self-similar processes, spectral density functions of them are presented. We assume that the process {X(t), t in R + } is also Markov in the wide sense and provide a discrete time scale invariant Markov (DT-SIM) process with the above scheme of sampling. We present an example of the DT-SIM process, simple Brownian motion, by the above sampling scheme and verify our results. Finally, we find the spectral density matrix of such a DT-SIM process and show that its associated T-dimensional self-similar Markov process is fully specified by {R H j (1), R j H (0), j = 0, 1, ..., T - 1}, where R H j (τ) is the covariance function of jth and (j + τ)th observations of the process.

Molecular beam kinetics

International Nuclear Information System (INIS)

Behrens, R. Jr.

1975-11-01

The design of a crossed molecular beam ''supermachine'' for neutral--neutral collisions is discussed. The universal electron bombardment ionizer, mass filter, and ion detection system of the detector, the supersonic nozzle sources, the differential pumping arrangement for the sources and detector, the time-of-flight detection of scattered products, and the overall configuration of the apparatus are described. The elastic scattering of two systems, CH 4 + Ar and NH 3 + Ar, has been measured using the supermachine with two supersonic nozzle sources. The rainbow structure and the interference oscillations are seen in each system. The best fit to the data was found using a Morse--Spline--Van der Waals (MSV) potential. The three potential parameters epsilon, r/sub m/, and β were found to be 2.20(+-0.04) x 10 -14 ergs, 3.82(+-0.04)A, and 7.05 +- 0.20 for CH 4 + Ar, and 2.21(+-0.04) x 10 -14 ergs 3.93 (+-0.05)A, and 8.45 +- 0.30 for NH 3 + Ar. A new phenomenon in crossed molecular beams of condensation of a molecule on a cluster to form a complex was observed. A bromine molecule condensed on clusters of chlorine (Cl 2 )/sub chi/ and ammonia (NH 3 )/sub chi/. The value of chi for measurements in these experiments ranges from 7 to 40 for chlorine clusters and from 10 to 70 ammonia clusters

The kinetic and thermodynamic sorption and stabilization of multiwalled carbon nanotubes in natural organic matter surrogate solutions: The effect of surrogate molecular weight

International Nuclear Information System (INIS)

Li, Tingting; Lin, Daohui; Li, Lu; Wang, Zhengyu; Wu, Fengchang

2014-01-01

Styrene sulfonate (SS) and polystyrene sulfonates (PSSs) were used as surrogates of natural organic matter to study the effect of molecular weight (from 206.2 to 70,000 Da) on their sorption by a multiwalled carbon nanotube (MWCNT) and an activated carbon (AC) and on their stabilization of MWCNT suspension. Results indicate that surface-diffusion through the liquid-sorbent boundary was the rate-controlling step of the kinetic sorption of both MWCNTs and AC, and surface-occupying and pore-filling mechanisms respectively dominated the thermodynamic sorption of MWCNTs and AC. Sorption rates and capacities of MWCNTs and AC in molecular concentration of SS and PSS decreased with increasing molecular weight. The PSSs but not SS facilitated the stabilization of MWCNT suspension because of the increased electrosteric repulsion. The PSSs with more monomers had greater capabilities to stabilize the MWCNT suspension, but the capabilities were comparable after being normalized by the total monomer number. -- Highlights: • Surface-diffusion controlled the kinetic sorption of NOM surrogates to MWCNTs and AC. • Surface-occupying mechanism dominates the thermodynamic sorption of MWCNTs. • The sorption in molecular concentration decreased with increasing M w of the PSSs. • PSS but not SS stabilized MWCNT suspension through electrosteric repulsion. • Stabilization capabilities normalized by monomer number of the PSSs were comparable. -- Molecular weight of NOM influences its sorption on and stabilizing MWCNTs

Probing the energy landscape of alanine dipeptide and decalanine using temperature as a tunable parameter in molecular dynamics

International Nuclear Information System (INIS)

Chatterjee, A; Bhattacharya, S

2016-01-01

We perform several molecular dynamics (MD) calculations of solvated alanine dipeptide and decalanine in vacuum with temperature as a tunable parameter and in the process, generate Markov state models (MSMs) at each temperature. An interesting observation that the kinetic rates appear to obey the Arrhenius rate law allows us to predict the dynamics of alanine dipeptide at 300 K at the microsecond timescales using the nanoseconds long high temperature calculations without actually performing MD simulations at 300 K. We conclude that the energy landscape of alanine dipeptide contains superbasins deeper than k B T and determine the energy barriers associated with the moves from the Arrhenius rate expression. Similar insights regarding the energy landscape associated with folding/unfolding pathways of a deca-alanine molecule are obtained using kinetic rates calculated at different temperatures. (paper)

Molecular Force Spectroscopy on Cells

Science.gov (United States)

Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

Atomic and molecular processes in fusion plasmas

Energy Technology Data Exchange (ETDEWEB)

Janev, R.K. [International Atomic Energy Agency, Vienna (Austria)

1997-01-01

The role of atomic and molecular processes in achieving and maintaining the conditions for thermonuclear burn in a magnetically confined fusion plasma is described. Emphasis is given to the energy balance and power and particle exhaust issues. The most important atomic and molecular processes which affect the radiation losses and impurity transport in the core plasma, the neutral particle transport in the plasma edge and the radiative cooling of divertor plasmas are discussed in greater detail. (author)

Material Balance And Reaction Kinetics Modeling For Penex Isomerization Process In Daura Refinery

Directory of Open Access Journals (Sweden)

Hamadi Adel Sharif

2017-01-01

Full Text Available Penex Deisohexanizer isomerization of light straight run naphtha is a significant process for petroleum refining and proved to be effective technology to produce gasoline components with a high octane number. Modeling of the chemical kinetic reactions is an important tool because it is a better tool for optimization of the experimental data into parameters used for industrial reactors. The present study deals on the isomerization process in Daura refinery. Material balance calculations were done mathematically on the unit for the kinetics prediction purpose. A kinetic mathematical model was derived for the prediction rate constants K1 and K2 and activation energy Ea at operating temperatures range 120-180°C. According to the model, the results show that with increasing of temperature leads to increased K1 directly, where the K2 values proportional inversely. The activation energy results show that Ea1(nC6

Process Analytical Technology for Advanced Process Control in Biologics Manufacturing with the Aid of Macroscopic Kinetic Modeling

Directory of Open Access Journals (Sweden)

Martin Kornecki

2018-03-01

Full Text Available Productivity improvements of mammalian cell culture in the production of recombinant proteins have been made by optimizing cell lines, media, and process operation. This led to enhanced titers and process robustness without increasing the cost of the upstream processing (USP; however, a downstream bottleneck remains. In terms of process control improvement, the process analytical technology (PAT initiative, initiated by the American Food and Drug Administration (FDA, aims to measure, analyze, monitor, and ultimately control all important attributes of a bioprocess. Especially, spectroscopic methods such as Raman or near-infrared spectroscopy enable one to meet these analytical requirements, preferably in-situ. In combination with chemometric techniques like partial least square (PLS or principal component analysis (PCA, it is possible to generate soft sensors, which estimate process variables based on process and measurement models for the enhanced control of bioprocesses. Macroscopic kinetic models can be used to simulate cell metabolism. These models are able to enhance the process understanding by predicting the dynamic of cells during cultivation. In this article, in-situ turbidity (transmission, 880 nm and ex-situ Raman spectroscopy (785 nm measurements are combined with an offline macroscopic Monod kinetic model in order to predict substrate concentrations. Experimental data of Chinese hamster ovary cultivations in bioreactors show a sufficiently linear correlation (R2 ≥ 0.97 between turbidity and total cell concentration. PLS regression of Raman spectra generates a prediction model, which was validated via offline viable cell concentration measurement (RMSE ≤ 13.82, R2 ≥ 0.92. Based on these measurements, the macroscopic Monod model can be used to determine different process attributes, e.g., glucose concentration. In consequence, it is possible to approximately calculate (R2 ≥ 0.96 glucose concentration based on online cell

Process Analytical Technology for Advanced Process Control in Biologics Manufacturing with the Aid of Macroscopic Kinetic Modeling.

Science.gov (United States)

Kornecki, Martin; Strube, Jochen

2018-03-16

Productivity improvements of mammalian cell culture in the production of recombinant proteins have been made by optimizing cell lines, media, and process operation. This led to enhanced titers and process robustness without increasing the cost of the upstream processing (USP); however, a downstream bottleneck remains. In terms of process control improvement, the process analytical technology (PAT) initiative, initiated by the American Food and Drug Administration (FDA), aims to measure, analyze, monitor, and ultimately control all important attributes of a bioprocess. Especially, spectroscopic methods such as Raman or near-infrared spectroscopy enable one to meet these analytical requirements, preferably in-situ. In combination with chemometric techniques like partial least square (PLS) or principal component analysis (PCA), it is possible to generate soft sensors, which estimate process variables based on process and measurement models for the enhanced control of bioprocesses. Macroscopic kinetic models can be used to simulate cell metabolism. These models are able to enhance the process understanding by predicting the dynamic of cells during cultivation. In this article, in-situ turbidity (transmission, 880 nm) and ex-situ Raman spectroscopy (785 nm) measurements are combined with an offline macroscopic Monod kinetic model in order to predict substrate concentrations. Experimental data of Chinese hamster ovary cultivations in bioreactors show a sufficiently linear correlation (R² ≥ 0.97) between turbidity and total cell concentration. PLS regression of Raman spectra generates a prediction model, which was validated via offline viable cell concentration measurement (RMSE ≤ 13.82, R² ≥ 0.92). Based on these measurements, the macroscopic Monod model can be used to determine different process attributes, e.g., glucose concentration. In consequence, it is possible to approximately calculate (R² ≥ 0.96) glucose concentration based on online cell

Tandem mass spectrometry at low kinetic energy

International Nuclear Information System (INIS)

Cooks, R.G.; Hand, O.W.

1987-01-01

Recent progress in mass spectrometry, as applied to molecular analysis, is reviewed with emphasis on tandem mass spectrometry. Tandem instruments use multiple analyzers (sector magnets, quadrupole mass filters and time-of-flight devices) to select particular molecules in ionic form, react them in the gas-phase and then record the mass, momenta or kinetic energies of their products. The capabilities of tandem mass spectrometry for identification of individual molecules or particular classes of compounds in complex mixtures are illustrated. Several different types of experiments can be run using a tandem mass spectrometer; all share the feature of sifting the molecular mixture being analyzed on the basis of chemical properties expressed in terms of ionic mass, kinetic energy or charge state. Applications of mass spectrometry to biological problems often depend upon desorption methods of ionization in which samples are bombarded with particle beams. Evaporation of preformed charged species from the condensed phase into the vacuum is a particularly effective method of ionization. It is suggested that the use of accelerator mass spectrometers be extended to include problems of molecular analysis. In such experiments, low energy tandem mass spectrometry conducted in the eV or keV range of energies, would be followed by further characterization of the production ion beam using high selective MeV collision processes

p-Nitrophenol degradation by electro-Fenton process: Pathway, kinetic model and optimization using central composite design.

Science.gov (United States)

Meijide, J; Rosales, E; Pazos, M; Sanromán, M A

2017-10-01

The chemical process scale-up, from lab studies to industrial production, is challenging and requires deep knowledge of the kinetic model and the reactions that take place in the system. This knowledge is also useful in order to be employed for the reactor design and the determination of the optimal operational conditions. In this study, a model substituted phenol such as p-nitrophenol was degraded by electro-Fenton process and the reaction products yielded along the treatment were recorded. The kinetic model was developed using Matlab software and was based on main reactions that occurred until total mineralization which allowed predicting the degradation pathway under this advanced oxidation process. The predicted concentration profiles of p-nitrophenol, their intermediates and by-products in electro-Fenton process were validated with experimental assays and the results were consistent. Finally, based on the developed kinetic model the degradation process was optimized using central composite design taking as key parameters the ferrous ion concentration and current density. Copyright © 2017 Elsevier Ltd. All rights reserved.

Heart Rate and Oxygen Uptake Kinetics in Type 2 Diabetes Patients - A Pilot Study on the Influence of Cardiovascular Medication on Regulatory Processes.

Science.gov (United States)

Koschate, Jessica; Drescher, Uwe; Baum, Klaus; Brinkmann, Christian; Schiffer, Thorsten; Latsch, Joachim; Brixius, Klara; Hoffmann, Uwe

2017-05-01

The aim of this pilot study was to investigate whether there are differences in heart rate and oxygen uptake kinetics in type 2 diabetes patients, considering their cardiovascular medication. It was hypothesized that cardiovascular medication would affect heart rate and oxygen uptake kinetics and that this could be detected using a standardized exercise test. 18 subjects were tested for maximal oxygen uptake. Kinetics were measured in a single test session with standardized, randomized moderate-intensity work rate changes. Time series analysis was used to estimate kinetics. Greater maxima in cross-correlation functions indicate faster kinetics. 6 patients did not take any cardiovascular medication, 6 subjects took peripherally acting medication and 6 patients were treated with centrally acting medication. Maximum oxygen uptake was not significantly different between groups. Significant main effects were identified regarding differences in muscular oxygen uptake kinetics and heart rate kinetics. Muscular oxygen uptake kinetics were significantly faster than heart rate kinetics in the group with no cardiovascular medication (maximum in cross-correlation function of muscular oxygen uptake vs. heart rate; 0.32±0.08 vs. 0.25±0.06; p=0.001) and in the group taking peripherally acting medication (0.34±0.05 vs. 0.28±0.05; p=0.009) but not in the patients taking centrally acting medication (0.28±0.05 vs. 0.30±0.07; n.s.). It can be concluded that regulatory processes for the achievement of a similar maximal oxygen uptake are different between the groups. The used standardized test provided plausible results for heart rate and oxygen uptake kinetics in a single measurement session in this patient group. © Georg Thieme Verlag KG Stuttgart · New York.

QSAR models based on quantum topological molecular similarity.

Science.gov (United States)

Popelier, P L A; Smith, P J

2006-07-01

A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

Quantum field kinetics of QCD quark-gluon transport theory for light-cone dominated processes

CERN Document Server

Kinder-Geiger, Klaus

1996-01-01

A quantum kinetic formalism is developed to study the dynamical interplay of quantum and statistical-kinetic properties of non-equilibrium multi-parton systems produced in high-energy QCD processes. The approach provides the means to follow the quantum dynamics in both space-time and energy-momentum, starting from an arbitrary initial configuration of high-momentum quarks and gluons. Using a generalized functional integral representation and adopting the `closed-time-path' Green function techniques, a self-consistent set of equations of motions is obtained: a Ginzburg-Landau equation for a possible color background field, and Dyson-Schwinger equations for the 2-point functions of the gluon and quark fields. By exploiting the `two-scale nature' of light-cone dominated QCD processes, i.e. the separation between the quantum scale that specifies the range of short-distance quantum fluctuations, and the kinetic scale that characterizes the range of statistical binary inter- actions, the quantum-field equations of ...

Non-equilibrium reacting gas flows kinetic theory of transport and relaxation processes

CERN Document Server

Nagnibeda, Ekaterina; Nagnibeda, Ekaterina

2009-01-01

This volume develops the kinetic theory of transport phenomena and relaxation processes in the flows of reacting gas mixtures. The theory is applied to the modeling of non-equilibrium flows behind strong shock waves, in the boundary layer, and in nozzles.

Photodissociation dynamics of propene at 157.6 nm: Kinetic energy distributions and branching ratios

International Nuclear Information System (INIS)

Lee, S.-H.; Lee, Y.-Y.; Lee, Yuan T.; Yang Xueming

2003-01-01

Photodissociation dynamics of propene at 157.6 nm has been investigated in a molecular beam apparatus using the photofragment translational spectroscopic technique combined with the vacuum ultraviolet ionization method. Eleven photofragments have been successfully detected and ascribed to eight (five binary and three triple) dissociation channels: namely, C 3 H 5 +H, C 3 H 4 +H+H, C 3 H 4 +H 2 , C 3 H 3 +H 2 +H, C 2 H 4 +CH 2 , C 2 H 3 +CH 3 , C 2 H 2 +CH 4 , and C 2 H 2 +CH 3 +H. Their branching ratios have been determined to be 1%, 7%, 2 H 2 +CH 3 +H channel. In addition, the averaged kinetic energy releases and the fractions in translational energy have also been determined from the measured kinetic energy distributions. For the binary dissociation channels, the fractions in translational energy are less than 18% except the C 3 H 5 +H channel, whereas they are more than 42% for the triple dissociation channels. An intriguing finding indicates that the C 2 H 4 +CH 2 channel has a nearly identical kinetic energy distribution and a similar branching ratio to the C 2 H 3 +CH 3 channel, although the former undergoes a three-center elimination process different from the C-C bond rupture occurring in the latter

Kinetics approach to modeling of polymer additive degradation in lubricants

Institute of Scientific and Technical Information of China (English)

llyaI.KUDISH; RubenG.AIRAPETYAN; Michael; J.; COVITCH

2001-01-01

A kinetics problem for a degrading polymer additive dissolved in a base stock is studied.The polymer degradation may be caused by the combination of such lubricant flow parameters aspressure, elongational strain rate, and temperature as well as lubricant viscosity and the polymercharacteristics (dissociation energy, bead radius, bond length, etc.). A fundamental approach tothe problem of modeling mechanically induced polymer degradation is proposed. The polymerdegradation is modeled on the basis of a kinetic equation for the density of the statistical distribu-tion of polymer molecules as a function of their molecular weight. The integrodifferential kineticequation for polymer degradation is solved numerically. The effects of pressure, elongational strainrate, temperature, and lubricant viscosity on the process of lubricant degradation are considered.The increase of pressure promotes fast degradation while the increase of temperature delaysdegradation. A comparison of a numerically calculated molecular weight distribution with an ex-perimental one obtained in bench tests showed that they are in excellent agreement with eachother.

Melting of superheated molecular crystals

Science.gov (United States)

Cubeta, Ulyana; Bhattacharya, Deepanjan; Sadtchenko, Vlad

2017-07-01

Melting dynamics of micrometer scale, polycrystalline samples of isobutane, dimethyl ether, methyl benzene, and 2-propanol were investigated by fast scanning calorimetry. When films are superheated with rates in excess of 105 K s-1, the melting process follows zero-order, Arrhenius-like kinetics until approximately half of the sample has transformed. Such kinetics strongly imply that melting progresses into the bulk via a rapidly moving solid-liquid interface that is likely to originate at the sample's surface. Remarkably, the apparent activation energies for the phase transformation are large; all exceed the enthalpy of vaporization of each compound and some exceed it by an order of magnitude. In fact, we find that the crystalline melting kinetics are comparable to the kinetics of dielectric α-relaxation in deeply supercooled liquids. Based on these observations, we conclude that the rate of non-isothermal melting for superheated, low-molecular-weight crystals is limited by constituent diffusion into an abnormally dense, glass-like, non-crystalline phase.

Deducing the kinetics of protein synthesis in vivo from the transition rates measured in vitro.

Directory of Open Access Journals (Sweden)

Sophia Rudorf

2014-10-01

Full Text Available The molecular machinery of life relies on complex multistep processes that involve numerous individual transitions, such as molecular association and dissociation steps, chemical reactions, and mechanical movements. The corresponding transition rates can be typically measured in vitro but not in vivo. Here, we develop a general method to deduce the in-vivo rates from their in-vitro values. The method has two basic components. First, we introduce the kinetic distance, a new concept by which we can quantitatively compare the kinetics of a multistep process in different environments. The kinetic distance depends logarithmically on the transition rates and can be interpreted in terms of the underlying free energy barriers. Second, we minimize the kinetic distance between the in-vitro and the in-vivo process, imposing the constraint that the deduced rates reproduce a known global property such as the overall in-vivo speed. In order to demonstrate the predictive power of our method, we apply it to protein synthesis by ribosomes, a key process of gene expression. We describe the latter process by a codon-specific Markov model with three reaction pathways, corresponding to the initial binding of cognate, near-cognate, and non-cognate tRNA, for which we determine all individual transition rates in vitro. We then predict the in-vivo rates by the constrained minimization procedure and validate these rates by three independent sets of in-vivo data, obtained for codon-dependent translation speeds, codon-specific translation dynamics, and missense error frequencies. In all cases, we find good agreement between theory and experiment without adjusting any fit parameter. The deduced in-vivo rates lead to smaller error frequencies than the known in-vitro rates, primarily by an improved initial selection of tRNA. The method introduced here is relatively simple from a computational point of view and can be applied to any biomolecular process, for which we have

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Science.gov (United States)

Srinivas, Niranjan

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

125IdUrd-induced chromosome fragments, assayed by premature chromosome condensation, and DNA double-strand breaks have similar repair kinetics in G1-phase CHO-cells

International Nuclear Information System (INIS)

Iliakis, George; Pantelias, G.E.; Okayasu, Ryuichi; Seaner, Robert

1987-01-01

The effect of 125 I-decay on cell lethality, and induction of chromosome and DNA damage, was studied in synchronous non-cycling, G 1 -phase CHO-cells. Neutral filter elution was used to assay repair of DNA double-strand breaks (dsbs), and premature chromosome condensation was used to assay repair of chromosome fragments and induction of ring chromosomes. The results indicate very little repair at the cell survival level (repair of PLD). At the DNA level an efficient repair of DNA dsbs was observed, with kinetics similar to those observed after exposure to X-rays. At the chromosome level a fast repair of prematurely condensed chromosome fragments was observed, with a concomitant increase in the number of ring chromosomes induced. The repair kinetics of chromosome fragments and DNA dsbs were very similar, suggesting that DNA dsbs may underlie chromosome fragmentation. (author)

Molecular Surveillance of Viral Processes Using Silicon Nitride Membranes

Directory of Open Access Journals (Sweden)

Deborah F. Kelly

2013-03-01

Full Text Available Here we present new applications for silicon nitride (SiN membranes to evaluate biological processes. We determined that 50-nanometer thin films of SiN produced from silicon wafers were sufficiently durable to bind active rotavirus assemblies. A direct comparison of SiN microchips with conventional carbon support films indicated that SiN performs equivalent to the traditional substrate to prepare samples for Electron Microscopy (EM imaging. Likewise, SiN films coated with Ni-NTA affinity layers concentrated rotavirus particles similarly to affinity-coated carbon films. However, affinity-coated SiN membranes outperformed glow-discharged conventional carbon films 5-fold as indicated by the number of viral particles quantified in EM images. In addition, we were able to recapitulate viral uncoating and transcription mechanisms directed onto the microchip surfaces. EM images of these processes revealed the production of RNA transcripts emerging from active rotavirus complexes. These results were confirmed by the functional incorporation of radiolabeled nucleotides into the nascent RNA transcripts. Collectively, we demonstrate new uses for SiN membranes to perform molecular surveillance on life processes in real-time.

Hamiltonian kinetic theory of plasma ponderomotive processes

International Nuclear Information System (INIS)

McDonald, S.W.; Kaufman, A.N.

1981-12-01

The nonlinear nonresonant interaction of plasma waves and particles is formulated in a Hamiltonian kinetic theory which treats the wave-action and particle distributions on an equal footing, thereby displaying reciprocity relations. In the quasistatic limit, a nonlinear wave-kinetic equation is obtained. The generality of the formalism allows for applications to arbitrary geometry, with the nonlinear effects expressed in terms of the linear susceptibility

Hamiltonian kinetic theory of plasma ponderomotive processes

International Nuclear Information System (INIS)

McDonald, S.W.; Kaufman, A.N.

1982-01-01

The nonlinear nonresonant interaction of plasma waves and particles is formulated in Hamiltonian kinetic theory which treats the wave-action and particle distributions on an equal footing, thereby displaying reciprocity relations. In the quasistatic limit, a nonlinear wave-kinetic equation is obtained. The generality of the formalism allows for applications to arbitrary geometry, with the nonlinear effects expressed in terms of the linear susceptibility

Investigations into the process kinetics of immobilized microorganisms

Energy Technology Data Exchange (ETDEWEB)

Voss, H; Geipel, F

1987-01-01

The authors present a population-structured process model of ethanol production by S. cerevisiae cells fixed in Ca alginate. Experiments were made in discontinuous and continuous fluidized-bed reactors. Living cells, both reproductive and non-reproductive, are distinguished from dead cells in the segregated reactor model. The rates of cell state change are described as a function of the ethanol concentration. The growth rate is described by a Monod model extended by inhibition functions and supplemented by a cell inhibition function. Product formation comprises a growth-associated component and a non-associated component resulting from the endogenous and maintenance metabolism. Further, a cell discharge rate from the gel is considered which is dependent both on growth and on the biomass concentration. The simulation of process kinetics and reactor dynamics with an optimum parameter vector shows an excellent adaptation for all experiments.

A kinetic reaction model for biomass pyrolysis processes in Aspen Plus

International Nuclear Information System (INIS)

Peters, Jens F.; Banks, Scott W.; Bridgwater, Anthony V.; Dufour, Javier

2017-01-01

Highlights: • Predictive kinetic reaction model applicable to any lignocellulosic feedstock. • Calculates pyrolysis yields and product composition as function of reactor conditions. • Detailed modelling of product composition (33 model compounds for the bio-oil). • Good agreement with literature regarding yield curves and product composition. • Successful validation with pyrolysis experiments in bench scale fast pyrolysis rig. - Abstract: This paper presents a novel kinetic reaction model for biomass pyrolysis processes. The model is based on the three main building blocks of lignocellulosic biomass, cellulose, hemicellulose and lignin and can be readily implemented in Aspen Plus and easily adapted to other process simulation software packages. It uses a set of 149 individual reactions that represent the volatilization, decomposition and recomposition processes of biomass pyrolysis. A linear regression algorithm accounts for the secondary pyrolysis reactions, thus allowing the calculation of slow and intermediate pyrolysis reactions. The bio-oil is modelled with a high level of detail, using up to 33 model compounds, which allows for a comprehensive estimation of the properties of the bio-oil and the prediction of further upgrading reactions. After showing good agreement with existing literature data, our own pyrolysis experiments are reported for validating the reaction model. A beech wood feedstock is subjected to pyrolysis under well-defined conditions at different temperatures and the product yields and compositions are determined. Reproducing the experimental pyrolysis runs with the simulation model, a high coincidence is found for the obtained fraction yields (bio-oil, char and gas), for the water content and for the elemental composition of the pyrolysis products. The kinetic reaction model is found to be suited for predicting pyrolysis yields and product composition for any lignocellulosic biomass feedstock under typical pyrolysis conditions

1978 bibliography of atomic and molecular processes

International Nuclear Information System (INIS)

1980-03-01

This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

1979 bibliography of atomic and molecular processes

International Nuclear Information System (INIS)

1980-08-01

This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

1980 bibliography of atomic and molecular processes

International Nuclear Information System (INIS)

1982-02-01

This annotated bibliography lists 2866 works on atomic and molecular processes reported in publications dated 1980. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

Probing the hydrogen equilibrium and kinetics in zeolite imidazolate frameworks via molecular dynamics and quasi-elastic neutron scattering experiments.

Science.gov (United States)

Pantatosaki, Evangelia; Jobic, Hervé; Kolokolov, Daniil I; Karmakar, Shilpi; Biniwale, Rajesh; Papadopoulos, George K

2013-01-21

The problem of simulating processes involving equilibria and dynamics of guest sorbates within zeolitic imidazolate frameworks (ZIF) by means of molecular dynamics (MD) computer experiments is of growing importance because of the promising role of ZIFs as molecular "traps" for clean energy applications. A key issue for validating such an atomistic modeling attempt is the possibility of comparing the MD results, with real experiments being able to capture analogous space and time scales to the ones pertained to the computer experiments. In the present study, this prerequisite is fulfilled through the quasi-elastic neutron scattering technique (QENS) for measuring self-diffusivity, by elaborating the incoherent scattering signal of hydrogen nuclei. QENS and MD experiments were performed in parallel to probe the hydrogen motion, for the first time in ZIF members. The predicted and measured dynamics behaviors show considerable concentration variation of the hydrogen self-diffusion coefficient in the two topologically different ZIF pore networks of this study, the ZIF-3 and ZIF-8. Modeling options such as the flexibility of the entire matrix versus a rigid framework version, the mobility of the imidazolate ligand, and the inclusion of quantum mechanical effects in the potential functions were examined in detail for the sorption thermodynamics and kinetics of hydrogen and also of deuterium, by employing MD combined with Widom averaging towards studying phase equilibria. The latter methodology ensures a rigorous and efficient way for post-processing the dynamics trajectory, thereby avoiding stochastic moves via Monte Carlo simulation, over the large number of configurational degrees of freedom a nonrigid framework encompasses.

Adsorption kinetics of c-Fos and c-Jun to air-water interfaces.

Science.gov (United States)

Del Boca, Maximiliano; Nobre, Thatyane Morimoto; Zaniquelli, Maria Elisabete Darbello; Maggio, Bruno; Borioli, Graciela A

2007-11-01

The kinetics of adsorption to air-water interfaces of the biomembrane active transcription factors c-Fos, c-Jun and their mixtures is investigated. The adsorption process shows three distinct stages: a lag time, a fast pseudo zero-order stage, and a halting stage. The initial stage determines the course of the process, which is concentration dependent until the end of the fast stage. We show that c-Fos has faster adsorption kinetics than c-Jun over all three stages and that the interaction between both proteins is apparent in the adsorption profiles of the mixtures. Protein molecular reorganization at the interface determines the transition to the final adsorption stage of the pure proteins as well as that of the mixtures.

Molecular dynamics study of kinetic boundary condition at an interface between a polyatomic vapor and its condensed phase

OpenAIRE

Ishiyama, Tatsuya; Yano, Takeru; Fujikawa, Shigeo

2004-01-01

The kinetic boundary condition for the Boltzmann equation at an interface between a polyatomic vapor and its liquid phase is investigated by the numerical method of molecular dynamics, with particular emphasis on the functional form of the evaporation part of the boundary condition, including the evaporation coefficient. The present study is an extension of a previous one for argon [Ishiyama, Yano, and Fujikawa, Phys. Fluids 16, 2899 (2004)] to water and methanol, typical examples of polyatom...

A kinetic model for the burst phase of processive cellulases

DEFF Research Database (Denmark)

Præstgaard, Eigil; Olsen, Jens Elmerdahl; Murphy, Leigh

2011-01-01

. This approach generally accounts well for the initial time course (approximately 1 h) of the hydrolysis. We suggest that the models will be useful in attempts to rationalize the initial kinetics of processive cellulases, and demonstrate their application to some open questions, including the effect of repeated......Cellobiohydrolases (exocellulases) hydrolyze cellulose processively, i.e. by sequential cleaving of soluble sugars from one end of a cellulose strand. Their activity generally shows an initial burst, followed by a pronounced slowdown, even when substrate is abundant and product accumulation...... of the model, which can be solved analytically, shows that the burst and slowdown can be explained by the relative rates of the sequential reactions in the hydrolysis process and the occurrence of obstacles for the processive movement along the cellulose strand. More specifically, the maximum enzyme activity...

Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies.

Science.gov (United States)

Deganutti, Giuseppe; Moro, Stefano

2017-04-01

Kinetic and thermodynamic ligand-protein binding parameters are gaining growing importance as key information to consider in drug discovery. The determination of the molecular structures, using particularly x-ray and NMR techniques, is crucial for understanding how a ligand recognizes its target in the final binding complex. However, for a better understanding of the recognition processes, experimental studies of ligand-protein interactions are needed. Even though several techniques can be used to investigate both thermodynamic and kinetic profiles for a ligand-protein complex, these procedures are very often laborious, time consuming and expensive. In the last 10 years, computational approaches have enormous potential in providing insights into each of the above effects and in parsing their contributions to the changes in both kinetic and thermodynamic binding parameters. The main purpose of this review is to summarize the state of the art of computational strategies for estimating the kinetic and thermodynamic parameters of a ligand-protein binding.

Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

Science.gov (United States)

Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

2018-04-01

A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

Kinetic analysis of interaction between N atoms and O-covered Ru(0001)

International Nuclear Information System (INIS)

Kang, Kai; Kleyn, A. W.; Gleeson, M. A.

2015-01-01

Eley-Rideal (ER) reactions involving neutral atoms heavier than hydrogen reacting with adsorbed atoms of similar mass were first observed in recent molecular beam experiments by Zaharia et al. [Phys. Rev. Lett. 113, 053201 (2014)]. Through analysis of two types of measurements, they obtained different estimations for the N–O ER reaction cross section, one of which is unexpectedly high. This was qualitatively accounted for by invoking a secondary effect whereby the presence of N adatoms on the surface acted to “shield” O adatoms from prompt recombinative desorption. We apply a rate equation model that includes two ER processes involving different adsorbed species (N–O ad and N–N ad ) and an N-adsorption process to the full-beam exposure subset of the experimental data in order to study the reaction kinetics. Values for the individual reaction cross sections are derived. The measured N 2 response can be well described by the model, but it is insufficient to completely describe the NO response. Modeling of different exposures is used to evaluate the qualitative picture presented by Zaharia et al

Dry/Wet Cycling and the Thermodynamics and Kinetics of Prebiotic Polymer Synthesis

Directory of Open Access Journals (Sweden)

David S. Ross

2016-07-01

Full Text Available The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life’s origins: (i how did the polymers arise in an aqueous prebiotic world; and (ii once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium Nm + Nn ↔ Nm+n + H2O is endoergic by about 3.3 kcal/mol for polynucleotide formation, and the system thus lies far to the left in the starting solutions. Kinetic simulations of the evaporation showed that simple Le Châtelier’s principle shifts were insufficient, but the introduction of oligomer-stabilizing factors of 5–10 kcal/mol both moved the process to the right and respectively boosted and retarded the elongation and hydrolysis rates. Molecular crowding and excluded volume effects in present-day cells yield stabilizing factors of that order, and we argue here that the crowded conditions in the evaporites generate similar effects. Oligomer formation is thus energetically preferred in those settings, but the process is thwarted in each evaporation step as diffusion becomes rate limiting. Rehydration dissipates disordered oligomer clusters in the evaporites, however, and subsequent dry/wet cycling accordingly “ratchets up” the system to an ultimate population of kinetically trappedthermodynamically preferred biopolymers.

Kinetics of the chiral phase transition

Energy Technology Data Exchange (ETDEWEB)

Hees, Hendrik van [Johann-Wolfgang-Goethe-Universitaet Frankfurt, Institut fuer Theoretische Physik, Frankfurt (Germany); Frankfurt Institute for Advanced Studies (FIAS), Frankfurt (Germany); Wesp, Christian; Meistrenko, Alex; Greiner, Carsten [Johann-Wolfgang-Goethe-Universitaet Frankfurt, Institut fuer Theoretische Physik, Frankfurt (Germany)

2016-07-01

We simulate the kinetics of the chiral phase transition in hot and dense strongly interacting matter within a novel kinetic-theory approach. Employing an effective linear σ model for quarks, σ mesons, and pions we treat the quarks within a test-particle ansatz for solving the Boltzmann transport equation and the mesons in terms of classical fields. The decay-recombination processes like σ <-> anti q+q are treated using a kind of wave-particle dualism using the exact conservation of energy and momentum. After demonstrating the correct thermodynamic limit for particles and fields in a ''box calculation'' we apply the simulation to the dynamics of an expanding fireball similar to the medium created in ultrarelativistic heavy-ion collisions.

water alteration processes and kinetics of basaltic glasses, natural analogue of nuclear glasses

International Nuclear Information System (INIS)

Techer, I.; Advocat, Th.; Vernaz, E.; Lancelot, J.R.; Liotard, J.M.

1997-01-01

Dissolution experiments of a basaltic glass were carried out at 90 deg C for different reaction progresses. The initial dissolution rate was compared with values obtained for rhyolitic glass and the R7T7 nuclear glass. The activation energy was also determined by computing literature data. The results provide similar reactional mechanism for basaltic and nuclear glasses. Dissolution rates measured under saturation conditions were compared to theoretical dissolution rates. These ones were calculated using two kinetic models: the first rate equation is the Grambow's law which only takes into account ortho-silica acid activity; the second rate equation was proposed by Daux et al., where silica and aluminum are combined to formulate the affinity. The comparison between experimental and theoretical results point out that these two models are not appropriate to describe the alteration kinetic of basaltic glasses. (authors)

Kinetic theory of age-structured stochastic birth-death processes

Science.gov (United States)

Greenman, Chris D.; Chou, Tom

2016-01-01

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

Progress in molecular precursors for electronic materials

Energy Technology Data Exchange (ETDEWEB)

Buhro, W.E. [Washington Univ., St. Louis, MO (United States)

1996-09-01

Molecular-precursor chemistry provides an essential underpinning to all electronic-materials technologies, including photovoltaics and related areas of direct interest to the DOE. Materials synthesis and processing is a rapidly developing field in which advances in molecular precursors are playing a major role. This article surveys selected recent research examples that define the exciting current directions in molecular-precursor science. These directions include growth of increasingly complex structures and stoichiometries, surface-selective growth, kinetic growth of metastable materials, growth of size-controlled quantum dots and quantum-dot arrays, and growth at progressively lower temperatures. Continued progress in molecular-precursor chemistry will afford precise control over the crystal structures, nanostructures, and microstructures of electronic materials.

1982 bibliography of atomic and molecular processes

International Nuclear Information System (INIS)

Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

1984-05-01

This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

Bibliography of atomic and molecular processes, 1983

International Nuclear Information System (INIS)

Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

1984-10-01

This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

1985 bibliography of atomic and molecular processes

Energy Technology Data Exchange (ETDEWEB)

Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

1986-06-01

This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

1985 bibliography of atomic and molecular processes

International Nuclear Information System (INIS)

Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

1986-06-01

This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

Bibliography of atomic and molecular processes, 1983

Energy Technology Data Exchange (ETDEWEB)

Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

1984-10-01

This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

1984 Bibliography of atomic and molecular processes

International Nuclear Information System (INIS)

Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

1985-04-01

This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

1982 bibliography of atomic and molecular processes

Energy Technology Data Exchange (ETDEWEB)

Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

1984-05-01

This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

Testicular cells exhibit similar molecular responses to cigarette smoke condensate ex vivo and in vivo.

Science.gov (United States)

Esakky, Prabagaran; Hansen, Deborah A; Drury, Andrea M; Felder, Paul; Cusumano, Andrew; Moley, Kelle H

2018-01-01

Male exposure to cigarette smoke is associated with seminal defects and with congenital anomalies and childhood cancers in offspring. In mice, paternal exposure to cigarette smoke condensate (CSC) causes molecular defects in germ cells and phenotypic effects in their offspring. Here we used an ex vivo testicular explant model and in vivo exposure to determine the concentration at which CSC impairs spermatogenesis and offspring development. We explanted testis tissue at postnatal day (P)5.5 and cultured it until P11.5. Assessment of growth parameters by analyzing expression of cell-specific markers revealed that the explant system maintained structural and functional integrity. We exposed the P5.5 to -11.5 explants to various concentrations (40-160 µg/ml) of CSC and confirmed that nicotine in the CSC was metabolized to cotinine. We assessed various growth and differentiation parameters, as well as testosterone production, and observed that many spermatogenesis features were impaired at 160 µg/ml CSC. The same parameters were impaired by a similar CSC concentration in vivo Finally, females mated to males that were exposed to 160 µg/ml CSC neonatally had increased rates of pup resorption. We conclude that male exposure to CSC impairs offspring development and that the concentration at which CSC impairs spermatogenesis is similar in vivo and ex vivo. Given that the concentrations of CSC we used contained similar doses of nicotine as human smokers are exposed to, we argue that our model mimics human male reproductive effects of smoking.-Esakky, P., Hansen, D. A., Drury, A. M., Felder, P., Cusumano, A., Moley, K. H. Testicular cells exhibit similar molecular responses to cigarette smoke condensate ex vivo and in vivo . © FASEB.

High-temperature spreading kinetics of metals

Energy Technology Data Exchange (ETDEWEB)

Rauch, N.

2005-05-15

In this PhD work a drop transfer setup combined with high speed photography has been used to analyze the spreading of Ag on polished polycrystalline Mo and single crystalline Mo (110) and (100) substrates. The objective of this work was to unveil the basic phenomena controlling spreading in metal-metal systems. The observed spreading kinetics were compared with current theories of low and high temperature spreading such as a molecular kinetic model and a fluid flow model. Analyses of the data reveal that the molecular model does describe the fastest velocity data well for all the investigated systems. Therefore, the energy which is dissipated during the spreading process is a dissipation at the triple line rather than dissipation due to the viscosity in the liquid. A comparison of the determined free activation energy for wetting of {delta}G95{approx}145kJ/mol with literature values allows the statement that the rate determining step seems to be a surface diffusion of the Ag atoms along the triple line. In order to investigate possible ridge formation, due to local atomic diffusion of atoms of the substrate at the triple during the spreading process, grooving experiments of the polycrystalline Mo were performed to calculate the surface diffusities that will control ridge evolution. The analyses of this work showed that a ridge formation at the fastest reported wetting velocities was not possible if there is no initial perturbation for a ridge. If there was an initial perturbation for a ridge the ridge had to be much smaller than 1 nm in order to be able to move with the liquid font. Therefore ridge formation does not influence the spreading kinetics for the studied system and the chosen conditions. SEM, AFM and TEM investigations of the triple line showed that ridge formation does also not occur at the end of the wetting experiment when the drop is close to equilibrium and the wetting velocity is slow. (orig.)

Surface grafted chitosan gels. Part I. Molecular insight into the formation of chitosan and poly(acrylic acid) multilayers

DEFF Research Database (Denmark)

Liu, Chao; Thormann, Esben; Claesson, Per M.

2014-01-01

Composite polyelectrolyte multilayers of chitosan and low molecular weight poly(acrylic acid) (PAA) have been assembled by sequential adsorption as a first step toward building a surface anchored chitosan gel. Silane chemistry was used to graft the first chitosan layer to prevent film detachment...... and decomposition. The assembly process is characterized by nonlinear growth behavior, with different adsorption kinetics for chitosan and PAA. In situ analysis of the multilayer by means of surface sensitive total internal reflection Raman (TIRR) spectroscopy, combined with target factor analysis of the spectra...... molecular weight chitosan shows a similar behavior, although to a much lower extent. Our data demonstrate that the charged monomeric units of chitosan are mainly compensated by carboxylate ions from PAA. Furthermore, the morphology and mechanical properties of the multilayers were investigated in situ using...

Coarse-grained molecular dynamics modeling of the kinetics of lamellar BCP defect annealing

Science.gov (United States)

Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

2015-03-01

Directed self-assembly of block copolymers (BCPs) is a process that has received great interest in the field of nanomanufacturing in the past decade, and great strides towards forming high quality aligned patterns have been made. But state of the art methods still yield defectivities orders of magnitude higher than is necessary in semi-conductor fabrication even though free energy calculations suggest that equilibrium defectivities are much lower than is necessary for economic semi-conductor fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that infinitely thick films yield an exponential drop in defect heal rate above χN ~ 30. Below χN ~ 30, the rate of transport was similar to the rate at which the transition state was reached so that the overall rate changed only slightly. The energy barrier in periodic simulations increased with 0.31 χN on average. Thin film simulations show no change in rate associated with the energy barrier below χN ~ 50, and then show an increase in energy barrier scaling with 0.16χN. Thin film simulations always begin to heal at either the free interface or the BCP-underlayer interface where the increased A-B contact area associated with the transition state will be minimized, while the infinitely thick films must start healing in the bulk where the A-B contact area is increased. It is also found that cooperative chain movement is required for the defect to start healing.

Addressing the Recalcitrance of Cellulose Degradation through Cellulase Discovery, Nano-scale Elucidation of Molecular Mechanisms, and Kinetic Modeling

Energy Technology Data Exchange (ETDEWEB)

Walker, Larry P., Bergstrom, Gary; Corgie, Stephane; Craighead, Harold; Gibson, Donna; Wilson, David

2011-06-13

This research project was designed to play a vital role in the development of low cost sugars from cellulosic biomass and contributing to the national effort to displace fossil fuel usage in the USA transportation sector. The goal was to expand the portfolio of cell wall degrading enzymes through innovative research at the nano-scale level, prospecting for novel cellulases and building a kinetic framework for the development of more effective enzymatic conversion processes. More precisely, the goal was to elucidate the molecular mechanisms for some cellulases that are very familiar to members of our research team and to investigate what we hope are novel cellulases or new enzyme combinations from the world of plant pathogenic fungi and bacteria. Hydrolytic activities of various cellulases and cellulase cocktails were monitored at the nanoscale of cellulose fibrils and the microscale of pretreated cellulose particles, and we integrated this insight into a heterogeneous reaction framework. The over-riding approach for this research program was the application of innovative and cutting edge optical and high-throughput screening and analysis techniques for observing how cellulases hydrolyze real substrates.

Kinetics and Thermodynamics of Ultrasound-Assisted Depolymerization of κ-Carrageenan

Directory of Open Access Journals (Sweden)

Ratnawati Ratnawati

2016-03-01

Full Text Available The ultrasound-assisted depolymerization of κ-carrageenan has been studied at various temperatures and times. The κ-carrageenan with initial molecular weight of 545 kDa was dispersed in water to form a 5 g/L solution, which was then depolymerized in an ultrasound device at various temperatures and times. The viscosity of the solution was measured using Brookfield viscometer, which was then used to find the number-average molecular weight by Mark-Houwink equation. To obtain the kinetics of κ-carrageenan depolymerization, the number-average molecular weight data was treated using midpoint-chain scission kinetics model. The pre-exponential factor and activation energies for the reaction are 2.683×10-7 mol g-1 min-1 and 6.43 kJ mol-1, respectively. The limiting molecular weight varies from 160 kDa to 240 kDa, and it is linearly correlated to temperature. The results are compared to the result of thermal depolymerization by calculating the half life. It is revealed that ultrasound assisted depolymerization of κ-carrageenan is faster than thermal depolymerization at temperatures below 72.2°C. Compared to thermal depolymerization, the ultrasound-assisted process has lower values of Ea, ΔG‡, ΔH‡, and ΔS‡, which can be attributed to the ultrasonically induced breakage of non-covalent bonds in κ-carrageenan molecules. Copyright © 2016 BCREC GROUP. All rights reserved Received: 10th November 2015; Revised: 18th January 2016; Accepted: 19th January 2016 How to Cite: Ratnawati, R., Prasetyaningrum, A., Wardhani, D.H. (2016. Kinetics and Thermodynamics of Ultrasound-Assisted Depolymerization of κ-Carrageenan. Bulletin of Chemical Reaction Engineering & Catalysis, 11(1: 48-58. (doi:10.9767/bcrec.11.1.415.48-58 Permalink/DOI: http://dx.doi.org/10.9767/bcrec.11.1.415.48-58

Effects of substrate anisotropy and edge diffusion on submonolayer growth during molecular beam epitaxy: A Kinetic Monte Carlo study

International Nuclear Information System (INIS)

Devkota, J.; Shrestha, S.P.

2007-12-01

We have performed Kinetic Monte Carlo simulation work to study the effect of diffusion anisotropy, bonding anisotropy and edge diffusion on island formation at different temperatures during the sub-monolayer film growth in Molecular Beam Epitaxy. We use simple cubic solid on solid model and event based Bortz, Kalos and Labowitch (BKL) algorithm on the Kinetic Monte Carlo method to simulate the physical phenomena. We have found that the island morphology and growth exponent are found to be influenced by substrate anisotropy as well as edge diffusion, however they do not play a significant role in island elongation. The growth exponent and island size distribution are observed to be influenced by substrate anisotropy but are negligibly influenced by edge diffusion. We have found fractal islands when edge diffusion is excluded and compact islands when edge diffusion is included. (author)

Evidence for Dynamic Chemical Kinetics at Individual Molecular Ruthenium Catalysts.

Science.gov (United States)

Easter, Quinn T; Blum, Suzanne A

2018-02-05

Catalytic cycles are typically depicted as possessing time-invariant steps with fixed rates. Yet the true behavior of individual catalysts with respect to time is unknown, hidden by the ensemble averaging inherent to bulk measurements. Evidence is presented for variable chemical kinetics at individual catalysts, with a focus on ring-opening metathesis polymerization catalyzed by the second-generation Grubbs' ruthenium catalyst. Fluorescence microscopy is used to probe the chemical kinetics of the reaction because the technique possesses sufficient sensitivity for the detection of single chemical reactions. Insertion reactions in submicron regions likely occur at groups of many (not single) catalysts, yet not so many that their unique kinetic behavior is ensemble averaged. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Making waves: Kinetic processes controlling surface evolution during low energy ion sputtering

International Nuclear Information System (INIS)

Chan, W.L.; Chason, Eric

2007-01-01

When collimated beams of low energy ions are used to bombard materials, the surface often develops a periodic pattern or ''ripple'' structure. Different types of patterns are observed to develop under different conditions, with characteristic features that depend on the substrate material, the ion beam parameters, and the processing conditions. Because the patterns develop spontaneously, without applying any external mask or template, their formation is the expression of a dynamic balance among fundamental surface kinetic processes, e.g., erosion of material from the surface, ion-induced defect creation, and defect-mediated evolution of the surface morphology. In recent years, a comprehensive picture of the different kinetic mechanisms that control the different types of patterns that form has begun to emerge. In this article, we provide a review of different mechanisms that have been proposed and how they fit together in terms of the kinetic regimes in which they dominate. These are grouped into regions of behavior dominated by the directionality of the ion beam, the crystallinity of the surface, the barriers to surface roughening, and nonlinear effects. In sections devoted to each type of behavior, we relate experimental observations of patterning in these regimes to predictions of continuum models and to computer simulations. A comparison between theory and experiment is used to highlight strengths and weaknesses in our understanding. We also discuss the patterning behavior that falls outside the scope of the current understanding and opportunities for advancement

Quasi-molecular processes in dense plasmas

International Nuclear Information System (INIS)

Younger, S.M.

1991-01-01

Quasi-molecular phenomena occur in dense plasmas when the interatomic spacing is comparable to the characteristic wavelength of the electrons. If the electronic states are bound, covalent orbitals arise with different excitation energies, radiative rates, and collisional rates than for isolated ions. For continuum electrons, charge localization near transient clusters of nuclei can influence many scattering and transport processes. We identify several novel consequences of quasi-molecular phenomena in plasmas and give a possible explanation of high energy features associated with helium-like emissions lines observed in recent inertial fusion experiments. 7 refs

Fluorescence kinetics and positron annihilation kinetics investigations in cadmium sulfide crystals

Energy Technology Data Exchange (ETDEWEB)

Grillot, E; Bancie-Grillot, M; Egee, M [Reims Univ., 51 (France)

1976-03-01

Fluorescence kinetics and positrons annihilation kinetics investigations on CdS crystals, either very pure or with increasing contents of Ag-ions, led to similar and complementary results. Ag-ions mainly fill the cadmium vacancies of the lattice, building red emission luminogene centres, while green 'edge-emission' ones are destroyed. These latter, which involve an excited level active for high energy series fluorescence, seems actually related to cadmium vacancies.

Kinetic mechanism of molecular energy transfer and chemical reactions in low-temperature air-fuel plasmas.

Science.gov (United States)

Adamovich, Igor V; Li, Ting; Lempert, Walter R

2015-08-13

This work describes the kinetic mechanism of coupled molecular energy transfer and chemical reactions in low-temperature air, H2-air and hydrocarbon-air plasmas sustained by nanosecond pulse discharges (single-pulse or repetitive pulse burst). The model incorporates electron impact processes, state-specific N(2) vibrational energy transfer, reactions of excited electronic species of N(2), O(2), N and O, and 'conventional' chemical reactions (Konnov mechanism). Effects of diffusion and conduction heat transfer, energy coupled to the cathode layer and gasdynamic compression/expansion are incorporated as quasi-zero-dimensional corrections. The model is exercised using a combination of freeware (Bolsig+) and commercial software (ChemKin-Pro). The model predictions are validated using time-resolved measurements of temperature and N(2) vibrational level populations in nanosecond pulse discharges in air in plane-to-plane and sphere-to-sphere geometry; temperature and OH number density after nanosecond pulse burst discharges in lean H(2)-air, CH(4)-air and C(2)H(4)-air mixtures; and temperature after the nanosecond pulse discharge burst during plasma-assisted ignition of lean H2-mixtures, showing good agreement with the data. The model predictions for OH number density in lean C(3)H(8)-air mixtures differ from the experimental results, over-predicting its absolute value and failing to predict transient OH rise and decay after the discharge burst. The agreement with the data for C(3)H(8)-air is improved considerably if a different conventional hydrocarbon chemistry reaction set (LLNL methane-n-butane flame mechanism) is used. The results of mechanism validation demonstrate its applicability for analysis of plasma chemical oxidation and ignition of low-temperature H(2)-air, CH(4)-air and C(2)H(4)-air mixtures using nanosecond pulse discharges. Kinetic modelling of low-temperature plasma excited propane-air mixtures demonstrates the need for development of a more accurate

Efficient integration of stiff kinetics with phase change detection for reactive reservoir processes

DEFF Research Database (Denmark)

Kristensen, Morten Rode; Gerritsen, Margot G.; Thomsen, Per Grove

2007-01-01

We propose the use of implicit one-step Explicit Singly Diagonal Implicit Runge-Kutta (ESDIRK) methods for integration of the stiff kinetics in reactive, compositional and thermal processes that are solved using operator-splitting type approaches. To facilitate the algorithmic development we...

Simulation of the organic-waste processing in plasma with allowance for kinetics of thermochemical transformations

Science.gov (United States)

Messerle, V. E.; Ustimenko, A. B.

2017-07-01

Kinetic calculations of the plasma processing/utilization process of organic waste in air and steam ambient were carried out. It is shown that, during the time of waste residence in the plasma reactor, 0.7 and 1.2 s, at the exit from the reactor there forms a high-calorific fuel gas with a combustion heat of 3540 and 5070 kcal/kg, respectively. In this process, 1 kg of waste yields 1.16 kg of fuel gas at air gasification of waste and 0.87 kg of pure synthesis gas at steam gasification. The energy efficiency of the waste gasification process, defined by the ratio between the calorific value of the resultant fuel gas and the initial calorific value of the waste amounts to 91 % in air plasma and 98 % in steam plasma. A comparison between the results of kinetic and thermodynamic calculations has revealed their good agreement.

Families of birth-death processes with similar time-dependent behaviour.

NARCIS (Netherlands)

Lenin, R.B.; Parthasarathy, P.R.; Scheinhardt, Willem R.W.; van Doorn, Erik A.

2000-01-01

We consider birth-death processes taking values in N ≡ {0,1,... }, but allow the death rate in state 0 to be positive, so that escape from N is possible. Two such processes with transition functions { pij(t) } and { ̃pij(t) } are said to be similar if, for all i, j ∈ N, there are constants cij such

Kinetic and spectral descriptions of autoionization phenomena associated with atomic processes in plasmas

Science.gov (United States)

Jacobs, Verne L.

2017-06-01

This investigation has been devoted to the theoretical description and computer modeling of atomic processes giving rise to radiative emission in energetic electron and ion beam interactions and in laboratory plasmas. We are also interested in the effects of directed electron and ion collisions and of anisotropic electric and magnetic fields. In the kinetic-theory description, we treat excitation, de-excitation, ionization, and recombination in electron and ion encounters with partially ionized atomic systems, including the indirect contributions from processes involving autoionizing resonances. These fundamental collisional and electromagnetic interactions also provide particle and photon transport mechanisms. From the spectral perspective, the analysis of atomic radiative emission can reveal detailed information on the physical properties in the plasma environment, such as non-equilibrium electron and charge-state distributions as well as electric and magnetic field distributions. In this investigation, a reduced-density-matrix formulation is developed for the microscopic description of atomic electromagnetic interactions in the presence of environmental (collisional and radiative) relaxation and decoherence processes. Our central objective is a fundamental microscopic description of atomic electromagnetic processes, in which both bound-state and autoionization-resonance phenomena can be treated in a unified and self-consistent manner. The time-domain (equation-of-motion) and frequency-domain (resolvent-operator) formulations of the reduced-density-matrix approach are developed in a unified and self-consistent manner. This is necessary for our ultimate goal of a systematic and self-consistent treatment of non-equilibrium (possibly coherent) atomic-state kinetics and high-resolution (possibly overlapping) spectral-line shapes. We thereby propose the introduction of a generalized collisional-radiative atomic-state kinetics model based on a reduced

Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments.

Directory of Open Access Journals (Sweden)

Tihamér Geyer

Full Text Available Metabolic processes in biological cells are commonly either characterized at the level of individual enzymes and metabolites or at the network level. Often these two paradigms are considered as mutually exclusive because concepts from neither side are suited to describe the complete range of scales. Additionally, when modeling metabolic or regulatory cellular systems, often a large fraction of the required kinetic parameters are unknown. This even applies to such simple and extensively studied systems like the photosynthetic apparatus of purple bacteria. Using the chromatophore vesicles of Rhodobacter sphaeroides as a model system, we show that a consistent kinetic model emerges when fitting the dynamics of a molecular stochastic simulation to a set of time dependent experiments even though about two thirds of the kinetic parameters in this system are not known from experiment. Those kinetic parameters that were previously known all came out in the expected range. The simulation model was built from independent protein units composed of elementary reactions processing single metabolites. This pools-and-proteins approach naturally compiles the wealth of available molecular biological data into a systemic model and can easily be extended to describe other systems by adding new protein or nucleic acid types. The automated parameter optimization, performed with an evolutionary algorithm, reveals the sensitivity of the model to the value of each parameter and the relative importances of the experiments used. Such an analysis identifies the crucial system parameters and guides the setup of new experiments that would add most knowledge for a systemic understanding of cellular compartments. The successful combination of the molecular model and the systemic parametrization presented here on the example of the simple machinery for bacterial photosynthesis shows that it is actually possible to combine molecular and systemic modeling. This framework can now

Energy partitioning constraints at kinetic scales in low-β turbulence

Science.gov (United States)

Gershman, Daniel J.; F.-Viñas, Adolfo; Dorelli, John C.; Goldstein, Melvyn L.; Shuster, Jason; Avanov, Levon A.; Boardsen, Scott A.; Stawarz, Julia E.; Schwartz, Steven J.; Schiff, Conrad; Lavraud, Benoit; Saito, Yoshifumi; Paterson, William R.; Giles, Barbara L.; Pollock, Craig J.; Strangeway, Robert J.; Russell, Christopher T.; Torbert, Roy B.; Moore, Thomas E.; Burch, James L.

2018-02-01

Turbulence is a fundamental physical process through which energy injected into a system at large scales cascades to smaller scales. In collisionless plasmas, turbulence provides a critical mechanism for dissipating electromagnetic energy. Here, we present observations of plasma fluctuations in low-β turbulence using data from NASA's Magnetospheric Multiscale mission in Earth's magnetosheath. We provide constraints on the partitioning of turbulent energy density in the fluid, ion-kinetic, and electron-kinetic ranges. Magnetic field fluctuations dominated the energy density spectrum throughout the fluid and ion-kinetic ranges, consistent with previous observations of turbulence in similar plasma regimes. However, at scales shorter than the electron inertial length, fluctuation power in electron kinetic energy significantly exceeded that of the magnetic field, resulting in an electron-motion-regulated cascade at small scales. This dominance is highly relevant for the study of turbulence in highly magnetized laboratory and astrophysical plasmas.

Combining experimental and simulation data of molecular processes via augmented Markov models.

Science.gov (United States)

Olsson, Simon; Wu, Hao; Paul, Fabian; Clementi, Cecilia; Noé, Frank

2017-08-01

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

1978 bibliography of atomic and molecular processes. [Bibliography

Energy Technology Data Exchange (ETDEWEB)

1980-03-01

This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

1979 bibliography of atomic and molecular processes. [Bibliography

Energy Technology Data Exchange (ETDEWEB)

None

1980-08-01

This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

Sulfonamide-Linked Ciprofloxacin, Sulfadiazine and Amantadine Derivatives as a Novel Class of Inhibitors of Jack Bean Urease; Synthesis, Kinetic Mechanism and Molecular Docking.

Science.gov (United States)

Channar, Pervaiz Ali; Saeed, Aamer; Albericio, Fernando; Larik, Fayaz Ali; Abbas, Qamar; Hassan, Mubashir; Raza, Hussain; Seo, Sung-Yum

2017-08-16

Sulfonamide derivatives serve as an important building blocks in the drug design discovery and development (4D) process. Ciprofloxacin-, sulfadiazine- and amantadine-based sulfonamides were synthesized as potent inhibitors of jack bean urease and free radical scavengers. Molecular diversity was explored and electronic factors were also examined. All 24 synthesized compounds exhibited excellent potential against urease enzyme. Compound 3e (IC 50 = 0.081 ± 0.003 µM), 6a (IC 50 = 0.0022 ± 0.0002 µM), 9e (IC 50 = 0.0250 ± 0.0007 µM) and 12d (IC 50 = 0.0266 ± 0.0021 µM) were found to be the lead compounds compared to standard (thiourea, IC 50 = 17.814 ± 0.096 µM). Molecular docking studies were performed to delineate the binding affinity of the molecules and a kinetic mechanism of enzyme inhibition was propounded. Compounds 3e , 6a and 12d exhibited a mixed type of inhibition, while derivative 9e revealed a non-competitive mode of inhibition. Compounds 12a , 12b , 12d , 12e and 12f showed excellent radical scavenging potency in comparison to the reference drug vitamin C.

Actinorhizal nitrogen fixing nodules: infection process, molecular ...

African Journals Online (AJOL)

Actinorhizal nitrogen fixing nodules: infection process, molecular biology and genomics. Mariana Obertello, Mame Oureye SY, Laurent Laplaze, Carole Santi, Sergio Svistoonoff, Florence Auguy, Didier Bogusz, Claudine Franche ...

Report on the scientific activity for the CRP on data for molecular processes in edge plasmas

International Nuclear Information System (INIS)

Schneider, I.F.; Crumeyrolle, O.; Suzor-Weiner, A.; Florescu, A.I.; Motapon, O.; Nana Ngassam, V.; Waffeu Tamo, F.O.; Fifirig, M.; Stroe, M.C.

2006-01-01

Reactive collisions between electrons and molecular ions of hydrogen and oxides, relevant for fusion plasma kinetics have been investigated. The main results (advances in modelling and computed rates) achieved are: Reactive collisions between electrons and H 2 + ions at low energy (0.0001-1 eV): dissociative recombination, superelastic collisions, inelastic collisions and elastic collisions; Computation and comparison with TSR storage ring experimental data; Rigorous theory for intermediate energy; Critical update of molecular data (states and interactions) for H 2 and isotopes; computation and comparison with flowing afterglow Langmuir probe plasma experiments

Glass formability in medium-sized molecular systems/pharmaceuticals. I. Thermodynamics vs. kinetics

Energy Technology Data Exchange (ETDEWEB)

Tu, Wenkang; Li, Xiangqian; Chen, Zeming; Liu, Ying Dan; Wang, Li-Min, E-mail: simone.capaccioli@unipi.it, E-mail: Limin-Wang@ysu.edu.cn [State Key Lab of Metastable Materials Science and Technology, and College of Materials Science and Engineering, Yanshan University, Qinhuangdao, Hebei 066004 (China); Labardi, Massimiliano [CNR-IPCF, Sede Secondaria Pisa, Largo Pontecorvo 3, I-56127 Pisa (Italy); Capaccioli, Simone, E-mail: simone.capaccioli@unipi.it, E-mail: Limin-Wang@ysu.edu.cn [CNR-IPCF, Sede Secondaria Pisa, Largo Pontecorvo 3, I-56127 Pisa (Italy); Department of Physics, Pisa University, Largo Bruno Pontecorvo 3, I-56127 Pisa (Italy); Paluch, M. [Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland)

2016-05-07

Scrutinizing critical thermodynamic and kinetic factors for glass formation and the glass stability of materials would benefit the screening of the glass formers for the industry of glassy materials. The present work aims at elucidating the factors that contribute to the glass formation by investigating medium-sized molecules of pharmaceuticals. Glass transition related thermodynamics and kinetics are performed on the pharmaceuticals using calorimetric, dielectric, and viscosity measurements. The characteristic thermodynamic and kinetic parameters of glass transition are found to reproduce the relations established for small-molecule glass formers. The systematic comparison of the thermodynamic and kinetic contributions to glass formation reveals that the melting-point viscosity is the crucial quantity for the glass formation. Of more interest is the finding of a rough correlation between the melting-point viscosity and the entropy of fusion normalized by the number of beads of the pharmaceuticals, suggesting the thermodynamics can partly manifest its contribution to glass formation via kinetics.

Glass formability in medium-sized molecular systems/pharmaceuticals. I. Thermodynamics vs. kinetics.

Science.gov (United States)

Tu, Wenkang; Li, Xiangqian; Chen, Zeming; Liu, Ying Dan; Labardi, Massimiliano; Capaccioli, Simone; Paluch, M; Wang, Li-Min

2016-05-07

Scrutinizing critical thermodynamic and kinetic factors for glass formation and the glass stability of materials would benefit the screening of the glass formers for the industry of glassy materials. The present work aims at elucidating the factors that contribute to the glass formation by investigating medium-sized molecules of pharmaceuticals. Glass transition related thermodynamics and kinetics are performed on the pharmaceuticals using calorimetric, dielectric, and viscosity measurements. The characteristic thermodynamic and kinetic parameters of glass transition are found to reproduce the relations established for small-molecule glass formers. The systematic comparison of the thermodynamic and kinetic contributions to glass formation reveals that the melting-point viscosity is the crucial quantity for the glass formation. Of more interest is the finding of a rough correlation between the melting-point viscosity and the entropy of fusion normalized by the number of beads of the pharmaceuticals, suggesting the thermodynamics can partly manifest its contribution to glass formation via kinetics.

Chemical kinetics modeling of the influence of molecular structure on shock tube ignition delay

International Nuclear Information System (INIS)

Westbrook, C.K.; Pitz, W.J.

1985-07-01

The current capabilities of kinetic modeling of hydrocarbon oxidation in shock waves are discussed. The influence of molecular size and structure on ignition delay times are stressed. The n-paraffin fuels from CH 4 to n-C 5 H 12 are examined under shock tube conditions, as well as the branched chain fuel isobutane, and the computed results are compared with available experimental data. The modeling results show that it is important in the reaction mechanism to distinguish between abstraction of primary, secondary and tertiary H atom sites from the fuel molecule. This is due to the fact that both the rates and the product distributions of the subsequent alkyl radical decomposition reactions depend on which H atoms were abstracted. Applications of the reaction mechanisms to shock tube problems and to other practical problems such as engine knock are discussed

Kinetic modelling of a diesel-polluted clayey soil bioremediation process

Energy Technology Data Exchange (ETDEWEB)

Fernández, Engracia Lacasa; Merlo, Elena Moliterni [Chemical Engineering Department, Research Institute for Chemical and Environmental Technology (ITQUIMA), University of Castilla La Mancha, 13071 Ciudad Real (Spain); Mayor, Lourdes Rodríguez [National Institute for Hydrogen Research, C/Fernando el Santo, 13500 Puertollano (Spain); Camacho, José Villaseñor, E-mail: jose.villasenor@uclm.es [Chemical Engineering Department, Research Institute for Chemical and Environmental Technology (ITQUIMA), University of Castilla La Mancha, 13071 Ciudad Real (Spain)

2016-07-01

A mathematical model is proposed to describe a diesel-polluted clayey soil bioremediation process. The reaction system under study was considered a completely mixed closed batch reactor, which initially contacted a soil matrix polluted with diesel hydrocarbons, an aqueous liquid-specific culture medium and a microbial inoculation. The model coupled the mass transfer phenomena and the distribution of hydrocarbons among four phases (solid, S; water, A; non-aqueous liquid, NAPL; and air, V) with Monod kinetics. In the first step, the model simulating abiotic conditions was used to estimate only the mass transfer coefficients. In the second step, the model including both mass transfer and biodegradation phenomena was used to estimate the biological kinetic and stoichiometric parameters. In both situations, the model predictions were validated with experimental data that corresponded to previous research by the same authors. A correct fit between the model predictions and the experimental data was observed because the modelling curves captured the major trends for the diesel distribution in each phase. The model parameters were compared to different previously reported values found in the literature. Pearson correlation coefficients were used to show the reproducibility level of the model. - Highlights: • A mathematical model is proposed to describe a soil bioremediation process. • The model couples mass transfer phenomena among phases with biodegradation. • Model predictions were validated with previous data reported by the authors. • A correct fit and correlation coefficients were observed.

Kinetic modelling of a diesel-polluted clayey soil bioremediation process

International Nuclear Information System (INIS)

Fernández, Engracia Lacasa; Merlo, Elena Moliterni; Mayor, Lourdes Rodríguez; Camacho, José Villaseñor

2016-01-01

A mathematical model is proposed to describe a diesel-polluted clayey soil bioremediation process. The reaction system under study was considered a completely mixed closed batch reactor, which initially contacted a soil matrix polluted with diesel hydrocarbons, an aqueous liquid-specific culture medium and a microbial inoculation. The model coupled the mass transfer phenomena and the distribution of hydrocarbons among four phases (solid, S; water, A; non-aqueous liquid, NAPL; and air, V) with Monod kinetics. In the first step, the model simulating abiotic conditions was used to estimate only the mass transfer coefficients. In the second step, the model including both mass transfer and biodegradation phenomena was used to estimate the biological kinetic and stoichiometric parameters. In both situations, the model predictions were validated with experimental data that corresponded to previous research by the same authors. A correct fit between the model predictions and the experimental data was observed because the modelling curves captured the major trends for the diesel distribution in each phase. The model parameters were compared to different previously reported values found in the literature. Pearson correlation coefficients were used to show the reproducibility level of the model. - Highlights: • A mathematical model is proposed to describe a soil bioremediation process. • The model couples mass transfer phenomena among phases with biodegradation. • Model predictions were validated with previous data reported by the authors. • A correct fit and correlation coefficients were observed.

Tantalum high-temperature oxidation kinetics

International Nuclear Information System (INIS)

Grigor'ev, Yu.M.; Sarkisyan, A.A.; Merzhanov, A.G.

1981-01-01

Kinetics of heat release and scale growth during tantalum oxidation within 650-1300 deg C temperature range in oxygen-containing media is investigated. Kinetic equations and temperature and pressure dependences of constants are ound Applicability of the kinetic Lorie mechanism for the description of the tantalum oxidation kinetics applicably to rapid-passing processes is shown. It is stated that the process rate (reaction ability) is determined by adsorption desorption factors on the external surface of the ''protective'' oxide for the ''linear'' oxidation stage [ru

Production of carbon molecular sieves from Illinois coal

Science.gov (United States)

Lizzio, A.A.; Rostam-Abadi, M.

1993-01-01

Carbon molecular sieves (CMS) have become an increasingly important class of adsorbents for application in the separation of gas molecules that vary in size and shape. A study is in progress at the Illinois State Geological Survey to determine whether Illinois basin coals are suitable feedstocks for the production of CMS and to evaluate their potential application in gas separation processes of commercial importance. Chars were prepared from Illinois coal in a fixed-bed reactor under a wide range of heat treatment and activation conditions. The effects of various coal/char pretreatments, including coal demineralization, preoxidation, char activation, and carbon deposition, on the molecular sieve properties of the chars were also investigated. Chars with commercially significant BET surface areas of 1500 m2/g were produced by chemical activation using potassium hydroxide as the activant. These high-surface-area (HSA) chars had more than twice the adsorption capacity of commercial carbon and zeolite molecular sieves. The kinetics of adsorption of various gases, e.g., N2, O2, CO2, CH4, CO and H2, on these chars at 25??C was measured. The O2/N2 molecular sieve properties of one char prepared without chemical activation were similar to those of a commercial CMS. On the other hand, the O2/N2 selectivity of the HSA char was comparable to that of a commercial activated carbon, i.e., essentially unity. Carbon deposition, using methane as the cracking gas, increased the O2/N2 selectivity of the HSA char, but significantly decreased its adsorption capacity. Several chars showed good potential for efficient CO2/CH4 separation; both a relatively high CO2 adsorption capacity and CO2/CH4 selectivity were achieved. The micropore size distribution of selected chars was estimated by equilibrium adsorption of carbon dioxide, n-butane and iso-butane at O??C. The extent of adsorption of each gas corresponded to the effective surface area contained in pores with diameters greater than 3

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

Science.gov (United States)

Kouza, Maksim; Co, Nguyen Truong; Li, Mai Suan; Kmiecik, Sebastian; Kolinski, Andrzej; Kloczkowski, Andrzej; Buhimschi, Irina Alexandra

2018-06-01

Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite much progress in the understanding of the protein aggregation process, the factors governing fibril formation rates and fibril stability have not been fully understood. Using lattice models, we have shown that the fibril formation time is controlled by the kinetic stability of the fibril state but not by its energy. Having performed all-atom explicit solvent molecular dynamics simulations with the GROMOS43a1 force field for full-length amyloid beta peptides Aβ40 and Aβ42 and truncated peptides, we demonstrated that kinetic stability can be accessed via mechanical stability in such a way that the higher the mechanical stability or the kinetic stability, the faster the fibril formation. This result opens up a new way for predicting fibril formation rates based on mechanical stability that may be easily estimated by steered molecular dynamics.

Molecular outflows in protostellar evolution

International Nuclear Information System (INIS)

Fukui, Y.; Iwata, T.; Mizuno, A.; Ogawa, H.; Kawabata, K.; Sugitani, K.

1989-01-01

Molecular outflow is an energetic mass-ejection phenomenon associated with very early stage of stellar evolution. The large kinetic energy involved in the phenomenon indicates that outflow may play an essential role in the process of star formation, particularly by extracting angular momentum. Most of the previous searches have been strongly biased toward optical or near-infrared signposts of star formation. They are not able, therefore, to provide the complete database necessary for a statistical study of the evolutionary status of molecular outflow. To overcome this difficulty, it is of vital importance to make an unbiased search of single molecular clouds for molecular outflows; here we report the final result of such a survey of the Lynds 1641 dark cloud. We show that molecular outflows are characterized by a total luminosity significantly greater than that of T Tauri stars. This indicates that molecular outflow corresponds to the main accretion phase of protostellar evolution, in which the luminosity excess is due to the gravitational energy released by dynamical mass accretion onto the protostellar core. (author)

Evaluation of silage-fed biogas process performance using microbiological and kinetic methods

Energy Technology Data Exchange (ETDEWEB)

Jarvis, Aa

1996-10-01

In this study, different kinetic and microbiological methods were used to evaluate the growth and activity of key groups of bacteria degrading ley silage in one-phase and two-phase biogas processes. Emphasis was placed on studying the dynamic behaviour of different trophic groups resulting from the initiation of liquid recirculation in the processes. The microbiological methods included microscopy and most probable number (MPN) counts with different substrates. The kinetic methods included measurements of specific methanogenic activity (SMA) with acetate and H{sub 2}/CO{sub 2} as substrates, batch assays with trace element additions and measurement of conversion rates of mannitol and lactate in the digesters. In general, the initiation of liquid recirculation at first promoted the growth and/or activity of several trophic groups of bacteria, such as butyrate and propionate degraders and acetotrophic and hydrogenotrophic methanogens in the liquefaction/acidogenesis reactors of the two-phase processes. This was probably mainly due to the increased pH. However, after some time of liquid recirculation, an inhibition of some bacterial groups occurred, such as propionate degraders and methanogens in the methanogenic reactors of two-phase processes. This was probably due to increased concentrations of salts and free ammonia. The batch assays proved to be valuable tools in process optimization by the addition of trace elements. Here, the addition of cobalt significantly increased methane production from acetate. In this study, a more comprehensive understanding of the process behaviour in response to the initiation of liquid recirculation was achieved which could not have been obtained by only monitoring routine parameters such as pH, methane production and concentrations of organic acids and salts. 120 refs, 4 figs, 1 tab

First-principles molecular dynamics study of Al/Alq3 interfaces

Directory of Open Access Journals (Sweden)

Kousuke Takeuchi et al

2007-01-01

Full Text Available We have carried out first-principles molecular dynamics simulations of Al deposition on tris (8-hydroxyquinoline aluminum (Alq3 layers to investigate atomic geometries and electronic properties of Al/Alq3 interfaces. Al atoms were ejected to Alq3 one by one with the kinetic energy of 37.4 kJ/mol, which approximately corresponds to the average kinetic energy of Al at the boiling temperature of metal Al. The first Al atom interacts with two of the three O atoms of meridional Alq3. Following Al atoms interact with Alq3 rather weakly and they tend to aggregate each other to form Al clusters. During the deposition process, Alq3 was not broken and its molecular structure remained essentially intact. At the interface, weak bonds between deposited Al atoms and N and C atoms were formed. The projected density of states (PDOS onto the Alq3 molecular orbitals shows gap states in between the highest occupied molecular orbitals (HOMOs and the lowest unoccupied molecular orbitals (LUMOs, which were experimentally observed by ultraviolet photoelectron spectroscopy (UPS and metastable atom electron spectroscopy (MAES. Our results show that even though the Alq3 molecular structure is retained, weak N–Al and C–Al bonds induce gap states.

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

Science.gov (United States)

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

2018-03-01

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

The role of atomic and molecular processes in fusion research

International Nuclear Information System (INIS)

Harrison, M.F.A.

1977-01-01

This paper considers the relevance of atomic and molecular processes to research into controlled nuclear fusion and in particular their effects upon the magnetically confined plasma in Tokamak experiments and conceptual Tokamak reactors. The relative significance of collective phenomena and of single particle collisions to both plasma heating and loss processes are discussed and the pertinent principles of plasma refuelling and plasma diagnostics are outlined. The methods by which atomic and molecular data are applied to these problems, the contributing effects of surface interactions and the consequent implications upon the accuracy and the type of data needed are described in a qualitative manner. Whilst particular atomic and molecular processes are not discussed in detail, sufficient information is given of the physical environments of Tokamak devices for significant processes to be self evident. (author)

Comparison of the kinetics of different Markov models for ligand binding under varying conditions

International Nuclear Information System (INIS)

Martini, Johannes W. R.; Habeck, Michael

2015-01-01

We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest

Comparison of the kinetics of different Markov models for ligand binding under varying conditions

Energy Technology Data Exchange (ETDEWEB)

Martini, Johannes W. R., E-mail: jmartin2@gwdg.de [Max Planck Institute for Developmental Biology, Tübingen (Germany); Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen (Germany); Habeck, Michael, E-mail: mhabeck@gwdg.de [Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen (Germany); Max Planck Institute for Biophysical Chemistry, Göttingen (Germany)

2015-03-07

We recently derived a Markov model for macromolecular ligand binding dynamics from few physical assumptions and showed that its stationary distribution is the grand canonical ensemble [J. W. R. Martini, M. Habeck, and M. Schlather, J. Math. Chem. 52, 665 (2014)]. The transition probabilities of the proposed Markov process define a particular Glauber dynamics and have some similarity to the Metropolis-Hastings algorithm. Here, we illustrate that this model is the stochastic analog of (pseudo) rate equations and the corresponding system of differential equations. Moreover, it can be viewed as a limiting case of general stochastic simulations of chemical kinetics. Thus, the model links stochastic and deterministic approaches as well as kinetics and equilibrium described by the grand canonical ensemble. We demonstrate that the family of transition matrices of our model, parameterized by temperature and ligand activity, generates ligand binding kinetics that respond to changes in these parameters in a qualitatively similar way as experimentally observed kinetics. In contrast, neither the Metropolis-Hastings algorithm nor the Glauber heat bath reflects changes in the external conditions correctly. Both converge rapidly to the stationary distribution, which is advantageous when the major interest is in the equilibrium state, but fail to describe the kinetics of ligand binding realistically. To simulate cellular processes that involve the reversible stochastic binding of multiple factors, our pseudo rate equation model should therefore be preferred to the Metropolis-Hastings algorithm and the Glauber heat bath, if the stationary distribution is not of only interest.

Insight derived from molecular dynamics simulations into molecular motions, thermodynamics and kinetics of HIV-1 gp120.

Directory of Open Access Journals (Sweden)

Peng Sang

Full Text Available Although the crystal structures of the HIV-1 gp120 core bound and pre-bound by CD4 are known, the details of dynamics involved in conformational equilibrium and transition in relation to gp120 function have remained elusive. The homology models of gp120 comprising the N- and C-termini and loops V3 and V4 in the CD4-bound and CD4-unbound states were built and subjected to molecular dynamics (MD simulations to investigate the differences in dynamic properties and molecular motions between them. The results indicate that the CD4-bound gp120 adopted a more compact and stable conformation than the unbound form during simulations. For both the unbound and bound gp120, the large concerted motions derived from essential dynamics (ED analyses can influence the size/shape of the ligand-binding channel/cavity of gp120 and, therefore, were related to its functional properties. The differences in motion direction between certain structural components of these two forms of gp120 were related to the conformational interconversion between them. The free energy calculations based on the metadynamics simulations reveal a more rugged and complex free energy landscape (FEL for the unbound than for the bound gp120, implying that gp120 has a richer conformational diversity in the unbound form. The estimated free energy difference of ∼-6.0 kJ/mol between the global minimum free energy states of the unbound and bound gp120 indicates that gp120 can transform spontaneously from the unbound to bound states, revealing that the bound state represents a high-probability "ground state" for gp120 and explaining why the unbound state resists crystallization. Our results provide insight into the dynamics-and-function relationship of gp120, and facilitate understandings of the thermodynamics, kinetics and conformational control mechanism of HIV-1 gp120.

Light-operated machines based on threaded molecular structures.

Science.gov (United States)

Credi, Alberto; Silvi, Serena; Venturi, Margherita

2014-01-01

Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

Microtubule dynamics. II. Kinetics of self-assembly

DEFF Research Database (Denmark)

Flyvbjerg, H.; Jobs, E.

1997-01-01

Inverse scattering theory describes the conditions necessary and sufficient to determine an unknown potential from known scattering data. No similar theory exists for when and how one may deduce the kinetics of an unknown chemical reaction from quantitative information about its final state and i...... to analyze the self-assembly of microtubules from tubulin are general, and many other reactions and processes may be studied as inverse problems with these methods when enough experimental data are available....

Line emission processes in atomic and molecular shocks

International Nuclear Information System (INIS)

Shull, J.M.

1988-01-01

The review discusses the observations and theoretical models of interstellar shock waves in diffuse and molecular clouds. After summarizing the relevant gas dynamics, atomic, molecular and grain processes, and physics of radiative and magnetic precursors, the author describes observational diagnostics of shocks. This paper concludes with a discussion of two topics: unstable or non-steady shocks and thermal conduction in metal-rich shocks

Prediction of Proper Temperatures for the Hot Stamping Process Based on the Kinetics Models

Science.gov (United States)

Samadian, P.; Parsa, M. H.; Mirzadeh, H.

2015-02-01

Nowadays, the application of kinetics models for predicting microstructures of steels subjected to thermo-mechanical treatments has increased to minimize direct experimentation, which is costly and time consuming. In the current work, the final microstructures of AISI 4140 steel sheets after the hot stamping process were predicted using the Kirkaldy and Li kinetics models combined with new thermodynamically based models in order for the determination of the appropriate process temperatures. In this way, the effect of deformation during hot stamping on the Ae3, Acm, and Ae1 temperatures was considered, and then the equilibrium volume fractions of phases at different temperatures were calculated. Moreover, the ferrite transformation rate equations of the Kirkaldy and Li models were modified by a term proposed by Åkerström to consider the influence of plastic deformation. Results showed that the modified Kirkaldy model is satisfactory for the determination of appropriate austenitization temperatures for the hot stamping process of AISI 4140 steel sheets because of agreeable microstructure predictions in comparison with the experimental observations.

Quantum mechanics of molecular rate processes

CERN Document Server

Levine, Raphael D

1999-01-01

This survey of applications of the theory of collisions and rate processes to molecular problems explores collisions of molecules with internal structure, generalized Ehrenfest theorem, theory of reactive collisions, and role of symmetry. It also reviews partitioning technique, equivalent potentials and quasibound states, theory of direct reactions, more. 1969 edition.

Estimation of fundamental kinetic parameters of polyhydroxybutyrate fermentation process of Azohydromonas australica using statistical approach of media optimization.

Science.gov (United States)

Gahlawat, Geeta; Srivastava, Ashok K

2012-11-01

Polyhydroxybutyrate or PHB is a biodegradable and biocompatible thermoplastic with many interesting applications in medicine, food packaging, and tissue engineering materials. The present study deals with the enhanced production of PHB by Azohydromonas australica using sucrose and the estimation of fundamental kinetic parameters of PHB fermentation process. The preliminary culture growth inhibition studies were followed by statistical optimization of medium recipe using response surface methodology to increase the PHB production. Later on batch cultivation in a 7-L bioreactor was attempted using optimum concentration of medium components (process variables) obtained from statistical design to identify the batch growth and product kinetics parameters of PHB fermentation. A. australica exhibited a maximum biomass and PHB concentration of 8.71 and 6.24 g/L, respectively in bioreactor with an overall PHB production rate of 0.75 g/h. Bioreactor cultivation studies demonstrated that the specific biomass and PHB yield on sucrose was 0.37 and 0.29 g/g, respectively. The kinetic parameters obtained in the present investigation would be used in the development of a batch kinetic mathematical model for PHB production which will serve as launching pad for further process optimization studies, e.g., design of several bioreactor cultivation strategies to further enhance the biopolymer production.

On the problem of a consistent description of kinetic and hydrodynamic processes in dense gases and liquids

Directory of Open Access Journals (Sweden)

B.B. Markiv

2010-01-01

Full Text Available For a consistent description of kinetic and hydrodynamic processes in dense gases and liquids the generalized non-Markovian equations for the nonequilibrium one-particle distribution function and potential part of the averaged enthalpy density are obtained. The inner structure of the generalized transport kernels for these equations is established. It is shown that the collision integral of the kinetic equation has the Fokker-Planck form with the generalized friction coefficient in momentum space. It also contains contributions from the generalized diffusion coefficient and dissipative processes connected with the potential part of the enthalpy density.

Photodissociation processes in molecular beams

International Nuclear Information System (INIS)

Carlson, L.R.

1979-05-01

A description is presented of a study of the photodissociation dynamics of molecules in a molecular beam. Photo-fragmentation translational spectroscopy has been utilized to observe the photodissociation dynamics of ozone. Using a supersonic molecular beam and a 10 nanosecond pulsed laser at lambda = 266 nm, the velocities of the fragment products are measured by the method of time of flight. The resolution of the time of flight spectrum of ozone is sufficiently high that the electronic and vibrational states are clearly resolved and identified. Above the threshold (lambda 1 D) has been estimated in the past to be unity for the process O 3 ( 1 A 1 ) + hν)lambda 3 ( 1 B 2 ) → O 2 ( 1 Δ/sub g/) + O( 1 D). However a small production of O 2 ( 3 Σ/sub g/ - ) + O( 3 P) has been observed in this study. The O 2 ( 1 Δ/sub g/) product yields four vibrational states (v = 0, 1, 2, 3) which yields a vibrational temperature of 2700 0 K along with narrow energy distributions of rotational levels. These energy distributions are compared with photodissociation models along with the polarization dependence of the dissociative process which was also measured. 143 references

Kinetics of protein adsorption/desorption mediated by pH-responsive polymer layer

International Nuclear Information System (INIS)

Su Xiao-Hang; Lei Qun-Li; Ren Chun-Lai

2015-01-01

We propose a new way of regulating protein adsorption by using a pH-responsive polymer. According to the theoretical results obtained from the molecular theory and kinetic approaches, both thermodynamics and kinetics of protein adsorption are verified to be well controlled by the solution pH. The kinetics and the amount of adsorbed proteins at equilibrium are greatly increased when the solution environment changes from acid to neutral. The reason is that the increased pH promotes the dissociation of the weak polyelectrolyte, resulting in more charged monomers and more stretched chains. Thus the steric repulsion within the polymer layer is weakened, which effectively lowers the barrier felt by the protein during the process of adsorption. Interestingly, we also find that the kinetics of protein desorption is almost unchanged with the variation of pH. It is because although the barrier formed by the polymer layer changes along with the change of pH, the potential at contact with the surface varies equally. Our results may provide useful insights into controllable protein adsorption/desorption in practical applications. (paper)

A Detailed Chemical Kinetic Reaction Mechanism for Oxidation of Four Small Alkyl Esters in Laminar Premixed Flames

Energy Technology Data Exchange (ETDEWEB)

Westbrook, C K; Pitz, W J; Westmoreland, P R; Dryer, F L; Chaos, M; Osswald, P; Kohse-Hoinghaus, K; Cool, T A; Wang, J; Yang, B; Hansen, N; Kasper, T

2008-02-08

A detailed chemical kinetic reaction mechanism has been developed for a group of four small alkyl ester fuels, consisting of methyl formate, methyl acetate, ethyl formate and ethyl acetate. This mechanism is validated by comparisons between computed results and recently measured intermediate species mole fractions in fuel-rich, low pressure, premixed laminar flames. The model development employs a principle of similarity of functional groups in constraining the H atom abstraction and unimolecular decomposition reactions in each of these fuels. As a result, the reaction mechanism and formalism for mechanism development are suitable for extension to larger oxygenated hydrocarbon fuels, together with an improved kinetic understanding of the structure and chemical kinetics of alkyl ester fuels that can be extended to biodiesel fuels. Variations in concentrations of intermediate species levels in these flames are traced to differences in the molecular structure of the fuel molecules.

Thermodynamics and kinetics of molecular motors.

Science.gov (United States)

Astumian, R Dean

2010-06-02

Molecular motors are first and foremost molecules, governed by the laws of chemistry rather than of mechanics. The dynamical behavior of motors based on chemical principles can be described as a random walk on a network of states. A key insight is that any molecular motor in solution explores all possible motions and configurations at thermodynamic equilibrium. By using input energy and chemical design to prevent motion that is not wanted, what is left behind is the motion that is desired. This review is focused on two-headed motors such as kinesin and Myosin V that move on a polymeric track. By use of microscopic reversibility, it is shown that the ratio between the number of forward steps and the number of backward steps in any sufficiently long time period does not directly depend on the mechanical properties of the linker between the two heads. Instead, this ratio is governed by the relative chemical specificity of the heads in the front-versus-rear position for the fuel, adenosine triphosphate and its products, adenosine diphosphate and inorganic phosphate. These insights have been key factors in the design of biologically inspired synthetic molecular walkers constructed out of DNA or out of small organic molecules. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Hydrogen electrode reaction: A complete kinetic description

International Nuclear Information System (INIS)

Quaino, P.M.; Gennero de Chialvo, M.R.; Chialvo, A.C.

2007-01-01

The kinetic description of the hydrogen electrode reaction (HER) in the whole range of overpotentials (-0.2 < η (V) < 0.40) is presented. The Volmer-Heyrovsky-Tafel mechanism was solved considering simultaneously the following items: (i) the diffusional contribution of the molecular hydrogen from and towards the electrode surface, (ii) the forward and backward reaction rates of each elementary step and (iii) a Frumkin type adsorption for the reaction intermediate. In order to verify the descriptive capability of the kinetic expressions derived, an experimental study of the HER was carried out on a rotating platinum disc electrode in acid solution. From the correlation of these results the elementary kinetic parameters were evaluated and several aspects related to the kinetic mechanism were discussed. Finally, the use of these kinetic expressions to interpret results obtained on microelectrodes is also analysed

A unified approach for description of gas hydrate formation kinetics in the presence of kinetic promoters in gas hydrate converters

International Nuclear Information System (INIS)

ZareNezhad, Bahman; Varaminian, Farshad

2013-01-01

Highlights: • A unified kinetic model for description of promoted and non-promoted gas hydrate formation processes is presented. • Effects of impeller speed, promoter concentration and different kinetic promoters are investigated. • A unique region of gas hydrate formation is identified regarding gas hydrate formation processes. • The proposed model is useful for understanding the behavior of gas hydrate formation processes and design of GTH converters. - Abstract: The kinetic promoters have found wide applications in enhancing the rate of energy conversion and storage via gas hydrate formation processes. Effects of different kinetic promoters such as anionic surfactants sodium dodecyl sulfate (SDS), dodecylbenzene sulfonic acid (DBSA), and sodium dodecyl benzene sulfonate (SDBS); cationic surfactants, Cetyl trimethyl ammonium bromide (CTAB), dodecyl trimethyl ammonium bromide (DTAB) and non-ionic surfactants, alkylpolyglucoside (APG), dodecyl polysaccharide glycoside (DPG), TritonX-100 (TX100) on methane (CH 4 ), ethane (C 2 H 6 ) and propane (C 3 H 8 ) gas hydrate formation processes are investigated in this work. A macroscopic kinetic model based on the time variations of reaction chemical potential is also presented for global description of gas hydrate formation processes. Experimental gas hydrate formation data are employed to validate the proposed kinetic model. Effects of promoter’s concentrations and agitation intensities on the gas consumption profiles are also investigated. A universal correlation and a unified kinetic map have been proposed for macroscopic description of gas hydrate formation kinetics in the presence or absence of kinetic promoters. According to the presented unified kinetic map, a unique region of gas hydrate formation is identified for the first time. For negligible amounts of kinetic promoters, the presented region disappears and approaches to a unique path at high agitation intensities. The presented unified approach is

Kinetics of dodecanoic acid adsorption from caustic solution by activated carbon.

Science.gov (United States)

Pendleton, Phillip; Wu, Sophie Hua

2003-10-15

This study examines the influences of adsorbent porosity and surface chemistry and of carbon dosage on dodecanoic acid adsorption kinetics from aqueous and 2 M NaOH solutions as batch adsorption processes. Both adsorbents are steam-activated carbons prepared from either coconut or coal precursors. Prior to use the adsorbents were washed in deionized water or 2 M NaOH. Mass transfer coefficients and effective overall diffusion coefficients indicate a minor contribution from adsorbent porosity. In contrast, high surface oxygen content impedes transport to and into the adsorbent structure. Carbon dosage shows a proportional increase in transport coefficients with increasing mass; these coefficients are constant when normalized per unit mass. Neither water nor NaOH treatment of the adsorbents has a significant influence on dodecanoic acid adsorption kinetics. Molecular and Knudsen diffusion coefficients are defined to demonstrate that the overall effective diffusion coefficient values and the diffusion process are controlled by surface diffusion.

Modeling physiological processes in plankton on enzyme kinetic principles

Directory of Open Access Journals (Sweden)

Ted Packard

2004-04-01

Full Text Available Many ecologically important chemical transformations in the ocean are controlled by biochemical enzyme reactions in plankton. Nitrogenase regulates the transformation of N2 to ammonium in some cyanobacteria and serves as the entryway for N2 into the ocean biosphere. Nitrate reductase controls the reduction of NO3 to NO2 and hence new production in phytoplankton. The respiratory electron transfer system in all organisms links the carbon oxidation reactions of intermediary metabolism with the reduction of oxygen in respiration. Rubisco controls the fixation of CO2 into organic matter in phytoplankton and thus is the major entry point of carbon into the oceanic biosphere. In addition to these, there are the enzymes that control CO2 production, NH4 excretion and the fluxes of phosphate. Some of these enzymes have been recognized and researched by marine scientists in the last thirty years. However, until recently the kinetic principles of enzyme control have not been exploited to formulate accurate mathematical equations of the controlling physiological expressions. Were such expressions available they would increase our power to predict the rates of chemical transformations in the extracellular environment of microbial populations whether this extracellular environment is culture media or the ocean. Here we formulate from the principles of bisubstrate enzyme kinetics, mathematical expressions for the processes of NO3 reduction, O2 consumption, N2 fixation, total nitrogen uptake.

Software for Demonstration of Features of Chain Polymerization Processes

Science.gov (United States)

Sosnowski, Stanislaw

2013-01-01

Free software for the demonstration of the features of homo- and copolymerization processes (free radical, controlled radical, and living) is described. The software is based on the Monte Carlo algorithms and offers insight into the kinetics, molecular weight distribution, and microstructure of the macromolecules formed in those processes. It also…

Kinetics of two-stage fermentation process for the production of hydrogen

Energy Technology Data Exchange (ETDEWEB)

Nath, Kaushik [Department of Chemical Engineering, G.H. Patel College of Engineering and Technology, Vallabh Vidyanagar 388 120, Gujarat (India); Muthukumar, Manoj; Kumar, Anish; Das, Debabrata [Fermentation Technology Laboratory, Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India)

2008-02-15

Two-stage process described in the present work is a combination of dark and photofermentation in a sequential batch mode. In the first stage glucose is fermented to acetate, CO{sub 2} and H{sub 2} in an anaerobic dark fermentation by Enterobacter cloacae DM11. This is followed by a successive second stage where acetate is converted to H{sub 2} and CO{sub 2} in a photobioreactor by photosynthetic bacteria, Rhodobacter sphaeroides O.U. 001. The yield of hydrogen in the first stage was about 3.31molH{sub 2}(molglucose){sup -1} (approximately 82% of theoretical) and that in the second stage was about 1.5-1.72molH{sub 2}(molaceticacid){sup -1} (approximately 37-43% of theoretical). The overall yield of hydrogen in two-stage process considering glucose as preliminary substrate was found to be higher compared to a single stage process. Monod model, with incorporation of substrate inhibition term, has been used to determine the growth kinetic parameters for the first stage. The values of maximum specific growth rate ({mu} {sub max}) and K{sub s} (saturation constant) were 0.398h{sup -1} and 5.509gl{sup -1}, respectively, using glucose as substrate. The experimental substrate and biomass concentration profiles have good resemblance with those obtained by kinetic model predictions. A model based on logistic equation has been developed to describe the growth of R. sphaeroides O.U 001 in the second stage. Modified Gompertz equation was applied to estimate the hydrogen production potential, rate and lag phase time in a batch process for various initial concentration of glucose, based on the cumulative hydrogen production curves. Both the curve fitting and statistical analysis showed that the equation was suitable to describe the progress of cumulative hydrogen production. (author)

A Signal Processing Method to Explore Similarity in Protein Flexibility

Directory of Open Access Journals (Sweden)

Simina Vasilache

2010-01-01

Full Text Available Understanding mechanisms of protein flexibility is of great importance to structural biology. The ability to detect similarities between proteins and their patterns is vital in discovering new information about unknown protein functions. A Distance Constraint Model (DCM provides a means to generate a variety of flexibility measures based on a given protein structure. Although information about mechanical properties of flexibility is critical for understanding protein function for a given protein, the question of whether certain characteristics are shared across homologous proteins is difficult to assess. For a proper assessment, a quantified measure of similarity is necessary. This paper begins to explore image processing techniques to quantify similarities in signals and images that characterize protein flexibility. The dataset considered here consists of three different families of proteins, with three proteins in each family. The similarities and differences found within flexibility measures across homologous proteins do not align with sequence-based evolutionary methods.

Kinetics of physico-chemical processes during intensive mechanical processing of ZnO-MnO2 powder mixture

International Nuclear Information System (INIS)

Kakazey, M.; Vlasova, M.; Dominguez-Patino, M.; Juarez-Arellano, E.A.; Bykov, A.; Leon, I.; Siqueiros-Diaz, A.

2011-01-01

Experimental results of electron paramagnetic resonance spectra, X-ray diffraction, scanning electron microscopy and infrared spectroscopy demonstrate that the kinetic of the physical and chemical processes that takes place during prolonged intensive mechanical processing (MP, 0 MP >3120min) of powder mixtures of 50%wt ZnO+50%wt MnO 2 can be described as a three stage process. (1) 0 MP >30min, particles destruction, formation of superficial defects, fast increment of sample average temperature (from 290 to ∼600K) and annealing of defects with the lowest energy of activation E ac . (2) 30 MP >390min, further particle destruction, slow increment of sample average temperature (from ∼600 to ∼700K), formation and growth of a very disordered layer of β-MnO 2 around ZnO particles, dehydration of MnO 2 , formation of solid solution of Mn 2+ ions in ZnO, formation of nano-quasiamorphous states in the ZnO-MnO 2 mixture and onset of the formation of the ZnMnO 3 phase. (3) 390 MP >3120min, the sample average temperature remains constant (∼700K), the reaction is completed and the spinel ZnMnO 3 phase with a unit cell a=8.431(1) A and space group Fd3-barm is the only phase present in the sample. No ferromagnetism at room temperature was detected in this study. - Highlights: → The kinetics during mechanical processing of ZnO-MnO 2 samples is a three stage process. → First stage, reduction of crystallites size and accumulation of defects. → Second stage, nano-quasiamorphous states formation and onset of the ZnMnO 3 phase. → Third stage, complete reaction to the spinel ZnMnO 3 phase.

Drug-Target Kinetics in Drug Discovery.

Science.gov (United States)

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.

Incorporation of chemical kinetic models into process control

International Nuclear Information System (INIS)

Herget, C.J.; Frazer, J.W.

1981-01-01

An important consideration in chemical process control is to determine the precise rationing of reactant streams, particularly when a large time delay exists between the mixing of the reactants and the measurement of the product. In this paper, a method is described for incorporating chemical kinetic models into the control strategy in order to achieve optimum operating conditions. The system is first characterized by determining a reaction rate surface as a function of all input reactant concentrations over a feasible range. A nonlinear constrained optimization program is then used to determine the combination of reactants which produces the specified yield at minimum cost. This operating condition is then used to establish the nominal concentrations of the reactants. The actual operation is determined through a feedback control system employing a Smith predictor. The method is demonstrated on a laboratory bench scale enzyme reactor

Kinetics of a Migration－Driven Aggregation－Fragmentation Process

Institute of Scientific and Technical Information of China (English)

ZHUANGYou-Yi; LINZhen-Quan; KEJian-Hon~

2003-01-01

We propose a reversible model of the migration-driven aggregation-fragmentation process with the symmetric migration rate kernels K (k; j) = K′(k; j) =λkjv and the constant aggregation rates I1, I2 and fragmentation rates Jl, J2. Based on the mean-field theory, we investigate the evolution behavior of the aggregate size distributions in several cases with different values of index v. We find that the fragmentation reaction plays a more important role in the kinetic behaviors of the system than the aggregation and migration. When Jl = 0 and J2 = O, the aggregate size distributions αk(t) and bk(t) obey the conventional scaling law, while when Jl > 0 and J2 > O, they obey the modified scaling law with an exponential scaling function. The total mass of either species remains conserved.

Kinetics of a Migration-Driven Aggregation-Fragmentation Process

Institute of Scientific and Technical Information of China (English)

ZHUANG You-Yi; LIN Zhen-Quan; KE Jian-Hong

2003-01-01

We propose a reversible model of the migration-driven aggregation-fragmentation process with the sym-metric migration rate kernels K(k;j) = K'(k;j) = λkjv and the constant aggregation rates I1, I2 and fragmentationrates J1, J2. Based on the mean-field theory, we investigate the evolution behavior of the aggregate size distributions inseveral cases with different values of index v. We find that the fragmentation reaction plays a more important role in the kinetic behaviors of the system than the aggregation and migration. When J1 = 0 and J2 = 0, the aggregate sizedistributions ak(t) and bk(t) obey the conventional scaling law, while when J1 ＞ 0 and J2 ＞ 0, they obey the modifiedscaling law with an exponential scaling function. The total mass of either species remains conserved.

Development of a Procedure to Apply Detailed Chemical Kinetic Mechanisms to CFD Simulations as Post Processing

DEFF Research Database (Denmark)

Skjøth-Rasmussen, Martin Skov; Glarborg, Peter; Jensen, Anker

2003-01-01

mechanism. It involves post-processing of data extracted from computational fluid dynamics simulations. Application of this approach successfully describes combustion chemistry in a standard swirl burner, the so-called Harwell furnace. Nevertheless, it needs validation against more complex combustion models......It is desired to make detailed chemical kinetic mechanisms applicable to the complex geometries of practical combustion devices simulated with computational fluid dynamics tools. This work presents a novel general approach to combining computational fluid dynamics and a detailed chemical kinetic...

THE MATHEMATICAL MODEL DEVELOPMENT OF THE ETHYLBENZENE DEHYDROGENATION PROCESS KINETICS IN A TWO-STAGE ADIABATIC CONTINUOUS REACTOR

Directory of Open Access Journals (Sweden)

V. K. Bityukov

2015-01-01

Full Text Available The article is devoted to the mathematical modeling of the kinetics of ethyl benzene dehydrogenation in a two-stage adiabatic reactor with a catalytic bed functioning on continuous technology. The analysis of chemical reactions taking place parallel to the main reaction of styrene formation has been carried out on the basis of which a number of assumptions were made proceeding from which a kinetic scheme describing the mechanism of the chemical reactions during the dehydrogenation process was developed. A mathematical model of the dehydrogenation process, describing the dynamics of chemical reactions taking place in each of the two stages of the reactor block at a constant temperature is developed. The estimation of the rate constants of direct and reverse reactions of each component, formation and exhaustion of the reacted mixture was made. The dynamics of the starting material concentration variations (ethyl benzene batch was obtained as well as styrene formation dynamics and all byproducts of dehydrogenation (benzene, toluene, ethylene, carbon, hydrogen, ect.. The calculated the variations of the component composition of the reaction mixture during its passage through the first and second stages of the reactor showed that the proposed mathematical description adequately reproduces the kinetics of the process under investigation. This demonstrates the advantage of the developed model, as well as loyalty to the values found for the rate constants of reactions, which enable the use of models for calculating the kinetics of ethyl benzene dehydrogenation under nonisothermal mode in order to determine the optimal temperature trajectory of the reactor operation. In the future, it will reduce energy and resource consumption, increase the volume of produced styrene and improve the economic indexes of the process.

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

DEFF Research Database (Denmark)

Eelderink, Coby; Noort, Martijn W J; Sozer, Nesli

2017-01-01

PURPOSE: Underlying mechanisms of the beneficial health effects of low glycemic index starchy foods are not fully elucidated yet. We varied the wheat particle size to obtain fiber-rich breads with a high and low glycemic response and investigated the differences in postprandial glucose kinetics...... and metabolic response after their consumption. METHODS: Ten healthy male volunteers participated in a randomized, crossover study, consuming (13)C-enriched breads with different structures; a control bread (CB) made from wheat flour combined with wheat bran, and a kernel bread (KB) where 85 % of flour...... in a difference in glucose response and kinetics, but in a pronounced difference in GLP-1 response. Thus, changing the processing conditions of wheat for baking bread can influence the metabolic response beyond glycemia and may therefore influence health....

Kinetics of spoilage fermentation in radurized fish and optimization of irradiation process

International Nuclear Information System (INIS)

Tukenmez, I.; Ersen, M.S.; Bakioglu, A.T.

1997-01-01

Kinetic studies on radiation-inactivation and the postirradiation growth of spoilage microorganisms during chill storage and their product formation inradurized fish were carried out. Anchovy (Engraulis encrasicholus) samples unirradiated, and those irradiated at 1,2 and 3 kGy doses of gamma radiation were stored at +2 o C for 21 days. Microbiological analyses of mesophilic, psycrophilic and total bacterial counts (TBC) and chemical analyses of trimethylamine (TMA) and total volatile bases (TVB) of the samples were done immediately after irradiation and periodically during storage. Radiation induced inactivations of bacteria were expressed with a first-order decreasing kinetics. A spoilage fermentation modeling was used to evaluate the quality control parameters of radurized fish in which the increase in TBC of survivor microorganisms during storage was described by a first-order growth with a lag phase and the production of TMA and TVB was described by a growth associated product formation. Examinations of the dose effects on the kinetic parameters resulted in that the relation between the product formation rate constants and the irradiation dose represented a parabolic function which was satisfactorily used to determine optimum irradiation dose. Optimum irradiation dose was found 1.719+- 0.471 kGy with TVB data resulting in an extended shelf-life of 15-16 days of fish. It is suggested that the kinetic evaluation method developed in this study may be substitute for or used with the analytical estimate in use comprising microbiological chemical and organoleptic controls for quality assessment and dose optimization of radurization processing of fish and other sea foods.(2 tab s. and 24 refs.)

Approximate method for stochastic chemical kinetics with two-time scales by chemical Langevin equations

International Nuclear Information System (INIS)

Wu, Fuke; Tian, Tianhai; Rawlings, James B.; Yin, George

2016-01-01

The frequently used reduction technique is based on the chemical master equation for stochastic chemical kinetics with two-time scales, which yields the modified stochastic simulation algorithm (SSA). For the chemical reaction processes involving a large number of molecular species and reactions, the collection of slow reactions may still include a large number of molecular species and reactions. Consequently, the SSA is still computationally expensive. Because the chemical Langevin equations (CLEs) can effectively work for a large number of molecular species and reactions, this paper develops a reduction method based on the CLE by the stochastic averaging principle developed in the work of Khasminskii and Yin [SIAM J. Appl. Math. 56, 1766–1793 (1996); ibid. 56, 1794–1819 (1996)] to average out the fast-reacting variables. This reduction method leads to a limit averaging system, which is an approximation of the slow reactions. Because in the stochastic chemical kinetics, the CLE is seen as the approximation of the SSA, the limit averaging system can be treated as the approximation of the slow reactions. As an application, we examine the reduction of computation complexity for the gene regulatory networks with two-time scales driven by intrinsic noise. For linear and nonlinear protein production functions, the simulations show that the sample average (expectation) of the limit averaging system is close to that of the slow-reaction process based on the SSA. It demonstrates that the limit averaging system is an efficient approximation of the slow-reaction process in the sense of the weak convergence.

Thermodynamics and kinetics of a molecular motor ensemble.

Science.gov (United States)

Baker, J E; Thomas, D D

2000-10-01

If, contrary to conventional models of muscle, it is assumed that molecular forces equilibrate among rather than within molecular motors, an equation of state and an expression for energy output can be obtained for a near-equilibrium, coworking ensemble of molecular motors. These equations predict clear, testable relationships between motor structure, motor biochemistry, and ensemble motor function, and we discuss these relationships in the context of various experimental studies. In this model, net work by molecular motors is performed with the relaxation of a near-equilibrium intermediate step in a motor-catalyzed reaction. The free energy available for work is localized to this step, and the rate at which this free energy is transferred to work is accelerated by the free energy of a motor-catalyzed reaction. This thermodynamic model implicitly deals with a motile cell system as a dynamic network (not a rigid lattice) of molecular motors within which the mechanochemistry of one motor influences and is influenced by the mechanochemistry of other motors in the ensemble.

Drainage and Stratification Kinetics of Foam Films

Science.gov (United States)

Zhang, Yiran; Sharma, Vivek

2014-03-01

Baking bread, brewing cappuccino, pouring beer, washing dishes, shaving, shampooing, whipping eggs and blowing bubbles all involve creation of aqueous foam films. Foam lifetime, drainage kinetics and stability are strongly influenced by surfactant type (ionic vs non-ionic), and added proteins, particles or polymers modify typical responses. The rate at which fluid drains out from a foam film, i.e. drainage kinetics, is determined in the last stages primarily by molecular interactions and capillarity. Interestingly, for certain low molecular weight surfactants, colloids and polyelectrolyte-surfactant mixtures, a layered ordering of molecules, micelles or particles inside the foam films leads to a stepwise thinning phenomena called stratification. Though stratification is observed in many confined systems including foam films containing particles or polyelectrolytes, films containing globular proteins seem not to show this behavior. Using a Scheludko-type cell, we experimentally study the drainage and stratification kinetics of horizontal foam films formed by protein-surfactant mixtures, and carefully determine how the presence of proteins influences the hydrodynamics and thermodynamics of foam films.

A molecular dynamics approach to barrodiffusion

Science.gov (United States)

Cooley, James; Marciante, Mathieu; Murillo, Michael

2016-10-01

Unexpected phenomena in the reaction rates for Inertial Confinement Fusion (ICF) capsules have led to a renewed interest in the thermo-dynamically driven diffusion process for the past 10 years, often described collectively as barodiffusion. In the current context, barodiffusion would manifest as a process that separates ions of differing mass and charge ratios due to pressure and temperature gradients set-up through shock structures in the capsule core. Barrodiffusion includes additional mass transfer terms that account for the irreversible transport of species due to gradients in the system, both thermodynamic and electric e.g, i = - ρD [ ∇c +kp ∇ln(pi) +kT(i) ∇ln(Ti) +kt(e) ∇ln(Te) +eke/Ti ∇ϕ ] . Several groups have attacked this phenomena using continuum scale models and supplemented with kinetic theory to derive coefficients for the different diffusion terms based on assumptions about the collisional processes. In contrast, we have applied a molecular dynamics (MD) simulation to this system to gain a first-principle understanding of the rate kinetics and to assess the accuracy of the differin

Kinetics of iron redox reactions in silicate liquids: A high-temperature X-ray absorption and Raman spectroscopy study

Energy Technology Data Exchange (ETDEWEB)

Magnien, V. [Physique des Mineraux et Magmas, CNRS-IPGP, 4 place Jussieu, 75252 Paris cedex 05 (France); CEA VALRHO Marcoule, SCDV, LEBV, BP 17171, 30207 Bagnols/Ceze (France); Neuville, D.R. [Physique des Mineraux et Magmas, CNRS-IPGP, 4 place Jussieu, 75252 Paris cedex 05 (France)]. E-mail: neuville@ipgp.jussieu.fr; Cormier, L. [IMPMC, CNRS UMR 7590, Universites Paris 6 and 7 and IPGP, 4 place Jussieu, 75252 Paris cedex 05 (France); Roux, J. [Physique des Mineraux et Magmas, CNRS-IPGP, 4 place Jussieu, 75252 Paris cedex 05 (France); Hazemann, J.-L. [Laboratoire de cristallographie, UPR 5031, CNRS, 38043 Grenoble (France); Pinet, O. [CEA VALRHO Marcoule, SCDV, LEBV, BP 17171, 30207 Bagnols/Ceze (France); Richet, P. [Physique des Mineraux et Magmas, CNRS-IPGP, 4 place Jussieu, 75252 Paris cedex 05 (France)

2006-06-30

The oxidation kinetics of a Fe-bearing supercooled liquid of the system SiO{sub 2}-CaO-MgO-Na{sub 2}O-FeO has been determined near the glass transition range by X-ray absorption near edge structure (XANES) and Raman spectroscopies. Both techniques yield room-temperature iron redox ratios in accord with wet chemical, Moessbauer and electron microprobe analyses. Similar oxidation kinetics have also been observed with both methods. At constant temperature, the kinetics obey an exponential law with a characteristic time that follows an Arrhenian temperature dependence. As redox changes are too fast to be accounted for in terms of diffusion of either ionic or molecular oxygen, these results lend further support to the idea that the rate-limiting factor for oxidation near the glass transition is diffusion of network-modifying cations along with a flux of electron holes.

Further insights into the kinetics of thermal decomposition during continuous cooling.

Science.gov (United States)

Liavitskaya, Tatsiana; Guigo, Nathanaël; Sbirrazzuoli, Nicolas; Vyazovkin, Sergey

2017-07-26

Following the previous work (Phys. Chem. Chem. Phys., 2016, 18, 32021), this study continues to investigate the intriguing phenomenon of thermal decomposition during continuous cooling. The phenomenon can be detected and its kinetics can be measured by means of thermogravimetric analysis (TGA). The kinetics of the thermal decomposition of ammonium nitrate (NH 4 NO 3 ), nickel oxalate (NiC 2 O 4 ), and lithium sulfate monohydrate (Li 2 SO 4 ·H 2 O) have been measured upon heating and cooling and analyzed by means of the isoconversional methodology. The results have confirmed the hypothesis that the respective kinetics should be similar for single-step processes (NH 4 NO 3 decomposition) but different for multi-step ones (NiC 2 O 4 decomposition and Li 2 SO 4 ·H 2 O dehydration). It has been discovered that the differences in the kinetics can be either quantitative or qualitative. Physical insights into the nature of the differences have been proposed.

Photodissociation processes in molecular beams

Energy Technology Data Exchange (ETDEWEB)

Carlson, L.R.

1979-05-01

A description is presented of a study of the photodissociation dynamics of molecules in a molecular beam. Photo-fragmentation translational spectroscopy has been utilized to observe the photodissociation dynamics of ozone. Using a supersonic molecular beam and a 10 nanosecond pulsed laser at lambda = 266 nm, the velocities of the fragment products are measured by the method of time of flight. The resolution of the time of flight spectrum of ozone is sufficiently high that the electronic and vibrational states are clearly resolved and identified. Above the threshold (lambda < 310 nm), the quantum yield for the production of O(/sup 1/D) has been estimated in the past to be unity for the process O/sub 3/ (/sup 1/A/sub 1/) + h..nu..)lambda < 300 nm) ..-->.. O/sub 3/(/sup 1/B/sub 2/) ..-->.. O/sub 2/(/sup 1/..delta../sub g/) + O(/sup 1/D). However a small production of O/sub 2/ (/sup 3/..sigma../sub g//sup -/) + O(/sup 3/P) has been observed in this study. The O/sub 2/(/sup 1/..delta../sub g/) product yields four vibrational states (v = 0, 1, 2, 3) which yields a vibrational temperature of 2700/sup 0/K along with narrow energy distributions of rotational levels. These energy distributions are compared with photodissociation models along with the polarization dependence of the dissociative process which was also measured. 143 references.

Molecular-beam studies of primary photochemical processes

Energy Technology Data Exchange (ETDEWEB)

Lee, Y.T.

1982-12-01

Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser.

Molecular-beam studies of primary photochemical processes

International Nuclear Information System (INIS)

Lee, Y.T.

1982-12-01

Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser

Kinetics of tetracycline, oxytetracycline, and chlortetracycline adsorption and desorption on two acid soils

DEFF Research Database (Denmark)

Fernandez Calviño, David; Bermúdez-Couso, Alipio; Arias-Estévez, Manuel

2015-01-01

The purpose of this work was to quantify retention/release of tetracycline, oxytetracycline, and chlortetracycline on two soils, paying attention to sorption kinetics and to implications of the adsorption/desorption processes on transfer of these pollutants to the various environmental compartments...... tetracycline > oxytetracycline > chlortetracycline in soil 1, with similar values for the three antibiotics and the sequence tetracycline > chlortetracycline > oxytetracycline in soil 2. The desorption sequences were oxytetracycline > tetracycline > chlortetracycline in soil 1 and oxytetracycline...... > chlortetracycline > tetracycline in soil 2. In conclusion, the SFC technique has yielded new kinetic data regarding tetracycline, oxytetracycline, and chlortetracycline adsorption/desorption on soils, indicating that it can be used to shed further light on the retention and transport processes affecting antibiotics...

Molecular and Cellular Profiling of Scalp Psoriasis Reveals Differences and Similarities Compared to Skin Psoriasis

Science.gov (United States)

Ruano, Juan; Suárez-Fariñas, Mayte; Shemer, Avner; Oliva, Margeaux

2016-01-01

Scalp psoriasis shows a variable clinical spectrum and in many cases poses a great therapeutic challenge. However, it remains unknown whether the immune response of scalp psoriasis differs from understood pathomechanisms of psoriasis in other skin areas. We sought to determine the cellular and molecular phenotype of scalp psoriasis by performing a comparative analysis of scalp and skin using lesional and nonlesional samples from 20 Caucasian subjects with untreated moderate to severe psoriasis and significant scalp involvement and 10 control subjects without psoriasis. Our results suggest that even in the scalp, psoriasis is a disease of the inter-follicular skin. The immune mechanisms that mediate scalp psoriasis were found to be similar to those involved in skin psoriasis. However, the magnitude of dysregulation, number of differentially expressed genes, and enrichment of the psoriatic genomic fingerprint were more prominent in skin lesions. Furthermore, the scalp transcriptome showed increased modulation of several gene-sets, particularly those induced by interferon-gamma, compared with that of skin psoriasis, which was mainly associated with activation of TNFα/L-17/IL-22-induced keratinocyte response genes. We also detected differences in expression of gene-sets involving negative regulation, epigenetic regulation, epidermal differentiation, and dendritic cell or Th1/Th17/Th22-related T-cell processes. PMID:26849645

Quantum field kinetics of QCD: Quark-gluon transport theory for light-cone-dominated processes

International Nuclear Information System (INIS)

Geiger, K.

1996-01-01

A quantum-kinetic formalism is developed to study the dynamical interplay of quantum and statistical-kinetic properties of nonequilibrium multiparton systems produced in high-energy QCD processes. The approach provides the means to follow the quantum dynamics in both space-time and energy-momentum, starting from an arbitrary initial configuration of high-momentum quarks and gluons. Using a generalized functional integral representation and adopting the open-quote open-quote closed-time-path close-quote close-quote Green function techniques, a self-consistent set of equations of motions is obtained: a Ginzburg-Landau equation for a possible color background field, and Dyson-Schwinger equations for the two-point functions of the gluon and quark fields. By exploiting the open-quote open-quote two-scale nature close-quote close-quote of light-cone-dominated QCD processes, i.e., the separation between the quantum scale that specifies the range of short-distance quantum fluctuations, and the kinetic scale that characterizes the range of statistical binary interactions, the quantum field equations of motion are converted into a corresponding set of open-quote open-quote renormalization equations close-quote close-quote and open-quote open-quote transport equations.close-quote close-quote The former describe renormalization and dissipation effects through the evolution of the spectral density of individual, dressed partons, whereas the latter determine the statistical occurrence of scattering processes among these dressed partons. The renormalization equations and the transport equations are coupled, and, hence, must be solved self-consistently. This amounts to evolving the multiparton system, from a specified initial configuration, in time and full seven-dimensional phase space, constrained by the Heisenberg uncertainty principle. (Abstract Truncated)

New kinetic insight into the spontaneous oxidation process of lithium in air by EPMA

Energy Technology Data Exchange (ETDEWEB)

Otero, Manuel [IFEG, Facultad de Matemáticas, Astronomía y Física, Universidad Nacional de Córdoba, Córdoba (Argentina); INFICQ, Departamento de Matemáticas y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba (Argentina); Lener, German [INFAP, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, San Luis (Argentina); Trincavelli, Jorge, E-mail: trincavelli@famaf.unc.edu.ar [IFEG, Facultad de Matemáticas, Astronomía y Física, Universidad Nacional de Córdoba, Córdoba (Argentina); Barraco, Daniel [IFEG, Facultad de Matemáticas, Astronomía y Física, Universidad Nacional de Córdoba, Córdoba (Argentina); Nazzarro, Marcelo Sandro; Furlong, Octavio [INFAP, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, San Luis (Argentina); Leiva, Ezequiel Pedro Marcos [INFICQ, Departamento de Matemáticas y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba (Argentina)

2016-10-15

Highlights: • EPMA measurements and Monte Carlo simulations were applied to study the corrosion process of Li in air. • The kinetic mechanism of corrosion was discussed. • A diffusion process of water through LiOH was found and quantitatively studied. - Abstract: The exposure of metallic lithium to ambient air produces a fast corrosion reaction of the surface that continues to the bulk of the material. This spontaneous process was explored by means of X-ray Photoelectron Spectroscopy (XPS) and Electron Probe Micro-Analysis (EPMA). The combination of these techniques and Monte Carlo simulations allowed observing the formation of a film of lithium hydroxide (LiOH) and studying the growth within the material during the first 300 s. The corrosion is mainly due to the reaction of lithium with water and the diffusion of water through the growing LiOH film is the rate determining step. On the basis of a kinetic analysis we studied the mechanism of reaction and inferred a diffusion coefficient of D = (5.1 ± 0.4) × 10{sup −12} cm{sup 2}/s in agreement with results from the literature obtained using different techniques.

Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations.

Science.gov (United States)

Álvarez-Barcia, Sonia; Kästner, Johannes

2017-06-01

Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe═O cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value.

Physical principles of filamentous protein self-assembly kinetics

Science.gov (United States)

Michaels, Thomas C. T.; Liu, Lucie X.; Meisl, Georg; Knowles, Tuomas P. J.

2017-04-01

The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer’s and Parkinson’s diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.

Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks

Science.gov (United States)

Cloonan, Carrie A.; Nichol, Carolyn A.; Hutchinson, John S.

2011-01-01

Chemical reaction kinetics and equilibrium are essential core concepts of chemistry but are challenging topics for many students, both at the high school and undergraduate university level. Visualization at the molecular level is valuable to aid understanding of reaction kinetics and equilibrium. This activity provides a discovery-based method to…

Kinetics of contraction-induced GLUT4 translocation in skeletal muscle fibers from living mice

DEFF Research Database (Denmark)

Lauritzen, Hans Peter M. Mortensen; Galbo, Henrik; Toyoda, Taro

2010-01-01

Exercise is an important strategy for the treatment of type 2 diabetes. This is due in part to an increase in glucose transport that occurs in the working skeletal muscles. Glucose transport is regulated by GLUT4 translocation in muscle, but the molecular machinery mediating this process is poorl...... understood. The purpose of this study was to 1) use a novel imaging system to elucidate the kinetics of contraction-induced GLUT4 translocation in skeletal muscle and 2) determine the function of AMP-activated protein kinase alpha2 (AMPKalpha2) in this process.......Exercise is an important strategy for the treatment of type 2 diabetes. This is due in part to an increase in glucose transport that occurs in the working skeletal muscles. Glucose transport is regulated by GLUT4 translocation in muscle, but the molecular machinery mediating this process is poorly...

Kinetic modeling of ethane pyrolysis at high conversion.

Science.gov (United States)

Xu, Chen; Al Shoaibi, Ahmed Sultan; Wang, Chenguang; Carstensen, Hans-Heinrich; Dean, Anthony M

2011-09-29

The primary objective of this study is to develop an improved first-principle-based mechanism that describes the molecular weight growth kinetics observed during ethane pyrolysis. A proper characterization of the kinetics of ethane pyrolysis is a prerequisite for any analysis of hydrocarbon pyrolysis and oxidation. Flow reactor experiments were performed with ~50/50 ethane/nitrogen mixtures with temperatures ranging from 550 to 850 °C at an absolute pressure of ~0.8 atm and a residence time of ~5 s. These conditions result in ethane conversions ranging from virtually no reaction to ~90%. Comparisons of predictions using our original mechanism to these data yielded very satisfactory results in terms of the temperature dependence of ethane conversion and prediction of the major products ethylene and hydrogen. However, there were discrepancies in some of the minor species concentrations that are involved in the molecular weight growth kinetics. We performed a series of CBS-QB3 analyses for the C(3)H(7), C(4)H(7), and C(4)H(9) potential energy surfaces to better characterize the radical addition reactions that lead to molecular weight growth. We also extended a published C(6)H(9) PES to include addition of vinyl to butadiene. The results were then used to calculate pressure-dependent rate constants for the multiple reaction pathways of these addition reactions. Inclusion of the unadjusted rate constants resulting from these analyses in the mechanism significantly improved the description of several of the species involved in molecular weight growth kinetics. We compare the predictions of this improved model to those obtained with a consensus model recently published as well as to ethane steam cracking data. We find that a particularly important reaction is that of vinyl addition to butadiene. Another important observation is that several radical addition reactions are partially equilibrated. Not only does this mean that reliable thermodynamic parameters are essential

Kinetic Behavior of Exchange-Driven Growth with Catalyzed-Birth Processes

Science.gov (United States)

Wang, Hai-Feng; Lin, Zhen-Quan; Kong, Xiang-Mu

2006-12-01

Two catalyzed-birth models of n-species (n>=2) aggregates with exchange-driven growth processes are proposed and compared. In the first one, the exchange reaction occurs between any two aggregates Amk and Amj of the same species with the rate kernels Km(k,j) = Kmkj (m = 1,2,...,n, n>=2), and aggregates of An species catalyze a monomer-birth of Al species (l = 1,2,...,n-1) with the catalysis rate kernel Jl(k,j) = Jlkjυ. The kinetic behaviors are investigated by means of the mean-field theory. We find that the evolution behavior of aggregate-size distribution alk(t) of Al species depends crucially on the value of the catalysis rate parameter υ: (i) alk(t) obeys the conventional scaling law in the case of υ0. In the second model, the mechanism of monomer-birth of An-species catalyzed by Al species is added on the basis of the first model, that is, the aggregates of Al and An species catalyze each other to cause monomer-birth. The kinetic behaviors of Al and An species are found to fall into two categories for the different υ: (i) growth obeying conventional scaling form with υ0.

Flocculation kinetics of kaolinite : role of aqueous phase species

Energy Technology Data Exchange (ETDEWEB)

House, P.; Wang, C.; Dhadli, N. [Shell Canada Ltd., Calgary, AB (Canada)

2010-07-01

Flocculation kinetics were used to study the rate-based processes that lead to aggregate growth and breakage of kaolinite in oil sands tailings. The role of aqueous phase species on aggregate growth, breakage and flocculant de-activation was studied. Collision efficiency and deactivation parameters were presented. The study showed that collisions can be efficient when the adsorption of the polymer is thermodynamically favorable. Up to 94 percent of adsorption takes place at the kaolinite edge. Studies have shown that hydrogen bonding sites on the kaolinite disappear with increases in pH values. The impact of molecular level interactions on flocculation kinetics were assessed in order to determine collision efficiencies and aggregate breakage rates. A focused beam reflectance model was used to monitor flocculation kinetics in situ. The period over which reflectance was observed was coupled with the laser velocity to determine the chord length of the particle. The kinetics of flocculation were observed for a 10 minute period. The effects of pH, calcium additions, and EDTA chelating agent additions were investigated. The study showed that calcium additions accelerate the rate of flocculant growth dramatically, and provide a much higher collision efficiency. Flocculants formed in the presence of calcium were weaker. The presence of salts promoted polymer adsorption by non-specific Van der Waals forces. tabs., figs.

Microwave irradiation enhances kinetics of the biomimetic process of hydroxyapatite nanocomposites

International Nuclear Information System (INIS)

Guha, Avijit; Nayar, Suprabha; Thatoi, H N

2010-01-01

In situ synthesized hydroxyapatite-poly(vinyl) alcohol nanocomposite was subjected to microwave irradiation, post synthesis. Interestingly, the aging time of 1 week required for the normal biomimetic process was reduced to 1 h post microwave irradiation, as characterized by x-ray powder diffraction and transmission electron microscopy. The surface topography shows the tendency of tubules to cross-link with the help of microwave energy. The microwave energy seems to provide a directional pull to the polymer chains which could have led to an enhancement of the kinetics of phase formation. (communication)

Process and kinetics of the fundamental radiation-electrochemical reactions in the primary coolant loop of nuclear reactors

International Nuclear Information System (INIS)

Kozomara-Maic, S.

1987-06-01

In spite of the rather broad title of this report, its major part is devoted to the corrosion problems at the RA reactor, i.e. causes and consequences of the reactor shutdown in 1979 and 1982. Some problems of reactor chemistry are pointed out because they are significant for future reactor operation. The final conclusion of this report is that corrosion processes in the primary coolant circuit of the nuclear reactor are specific and that radiation effects cannot be excluded when processes and reaction kinetics are investigated. Knowledge about the kinetics of all the chemical reactions occurring in the primary coolant loop are of crucial significance for safe and economical reactor operation [sr

Levy Stable Processes. From Stationary to Self-Similar Dynamics and Back. An Application to Finance

International Nuclear Information System (INIS)

Burnecki, K.; Weron, A.

2004-01-01

We employ an ergodic theory argument to demonstrate the foundations of ubiquity of Levy stable self-similar processes in physics and present a class of models for anomalous and nonextensive diffusion. A relationship between stationary and self-similar models is clarified. The presented stochastic integral description of all Levy stable processes could provide new insights into the mechanism underlying a range of self-similar natural phenomena. Finally, this effect is illustrated by self-similar approach to financial modelling. (author)

Quantum Control of Molecular Processes

CERN Document Server

Shapiro, Moshe

2012-01-01

Written by two of the world's leading researchers in the field, this is a systematic introduction to the fundamental principles of coherent control, and to the underlying physics and chemistry.This fully updated second edition is enhanced by 80% and covers the latest techniques and applications, including nanostructures, attosecond processes, optical control of chirality, and weak and strong field quantum control. Developments and challenges in decoherence-sensitive condensed phase control as well as in bimolecular control are clearly described.Indispensable for atomic, molecular and chemical

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

Energy Technology Data Exchange (ETDEWEB)

Li, Minjing [School; Qian, Wei-jun [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Shi, Liang [School; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; School

2017-09-28

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

Transformation kinetics for nucleus clusters

International Nuclear Information System (INIS)

Villa, Elena; Rios, Paulo R.

2009-01-01

A rigorous mathematical approach based on stochastic geometry concepts is presented to extend previous Johnson-Mehl, Avrami, Kolmogorov treatment of transformation kinetics to situations in which nuclei are not homogeneously located in space but are located in clusters. An exact analytical solution is presented here for the first time assuming that nucleation sites follow a Matern cluster process. The influence of Matern cluster process parameters on subsequent growth kinetics and the microstructural path are illustrated by means of numerical examples. Moreover, using the superposition principle, exact analytical solutions are also obtained when nucleation takes place by a combination of a Matern cluster process and an inhomogeneous Poisson point process. The new solutions presented here significantly increase the number of exactly solvable cases available to formal kinetics.

Biochemical and molecular characterization of Coriolopsis rigida laccases involved in transformation of the solid waste from olive oil production.

Science.gov (United States)

Díaz, Rosario; Saparrat, Mario C N; Jurado, Miguel; García-Romera, Inmaculada; Ocampo, Juan Antonio; Martínez, María Jesús

2010-09-01

Two laccase isoenzymes were purified and characterized from the basidiomycete Coriolopsis rigida during transformation of the water-soluble fraction of "alpeorujo" (WSFA), a solid residue derived from the olive oil production containing high levels of toxic compounds. Zymogram assays of laccases secreted by the fungus growing on WSFA and WSFA supplemented with glucose showed two bands with isoelectric points of 3.3 and 3.4. The kinetic studies of the two purified isoenzymes showed similar affinity on 2,6-dimethoxyphenol and 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid), used as phenolic and non-phenolic model substrate, respectively. The molecular mass of both proteins was 66 kDa with 9% N-linked carbohydrate. Physico-chemical properties of the purified laccases from media containing WSFA were similar to those obtained from medium with glucose as the main carbon source. In-vitro studies performed with the purified laccases revealed a 42% phenol reduction of WSFA, as well as changes in the molecular mass distribution. These findings indicate that these laccases are involved in the process of transformation, via polymerization by the oxidation of phenolic compounds present in WSFA. A single laccase gene, containing an open reading frame of 1,488 bp, was obtained in PCR amplifications performed with cDNA extracted from mycelia grown on WSFA. The product of the gene shares 90% identity (95% similarity) with a laccase from Trametes trogii and 89% identity (95% similarity) with a laccase from Coriolopsis gallica. This is the first report on purification and molecular characterization of laccases directly involved in the transformation of olive oil residues.

Water in the physiology of plant: thermodynamics and kinetic

Directory of Open Access Journals (Sweden)

Maurizio Cocucci

2011-02-01

Full Text Available Molecular properties of water molecule determine its role in plant physiology. At molecular level the properties of water molecules determine the behaviour of other plant molecules; in particular its physic characteristics are important in the operativeness of macromolecules and in plant thermoregulation. Plant water supply primarily dependent on thermodynamics properties in particular water chemical potential and its components, more recently there are evidences that suggest an important role in the water kinetic characteristics, depending, at cell membrane level, in particular plasmalemma, on the presence of specific water channel, the aquaporines controlled in its activity by a number of physiological and biochemical factors. Thermodynamics and kinetic factors controlled by physiological, biochemical properties and molecular effectors, control water supply and level in plants to realize their survival, growth and differentiation and the consequent plant production.

Study on copper kinetics in processing sulphide ore mixed with copper and zinc with sulfuric acid leaching under pressure

Science.gov (United States)

Wen-bo, LUO; Ji-kun, WANG; Yin, GAN

2018-01-01

Sulphide ore mixed with copper and zinc is processed with pressure acid leaching. Research is conducted on the copper kinetic. The stirring rate is set at 600 rpm which could eliminate the influence of external diffusions. Research is conducted on the factors affecting the copper leaching kinetic are temperature, pressure, concentration of sulfuric acid, particle size. The result shows that the apparent activity energy is 50.7 KJ/mol. We could determine that the copper leaching process is shrinking core model of chemical reaction control and work out the leaching equation.

A kinetic study of the electrochemical hydrogenation of ethylene

International Nuclear Information System (INIS)

Sedighi, S.; Gardner, C.L.

2010-01-01

In this study, we have examined the kinetics of the electrochemical hydrogenation of ethylene in a PEM reactor. While in itself this reaction is of little industrial interest, this reaction can be looked upon as a model reaction for many of the important hydrogenation processes including the refining of heavy oils and the hydrogenation of vegetable oils. To study the electrochemical hydrogenation of ethylene, several experimental techniques have been used including polarization measurements, measurement of the composition of the exit gases and potential step, transient measurements. The results show that the hydrogenation reaction proceeds rapidly and essentially to completion. By fitting the experimental transient data to the results from a zero-dimensional mathematical model of the process, a set of kinetic parameters for the reactions has been obtained that give generally good agreement with the experimental results. It seems probable that similar experimental techniques could be used to study the electrochemical hydrogenation of other unsaturated organic molecules of more industrial significance.

Kinetics of protein adsorption/desorption mediated by pH-responsive polymer layer

Science.gov (United States)

Su, Xiao-Hang; Lei, Qun-Li; Ren, Chun-Lai

2015-11-01

We propose a new way of regulating protein adsorption by using a pH-responsive polymer. According to the theoretical results obtained from the molecular theory and kinetic approaches, both thermodynamics and kinetics of protein adsorption are verified to be well controlled by the solution pH. The kinetics and the amount of adsorbed proteins at equilibrium are greatly increased when the solution environment changes from acid to neutral. The reason is that the increased pH promotes the dissociation of the weak polyelectrolyte, resulting in more charged monomers and more stretched chains. Thus the steric repulsion within the polymer layer is weakened, which effectively lowers the barrier felt by the protein during the process of adsorption. Interestingly, we also find that the kinetics of protein desorption is almost unchanged with the variation of pH. It is because although the barrier formed by the polymer layer changes along with the change of pH, the potential at contact with the surface varies equally. Our results may provide useful insights into controllable protein adsorption/desorption in practical applications. Project supported by the National Natural Science Foundation of China (Grant Nos. 21274062, 11474155, and 91027040).

Strategic Planning Process and Organizational Structure: Impacts, Confluence and Similarities

Directory of Open Access Journals (Sweden)

Dyogo Felype Neis

2017-01-01

Full Text Available This article aims to analyze the relationship between the strategic planning process and organizational structure in the reality of a complex organization: the Public Prosecutor’s Office of Santa Catarina (MPSC. The research is set by the single case study research strategy and data were collected through the following instruments: bibliographical research, documentary research, semi-structured interviews and systematic observation. The conclusion indicates that the phases of the strategic planning process influence and are influenced by the elements of the organizational structure and highlights the confluences, the impacts and similarities between the stages of formulation and implementation of the strategic process with the various constituent elements of the organizational structure.

Spontaneous chiral symmetry breaking in early molecular networks

Directory of Open Access Journals (Sweden)

Markovitch Omer

2010-05-01

Full Text Available Abstract Background An important facet of early biological evolution is the selection of chiral enantiomers for molecules such as amino acids and sugars. The origin of this symmetry breaking is a long-standing question in molecular evolution. Previous models addressing this question include particular kinetic properties such as autocatalysis or negative cross catalysis. Results We propose here a more general kinetic formalism for early enantioselection, based on our previously described Graded Autocatalysis Replication Domain (GARD model for prebiotic evolution in molecular assemblies. This model is adapted here to the case of chiral molecules by applying symmetry constraints to mutual molecular recognition within the assembly. The ensuing dynamics shows spontaneous chiral symmetry breaking, with transitions towards stationary compositional states (composomes enriched with one of the two enantiomers for some of the constituent molecule types. Furthermore, one or the other of the two antipodal compositional states of the assembly also shows time-dependent selection. Conclusion It follows that chiral selection may be an emergent consequence of early catalytic molecular networks rather than a prerequisite for the initiation of primeval life processes. Elaborations of this model could help explain the prevalent chiral homogeneity in present-day living cells. Reviewers This article was reviewed by Boris Rubinstein (nominated by Arcady Mushegian, Arcady Mushegian, Meir Lahav (nominated by Yitzhak Pilpel and Sergei Maslov.

Kinetics of physico-chemical processes during intensive mechanical processing of ZnO-MnO{sub 2} powder mixture

Energy Technology Data Exchange (ETDEWEB)

Kakazey, M.; Vlasova, M.; Dominguez-Patino, M. [CIICAp-Universidad Autonoma del Estado de Morelos, Cuernavaca (Mexico); Juarez-Arellano, E.A., E-mail: eajuarez@unpa.edu.mx [Universidad del Papaloapan, Tuxtepec, Oaxaca (Mexico); Bykov, A. [Institute for Problems of Materials Science of NASU, Kyiv (Ukraine); Leon, I. [CIQ-Universidad Autonoma del Estado de Morelos, Cuernavaca (Mexico); Siqueiros-Diaz, A. [FCQI-Universidad Autonoma del Estado de Morelos, Cuernavaca (Mexico)

2011-10-15

Experimental results of electron paramagnetic resonance spectra, X-ray diffraction, scanning electron microscopy and infrared spectroscopy demonstrate that the kinetic of the physical and chemical processes that takes place during prolonged intensive mechanical processing (MP, 03120min) of powder mixtures of 50%wt ZnO+50%wt MnO{sub 2} can be described as a three stage process. (1) 030min, particles destruction, formation of superficial defects, fast increment of sample average temperature (from 290 to {approx}600K) and annealing of defects with the lowest energy of activation E{sub ac}. (2) 30390min, further particle destruction, slow increment of sample average temperature (from {approx}600 to {approx}700K), formation and growth of a very disordered layer of {beta}-MnO{sub 2} around ZnO particles, dehydration of MnO{sub 2}, formation of solid solution of Mn{sup 2+} ions in ZnO, formation of nano-quasiamorphous states in the ZnO-MnO{sub 2} mixture and onset of the formation of the ZnMnO{sub 3} phase. (3) 3903120min, the sample average temperature remains constant ({approx}700K), the reaction is completed and the spinel ZnMnO{sub 3} phase with a unit cell a=8.431(1) A and space group Fd3-barm is the only phase present in the sample. No ferromagnetism at room temperature was detected in this study. - Highlights: > The kinetics during mechanical processing of ZnO-MnO{sub 2} samples is a three stage process. > First stage, reduction of crystallites size and accumulation of defects. > Second stage, nano-quasiamorphous states formation and onset of the ZnMnO{sub 3} phase. > Third stage, complete reaction to the spinel ZnMnO{sub 3} phase.

Kinetic model of continuous ethanol fermentation in closed-circulating process with pervaporation membrane bioreactor by Saccharomyces cerevisiae.

Science.gov (United States)

Fan, Senqing; Chen, Shiping; Tang, Xiaoyu; Xiao, Zeyi; Deng, Qing; Yao, Peina; Sun, Zhaopeng; Zhang, Yan; Chen, Chunyan

2015-02-01

Unstructured kinetic models were proposed to describe the principal kinetics involved in ethanol fermentation in a continuous and closed-circulating fermentation (CCCF) process with a pervaporation membrane bioreactor. After ethanol was removed in situ from the broth by the membrane pervaporation, the secondary metabolites accumulated in the broth became the inhibitors to cell growth. The cell death rate related to the deterioration of the culture environment was described as a function of the cell concentration and fermentation time. In CCCF process, 609.8 g L(-1) and 750.1 g L(-1) of ethanol production were obtained in the first run and second run, respectively. The modified Gompertz model, correlating the ethanol production with the fermentation period, could be used to describe the ethanol production during CCCF process. The fitting results by the models showed good agreement with the experimental data. These models could be employed for the CCCF process technology development for ethanol fermentation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Kinetics of small particle activation in supersaturated vapors

Energy Technology Data Exchange (ETDEWEB)

McGraw, R.; Wang, J.

2010-08-29

We examine the nucleated (with barrier) activation of perfectly wetting (zero contact angle) particles ranging from bulk size down to one nanometer. Thermodynamic properties of the particles, coated with liquid layers of varying thickness and surrounded by vapor, are analyzed. Nano-size particles are predicted to activate at relative humidity below the Kelvin curve on crossing a nucleation barrier, located at a critical liquid layer thickness such that the total particle size (core + liquid layer) equals the Kelvin radius (Fig. 1). This barrier vanishes precisely as the critical layer thickness approaches the thin layer limit and the Kelvin radius equals the radius of the particle itself. These considerations are similar to those included in Fletcher's theory (Fletcher, 1958) however the present analysis differs in several important respects. Firstly, where Fletcher used the classical prefactor-exponent form for the nucleation rate, requiring separate estimation of the kinetic prefactor, we solve a diffusion-drift equation that is equivalent to including the full Becker-Doering (BD) multi-state kinetics of condensation/evaporation along the growth coordinate. We also determine the mean first passage time (MFPT) for barrier crossing (Wedekind et al., 2007), which is shown to provide a generalization of BD nucleation kinetics especially useful for barrier heights that are considerably lower than those typically encountered in homogeneous vapor-liquid nucleation, and make explicit comparisons between the MFPT and BD kinetic models. Barrier heights for heterogeneous nucleation are computed by a thermo-dynamic area construction introduced recently to model deliquescence and efflorescence of small particles (McGraw and Lewis, 2009). In addition to providing a graphical representation of the activation process that offers new insights, the area construction provides a molecular approach that avoids explicit use of the interfacial tension. Typical barrier profiles for

Kinetic proofreading at single molecular level: aminoacylation of tRNA(Ile and the role of water as an editor.

Directory of Open Access Journals (Sweden)

Mantu Santra

Full Text Available Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs hydrolysis of the wrong substrate as the discriminatory step in enzyme catalytic reactions. We consider aminoacylation of tRNA(Ile which is a crucial step in protein synthesis and for which experimental results are now available. We present an augmented kinetic scheme and then employ methods of stochastic simulation algorithm to obtain time dependent concentrations of different substances involved in the reaction and their rates of formation. We obtain the rates of product formation and ATP hydrolysis for both correct and wrong substrates (isoleucine and valine in our case, respectively, in single molecular enzyme as well as ensemble enzyme kinetics. The present theoretical scheme correctly reproduces (i the amplitude of the discrimination factor in the overall rates between isoleucine and valine which is obtained as (1.8×10(2.(4.33×10(2 = 7.8×10(4, (ii the rates of ATP hydrolysis for both Ile and Val at different substrate concentrations in the aminoacylation of tRNA(Ile. The present study shows a non-michaelis type dependence of rate of reaction on tRNA(Ile concentration in case of valine. The overall editing in steady state is found to be independent of amino acid concentration. Interestingly, the computed ATP hydrolysis rate for valine at high substrate concentration is same as the rate of formation of Ile-tRNA(Ile whereas at intermediate substrate concentration the ATP hydrolysis rate is relatively low. We find that the presence of additional editing domain in class I editing enzyme makes the kinetic proofreading more efficient through enhanced hydrolysis of wrong product at the editing CP1 domain.

Kinetics of transformation of deformation processed gold-matrix composite

Science.gov (United States)

Wongpreedee, Kageeporn

Gold matrix Ḏeformation-processed M&barbelow;etal M&barbelow;etal C&barbelow;omposites (DMMC) have been developed that have better strength and conductivity than conventional gold alloys. However, DMMC possess metastable two-phase microstructures, and their strength and conductivity decrease after prolonged exposure to elevated temperatures. The kinetics of the transformation from the metastable two-phase microstructure to the equilibrium single-phase solid solution is of interest. This document describes a study of the elevated temperature stability of Au DMMC's and the relationship between microstructure and resistivity of three compositions: Au-7 vol %Ag, Au-14 vol %Ag, and Au-vol 7%Pt. DMMC samples were prepared by a powder metallurgy technique and mechanical processes. The smallest final diameter of these wires was 120 mum. Avrami and Arrhenius relations were used to evaluate the kinetic transformation. The extensive deformation used to produce these composites reshaped the initially equi-axed powder particles into a nanofilamentary composite. Electrical resistivity measurements were used to determine the degree of transformation from the initial metastable nano-filamentary composite to the equilibrium solid solution condition. These measurements indicated that this transformation in Au-14 at%Ag, Au-7 at %Ag Au and Au-7 at %Pt DMMC wires proceeded with activation energies of 141, 156, and 167 kJ/mol, respectively. It is thought that these empirically determined activation energies differ from those determined in single crystal, planar interface Au-Ag and Au-Pt diffusion couples due to chemical potential, surface curvature, and strain effects. The DMMC systems reach the equilibrium solid solution condition faster than single crystal, planar interface systems for two reasons: (1) far more defects (dislocations, grain boundaries, vacancies from non-conservative dislocation motion, etc.) are present in the Au-Ag and Au-Pt DMMC composites, and (2) the small

Polarographic investigation of complexing kinetics of polyacrylate anions with cadmium ions

International Nuclear Information System (INIS)

Avlyanov, Zh.K.; Kabanov, N.M.; Zezin, A.B.; Askarov, M.A.

1990-01-01

The processes which occur during the reduction of cadmium ions from polymer-metallic complexes (PMC) are studied for the purposes of polarographic investigation of complexing kinetics of polyacrylate anions (PAA) of different molecular masses with cadmium ions in KCl aqueous solutions. An expression is derived for establishing semiwave potential. PMC formation and dissociation reduction rate constants are calculated. It is shown that intramolecular reorderings required for the formation of a two-coordinate complex proceed much slower as compared to the diffusion of free ions

Pyrolysis and Gasification Kinetics of Large Biomass Particles

Energy Technology Data Exchange (ETDEWEB)

Svenson, Jenny; Hagstroem, Magnus; Andersson, Patrik U.; Loenn, Benny; Pettersson, Jan B.C. [Goteborg Univ. (Sweden). Dep. of Chemistry, Atmospheric Science; Davidsson, Kent O. [Chalmers Univ. of Technology, Goeteborg (Sweden). Energy Conversion

2004-05-01

The aim of the project is to provide experimental data on single biomass particle pyrolysis that have an applied as well as a fundamental bearing. Transport phenomena and kinetics on the single particle level are characterized, including heat and mass transport processes. New experimental techniques and methods are applied and developed within the project. A single-particle reactor has been developed for the investigations, and several detection techniques including fast thermogravimetric analysis, molecular beam mass spectrometry, laser spectroscopy, video recording and pyrometry are applied. The experimental data are used to develop robust models for pyrolysis and gasification, which are essential components in the design of gasification and combustion reactors.

Radiodegradation process in PVDF with different molecular weight

International Nuclear Information System (INIS)

Silva, L.; Batista, A.S.M.; Nascimento, J.P.; Furtado, C.A.; Faria, L.O.

2017-01-01

Poly(vinylidene fluoride) (PVDF) is a semi-crystalline polymer with several industrial applications due to its mechanical, ferroelectric and biocompatibility properties. Due to the particularity of some of its applications this polymer is exposed to high energy radiation, for example in the aerospace industry and with biomaterial, in sterilization processes. In this sense it is of interest studies that evaluate the radiodegradation of this material, as a way to predict its mechanical behavior after processes of exposure to gamma radiation. In this study the radioresistance of PVDF with different molecular weights is evaluated, considering that large molecular chains can provide greater resistance than smaller chains. Method: PVDF samples with different molecular weights were produced by the solvent dilution process. They were irradiated with gamma doses of 100, 300, 500, 1000 and 2000 kGy with a source of cobalt in the Laboratório de Irradiação Gama (LIG) of the Centro de Desenvolvimento da Tecnologia Nuclear (CDTN). FTIR, UV-Vis, DSC and XRD analyzes were used to evaluate the induced radiodegradation processes immediately after irradiation and one month later. Results: The FTIR and UV-Vis analyzes showed formation of unsaturations in the polymer chains. The DSC technique showed a drop in the crystalline fraction of the polymer confirmed by the XRD technique. Conclusion: Post-irradiation sample evaluations are discussed in terms of the effect of high energy ionizing radiation on polymeric mate-rials for industrial and biomedical use for safety in quality assurance and performance in service. (author)

Radiodegradation process in PVDF with different molecular weight

Energy Technology Data Exchange (ETDEWEB)

Silva, L.; Batista, A.S.M., E-mail: adriananuclear@yahoo.com.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil); Nascimento, J.P.; Furtado, C.A.; Faria, L.O. [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

2017-07-01

Poly(vinylidene fluoride) (PVDF) is a semi-crystalline polymer with several industrial applications due to its mechanical, ferroelectric and biocompatibility properties. Due to the particularity of some of its applications this polymer is exposed to high energy radiation, for example in the aerospace industry and with biomaterial, in sterilization processes. In this sense it is of interest studies that evaluate the radiodegradation of this material, as a way to predict its mechanical behavior after processes of exposure to gamma radiation. In this study the radioresistance of PVDF with different molecular weights is evaluated, considering that large molecular chains can provide greater resistance than smaller chains. Method: PVDF samples with different molecular weights were produced by the solvent dilution process. They were irradiated with gamma doses of 100, 300, 500, 1000 and 2000 kGy with a source of cobalt in the Laboratório de Irradiação Gama (LIG) of the Centro de Desenvolvimento da Tecnologia Nuclear (CDTN). FTIR, UV-Vis, DSC and XRD analyzes were used to evaluate the induced radiodegradation processes immediately after irradiation and one month later. Results: The FTIR and UV-Vis analyzes showed formation of unsaturations in the polymer chains. The DSC technique showed a drop in the crystalline fraction of the polymer confirmed by the XRD technique. Conclusion: Post-irradiation sample evaluations are discussed in terms of the effect of high energy ionizing radiation on polymeric mate-rials for industrial and biomedical use for safety in quality assurance and performance in service. (author)

Process kinetics and digestion efficiency of anaerobic batch fermentation of brewer`s spent grains (BSG)

Energy Technology Data Exchange (ETDEWEB)

Ezeonu, F.C.; Okaka, A.N.C. [Nnamdi Azikiwe University, Awka (Nigeria). Dept. of Applied Biochemistry

1996-12-31

The process kinetics of optimized anaerobic batch digestion of brewer`s spent grains (BSG) reveal that biomethanation is essentially a first order reaction interrupted intermittently by mixed order reactions. An apparent cellulose degradation efficiency of approximately 60% and a lignin degradation efficiency of about 40% was observed in the optimized process. Using the Ken and Hashimoto model, the operational efficiency of the digester was determined to be 26%. (author)

Kinetics in radiation chemistry

International Nuclear Information System (INIS)

Hummel, A.

1987-01-01

In this chapter the authors first briefly review the kinetics of first- and second-order processes for continuous and pulsed irradiation, without taking the effects of nonhomogeneous formation of the species into consideration. They also discuss diffusion controlled reactions under conditions where interactions of more than two particles can be neglected, first the kinetics of the diffusion-controlled reaction of randomly generated species (homogeneous reaction) and then that of isolated pairs of reactants. The latter is often called geminate kinetics when dealing with pairs of oppositely charged species; they shall use this term for the kinetics of isolated pairs in general. In the last section they discuss briefly the kinetics of groups of more than two reactants

Kinetics of contraction-induced GLUT4 translocation in skeletal muscle fibers from living mice

DEFF Research Database (Denmark)

Lauritzen, Hans Peter M. Mortensen; Galbo, Henrik; Toyoda, Taro

2010-01-01

Exercise is an important strategy for the treatment of type 2 diabetes. This is due in part to an increase in glucose transport that occurs in the working skeletal muscles. Glucose transport is regulated by GLUT4 translocation in muscle, but the molecular machinery mediating this process is poorly...... understood. The purpose of this study was to 1) use a novel imaging system to elucidate the kinetics of contraction-induced GLUT4 translocation in skeletal muscle and 2) determine the function of AMP-activated protein kinase alpha2 (AMPKalpha2) in this process....

Flow chemistry and polymer-supported pseudoenantiomeric acylating agents enable parallel kinetic resolution of chiral saturated N-heterocycles

Science.gov (United States)

Kreituss, Imants; Bode, Jeffrey W.

2017-05-01

Kinetic resolution is a common method to obtain enantioenriched material from a racemic mixture. This process will deliver enantiopure unreacted material when the selectivity factor of the process, s, is greater than 1; however, the scalemic reaction product is often discarded. Parallel kinetic resolution, on the other hand, provides access to two enantioenriched products from a single racemic starting material, but suffers from a variety of practical challenges regarding experimental design that limit its applications. Here, we describe the development of a flow-based system that enables practical parallel kinetic resolution of saturated N-heterocycles. This process provides access to both enantiomers of the starting material in good yield and high enantiopurity; similar results with classical kinetic resolution would require selectivity factors in the range of s = 100. To achieve this, two immobilized quasienantiomeric acylating agents were designed for the asymmetric acylation of racemic saturated N-heterocycles. Using the flow-based system we could efficiently separate, recover and reuse the polymer-supported reagents. The amide products could be readily separated and hydrolysed to the corresponding amines without detectable epimerization.

Kinetics of evaporation of barium THD precursors used for organometallic chemical vapor deposition (OMCVD) thin films

Science.gov (United States)

Burtman, V.; Schieber, M.; Yitzchaik, S.; Yaroslavsky, Y.

1997-04-01

Various methods have been used to synthesize Ba(THD) 2 and its molecular structure has been studied using nuclear magnetic resonance. Compared with Raman and infrared spectroscopy it was found that NMR is very useful to determine quantitatively the decomposition through aging of Ba(THD) 2. The transport kinetics of Ba(THD) 2 has been studied under experimental conditions of a OMCVD reactor. It has been found that the freshly prepared Ba(THD) 2 by the reaction of Ba metal with THD ligand in anhydrous conditions with subsequent crystallization from methanol transported quantitatively without decomposition. A simple model shows that the transport kinetics corresponds to a diffusion controlled process.

Vector properties in molecular photodissociation

International Nuclear Information System (INIS)

Underwood, J.

1999-12-01

The technique of resonance enhanced multi-photon ionization (REMPI) of atomic and molecular species produced from a photofragmentation event combined with time-of flight (TOF) detection is used to examine scalar and vector properties following photodissociation. This technique is applied to the study of methyl bromide dissociation in a product state specific manner. We report measurements of the angular distributions and kinetic energy releases of the resulting bromine atoms in the ground and first spin-orbit excited state. Additionally we report measurements of the angular distributions and kinetic energy releases of the methyl fragment in the ground vibrational state, and also the excited state with one quanta in the ν 2 vibrational modes. These studies were carried out in the red wing of the absorption band at several wavelengths. For these measurements we were able to resolve the spin orbit state of the partner bromine fragment. From our observations we find new evidence for enhanced nonadiabatic curve crossing active in methyl bromide dissociation in comparison with earlier studies of methyl iodide. The atomic polarization produced following photodissociation of a diatomic molecule was investigated both theoretically and experimentally. We develop theoretical expressions relating the lab frame and molecular frame atomic polarization to the photoexcitation and subsequent dissociation of a diatomic molecule. This treatment includes both incoherent, coherent and non-adiabatic processes which may be active in the photodissociation process. We treat the general case of a polarized diatomic molecule yielding two fragments with non zero angular momentum. Experimentally, an investigation of the polarization of atomic Cl( 2 P 3/2 ) photofragments from the ∼330 nm photolysis of molecular chlorine using the REMPI-TOF technique is reported. We present a theoretical framework in which to treat such experiments allowing the extraction of parameters with direct physical

The Nature of the Chemical Process. 1. Symmetry Evolution – Revised Information Theory, Similarity Principle and Ugly Symmetry

Directory of Open Access Journals (Sweden)

Shu-Kun Lin

2001-03-01

Full Text Available Abstract: Symmetry is a measure of indistinguishability. Similarity is a continuous measure of imperfect symmetry. Lewis' remark that “gain of entropy means loss of information” defines the relationship of entropy and information. Three laws of information theory have been proposed. Labeling by introducing nonsymmetry and formatting by introducing symmetry are defined. The function L ( L=lnw, w is the number of microstates, or the sum of entropy and information, L=S+I of the universe is a constant (the first law of information theory. The entropy S of the universe tends toward a maximum (the second law law of information theory. For a perfect symmetric static structure, the information is zero and the static entropy is the maximum (the third law law of information theory. Based on the Gibbs inequality and the second law of the revised information theory we have proved the similarity principle (a continuous higher similarity−higher entropy relation after the rejection of the Gibbs paradox and proved the Curie-Rosen symmetry principle (a higher symmetry−higher stability relation as a special case of the similarity principle. The principles of information minimization and potential energy minimization are compared. Entropy is the degree of symmetry and information is the degree of nonsymmetry. There are two kinds of symmetries: dynamic and static symmetries. Any kind of symmetry will define an entropy and, corresponding to the dynamic and static symmetries, there are static entropy and dynamic entropy. Entropy in thermodynamics is a special kind of dynamic entropy. Any spontaneous process will evolve towards the highest possible symmetry, either dynamic or static or both. Therefore the revised information theory can be applied to characterizing all kinds of structural stability and process spontaneity. Some examples in chemical physics have been given. Spontaneous processes of all kinds of molecular

Erbium hydride decomposition kinetics.

Energy Technology Data Exchange (ETDEWEB)

Ferrizz, Robert Matthew

2006-11-01

Thermal desorption spectroscopy (TDS) is used to study the decomposition kinetics of erbium hydride thin films. The TDS results presented in this report are analyzed quantitatively using Redhead's method to yield kinetic parameters (E{sub A} {approx} 54.2 kcal/mol), which are then utilized to predict hydrogen outgassing in vacuum for a variety of thermal treatments. Interestingly, it was found that the activation energy for desorption can vary by more than 7 kcal/mol (0.30 eV) for seemingly similar samples. In addition, small amounts of less-stable hydrogen were observed for all erbium dihydride films. A detailed explanation of several approaches for analyzing thermal desorption spectra to obtain kinetic information is included as an appendix.

Complexity in Evolutionary Processes

International Nuclear Information System (INIS)

Schuster, P.

2010-01-01

Darwin's principle of evolution by natural selection is readily casted into a mathematical formalism. Molecular biology revealed the mechanism of mutation and provides the basis for a kinetic theory of evolution that models correct reproduction and mutation as parallel chemical reaction channels. A result of the kinetic theory is the existence of a phase transition in evolution occurring at a critical mutation rate, which represents a localization threshold for the population in sequence space. Occurrence and nature of such phase transitions depend critically on fitness landscapes. The fitness landscape being tantamount to a mapping from sequence or genotype space into phenotype space is identified as the true source of complexity in evolution. Modeling evolution as a stochastic process is discussed and neutrality with respect to selection is shown to provide a major challenge for understanding evolutionary processes (author)

Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

Science.gov (United States)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-10-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

The kinetics of steam-carbon dioxide conversion, rational ways and production catalysts of process gas

International Nuclear Information System (INIS)

Khamroev, F.B.

2016-01-01

The purpose of the present work is to study the kinetics of steam-carbon dioxide conversion, rational ways and production catalysts of process gas. The experimental equation of steam-carbon methane conversion, heat stability increasing and catalyst efficiency, decreasing of hydrodynamical resistance of catalyst layer were determined.

Behavioral similarity measurement based on image processing for robots that use imitative learning

Science.gov (United States)

Sterpin B., Dante G.; Martinez S., Fernando; Jacinto G., Edwar

2017-02-01

In the field of the artificial societies, particularly those are based on memetics, imitative behavior is essential for the development of cultural evolution. Applying this concept for robotics, through imitative learning, a robot can acquire behavioral patterns from another robot. Assuming that the learning process must have an instructor and, at least, an apprentice, the fact to obtain a quantitative measurement for their behavioral similarity, would be potentially useful, especially in artificial social systems focused on cultural evolution. In this paper the motor behavior of both kinds of robots, for two simple tasks, is represented by 2D binary images, which are processed in order to measure their behavioral similarity. The results shown here were obtained comparing some similarity measurement methods for binary images.

The Validity of 21 cm Spin Temperature as a Kinetic Temperature Indicator in Atomic and Molecular Gas

Energy Technology Data Exchange (ETDEWEB)

Shaw, Gargi [Dept. of Physics, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Mumbai 400098 (India); Ferland, G. J. [Department of Physics and Astronomy, University of Kentucky, Lexington, KY 40506 (United States); Hubeny, I., E-mail: gargishaw@gmail.com, E-mail: gary@uky.edu, E-mail: hubeny@as.arizona.edu [Steward Observatory, University of Arizona, Tucson, AZ 85721 (United States)

2017-07-10

The gas kinetic temperature ( T {sub K} ) of various interstellar environments is often inferred from observations that can deduce level populations of atoms, ions, or molecules using spectral line observations; H i 21 cm is perhaps the most widely used, and has a long history. Usually the H i 21 cm line is assumed to be in thermal equilibrium and the populations are given by the Boltzmann distribution. A variety of processes, many involving Ly α , can affect the 21 cm line. Here we show how this is treated in the spectral simulation code Cloudy, and present numerical simulations of environments where this temperature indicator is used, with a detailed treatment of the physical processes that determine level populations within H{sup 0}. We discuss situations where this temperature indicator traces T {sub K}, cases where it fails, as well as the effects of Ly α pumping on the 21 cm spin temperature. We also show that the Ly α excitation temperature rarely traces the gas kinetic temperature.

Kinetics of oxygen adsorption on ZnS nanoparticles synthesized by precipitation process

Directory of Open Access Journals (Sweden)

Ahmadi Reza

2016-06-01

Full Text Available ZnS nanoparticles were synthesized through a one-step precipitation process. Effect of time and temperature on the formation reaction was investigated. The synthesized samples were characterized by X-ray diffraction (XRD, ultraviolet (UV visible absorption and photoluminescence (PL spectrophotometry. Based on XRD and UV-Vis data, the particles produced at 70 °C had a mean particle size of about 5 nm. Increasing time and temperature of the synthesis reaction resulted in photoluminescence intensification. PL spectroscopy helped understanding the adsorption kinetics of oxygen on ZnS nanoparticles during the precipitation synthesis process. Fabrication of ZnS structures with appropriate oxygen adsorption capacity was suggested as a means of PL emission intensity control.

Kinetic studies of uranyl ion adsorption on acrylonitrile (AN)/polyethylene glycol (PEG) interpenetrating networks (IPN)

International Nuclear Information System (INIS)

Aycik, G.A.; Gurellier, R.

2004-01-01

Full text: The kinetics of the adsorption of uranyl ions on amidoximated acrylonitrile (AN)/ polyethylene glycol (PEG) interpenetrating network (IPNs) from aqueous solutions was studied as a function of time and temperature. The IPNs were prepared by irradiation initiated gamma polymerisation using Co-60 gamma source. Adsorption capacities were performed for definite uranyl ion concentrations of 1x10 -2 M and at four different temperatures as 290K, 298K, 308K and 318K by gamma spectrometer. Adsorption time was increased from zero to 48 hours. The results indicate that adsorption capacity increases linearly with increasing temperature. Temperature and agitation hardly influence equilibrium and kinetics and decreasing of temperature results in a slightly greater time to reach equilibrium. The adsorption of uranyl ions has been studied in a multi step mechanism processes thus comparing chemical sorption and diffusion sorption processes. The experimental data was analysed using various kinetic models to determine the best-fit equation for the adsorption mechanisms. However, it was shown that all models, in general according to the reaction time and uranyl ion concentration in the solution, could describe the adsorption of uranyl ion onto amidoximated IPN, the adsorption kinetics was best described by zeroth order and intraparticle diffusion model whereas that of in increasing time by pseudo first and pseudo second order response respectively. External-intraparticle diffusion and zeroth order process in the IPN structure is proposed as a mass transfer mechanism and the results indicate a diffusion-controlled process. The Mean Activation Energy Of Uranyl Ions Adsorption Was Found As 4,1 Kj/Mole By Using Arrhenius Equation. The Rate Constant, The Equilibrium Adsorption Capacity And The Initial Adsorption Rate Were Calculated For All Models At Each Temperature. Kinetic Parameters Of All Models And The Normalized Standard Deviations Between The Measured And Predicted

Functional neuronal processing of body odors differs from that of similar common odors.

Science.gov (United States)

Lundström, Johan N; Boyle, Julie A; Zatorre, Robert J; Jones-Gotman, Marilyn

2008-06-01

Visual and auditory stimuli of high social and ecological importance are processed in the brain by specialized neuronal networks. To date, this has not been demonstrated for olfactory stimuli. By means of positron emission tomography, we sought to elucidate the neuronal substrates behind body odor perception to answer the question of whether the central processing of body odors differs from perceptually similar nonbody odors. Body odors were processed by a network that was distinctly separate from common odors, indicating a separation in the processing of odors based on their source. Smelling a friend's body odor activated regions previously seen for familiar stimuli, whereas smelling a stranger activated amygdala and insular regions akin to what has previously been demonstrated for fearful stimuli. The results provide evidence that social olfactory stimuli of high ecological relevance are processed by specialized neuronal networks similar to what has previously been demonstrated for auditory and visual stimuli.

PET-based molecular imaging in neuroscience

International Nuclear Information System (INIS)

Jacobs, A.H.; Heiss, W.D.; Li, H.; Knoess, C.; Schaller, B.; Kracht, L.; Monfared, P.; Vollmar, S.; Bauer, B.; Wagner, R.; Graf, R.; Wienhard, K.; Winkeler, A.; Rueger, A.; Klein, M.; Hilker, R.; Galldiks, N.; Herholz, K.; Sobesky, J.

2003-01-01

Positron emission tomography (PET) allows non-invasive assessment of physiological, metabolic and molecular processes in humans and animals in vivo. Advances in detector technology have led to a considerable improvement in the spatial resolution of PET (1-2 mm), enabling for the first time investigations in small experimental animals such as mice. With the developments in radiochemistry and tracer technology, a variety of endogenously expressed and exogenously introduced genes can be analysed by PET. This opens up the exciting and rapidly evolving field of molecular imaging, aiming at the non-invasive localisation of a biological process of interest in normal and diseased cells in animal models and humans in vivo. The main and most intriguing advantage of molecular imaging is the kinetic analysis of a given molecular event in the same experimental subject over time. This will allow non-invasive characterisation and ''phenotyping'' of animal models of human disease at various disease stages, under certain pathophysiological stimuli and after therapeutic intervention. The potential broad applications of imaging molecular events in vivo lie in the study of cell biology, biochemistry, gene/protein function and regulation, signal transduction, transcriptional regulation and characterisation of transgenic animals. Most importantly, molecular imaging will have great implications for the identification of potential molecular therapeutic targets, in the development of new treatment strategies, and in their successful implementation into clinical application. Here, the potential impact of molecular imaging by PET in applications in neuroscience research with a special focus on neurodegeneration and neuro-oncology is reviewed. (orig.)

2D Numerical Modelling of the Resin Injection Pultrusion Process Including Experimental Resin Kinetics and Temperature Validation

DEFF Research Database (Denmark)

Rasmussen, Filip Salling; Sonne, Mads Rostgaard; Larsen, Martin

In the present study, a two-dimensional (2D) transient Eulerian thermo-chemical analysis of a carbon fibre epoxy thermosetting Resin Injection Pultrusion (RIP) process is carried out. The numerical model is implemented using the well known unconditionally stable Alternating Direction Implicit (ADI......) scheme. The total heat of reaction and the cure kinetics of the epoxy thermosetting are determined using Differential Scanning Calorimetry (DSC). A very good agreement is observed between the fitted cure kinetic model and the experimental measurements. The numerical steady state temperature predictions...

Application of a small molecule radiopharmaceutical concept to improve kinetics

International Nuclear Information System (INIS)

Jeong, Jae Min

2016-01-01

Recently, large molecules or nanoparticles are actively studied as radiopharmaceuticals. However, their kinetics is problematic because of a slow penetration through the capillaries and slow distribution to the target. To improve the kinetics, a two-step targeting method can be applied by using small molecules and very rapid copper-free click reaction. Although this method might have limitations such as internalization of the first targeted conjugate, it will provide high target-to-non-target ratio imaging of radiopharmaceuticals. The majority of radiopharmaceuticals belong to small molecules of which the molecular weight is less than 2000 Da, and the molecular size is smaller than 2 nm generally. The outstanding feature of the small molecule radiopharmaceuticals compared to large molecules is with their kinetics. Their distribution to target and clearance from non-target tissues are very rapid, which is the essential requirement of radiopharmaceuticals. In conclusion, the small molecule radiopharmaceuticals generally show excellent biodistribution properties; however, they show poor efficiency of radioisotope delivery. Large molecule or nanoparticle radiopharmaceuticals have advantages of multimodal and efficient delivery, but lower target-to-non-target ratio. Two-step targeting using a bio-orthogonal copper-free click reaction can be a solution of the problem of large molecule or nanoparticle radiopharmaceuticals. The majority of radiopharmaceuticals belong to small molecules of which the molecular weight is less than 2000 Da, and the molecular size is smaller than 2 nm generally. The outstanding feature of the small molecule radiopharmaceuticals compared to large molecules is with their kinetics. Their distribution to target and clearance from non-target tissues are very rapid, which is the essential requirement of radiopharmaceuticals

Application of a small molecule radiopharmaceutical concept to improve kinetics

Energy Technology Data Exchange (ETDEWEB)

Jeong, Jae Min [Dept. of Nuclear Medicine, Seoul National University College of Medicine, Seoul (Korea, Republic of)

2016-06-15

Recently, large molecules or nanoparticles are actively studied as radiopharmaceuticals. However, their kinetics is problematic because of a slow penetration through the capillaries and slow distribution to the target. To improve the kinetics, a two-step targeting method can be applied by using small molecules and very rapid copper-free click reaction. Although this method might have limitations such as internalization of the first targeted conjugate, it will provide high target-to-non-target ratio imaging of radiopharmaceuticals. The majority of radiopharmaceuticals belong to small molecules of which the molecular weight is less than 2000 Da, and the molecular size is smaller than 2 nm generally. The outstanding feature of the small molecule radiopharmaceuticals compared to large molecules is with their kinetics. Their distribution to target and clearance from non-target tissues are very rapid, which is the essential requirement of radiopharmaceuticals. In conclusion, the small molecule radiopharmaceuticals generally show excellent biodistribution properties; however, they show poor efficiency of radioisotope delivery. Large molecule or nanoparticle radiopharmaceuticals have advantages of multimodal and efficient delivery, but lower target-to-non-target ratio. Two-step targeting using a bio-orthogonal copper-free click reaction can be a solution of the problem of large molecule or nanoparticle radiopharmaceuticals. The majority of radiopharmaceuticals belong to small molecules of which the molecular weight is less than 2000 Da, and the molecular size is smaller than 2 nm generally. The outstanding feature of the small molecule radiopharmaceuticals compared to large molecules is with their kinetics. Their distribution to target and clearance from non-target tissues are very rapid, which is the essential requirement of radiopharmaceuticals.

Modern quantum kinetic theory and spectral line shapes

International Nuclear Information System (INIS)

Monchick, L.

1991-01-01

The modern quantum kinetic theory of spectral line shapes is outlined and a typical calculation of a Raman scattered line shape described. The distinguishing feature of this calculation is that it was completely ab initio and therefore constituted a test of modern quantum kinetic theory, the state of the art in computing molecular-scattering cross sections, and novel methods of solving kinetic equations. The computation employed a large assortment of tools: group theory, finite-element methods, classic methods of solving coupled sets of ordinary differential equations, graph methods of combining angular momenta, and matrix methods of solving integral equations. Agreement with experimental results was excellent. 13 refs

Oxidation kinetics of innovative carbon materials with respect to severe air ingress accidents in HTRs and graphite disposal or processing

International Nuclear Information System (INIS)

Schloegel, Baerbel

2010-01-01

Currently future nuclear reactor concepts of the Fourth Generation (Gen IV) are under development. To some extend they apply with new, innovative materials developed just for this purpose. This thesis work aims at a concept of Generation IV Very High Temperature Reactors (VHTR) in the framework of the European project RAPHAEL (ReActor for Process heat, Hydrogen And ELectricity generation). The concept named ANTARES (AREVA New Technology based on advanced gas-cooled Reactors for Energy Supply) was developed by AEVA NP. It is a helium cooled, graphite moderated modular reactor for electricity and hydrogen production, by providing the necessary process heat due to its high working temperature. Particular attention is given here to oxidation kinetics of newly developed carbon materials (NBG-17) with still unknown but needed information in context of severe air ingress accident in VHTR's. Special interest is paid to the Boudouard reaction, the oxidation of carbon by CO 2 . In case of an air ingress accident, carbon dioxide is produced in the primary reaction of atmospheric oxygen with reflector graphite. From there CO 2 could flow into the reactor core causing further damage by conversion into CO. The purpose of this thesis is to ascertain if and to what degree this could happen. First of all oxidation kinetic data of the Boudouard reaction with NBG-17 is determined by experiments in a thermo gravimetric facility. The measurements are evaluated and converted into a common formula and a Langmuir-Hinshelwood similar oxidation kinetic equation, as input for the computer code REACT/THERMIX. This code is then applied to analyse severe air ingress accidents for several air flow rates. The results are discussed for two accident situations, in which a certain graphite burn off is achieved. All cases show much more damage to the graphite bottom reflector than to the reactor core. Thus the bottom reflector will lose its structural integrity much earlier than the core itself will

Influence of film structure on the dewetting kinetics of thin polymer films in the solvent annealing process.

Science.gov (United States)

Zhang, Huanhuan; Xu, Lin; Lai, Yuqing; Shi, Tongfei

2016-06-28

On a non-wetting solid substrate, the solvent annealing process of a thin polymer film includes the swelling process and the dewetting process. Owing to difficulties in the in situ analysis of the two processes simultaneously, a quantitative study on the solvent annealing process of thin polymer films on the non-wetting solid substrate is extremely rare. In this paper, we design an experimental method by combining spectroscopic ellipsometry with optical microscopy to achieve the simultaneous in situ study. Using this method, we investigate the influence of the structure of swollen film on its dewetting kinetics during the solvent annealing process. The results show that for a thin PS film with low Mw (Mw = 4.1 kg mol(-1)), acetone molecules can form an ultrathin enriched layer between the PS film and the solid substrate during the swelling process. The presence of the acetone enriched layer accounts for the exponential kinetic behavior in the case of a thin PS film with low Mw. However, the acetone enriched layer is not observed in the case of a thin PS film with high Mw (Mw = 400 kg mol(-1)) and the slippage effect of polymer chains is valid during the dewetting process.

High-pressure processing of apple juice: kinetics of pectin methyl esterase inactivation.

Science.gov (United States)

Riahi, Esmaeil; Ramaswamy, Hosahalli S

2003-01-01

High-pressure (HP) inactivation kinetics of pectin methyl esterase (PME) in apple juice were evaluated. Commercial PME was dispensed in clarified apple juice, sealed in dual peel sterilizable plastic bags, and subjected to different high-pressure processing conditions (200-400 MPa, 0-180 min). Residual enzyme activity was determined by a titration method estimating the rate of free carboxyl group released by the enzyme acting on pectin substrate at pH 7.5 (30 degrees C). The effects of pressure level and pressure holding time on enzyme inactivation were significant (p < 0.05). PME from the microbial source was found to be more resistant (p < 0.05) to pressure inactivation than PME from the orange peel. Almost a full decimal reduction in the activity of commercial PME was achieved by HP treatment at 400 MPa for 25 min. Inactivation kinetics were evaluated on the basis of a dual effect model involving a pressure pulse effect and a first-order rate model, and the pressure sensitivity of rate constants was modeled by using the z-value concept.

Nonlinear and Nonsymmetric Single-Molecule Electronic Properties Towards Molecular Information Processing.

Science.gov (United States)

Tamaki, Takashi; Ogawa, Takuji

2017-09-05

This review highlights molecular design for nonlinear and nonsymmetric single-molecule electronic properties such as rectification, negative differential resistance, and switching, which are important components of future single-molecule information processing devices. Perspectives on integrated "molecular circuits" are also provided. Nonlinear and nonsymmetric single-molecule electronics can be designed by utilizing (1) asymmetric molecular cores, (2) asymmetric anchoring groups, (3) an asymmetric junction environment, and (4) asymmetric electrode materials. This review mainly focuses on the design of molecular cores.

Proceedings of the Conference on Isotopic and Molecular Processes

International Nuclear Information System (INIS)

Pamula, A.

1999-01-01

The proceedings of the Conference on Isotopic and Molecular Processes held on September 23 - 25, 1999 in Cluj - Napoca, Romania contains 8 plenary lectures, 12 oral presentations and 34 posters on isotopic processes (Section A) and 12 oral presentations plus 61 posters on molecular processes (Section B). The main topics treated in plenary lectures were isotope production, separation and enrichment as well as stable isotope applications. Also in this section studies on isotope effects in different fields are reported. In the section A, besides reports on isotope effects, exchange and separation, new methods of preparation and labelling compounds used particularly in nuclear medicine are presented. Also environmental studies by means of stable isotope and radon monitoring are described. In the section B several communications are treating the applications of radiation effects and different nuclear methods in medicine

Physical principles of filamentous protein self-assembly kinetics

International Nuclear Information System (INIS)

Michaels, Thomas C T; Liu, Lucie X; Meisl, Georg; Knowles, Tuomas P J

2017-01-01

The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer’s and Parkinson’s diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes. (topical review)

Fundamental aspects of plasma chemical physics kinetics

CERN Document Server

Capitelli, Mario; Colonna, Gianpiero; Esposito, Fabrizio; Gorse, Claudine; Hassouni, Khaled; Laricchiuta, Annarita; Longo, Savino

2016-01-01

Describing non-equilibrium "cold" plasmas through a chemical physics approach, this book uses the state-to-state plasma kinetics, which considers each internal state as a new species with its own cross sections. Extended atomic and molecular master equations are coupled with Boltzmann and Monte Carlo methods to solve the electron energy distribution function. Selected examples in different applied fields, such as microelectronics, fusion, and aerospace, are presented and discussed including the self-consistent kinetics in RF parallel plate reactors, the optimization of negative ion sources and the expansion of high enthalpy flows through nozzles of different geometries. The book will cover the main aspects of the state-to-state kinetic approach for the description of nonequilibrium cold plasmas, illustrating the more recent achievements in the development of kinetic models including the self-consistent coupling of master equations and Boltzmann equation for electron dynamics. To give a complete portrayal, the...

How to Measure Load-Dependent Kinetics of Individual Motor Molecules Without a Force-Clamp

DEFF Research Database (Denmark)

Sung, Jongmin; Mortensen, Kim; Spudich, James A.

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using a new method, Harmonic Force...... and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human beta-cardiac myosin molecules interacting with an actin filament...... at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load. This points to Kramer's Brownian diffusion model of chemical reactions as explanation why muscle contracts with a velocity inversely proportional to external load....

Kinetics of Low Temperature Polyester Dyeing with High Molecular Weight Disperse Dyes by Solvent Microemulsion and AgroSourced Auxiliaries

Directory of Open Access Journals (Sweden)

Shahram Radei

2018-02-01

Full Text Available This work focused on the evaluation of the kinetics of dyeing polyester fabrics with high molecular weight disperse dyes, at low temperature by solvent microemulsion. This study also compared the effect of two non-toxic agro-sourced auxiliaries (o-vanillin and coumarin using a non-toxic organic solvent. A dyeing bath consisting of a micro-emulsion system involving a small proportion of n-butyl acetate was used, and the kinetics of dyeing were analysed at four temperatures (83, 90, 95 and 100 °C. Moreover, the dyeing rate constants, correlation coefficient and activation energies were proposed for this system. It was found that o-vanillin yielded higher dye absorption levels than coumarin, leading to exhaustions of 88% and 87% for Disperse Red 167 and Disperse Blue 79, respectively. K/S values of dyed polyester were also found to be higher for dye baths containing o-vanillin with respect to the ones with coumarin. In terms of hot pressing fastness and wash fastness, generally no adverse influence on fastness properties was reported, while o-vanillin showed slightly better results compared to coumarin.

Film growth kinetics and electric field patterning during electrospray deposition of block copolymer thin films

Science.gov (United States)

Toth, Kristof; Hu, Hanqiong; Choo, Youngwoo; Loewenberg, Michael; Osuji, Chinedum

The delivery of sub-micron droplets of dilute polymer solutions to a heated substrate by electrospray deposition (ESD) enables precisely controlled and continuous growth of block copolymer (BCP) thin films. Here we explore patterned deposition of BCP films by spatially varying the electric field at the substrate using an underlying charged grid, as well as film growth kinetics. Numerical analysis was performed to examine pattern fidelity by considering the trajectories of charged droplets during flight through imposed periodic field variations in the vicinity of the substrate. Our work uncovered an unexpected modality for improving the resolution of the patterning process via stronger field focusing through the use of a second oppositely charged grid beneath a primary focusing array, with an increase in highly localized droplet deposition on the intersecting nodes of the grid. Substrate coverage kinetics are considered for homopolymer deposition in the context of simple kinetic models incorporating temperature and molecular weight dependence of diffusivity. By contrast, film coverage kinetics for block copolymer depositions are additionally convoluted with preferential wetting and thickness-periodicity commensurability effects. NSF GRFP.

Spectrophotometric Analysis of the Kinetic of Pd(II Chloride Complex Ions Sorption Process from Diluted Aqua Solutions Using Commercially Available Activated Carbon

Directory of Open Access Journals (Sweden)

Wojnicki M.

2017-12-01

Full Text Available In this paper, results of adsorption kinetic studies of Pd(II chloride complex ions on activated carbon Organosrob 10 CO are presented. Spectorphotometrical method was applied to investigate the process. Kinetic model was proposed, and fundamental thermodynamic parameters were determined. Proposed kinetic model describes well observed phenomenon in the studied range of concentration of Pd(II chloride complex ions as well, as concentration of activated carbon.

The kinetic study of oxidation of iodine by hydrogen peroxide

Energy Technology Data Exchange (ETDEWEB)

Cantrel, L [Institut de Protection et de Surete Nucleaire, IPNS, CEN Cadarache, Saint Paul lez Durance (France); Chopin, J [Laboratoire d` Electrochimie Inorganique, ENSSPICAM, Marseille (France)

1996-12-01

Iodine chemistry is one of the most important subjects of research in the field of reactor safety because this element can form volatile species which represent a biological hazard for environment. As the iodine and the peroxide are both present in the sump of the containment in the event of a severe accident on a light water nuclear reactor, it can be important to improve the knowledge on the reaction of oxidation of iodine by hydrogen peroxide. The kinetics of iodine by hydrogen peroxide has been studied in acid solution using two different analytical methods. The first is a UV/Vis spectrophotometer which records the transmitted intensity at 460 nm as a function of time to follow the decrease of iodine concentration, the second is an amperometric method which permits to record the increase of iodine+1 with time thanks to the current of reduction of iodine+1 to molecular iodine. The iodine was generated by Dushman reaction and the series of investigations were made at 40{sup o}C in a continuous stirring tank reactor. The influence of the initial concentrations of iodine, iodate, hydrogen peroxide, H{sup +} ions has been determined. The kinetics curves comprise two distinct chemical phases both for molecular iodine and for iodine+1. The relative importance of the two processes is connected to the initial concentrations of [I{sub 2}], [IO{sub 3}{sup -}], [H{sub 2}O{sub 2}] and [H{sup +}]. A rate law has been determined for the two steps for molecular iodine. (author) figs., tabs., 22 refs.

The kinetic study of oxidation of iodine by hydrogen peroxide

International Nuclear Information System (INIS)

Cantrel, L.; Chopin, J.

1996-01-01

Iodine chemistry is one of the most important subjects of research in the field of reactor safety because this element can form volatile species which represent a biological hazard for environment. As the iodine and the peroxide are both present in the sump of the containment in the event of a severe accident on a light water nuclear reactor, it can be important to improve the knowledge on the reaction of oxidation of iodine by hydrogen peroxide. The kinetics of iodine by hydrogen peroxide has been studied in acid solution using two different analytical methods. The first is a UV/Vis spectrophotometer which records the transmitted intensity at 460 nm as a function of time to follow the decrease of iodine concentration, the second is an amperometric method which permits to record the increase of iodine+1 with time thanks to the current of reduction of iodine+1 to molecular iodine. The iodine was generated by Dushman reaction and the series of investigations were made at 40 o C in a continuous stirring tank reactor. The influence of the initial concentrations of iodine, iodate, hydrogen peroxide, H + ions has been determined. The kinetics curves comprise two distinct chemical phases both for molecular iodine and for iodine+1. The relative importance of the two processes is connected to the initial concentrations of [I 2 ], [IO 3 - ], [H 2 O 2 ] and [H + ]. A rate law has been determined for the two steps for molecular iodine. (author) figs., tabs., 22 refs

Analysis of metal forming processes by using physical modeling and new plastic similarity condition

International Nuclear Information System (INIS)

Gronostajski, Z.; Hawryluk, M.

2007-01-01

In recent years many advances have been made in numerical methods, for linear and non-linear problems. However the success of them depends very much on the correctness of the problem formulation and the availability of the input data. Validity of the theoretical results can be verified by an experiment using the real or soft materials. An essential reduction of time and costs of the experiment can be obtained by using soft materials, which behaves in a way analogous to that of real metal during deformation. The advantages of using of the soft materials are closely connected with flow stress 500 to 1000 times lower than real materials. The accuracy of physical modeling depend on the similarity conditions between physical model and real process. The most important similarity conditions are materials similarity in the range of plastic and elastic deformation, geometrical, frictional and thermal similarities. New original plastic similarity condition for physical modeling of metal forming processes is proposed in the paper. It bases on the mathematical description of similarity of the flow stress curves of soft materials and real ones

Designing Antibacterial Peptides with Enhanced Killing Kinetics

Directory of Open Access Journals (Sweden)

Faiza H. Waghu

2018-02-01

Full Text Available Antimicrobial peptides (AMPs are gaining attention as substitutes for antibiotics in order to combat the risk posed by multi-drug resistant pathogens. Several research groups are engaged in design of potent anti-infective agents using natural AMPs as templates. In this study, a library of peptides with high sequence similarity to Myeloid Antimicrobial Peptide (MAP family were screened using popular online prediction algorithms. These peptide variants were designed in a manner to retain the conserved residues within the MAP family. The prediction algorithms were found to effectively classify peptides based on their antimicrobial nature. In order to improve the activity of the identified peptides, molecular dynamics (MD simulations, using bilayer and micellar systems could be used to design and predict effect of residue substitution on membranes of microbial and mammalian cells. The inference from MD simulation studies well corroborated with the wet-lab observations indicating that MD-guided rational design could lead to discovery of potent AMPs. The effect of the residue substitution on membrane activity was studied in greater detail using killing kinetic analysis. Killing kinetics studies on Gram-positive, negative and human erythrocytes indicated that a single residue change has a drastic effect on the potency of AMPs. An interesting outcome was a switch from monophasic to biphasic death rate constant of Staphylococcus aureus due to a single residue mutation in the peptide.

Molecular-Level Simulations of the Turbulent Taylor-Green Flow

Science.gov (United States)

Gallis, M. A.; Bitter, N. P.; Koehler, T. P.; Plimpton, S. J.; Torczynski, J. R.; Papadakis, G.

2017-11-01

The Direct Simulation Monte Carlo (DSMC) method, a statistical, molecular-level technique that provides accurate solutions to the Boltzmann equation, is applied to the turbulent Taylor-Green vortex flow. The goal of this work is to investigate whether DSMC can accurately simulate energy decay in a turbulent flow. If so, then simulating turbulent flows at the molecular level can provide new insights because the energy decay can be examined in detail from molecular to macroscopic length scales, thereby directly linking molecular relaxation processes to macroscopic transport processes. The DSMC simulations are performed on half a million cores of Sequoia, the 17 Pflop platform at Lawrence Livermore National Laboratory, and the kinetic-energy dissipation rate and the energy spectrum are computed directly from the molecular velocities. The DSMC simulations are found to reproduce the Kolmogorov -5/3 law and to agree with corresponding Navier-Stokes simulations obtained using a spectral method. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

NATO Advanced Study Institute on Molecular Physics and Hypersonic Flows

CERN Document Server

1996-01-01

Molecular Physics and Hypersonic Flows bridges the gap between the fluid dynamics and molecular physics communities, emphasizing the role played by elementary processes in hypersonic flows. In particular, the work is primarily dedicated to filling the gap between microscopic and macroscopic treatments of the source terms to be inserted in the fluid dynamics codes. The first part of the book describes the molecular dynamics of elementary processes both in the gas phase and in the interaction with surfaces by using quantum mechanical and phenomenological approaches. A second group of contributions describes thermodynamics and transport properties of air components, with special attention to the transport of internal energy. A series of papers is devoted to the experimental and theoretical study of the flow of partially ionized gases. Subsequent contributions treat modern computational techniques for 3-D hypersonic flow. Non-equilibrium vibrational kinetics are then described, together with the coupling of vibra...

Butia Yatay coconut oil: Process development for biodiesel production and kinetics of esterification with ethanol

International Nuclear Information System (INIS)

Zanuttini, M.S.; Pisarello, M.L.; Querini, C.A.

2014-01-01

Highlights: • Coconut oil contains high levels of phosphorous and free fatty acids. • Especial degumming process is needed in order to decrease the phosphorous content. • Kinetic constant for esterification reaction decreases as a function of time. • Two-step esterification is more efficient to reduce acidity than one-step. • Approximately 15% of esters are formed by acid-catalyzed transesterification. - Abstract: The aim of this work is to study biodiesel production using Butia Yatay coconut oil. This oil has acid values between 109 and 140 mg KOH/g, and phosphorus content in the order of 600 ppm. A three-step degumming pre-treatment of the raw material was adjusted in order to decrease the phosphorus content to approximately 200 ppm. Afterwards, a two-step esterification followed by transesterification was required in order to obtain a high-quality product. The esterification kinetics was studied including the simultaneous reactions that take place during the esterification of free fatty acids: autocatalysis, triacylglycerides hydrolysis, transesterification, and the reaction of sulphuric acid with the alcohol, being the most important ones. The kinetic parameters for the esterification and autocatalysis reactions were also obtained, being different compared to sunflower oil, due to the presence of short chain fatty acids. The kinetic constant for the esterification reaction rapidly decreases as a function of time, due to the consumption of the catalyst by the alkyl-sulphate formation reaction

Simplified modeling of simultaneous reaction kinetics of carbon oxidation and nitrification in biofilm processes

Energy Technology Data Exchange (ETDEWEB)

Tsuneda, S.; Auresenia, J.; Hibiya, K.; Hirata, A. [Waseda University, Department of Chemical Engineering, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555 (Japan)

2004-06-01

Batch experiments with varying initial substrate concentrations and biomass volumes were performed in a three-phase fluidized bed biofilm reactor treating simulated domestic wastewater to study the simultaneous carbon oxidation and nitrification in the biofilm process. A simplified mass balance equation for the biofilm was proposed and five different kinetic rate equations were used to match the actual data. The kinetic parameters were obtained by nonlinear regression analysis on a set of two differential equations representing the simultaneous carbon oxidation and nitrification. The competitive inhibition model incorporating the effects of total organic carbon (TOC) concentrations on nitrification rates was the best-suited model based on the average r{sup 2}. In this model, oxygen concentration and its affinity constants were not included. Instead, it was assumed that the rate of carbon oxidation is independent of the NH{sub 4}{sup +}-N, while nitrification is affected by TOC. The number of parameters was successfully minimized without reducing its ability to accurately predict the bulk concentration time course, which would reduce computational complexity and possibly enhance the availability for an actual wastewater treatment process. (Abstract Copyright [2004], Wiley Periodicals, Inc.)

A new kinetic biphasic approach applied to biodiesel process intensification

Energy Technology Data Exchange (ETDEWEB)

Russo, V.; Tesser, R.; Di Serio, M.; Santacesaria, E. [Naples Univ. (Italy). Dept. of Chemistry

2012-07-01

Many different papers have been published on the kinetics of the transesterification of vegetable oil with methanol, in the presence of alkaline catalysts to produce biodiesel. All the proposed approaches are based on the assumption of a pseudo-monophasic system. The consequence of these approaches is that some experimental aspects cannot be described. For the reaction performed in batch conditions, for example, the monophasic approach is not able to reproduce the different plateau obtained by using different amount of catalyst or the induction time observed at low stirring rates. Moreover, it has been observed by operating in continuous reactors that micromixing has a dramatic effect on the reaction rate. At this purpose, we have recently observed that is possible to obtain a complete conversion to biodiesel in less than 10 seconds of reaction time. This observation is confirmed also by other authors using different types of reactors like: static mixers, micro-reactors, oscillatory flow reactors, cavitational reactors, microwave reactors or centrifugal contactors. In this work we will show that a recently proposed biphasic kinetic approach is able to describe all the aspects before mentioned that cannot be described by the monophasic kinetic model. In particular, we will show that the biphasic kinetic model can describe both the induction time observed in the batch reactors, at low stirring rate, and the very high conversions obtainable in a micro-channel reactor. The adopted biphasic kinetic model is based on a reliable reaction mechanism that will be validated by the experimental evidences reported in this work. (orig.)

Vibrational energy transfer kinetics in molecular disequilibrium. Final technical report

International Nuclear Information System (INIS)

Rich, J.W.

1982-09-01

The present Calspan experiments have shown direct evidence of preferential vibrational pumping of two heavy isotopes of CO: 13 C 16 O and 12 C 18 O. The nature of the enhancement is generally consistent with the predictions of theoretical modeling. These are the first direct experimental demonstrations of this isotope selection method. The potential advantages of such a means of isotope separation are inherent in the V-V pumping process itself. Summarizing these: (1) Selectivity actually increases at higher reactant pressures, since the selection mechanism is collisional. Accordingly, rather high throughputs are possible, unlike other techniques in which molecular collisions actually decrease selectivity. (2) A variety of excitation methods can potentially be used - electric discharge, optical excitation by coherent or incoherent sources, or chemical excitation; laser excitation is not critical to the process. (3) The method can be applied to many isotopes of the lighter atoms. It is not inherently species-specific

Selective Adsorption on Fluorinated Plastic Enables the Optical Detection of Molecular Pollutants in Water

Science.gov (United States)

Lanfranco, R.; Giavazzi, F.; Salina, M.; Tagliabue, G.; Di Nicolò, E.; Bellini, T.; Buscaglia, M.

2016-05-01

Amorphous fluorinated plastic can be produced with a refractive index similar to that of water, a condition that makes it essentially invisible when immersed in aqueous solutions. Because of this property, even a small amount of adsorbed molecules on the plastic-water interface provides a detectable optical signal. We investigate two distinct substrates made of this material, characterized by different interface areas: a prism and a microporous membrane. We demonstrate that both substrates enable the label-free detection of molecular compounds in water even without any surface functionalization. The adsorption of molecules on the planar surface of the prism provides an increase of optical reflectivity, whereas the adsorption on the internal surface of the microporous membrane yields an increase of scattered light. Despite the different mechanisms, we find a similar optical response upon adsorption. We confirm this result by a theoretical model accounting for both reflection and scattering. We investigate the spontaneous adsorption process for different kinds of molecules: surfactants with different charges, a protein (lysozyme), and a constituent of gasoline (hexane). The measured equilibrium and kinetic constants for adsorption differ by orders of magnitudes among the different classes of molecules. By suitable analytical models, accounting for the effects of mass limitation and transport, we find a simple and general scaling of the adsorption parameters with the molecular size.

Arabidopsis peroxidase-catalyzed copolymerization of coniferyl and sinapyl alcohols: kinetics of an endwise process.

Science.gov (United States)

Demont-Caulet, Nathalie; Lapierre, Catherine; Jouanin, Lise; Baumberger, Stéphanie; Méchin, Valérie

2010-10-01

In order to determine the mechanism of the earlier copolymerization steps of two main lignin precursors, sinapyl (S) alcohol and coniferyl (G) alcohol, microscale in vitro oxidations were carried out with a PRX34 Arabidopsis thaliana peroxidase in the presence of H(2)O(2). This plant peroxidase was found to have an in vitro polymerization activity similar to the commonly used horseradish peroxidase. The selected polymerization conditions lead to a bulk polymerization mechanism when G alcohol was the only phenolic substrate available. In the same conditions, the presence of S alcohol at a 50/50 S/G molar ratio turned this bulk mechanism into an endwise one. A kinetics monitoring (size-exclusion chromatography and liquid chromatography-mass spectrometry) of the different species formed during the first 24h oxidation of the S/G mixture allowed sequencing the bondings responsible for oligomerization. Whereas G homodimers and GS heterodimers exhibit low reactivity, the SS pinoresinol structure act as a nucleating site of the polymerization through an endwise process. This study is particularly relevant to understand the impact of S units on lignin structure in plants and to identify the key step at which this structure is programmed. Copyright © 2010 Elsevier Ltd. All rights reserved.

Decohesion Kinetics in Polymer Organic Solar Cells

KAUST Repository

Bruner, Christopher; Novoa, Fernando; Dupont, Stephanie; Dauskardt, Reinhold

2014-01-01

© 2014 American Chemical Society. We investigate the role of molecular weight (MW) of the photoactive polymer poly(3-hexylthiophene) (P3HT) on the temperature-dependent decohesion kinetics of bulk heterojunction (BHJ) organic solar cells (OSCs). The MW of P3HT has been directly correlated to its carrier field effect mobilities and the ambient temperature also affects OSC in-service performance and P3HT arrangement within the BHJ layer. Under inert conditions, time-dependent decohesion readily occurs within the BHJ layer at loads well below its fracture resistance. We observe that by increasing the MW of P3HT, greater resistance to decohesion is achieved. However, failure consistently occurs within the BHJ layer representing the weakest layer within the device stack. Additionally, it was found that at temperatures below the glass transition temperature (∼41-45 °C), decohesion was characterized by brittle failure via molecular bond rupture. Above the glass transition temperature, decohesion growth occurred by a viscoelastic process in the BHJ layer, leading to a significant degree of viscoelastic deformation. We develop a viscoelastic model based on molecular relaxation to describe the resulting behavior. The study has implications for OSC long-term reliability and device performance, which are important for OSC production and implementation.

Decohesion Kinetics in Polymer Organic Solar Cells

KAUST Repository

Bruner, Christopher

2014-12-10

© 2014 American Chemical Society. We investigate the role of molecular weight (MW) of the photoactive polymer poly(3-hexylthiophene) (P3HT) on the temperature-dependent decohesion kinetics of bulk heterojunction (BHJ) organic solar cells (OSCs). The MW of P3HT has been directly correlated to its carrier field effect mobilities and the ambient temperature also affects OSC in-service performance and P3HT arrangement within the BHJ layer. Under inert conditions, time-dependent decohesion readily occurs within the BHJ layer at loads well below its fracture resistance. We observe that by increasing the MW of P3HT, greater resistance to decohesion is achieved. However, failure consistently occurs within the BHJ layer representing the weakest layer within the device stack. Additionally, it was found that at temperatures below the glass transition temperature (∼41-45 °C), decohesion was characterized by brittle failure via molecular bond rupture. Above the glass transition temperature, decohesion growth occurred by a viscoelastic process in the BHJ layer, leading to a significant degree of viscoelastic deformation. We develop a viscoelastic model based on molecular relaxation to describe the resulting behavior. The study has implications for OSC long-term reliability and device performance, which are important for OSC production and implementation.

Decohesion kinetics in polymer organic solar cells.

Science.gov (United States)

Bruner, Christopher; Novoa, Fernando; Dupont, Stephanie; Dauskardt, Reinhold

2014-12-10

We investigate the role of molecular weight (MW) of the photoactive polymer poly(3-hexylthiophene) (P3HT) on the temperature-dependent decohesion kinetics of bulk heterojunction (BHJ) organic solar cells (OSCs). The MW of P3HT has been directly correlated to its carrier field effect mobilities and the ambient temperature also affects OSC in-service performance and P3HT arrangement within the BHJ layer. Under inert conditions, time-dependent decohesion readily occurs within the BHJ layer at loads well below its fracture resistance. We observe that by increasing the MW of P3HT, greater resistance to decohesion is achieved. However, failure consistently occurs within the BHJ layer representing the weakest layer within the device stack. Additionally, it was found that at temperatures below the glass transition temperature (∼41-45 °C), decohesion was characterized by brittle failure via molecular bond rupture. Above the glass transition temperature, decohesion growth occurred by a viscoelastic process in the BHJ layer, leading to a significant degree of viscoelastic deformation. We develop a viscoelastic model based on molecular relaxation to describe the resulting behavior. The study has implications for OSC long-term reliability and device performance, which are important for OSC production and implementation.

Adsorption analysis equilibria and kinetics

CERN Document Server

Do, Duong D

1998-01-01

This book covers topics of equilibria and kinetics of adsorption in porous media. Fundamental equilibria and kinetics are dealt with for homogeneous as well as heterogeneous particles. Five chapters of the book deal with equilibria and eight chapters deal with kinetics. Single component as well as multicomponent systems are discussed. In kinetics analysis, we deal with the various mass transport processes and their interactions inside a porous particle. Conventional approaches as well as the new approach using Maxwell-Stefan equations are presented. Various methods to measure diffusivity, such

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

Science.gov (United States)

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

2018-04-01

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

The 2-nd Conference on Isotopic and Molecular Processes. Abstracts

International Nuclear Information System (INIS)

Bogdan, Mircea

2001-01-01

The proceedings of the 2-nd Conference on Isotopic and Molecular Processes held on September 27 - 29, 2001 in Cluj - Napoca, Romania, contains contributions presented as: 11 plenary lectures, 24 oral presentations and 103 posters in two sections, namely, isotopic processes and molecular processes. The main topics treated in this conference were isotope production, separation and enrichment as well as stable isotope applications. Also, studies on isotope effects in different fields are reported. Besides reports on isotope effects, exchange and separation, new methods of preparation and labelling compounds used particularly in nuclear medicine are presented. Environmental studies by means of stable isotope and radon monitoring are described. Applications of radiation effects and different nuclear methods in medicine are also addressed

Kinetics of Slurry Phase Fischer-Tropsch Synthesis

Energy Technology Data Exchange (ETDEWEB)

Dragomir B. Bukur; Gilbert F. Froment; Tomasz Olewski; Lech Nowicki; Madhav Nayapati

2006-12-31

The overall objective of this project is to develop a comprehensive kinetic model for slurry-phase Fischer-Tropsch synthesis (FTS) employing iron-based catalysts. This model will be validated with experimental data obtained in a stirred-tank slurry reactor (STSR) over a wide range of process conditions. Three STSR tests of the Ruhrchemie LP 33/81 catalyst were conducted to collect data on catalyst activity and selectivity under 25 different sets of process conditions. The observed decrease in 1-olefin content and increase in 2-olefin and n-paraffin contents with the increase in conversion are consistent with a concept that 1-olefins participate in secondary reactions (e.g. 1-olefin hydrogenation, isomerization and readsorption), whereas 2-olefins and n-paraffins are formed in these reactions. Carbon number product distribution showed an increase in chain growth probability with increase in chain length. Vapor-liquid equilibrium calculations were made to check validity of the assumption that the gas and liquid phases are in equilibrium during FTS in the STSR. Calculated vapor phase compositions were in excellent agreement with experimental values from the STSR under reaction conditions. Discrepancies between the calculated and experimental values for the liquid-phase composition (for some of the experimental data) are ascribed to experimental errors in the amount of wax collected from the reactor, and the relative amounts of hydrocarbon wax and Durasyn 164 oil (start-up fluid) in the liquid samples. Kinetic parameters of four kinetic models (Lox and Froment, 1993b; Yang et al., 2003; Van der Laan and Beenackers, 1998, 1999; and an extended kinetic model of Van der Laan and Beenackers) were estimated from experimental data in the STSR tests. Two of these kinetic models (Lox and Froment, 1993b; Yang et al., 2003) can predict a complete product distribution (inorganic species and hydrocarbons), whereas the kinetic model of Van der Laan and Beenackers (1998, 1999) can

Kinetics of Slurry Phase Fischer-Tropsch Synthesis

International Nuclear Information System (INIS)

Dragomir B. Bukur; Gilbert F. Froment; Tomasz Olewski; Lech Nowicki; Madhav Nayapati

2006-01-01

The overall objective of this project is to develop a comprehensive kinetic model for slurry-phase Fischer-Tropsch synthesis (FTS) employing iron-based catalysts. This model will be validated with experimental data obtained in a stirred-tank slurry reactor (STSR) over a wide range of process conditions. Three STSR tests of the Ruhrchemie LP 33/81 catalyst were conducted to collect data on catalyst activity and selectivity under 25 different sets of process conditions. The observed decrease in 1-olefin content and increase in 2-olefin and n-paraffin contents with the increase in conversion are consistent with a concept that 1-olefins participate in secondary reactions (e.g. 1-olefin hydrogenation, isomerization and readsorption), whereas 2-olefins and n-paraffins are formed in these reactions. Carbon number product distribution showed an increase in chain growth probability with increase in chain length. Vapor-liquid equilibrium calculations were made to check validity of the assumption that the gas and liquid phases are in equilibrium during FTS in the STSR. Calculated vapor phase compositions were in excellent agreement with experimental values from the STSR under reaction conditions. Discrepancies between the calculated and experimental values for the liquid-phase composition (for some of the experimental data) are ascribed to experimental errors in the amount of wax collected from the reactor, and the relative amounts of hydrocarbon wax and Durasyn 164 oil (start-up fluid) in the liquid samples. Kinetic parameters of four kinetic models (Lox and Froment, 1993b; Yang et al., 2003; Van der Laan and Beenackers, 1998, 1999; and an extended kinetic model of Van der Laan and Beenackers) were estimated from experimental data in the STSR tests. Two of these kinetic models (Lox and Froment, 1993b; Yang et al., 2003) can predict a complete product distribution (inorganic species and hydrocarbons), whereas the kinetic model of Van der Laan and Beenackers (1998, 1999) can

Early stage oxynitridation process of Si(001) surface by NO gas: Reactive molecular dynamics simulation study

International Nuclear Information System (INIS)

Cao, Haining; Kim, Seungchul; Lee, Kwang-Ryeol; Srivastava, Pooja; Choi, Keunsu

2016-01-01

Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathway for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.

Early stage oxynitridation process of Si(001) surface by NO gas: Reactive molecular dynamics simulation study

Energy Technology Data Exchange (ETDEWEB)

Cao, Haining; Kim, Seungchul; Lee, Kwang-Ryeol, E-mail: krlee@kist.re.kr [Computational Science Research Center, Korea Institute of Science and Technology, 5, Hwarangno 14-gil, Seongbuk-gu, Seoul 02792 (Korea, Republic of); Department of Nanomaterial Science and Technology, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113 (Korea, Republic of); Srivastava, Pooja; Choi, Keunsu [Computational Science Research Center, Korea Institute of Science and Technology, 5, Hwarangno 14-gil, Seongbuk-gu, Seoul 02792 (Korea, Republic of)

2016-03-28

Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathway for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.

Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes.

Science.gov (United States)

Bonachéra, Fanny; Parent, Benjamin; Barbosa, Frédérique; Froloff, Nicolas; Horvath, Dragos

2006-01-01

This paper introduces a novel molecular description--topological (2D) fuzzy pharmacophore triplets, 2D-FPT--using the number of interposed bonds as the measure of separation between the atoms representing pharmacophore types (hydrophobic, aromatic, hydrogen-bond donor and acceptor, cation, and anion). 2D-FPT features three key improvements with respect to the state-of-the-art pharmacophore fingerprints: (1) The first key novelty is fuzzy mapping of molecular triplets onto the basis set of pharmacophore triplets: unlike in the binary scheme where an atom triplet is set to highlight the bit of a single, best-matching basis triplet, the herein-defined fuzzy approach allows for gradual mapping of each atom triplet onto several related basis triplets, thus minimizing binary classification artifacts. (2) The second innovation is proteolytic equilibrium dependence, by explicitly considering all of the conjugated acids and bases (microspecies). 2D-FPTs are concentration-weighted (as predicted at pH=7.4) averages of microspecies fingerprints. Therefore, small structural modifications, not affecting the overall pharmacophore pattern (in the sense of classical rule-based assignment), but nevertheless triggering a pKa shift, will have a major impact on 2D-FPT. Pairs of almost identical compounds with significantly differing activities ("activity cliffs" in classical descriptor spaces) were in many cases predictable by 2D-FPT. (3) The third innovation is a new similarity scoring formula, acknowledging that the simultaneous absence of a triplet in two molecules is a less-constraining indicator of similarity than its simultaneous presence. It displays excellent neighborhood behavior, outperforming 2D or 3D two-point pharmacophore descriptors or chemical fingerprints. The 2D-FPT calculator was developed using the chemoinformatics toolkit of ChemAxon (www.chemaxon.com).

PHOTOCHEMICAL HEATING OF DENSE MOLECULAR GAS

Energy Technology Data Exchange (ETDEWEB)

Glassgold, A. E. [Astronomy Department, University of California, Berkeley, CA 94720 (United States); Najita, J. R. [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States)

2015-09-10

Photochemical heating is analyzed with an emphasis on the heating generated by chemical reactions initiated by the products of photodissociation and photoionization. The immediate products are slowed down by collisions with the ambient gas and then heat the gas. In addition to this direct process, heating is also produced by the subsequent chemical reactions initiated by these products. Some of this chemical heating comes from the kinetic energy of the reaction products and the rest from collisional de-excitation of the product atoms and molecules. In considering dense gas dominated by molecular hydrogen, we find that the chemical heating is sometimes as large, if not much larger than, the direct heating. In very dense gas, the total photochemical heating approaches 10 eV per photodissociation (or photoionization), competitive with other ways of heating molecular gas.

Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes

Energy Technology Data Exchange (ETDEWEB)

García-Gen, Santiago [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Sousbie, Philippe; Rangaraj, Ganesh [INRA, UR50, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne F-11100 (France); Lema, Juan M. [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Rodríguez, Jorge, E-mail: jrodriguez@masdar.ac.ae [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, PO Box 54224 Abu Dhabi (United Arab Emirates); Steyer, Jean-Philippe; Torrijos, Michel [INRA, UR50, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne F-11100 (France)

2015-01-15

Highlights: • Fractionation of solid wastes into readily and slowly biodegradable fractions. • Kinetic coefficients estimation from mono-digestion batch assays. • Validation of kinetic coefficients with a co-digestion continuous experiment. • Simulation of batch and continuous experiments with an ADM1-based model. - Abstract: A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowly biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 g VS/L d. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes.

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

Directory of Open Access Journals (Sweden)

Moye Wang

2016-04-01

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

Determination of molecular-ion structures through the use of accelerated beams

International Nuclear Information System (INIS)

Gemmell, D.S.

1987-01-01

In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs

Kinetics of DNA tile dimerization.

Science.gov (United States)

Jiang, Shuoxing; Yan, Hao; Liu, Yan

2014-06-24

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

Prediction of vapour-liquid equilibria for the kinetic study of processes based on synthesis gas

Energy Technology Data Exchange (ETDEWEB)

Di Serio, M.; Tesser, R.; Cozzolino, M.; Santacesaria, E. [Naples Univ., Napoli (Italy). Dept. of Chemistry

2006-07-01

Syngas is normally used in the production of a broad range of chemicals and fuels. In many of these processes multiphase reactors, gas-liquid or gas-liquid-solid are used. Kinetic studies in multiphase systems are often complicated by the non-ideal behaviour of reagents and/or products that are consistently partitioned between the liquid and the vapour phase. Moreover, as often kinetic data are collected in batch conditions for the liquid phase, activity coefficients of the partitioned components can consistently change during the time as a consequence of changing the composition of the reaction mixture. Therefore, it is necessary, in these cases, to known the vapor-liquid equilibria (VLE) in order to collect and to interpret correctly the kinetic data. The description of phase equilibria, at high pressures, is usually performed by means of an EOS (Equation of State) allowing the calculation of fugacity coefficients, for each component, in both phases and determining the partition coefficients but the EOS approach involves the experimental determination of the interaction parameters for all the possible binary system of the mixture. For multicomponent mixtures a complete experimental determination of vapourliquid equilibria is very hard, also considering the high pressure and temperatures used. Some predictive group contribution methods have been recently developed. In this paper, we will describe in detail the application of these methods to the methanol homologation, as an example, with the scope of determining more reliable kinetic parameters for this reaction. (orig.)

Kinetics of the reactions of hydrated electrons with metal complexes

International Nuclear Information System (INIS)

Korsse, J.

1983-01-01

The reactivity of the hydrated electron towards metal complexes is considered. Experiments are described involving metal EDTA and similar complexes. The metal ions studied are mainly Ni 2+ , Co 2+ and Cu 2+ . Rates of the reactions of the complexes with e - (aq) were measured using the pulse radiolysis technique. It is shown that the reactions of e - (aq) with the copper complexes display unusually small kinetic salt effects. The results suggest long-range electron transfer by tunneling. A tunneling model is presented and the experimental results are discussed in terms of this model. Results of approximate molecular orbital calculations of some redox potentials are given, for EDTA chelates as well as for series of hexacyano and hexaquo complexes. Finally, equilibrium constants for the formation of ternary complexes are reported. (Auth./G.J.P.)

Kinetics of the nitridation of dysprosium during mechanochemical processing

Energy Technology Data Exchange (ETDEWEB)

Alanko, Gordon A.; Osterberg, Daniel D.; Jaques, Brian J. [Department of Materials Science and Engineering, College of Engineering, Boise State University, 1910 University Drive, Boise, ID 83725 (United States); Hurley, Michael F. [Department of Materials Science and Engineering, College of Engineering, Boise State University, 1910 University Drive, Boise, ID 83725 (United States); Center for Advanced Energy Studies, 995 University Boulevard, Idaho Falls, ID 83401 (United States); Butt, Darryl P., E-mail: darrylbutt@boisestate.edu [Department of Materials Science and Engineering, College of Engineering, Boise State University, 1910 University Drive, Boise, ID 83725 (United States); Center for Advanced Energy Studies, 995 University Boulevard, Idaho Falls, ID 83401 (United States)

2015-01-25

Highlights: • DyN was mechanochemically synthesized by milling pure metal under nitrogen. • Temperature and pressure were monitored to investigate reaction progress. • The effects of metal adhered to media on the impact energetics was measured. • The reactive milling kinetics are described in terms of reactive surface formation. - Abstract: Dysprosium nitride was synthesized by the reactive milling of the rare earth metal under 400 kPa nitrogen gas in a planetary ball mill. The nitrogen consumption rate was calculated from in situ temperature and pressure measurements to find the reaction extent as a function of milling time at milling speeds from 350 to 650 rpm. The results are analyzed in terms of a fundamental milling dynamics model in which the input milling energy is the primary driving force for reaction and the rate limiting step of the nitridation kinetics is the formation of chemically active surfaces. The model differs from traditional gas–solid reactions which are often limited by diffusion of a species through a surface layer or by dissociation of the gas molecule. These results give fresh insight into reactive gas–solid milling kinetics.

A kinetic Monte Carlo simulation method of van der Waals epitaxy for atomistic nucleation-growth processes of transition metal dichalcogenides.

Science.gov (United States)

Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

2017-06-07

Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.

Derivation of kinetic coefficients by atomistic methods for studying defect behavior in Mo

International Nuclear Information System (INIS)

Insepov, Z.; Rest, J.; Yacout, A.M.; Kuksin, A.Yu.; Norman, G.E.; Stegailov, V.V.; Starikov, S.V.; Yanilkin, A.V.

2012-01-01

Highlights: ► A multiscale concept couples molecular dynamics (MD) with ab initio and kinetic rate theory. ► Evolution of a system of self-interstitial atoms and vacancies in Mo is studied by MD. ► Formation of di-SIA clusters and SIA–vacancy recombination is analyzed. ► 1D diffusion of self-interstitials at various temperature and defect concentrations were studied. ► This paper provides a powerful predictive tool for simulating irradiation of nuclear materials. - Abstract: A multiscale concept for irradiated materials simulation is formulated based on coupling molecular dynamics simulations (MD) where the potential was obtained from ab initio data of energies of the basic defect structures, with kinetic mesoscale models. The evolution of a system containing self-interstitial atoms (SIAs) and vacancies in crystalline molybdenum is investigated by means of MD. The kinetics of formation of di-SIA clusters and SIA–vacancy recombination is analyzed via approaches used in the kinetic theory of radiation ageing. The effects of 1D diffusion of SIAs, temperature, and defect concentrations on the reaction rates are also studied. This approach can validate both the kinetic mechanisms and the appropriate kinetic coefficients, offering the potential to significantly reduce the uncertainty of the kinetic methodology and providing a powerful predictive tool for simulating irradiation behavior of nuclear materials.

Kinetics of the Leaching Process of an Australian Gibbsitic Bauxite by Hydrochloric Acid

Directory of Open Access Journals (Sweden)

Aichun Zhao

2016-01-01

Full Text Available Gibbsitic bauxite from Australia was leached by hydrochloric acid in this work. Analysis on kinetics for the extraction of Al2O3 was quantitatively studied. It was concluded that the hydrochloric acid leaching process of gibbsitic bauxite was controlled by chemical reaction. Moreover, the mechanism for the dissolution followed the equation, ln⁡k=39.44-1.66×104(1/T, with an apparent activation energy of 137.90 kJ/mol, according to the equation of k=Ae-Ea/RT. This work aims to provide a good theory support for the process control by using a new method of alumina production from the low grade bauxite.

Analysis of dechlorination kinetics of chlorinated aliphatic hydrocarbons by Fe(II) in cement slurries

Energy Technology Data Exchange (ETDEWEB)

Jung, Bahngmi [Department of Earth and Environmental Sciences, Wright State University, Dayton, OH 45435-0001 (United States)], E-mail: jung.bahngmi@gmail.com; Batchelor, Bill [Department of Civil Engineering, Texas A and M University, College Station, TX 77843-3136 (United States)

2008-03-21

Degradative solidification/stabilization with ferrous iron (DS/S-Fe(II)) has been found to be effective in degrading a number of chlorinated aliphatic hydrocarbons including 1,1,1-trichloroethane (1,1,1-TCA), 1,1,2,2-tetrachloroethane (1,1,2,2-TeCA), tetrachloroethylene (PCE), trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), vinyl chloride (VC), carbon tetrachloride (CT) and chloroform (CF). Previous studies have characterized degradation kinetics in DS/S-Fe(II) systems as affected by Fe(II) dose, pH and initial target organic concentration. The goal of this study is to investigate the importance of various chemical properties on degradation kinetics of DS/S-Fe(II). This was accomplished by first measuring rate constants for degradation of 1,1,1-TCA, 1,1,2,2-TeCA and 1,2-dichloroethane (1,2-DCA) in individual batch experiments. Rate constants developed in these experiments and those obtained from the literature were related to thermodynamic parameters including one-electron reduction potential, two-electron reduction potential, bond dissociation energy and lowest unoccupied molecular orbital energies. Degradation kinetics by Fe(II) in cement slurries were generally represented by a pseudo-first-order rate law. The results showed that the rate constants for chlorinated methanes (e.g. CT, CF) and chlorinated ethanes (e.g. 1,1,1-TCA) were higher than those for chlorinated ethylenes (e.g. PCE, TCE, 1,1-DCE and VC) under similar experimental conditions. The log of the pseudo-first-order rate constant (k) was found to correlate better with lowest unoccupied molecular orbital energies (E{sub LUMO}) (R{sup 2} = 0.874) than with other thermodynamic parameter descriptors.

Thermodynamic-state and kinetic-process dependent dual ferromagnetic states in high-Si content FeMn(PSi) alloys

International Nuclear Information System (INIS)

Li, Guijiang; Eriksson, Olle; Johansson, Börje; Vitos, Levente

2015-01-01

We have found that thermodynamic state and kinetic process co-determine the dual ferromagnetic (FM) orders in high-Si content FeMnP 1−x Si x (0.25 < x < 0.5). Alloys undergoing high temperature annealing and quenching process prefer a high magnetic moment FM state in a chemically partial disordered structure with low c/a ratio. This mechanism is suggested to be responsible for the often discussed virgin effect as well. A chemically ordered structure obtained by a slow cooling process from a relatively low annealing temperature and the increase in Si content stabilize a metastable lattice with high c/a ratio and FM order with low magnetic moment. The non-simultaneity of the magnetic and structural transitions can be responsible for the occurrence of FM state in the high c/a range. Thus, a c/a ratio that changes from high to low is physically plausible to stabilize the metastable FM order at low temperature. Our theoretical observations indicate that suitable thermodynamic state and kinetic diffusion process is crucial for optimizing magnetocaloric properties and exploring feasible magnetocaloric materials

Application potential of ATR-FT/IR molecular spectroscopy in animal nutrition: revelation of protein molecular structures of canola meal and presscake, as affected by heat-processing methods, in relationship with their protein digestive behavior and utilization for dairy cattle.

Science.gov (United States)

Theodoridou, Katerina; Yu, Peiqiang

2013-06-12

Protein quality relies not only on total protein but also on protein inherent structures. The most commonly occurring protein secondary structures (α-helix and β-sheet) may influence protein quality, nutrient utilization, and digestive behavior. The objectives of this study were to reveal the protein molecular structures of canola meal (yellow and brown) and presscake as affected by the heat-processing methods and to investigate the relationship between structure changes and protein rumen degradations kinetics, estimated protein intestinal digestibility, degraded protein balance, and metabolizable protein. Heat-processing conditions resulted in a higher value for α-helix and β-sheet for brown canola presscake compared to brown canola meal. The multivariate molecular spectral analyses (PCA, CLA) showed that there were significant molecular structural differences in the protein amide I and II fingerprint region (ca. 1700-1480 cm(-1)) between the brown canola meal and presscake. The in situ degradation parameters, amide I and II, and α-helix to β-sheet ratio (R_a_β) were positively correlated with the degradable fraction and the degradation rate. Modeling results showed that α-helix was positively correlated with the truly absorbed rumen synthesized microbial protein in the small intestine when using both the Dutch DVE/OEB system and the NRC-2001 model. Concerning the protein profiles, R_a_β was a better predictor for crude protein (79%) and for neutral detergent insoluble crude protein (68%). In conclusion, ATR-FT/IR molecular spectroscopy may be used to rapidly characterize feed structures at the molecular level and also as a potential predictor of feed functionality, digestive behavior, and nutrient utilization of canola feed.

Bibliography of atomic and molecular processes. Volume 1, 1978-1981

International Nuclear Information System (INIS)

Barnett, C.F.; Crandall, D.H.; Farmer, B.J.

1982-10-01

This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

Bibliography of atomic and molecular processes. Volume 1, 1978-1981

Energy Technology Data Exchange (ETDEWEB)

Barnett, C.F.; Crandall, D.H.; Farmer, B.J. (comps.)

1982-10-01

This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

Non-isothermal kinetic studies on co-processing of olive residue and polypropylene

International Nuclear Information System (INIS)

Aboulkas, A.; El Harfi, K.; El Bouadili, A.

2008-01-01

Co-processing of olive residue with polypropylene was performed in a thermogravimetric analyzer (TGA) reaction system in a nitrogen atmosphere with a view to comparing the process of the mixture with those of the individual components. Experiments were conducted at different heating rates of 2, 10, 20 and 50 K min -1 in the temperature range of 300-975 K based on the results obtained, three thermal stages were identified during the thermal degradation. The first two were dominated by olive residue pyrolysis, while the third was linked to polypropylene pyrolysis, which occurred at much higher temperatures. Discrepancies between the experimental and calculated TG/DTG profiles were considered as a measurement of the extent of interactions occurring on co-pyrolysis. The maximum degradation temperature of each component in the mixture was higher than those of the individual components alone; thus, an increase in thermal stability was expected. The kinetic processing of thermogravimetric data was conducted using the Friedman method

Giant molecular cloud scaling relations: the role of the cloud definition

Science.gov (United States)