WorldWideScience

Sample records for modeling molecular processes

  1. 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.

  2. Molecular Modeling

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

  3. Molecular modeling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-01-01

    Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

  4. Molecular Modelling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-12-01

    Full Text Available

    The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important
    tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and
    the exponential growth of the knowledge of protein structures have made it possible for organic compounds to tailored to
    decrease harmful side effects and increase the potency. This article provides a detailed description of the techniques
    employed in molecular modeling. Molecular modelling is a rapidly developing discipline, and has been supported from
    the dramatic improvements in computer hardware and software in recent years.

  5. Cellular Automata Modelling of Photo-Induced Oxidation Processes in Molecularly Doped Polymers

    Directory of Open Access Journals (Sweden)

    David M. Goldie

    2016-11-01

    Full Text Available The possibility of employing cellular automata (CA to model photo-induced oxidation processes in molecularly doped polymers is explored. It is demonstrated that the oxidation dynamics generated using CA models exhibit stretched-exponential behavior. This dynamical characteristic is in general agreement with an alternative analysis conducted using standard rate equations provided the molecular doping levels are sufficiently low to prohibit the presence of safe-sites which are impenetrable to dissolved oxygen. The CA models therefore offer the advantage of exploring the effect of dopant agglomeration which is difficult to assess from standard rate equation solutions. The influence of UV-induced bleaching or darkening upon the resulting oxidation dynamics may also be easily incorporated into the CA models and these optical effects are investigated for various photo-oxidation product scenarios. Output from the CA models is evaluated for experimental photo-oxidation data obtained from a series of hydrazone-doped polymers.

  6. Mathematical models of non-linear phenomena, processes and systems: from molecular scale to planetary atmosphere

    CERN Document Server

    2013-01-01

    This book consists of twenty seven chapters, which can be divided into three large categories: articles with the focus on the mathematical treatment of non-linear problems, including the methodologies, algorithms and properties of analytical and numerical solutions to particular non-linear problems; theoretical and computational studies dedicated to the physics and chemistry of non-linear micro-and nano-scale systems, including molecular clusters, nano-particles and nano-composites; and, papers focused on non-linear processes in medico-biological systems, including mathematical models of ferments, amino acids, blood fluids and polynucleic chains.

  7. WE-DE-202-03: Modeling of Biological Processes - What Happens After Early Molecular Damage?

    International Nuclear Information System (INIS)

    McMahon, S.

    2016-01-01

    Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

  8. WE-DE-202-03: Modeling of Biological Processes - What Happens After Early Molecular Damage?

    Energy Technology Data Exchange (ETDEWEB)

    McMahon, S. [Massachusetts General Hospital and Harvard Medical School (United States)

    2016-06-15

    Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

  9. 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.

  10. Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo.

    Science.gov (United States)

    Parsons, Neal; Levin, Deborah A; van Duin, Adri C T; Zhu, Tong

    2014-12-21

    The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N2(Σg+1)-N2(Σg+1) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections.

  11. Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo

    International Nuclear Information System (INIS)

    Parsons, Neal; Levin, Deborah A.; Duin, Adri C. T. van; Zhu, Tong

    2014-01-01

    The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N 2 ( 1 Σ g + )-N 2 ( 1 Σ g + ) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections

  12. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.

    Science.gov (United States)

    Quesne, Matthew G; Borowski, Tomasz; de Visser, Sam P

    2016-02-18

    Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. 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

  14. 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.

  15. Mathematical model and calculation algorithm of micro and meso levels of separation process of gaseous mixtures in molecular sieves

    Energy Technology Data Exchange (ETDEWEB)

    Umarova, Zhanat; Botayeva, Saule; Yegenova, Aliya; Usenova, Aisaule [South Kazakhstan State University, 5, Tauke Khan Avenue, 160012 Shymkent (Kazakhstan)

    2015-05-15

    In the given article, the main thermodynamic aspects of the issue of modeling diffusion transfer in molecular sieves have been formulated. Dissipation function is used as a basic notion. The differential equation, connecting volume flow with the change of the concentration of catchable component has been derived. As a result, the expression for changing the concentration of the catchable component and the coefficient of membrane detecting has been received. As well, the system approach to describing the process of gases separation in ultra porous membranes has been realized and micro and meso-levels of mathematical modeling have been distinguished. The non-ideality of the shared system is primarily taken into consideration at the micro-level and the departure from the diffusion law of Fick has been taken into account. The calculation method of selectivity considering fractal structure of membranes has been developed at the meso level. The calculation algorithm and its software implementation have been suggested.

  16. Mathematical model and calculation algorithm of micro and meso levels of separation process of gaseous mixtures in molecular sieves

    International Nuclear Information System (INIS)

    Umarova, Zhanat; Botayeva, Saule; Yegenova, Aliya; Usenova, Aisaule

    2015-01-01

    In the given article, the main thermodynamic aspects of the issue of modeling diffusion transfer in molecular sieves have been formulated. Dissipation function is used as a basic notion. The differential equation, connecting volume flow with the change of the concentration of catchable component has been derived. As a result, the expression for changing the concentration of the catchable component and the coefficient of membrane detecting has been received. As well, the system approach to describing the process of gases separation in ultra porous membranes has been realized and micro and meso-levels of mathematical modeling have been distinguished. The non-ideality of the shared system is primarily taken into consideration at the micro-level and the departure from the diffusion law of Fick has been taken into account. The calculation method of selectivity considering fractal structure of membranes has been developed at the meso level. The calculation algorithm and its software implementation have been suggested

  17. A Model of the Molecular Aggregate Processes of Hemoglobin S. Absence of Cristallization

    Directory of Open Access Journals (Sweden)

    Carlos Cabal-Mirabal

    2008-01-01

    Full Text Available Aquí se propone un mecanismo y un modelo matemático. el modelo postula la existencia de microtúbulos defectivos formados por deoxihemoglobina S y oxihemoglobina S, y explica la dependencia de la polimerización de la concentración de hemoglobina, la temperatura y la presión parcial de oxígeno. El análisis hace énfasis en la polimerización de hemoglobina S en la ausencia de cristalización. La acción de otras clases de hemoglobinas en la formación molecular agregada puede ser explicada.

  18. Pressure effects on martensitic transformation under quenching process in a molecular dynamics model of NiAl alloy

    International Nuclear Information System (INIS)

    Kazanc, S.; Ozgen, S.; Adiguzel, O.

    2003-01-01

    The solid-solid phase transitions in NiAl alloys occur by the temperature changes and application of a pressure on the system. Both types of transitions are called martensitic transformation and have displacive and thermoelastic characters. Pressure effects on thermoelastic transformation in Ni 62.5 Al 37.5 alloy model have been studied by means of molecular dynamics method proposed by Parrinello-Rahman. Interaction forces between atoms in the model system were calculated by Lennard-Jones potential energy function. Thermodynamics and structural analysis of the martensitic transformations under hydrostatic pressure during the quenching processes have been performed. The simulation runs have been carried out in different hydrostatic pressures changing from zero to 40.65 GPa during the quenching process of the model alloy. At the zero and nonzero pressures, the system with B2-type ordered structure undergoes the product phase with L1 0 -type ordered structure by Bain distortion in the first step of martensitic transformation under the quenching process. The increase in hydrostatic pressure causes decrease in the formation time of the product phase, and twin-like lattice distortion is observed in low temperature L1 0 phase

  19. Open source molecular modeling.

    Science.gov (United States)

    Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

    2016-09-01

    The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  20. 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

  1. Molecular modeling of directed self-assembly of block copolymers: Fundamental studies of processing conditions and evolutionary pattern design

    Science.gov (United States)

    Khaira, Gurdaman Singh

    Rapid progress in the semi-conductor industry has pushed for smaller feature sizes on integrated electronic circuits. Current photo-lithographic techniques for nanofabrication have reached their technical limit and are problematic when printing features small enough to meet future industrial requirements. "Bottom-up'' techniques, such as the directed self-assembly (DSA) of block copolymers (BCP), are the primary contenders to compliment current "top-down'' photo-lithography ones. For industrial requirements, the defect density from DSA needs to be less than 1 defect per 10 cm by 10 cm. Knowledge of both material synthesis and the thermodynamics of the self-assembly process are required before optimal operating conditions can be found to produce results adequate for industry. The work present in this thesis is divided into three chapters, each discussing various aspects of DSA as studied via a molecular model that contains the essential physics of BCP self-assembly. Though there are various types of guiding fields that can be used to direct BCPs over large wafer areas with minimum defects, this study focuses only on chemically patterned substrates. The first chapter addresses optimal pattern design by describing a framework where molecular simulations of various complexities are coupled with an advanced optimization technique to find a pattern that directs a target morphology. It demonstrates the first ever study where BCP self-assembly on a patterned substrate is optimized using a three-dimensional description of the block-copolymers. For problems pertaining to DSA, the methodology is shown to converge much faster than the traditional random search approach. The second chapter discusses the metrology of BCP thin films using TEM tomography and X-ray scattering techniques, such as CDSAXS and GISAXS. X-ray scattering has the advantage of being able to quickly probe the average structure of BCP morphologies over large wafer areas; however, deducing the BCP morphology

  2. Atomic and molecular collision processes

    International Nuclear Information System (INIS)

    Norcross, D.W.

    1991-01-01

    530Accomplishments during the course of a 44-month program of code development and high precision calculations for electron collisions with atoms, atomic ions, and molecules are summarized. In electron-atom and -ion collisions, we were primarily concerned with the fundamental physics of the process that controls excitation in high temperature plasmas. In the molecular work, we pursued the development of techniques for accurate calculations of ro-vibrational excitation of polyatomic molecules, to the modeling of gas-phase laser systems. Highlights from the seven technical paper published as a result of this contract include: The resolution of a long history of unexplained anomalies and experimental/theoretical discrepancies by a demonstration that the Coulomb phase must be included in scattering amplitudes for electron-ion collisions. Definitive close-coupling calculations of cross sections for electron impact excitation of Be + , using a very elaborate expansion for the collision system and inclusion of both one- and two-body terms for the effect of core polarization. Detailed state-of-the-art calculations for electron-impact excitation of the sodium-like ion A ell 2+ that included core-polarization interactions, and which also produced new data on bound-state energy levels for the magnesium-like ion A ell + and oscillator strengths for A ell 2+ . Partial cross sections for excitation of the 3p level of sodium at energies just above threshold calculated using a four-state close-coupling approach, including both total cross sections and those for excitation as a function of the change in the spin and orbital angular momentum projection quantum numbers of the target electron. Generalization of our electron-molecule scattering code to carry out full vibrational close-coupling calculations with an exact treatment of exchange and with a parameter-free representation of correlation and polarization interactions, and application to HF and H 2

  3. 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

  4. Multi-Scale Modelling of Deformation and Fracture in a Biomimetic Apatite-Protein Composite: Molecular-Scale Processes Lead to Resilience at the μm-Scale.

    Directory of Open Access Journals (Sweden)

    Dirk Zahn

    Full Text Available Fracture mechanisms of an enamel-like hydroxyapatite-collagen composite model are elaborated by means of molecular and coarse-grained dynamics simulation. Using fully atomistic models, we uncover molecular-scale plastic deformation and fracture processes initiated at the organic-inorganic interface. Furthermore, coarse-grained models are developed to investigate fracture patterns at the μm-scale. At the meso-scale, micro-fractures are shown to reduce local stress and thus prevent material failure after loading beyond the elastic limit. On the basis of our multi-scale simulation approach, we provide a molecular scale rationalization of this phenomenon, which seems key to the resilience of hierarchical biominerals, including teeth and bone.

  5. Molecular dynamics modeling of bonding two materials by atomic scale friction stir welding at different process parameters

    Science.gov (United States)

    Konovalenko S., Iv.; Psakhie, S. G.

    2017-12-01

    Using the molecular dynamics method, we simulated the atomic scale butt friction stir welding on two crystallites and varied the onset FSW tool plunge depth. The effects of the plunge depth value on the thermomechanical evolution of nanosized crystallites and mass transfer in the course of FSW have been studied. The increase of plunge depth values resulted in more intense heating and reducing the plasticized metal resistance to the tool movement. The mass transfer intensity was hardly dependent on the plunge depth value. The plunge depth was recommended to be used as a FSW process control parameter in addition to the commonly used ones.

  6. Assessment of Molecular Modeling & Simulation

    Energy Technology Data Exchange (ETDEWEB)

    None

    2002-01-03

    This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

  7. The use of artificial neural network modeling to represent the process of concentration by molecular distillation of omega-3 from squid oil

    Directory of Open Access Journals (Sweden)

    Rossi, P.

    2014-12-01

    Full Text Available The concentration of omega-3 compounds obtained for the esterification of squid oil by molecular distillation was carried out in two stages. This operation can process these thermolabile and high molecular weight components at very low temperatures. Given the mathematical complexity of the theoretical model, artificial neural networks (ANN have provided an alternative to a classical computing analysis. The objective of this study was to create a predictive model using artificial neural network techniques to represent the concentration process of omega-3 compounds obtained from squid oil using molecular distillation. Another objective of this study was to analyze the performance of two different alternatives of ANN modeling; one of them is a model that represents all variables in the process and the other is a global model that simulates only the input and output variables of the process. The alternative of the ANN global model showed the best fit to the experimental data.La concentración de compuestos omega-3, obtenidos de la esterificación de aceite de calamar, por destilación molecular fue llevada a cabo en dos etapas. Esta operación permite procesar componentes termolábiles y de alto peso molecular a muy bajas temperaturas. Dada la alta complejidad de los modelos teóricos, las redes neuronales artificiales (RNA conforman una alternativa al análisis computacional clásico. El objetivo de este estudio fue crear un modelo predictivo usando modelos de redes neuronales artificiales para representar el proceso de concentración de compuestos omega-3 obtenidos del aceite de calamar por destilación molecular. Otro objetivo de este estudio fue analizar el desenvolvimiento de dos alternativas de modelos RNA; uno de ellos es un modelo que representa todas las variables en el proceso y otro es un modelo global que simula solo las variables de entrada y de salida del proceso. La alternativa de un modelo RNA global mostró el mejor ajuste de los

  8. 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

  9. A Process for Modelling Diffuse Scattering from Disordered Molecular Crystals, Illustrated by Application to Monoclinic 9-Chloro-10-methylanthracene

    Directory of Open Access Journals (Sweden)

    D. J. Goossens

    2015-01-01

    Full Text Available Diffuse scattering from a crystal contains valuable information about the two-body correlations (related to the nanoscale order in the material. Despite years of development, the detailed analysis of single crystal diffuse scattering (SCDS has yet to become part of the everyday toolbox of the structural scientist. Recent decades have seen the pair distribution function approach to diffuse scattering (in fact, total scattering from powders become a relatively routine tool. However, analysing the detailed, complex, and often highly anisotropic three-dimensional distribution of SCDS remains valuable yet rare because there is no routine method for undertaking the analysis. At present, analysis requires significant investment of time to develop specialist expertise, which means that the analysis of diffuse scattering, which has much to offer, is not incorporated thorough studies of many compounds even though it has the potential to be a very useful adjunct to existing techniques. This article endeavours to outline in some detail how the diffuse scattering from a molecular crystal can be modelled relatively quickly and largely using existing software tools. It is hoped this will provide a template for other studies. To enable this, the entire simulation is included as deposited material.

  10. Magnetohydrodynamic Models of Molecular Tornadoes

    Science.gov (United States)

    Au, Kelvin; Fiege, Jason D.

    2017-07-01

    Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

  11. Magnetohydrodynamic Models of Molecular Tornadoes

    Energy Technology Data Exchange (ETDEWEB)

    Au, Kelvin; Fiege, Jason D., E-mail: fiege@physics.umanitoba.ca [Department of Physics and Astronomy, University of Manitoba Winnipeg, MB R3T 2N2 (Canada)

    2017-07-10

    Recent observations near the Galactic Center (GC) have found several molecular filaments displaying striking helically wound morphology that are collectively known as molecular tornadoes. We investigate the equilibrium structure of these molecular tornadoes by formulating a magnetohydrodynamic model of a rotating, helically magnetized filament. A special analytical solution is derived where centrifugal forces balance exactly with toroidal magnetic stress. From the physics of torsional Alfvén waves we derive a constraint that links the toroidal flux-to-mass ratio and the pitch angle of the helical field to the rotation laws, which we find to be an important component in describing the molecular tornado structure. The models are compared to the Ostriker solution for isothermal, nonmagnetic, nonrotating filaments. We find that neither the analytic model nor the Alfvén wave model suffer from the unphysical density inversions noted by other authors. A Monte Carlo exploration of our parameter space is constrained by observational measurements of the Pigtail Molecular Cloud, the Double Helix Nebula, and the GC Molecular Tornado. Observable properties such as the velocity dispersion, filament radius, linear mass, and surface pressure can be used to derive three dimensionless constraints for our dimensionless models of these three objects. A virial analysis of these constrained models is studied for these three molecular tornadoes. We find that self-gravity is relatively unimportant, whereas magnetic fields and external pressure play a dominant role in the confinement and equilibrium radial structure of these objects.

  12. 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 ...

  13. 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)

  14. Charge Transport Processes in Molecular Junctions

    Science.gov (United States)

    Smith, Christopher Eugene

    Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

  15. 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

  16. Molecular modeling of the process of reversible dissolution of the collagen protein under the action of tissue-clearing agents

    Science.gov (United States)

    Dvoretsky, K. N.; Berezin, K. V.; Chernavina, M. L.; Likhter, A. M.; Shagautdinova, I. T.; Antonova, E. M.; Rybakov, A. V.; Grechukhina, O. N.; Tuchin, V. V.

    2018-04-01

    The interaction of glycerol immersion agent with collagen mimetic peptide ((GPH)9)3 and a fragment of the microfibril 5((GPH)12)3 was studied by the classical molecular dynamics method using the GROMACS software. The change in geometric parameters of collagen α-chains at various concentrations of an aqueous solution of glycerol is analyzed. It is shown that these changes nonlinearly depend on the concentration and are limited to a certain level, which correlates with the experimental data on optical clearing efficiency of human skin. A hypothesis on the cause of the decreased efficiency of optical skin clearing at high immersion agent concentrations is put forward. The molecular mechanism of immersion optical clearing of biological tissues is discussed.

  17. Integrated multiscale modeling of molecular computing devices

    International Nuclear Information System (INIS)

    Cummings, Peter T; Leng Yongsheng

    2005-01-01

    Molecular electronics, in which single organic molecules are designed to perform the functions of transistors, diodes, switches and other circuit elements used in current siliconbased microelecronics, is drawing wide interest as a potential replacement technology for conventional silicon-based lithographically etched microelectronic devices. In addition to their nanoscopic scale, the additional advantage of molecular electronics devices compared to silicon-based lithographically etched devices is the promise of being able to produce them cheaply on an industrial scale using wet chemistry methods (i.e., self-assembly from solution). The design of molecular electronics devices, and the processes to make them on an industrial scale, will require a thorough theoretical understanding of the molecular and higher level processes involved. Hence, the development of modeling techniques for molecular electronics devices is a high priority from both a basic science point of view (to understand the experimental studies in this field) and from an applied nanotechnology (manufacturing) point of view. Modeling molecular electronics devices requires computational methods at all length scales - electronic structure methods for calculating electron transport through organic molecules bonded to inorganic surfaces, molecular simulation methods for determining the structure of self-assembled films of organic molecules on inorganic surfaces, mesoscale methods to understand and predict the formation of mesoscale patterns on surfaces (including interconnect architecture), and macroscopic scale methods (including finite element methods) for simulating the behavior of molecular electronic circuit elements in a larger integrated device. Here we describe a large Department of Energy project involving six universities and one national laboratory aimed at developing integrated multiscale methods for modeling molecular electronics devices. The project is funded equally by the Office of Basic

  18. Molecular modeling of inorganic compounds

    National Research Council Canada - National Science Library

    Comba, Peter; Hambley, Trevor W; Martin, Bodo

    2009-01-01

    ... mechanics to inorganic and coordination compounds. Initially, simple metal complexes were modeled, but recently the field has been extended to include organometallic compounds, catalysis and the interaction of metal ions with biological macromolecules. The application of molecular mechanics to coordination compounds is complicated by the numbe...

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. Mathematical modeling of molecular motors

    OpenAIRE

    Keller, Peter

    2013-01-01

    Amongst the many complex processes taking place in living cells, transport of cargoes across the cytosceleton is fundamental to cell viability and activity. To move cargoes between the different cell parts, cells employ Molecular Motors. The motors operate by transporting cargoes along the so-called cellular micro-tubules, namely rope-like structures that connect, for instance, the cell-nucleus and outer membrane. We introduce a new Markov Chain, the killed Quasi-Random-Walk, for such transpo...

  12. 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

  13. Semantic Business Process Modeling

    OpenAIRE

    Markovic, Ivan

    2010-01-01

    This book presents a process-oriented business modeling framework based on semantic technologies. The framework consists of modeling languages, methods, and tools that allow for semantic modeling of business motivation, business policies and rules, and business processes. Quality of the proposed modeling framework is evaluated based on the modeling content of SAP Solution Composer and several real-world business scenarios.

  14. Variational methods in molecular modeling

    CERN Document Server

    2017-01-01

    This book presents tutorial overviews for many applications of variational methods to molecular modeling. Topics discussed include the Gibbs-Bogoliubov-Feynman variational principle, square-gradient models, classical density functional theories, self-consistent-field theories, phase-field methods, Ginzburg-Landau and Helfrich-type phenomenological models, dynamical density functional theory, and variational Monte Carlo methods. Illustrative examples are given to facilitate understanding of the basic concepts and quantitative prediction of the properties and rich behavior of diverse many-body systems ranging from inhomogeneous fluids, electrolytes and ionic liquids in micropores, colloidal dispersions, liquid crystals, polymer blends, lipid membranes, microemulsions, magnetic materials and high-temperature superconductors. All chapters are written by leading experts in the field and illustrated with tutorial examples for their practical applications to specific subjects. With emphasis placed on physical unders...

  15. Molecular modeling of fentanyl analogs

    Directory of Open Access Journals (Sweden)

    LJILJANA DOSEN-MICOVIC

    2004-11-01

    Full Text Available Fentanyl is a highly potent and clinically widely used narcotic analgesic. A large number of its analogs have been synthesized, some of which (sufentanil and alfentanyl are also in clinical use. Theoretical studies, in recent years, afforded a better understanding of the structure-activity relationships of this class of opiates and allowed insight into the molecular mechanism of the interactions of fentanyl analogs with their receptors. An overview of the current computational techniques for modeling fentanyl analogs, their receptors and ligand-receptor interactions is presented in this paper.

  16. Molecular modelling and radiopharmaceutical design

    International Nuclear Information System (INIS)

    Neves, M.; Gano, L.; Costa, M.C.; Raminhos, H.; Rosado, M.; Fausto, R.

    2002-01-01

    Aim: Among several headings for radiopharmaceuticals (RPs) design, molecular modelling (MM) could be used for the prediction of ligands and metal-complexes structures. Using MM it is also possible to simulate molecular interactions between predicted structures and specific biomolecules. Bisphosphonates (BPs) are ligands that are able to coordinate radioactive metals, such as 153 Sm, 166 Ho, 186 Re, etc., but they are all polymeric complexes difficult to characterize. It is reported that the bone uptake does not depend on the nature of metal center, but is primarily driven by the nature of the ligand, as in the case of HEDP-M (M= 99m Tc, 186 Re, 113 Sn). So, it would be interesting to estimate the relevant molecular properties of BPs by MM, simulate their interaction with hydroxyapatite (HAP) the main bone component, and then correlate the predicted molecular parameters with experimental data obtained from HAP binding and biodistribution studies of BPs carrying radioactive metals. Materials and Methods: The molecular structures and preferred conformations of BPs differing in the length of the aliphatic chain attached to their substituted amine groups (pami-dronate, olpadronate and ibandronate) were obtained using the second-generation CVFF 950 (version 1.01) force field of Hwang et al. Simulation of the interactions between the studied BPs and HAP were performed using a Cerius-2 system of programs running on a Silicon Graphics O2 workstation. BPs- 153 Sm complexes were synthesized and characterized by ITLC. Their binding to HAP and in vivo biodistribution studies were carried out as usual described in literature. Results: A direct correlation could be established between in vitro BPs affinity towards HAP and their corresponding energies from the Coulomb interactions involving the N and P atoms of the studied BPs bound to the HAP (0,0,1) surface and the nearest Ca atoms of HAP. The BPs- 153 Sm showing the highest binding to HAP and skeletal uptake are those which

  17. Modeling multiphase materials processes

    CERN Document Server

    Iguchi, Manabu

    2010-01-01

    ""Modeling Multiphase Materials Processes: Gas-Liquid Systems"" describes the methodology and application of physical and mathematical modeling to multi-phase flow phenomena in materials processing. The book focuses on systems involving gas-liquid interaction, the most prevalent in current metallurgical processes. The performance characteristics of these processes are largely dependent on transport phenomena. This volume covers the inherent characteristics that complicate the modeling of transport phenomena in such systems, including complex multiphase structure, intense turbulence, opacity of

  18. Process and apparatus for determining molecular spectra

    International Nuclear Information System (INIS)

    Boesl, U.; Neusser, H.J.; Schlag, E.W.

    1984-01-01

    A process for determining molecular spectra in unseparated mixtures, in particular unseparated isotopic mixtures, which comprises allowing said mixture to successively flow through a photoreactor which is irradiated by an adjustable-wavelength laser and then through a mass spectrometer wherein the concentration of particles of specified mass is determined by variation of the wavelength of the laser or variation of the mass setting of the mass spectrometer in such a manner that a two-dimensional spectrum results having the parameters of wavelength and mass

  19. Process modeling style

    CERN Document Server

    Long, John

    2014-01-01

    Process Modeling Style focuses on other aspects of process modeling beyond notation that are very important to practitioners. Many people who model processes focus on the specific notation used to create their drawings. While that is important, there are many other aspects to modeling, such as naming, creating identifiers, descriptions, interfaces, patterns, and creating useful process documentation. Experience author John Long focuses on those non-notational aspects of modeling, which practitioners will find invaluable. Gives solid advice for creating roles, work produ

  20. 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.

  1. Quantifying and Visualizing Uncertainties in Molecular Models

    OpenAIRE

    Rasheed, Muhibur; Clement, Nathan; Bhowmick, Abhishek; Bajaj, Chandrajit

    2015-01-01

    Computational molecular modeling and visualization has seen significant progress in recent years with sev- eral molecular modeling and visualization software systems in use today. Nevertheless the molecular biology community lacks techniques and tools for the rigorous analysis, quantification and visualization of the associated errors in molecular structure and its associated properties. This paper attempts at filling this vacuum with the introduction of a systematic statistical framework whe...

  2. Product and Process Modelling

    DEFF Research Database (Denmark)

    Cameron, Ian T.; Gani, Rafiqul

    . These approaches are put into the context of life cycle modelling, where multiscale and multiform modelling is increasingly prevalent in the 21st century. The book commences with a discussion of modern product and process modelling theory and practice followed by a series of case studies drawn from a variety......This book covers the area of product and process modelling via a case study approach. It addresses a wide range of modelling applications with emphasis on modelling methodology and the subsequent in-depth analysis of mathematical models to gain insight via structural aspects of the models...... to biotechnology applications, food, polymer and human health application areas. The book highlights to important nature of modern product and process modelling in the decision making processes across the life cycle. As such it provides an important resource for students, researchers and industrial practitioners....

  3. Standard Model processes

    CERN Document Server

    Mangano, M.L.; Aguilar-Saavedra, Juan Antonio; Alekhin, S.; Badger, S.; Bauer, C.W.; Becher, T.; Bertone, V.; Bonvini, M.; Boselli, S.; Bothmann, E.; Boughezal, R.; Cacciari, M.; Carloni Calame, C.M.; Caola, F.; Campbell, J.M.; Carrazza, S.; Chiesa, M.; Cieri, L.; Cimaglia, F.; Febres Cordero, F.; Ferrarese, P.; D'Enterria, D.; Ferrera, G.; Garcia i Tormo, X.; Garzelli, M.V.; Germann, E.; Hirschi, V.; Han, T.; Ita, H.; Jäger, B.; Kallweit, S.; Karlberg, A.; Kuttimalai, S.; Krauss, F.; Larkoski, A.J.; Lindert, J.; Luisoni, G.; Maierhöfer, P.; Mattelaer, O.; Martinez, H.; Moch, S.; Montagna, G.; Moretti, M.; Nason, P.; Nicrosini, O.; Oleari, C.; Pagani, D.; Papaefstathiou, A.; Petriello, F.; Piccinini, F.; Pierini, M.; Pierog, T.; Pozzorini, S.; Re, E.; Robens, T.; Rojo, J.; Ruiz, R.; Sakurai, K.; Salam, G.P.; Salfelder, L.; Schönherr, M.; Schulze, M.; Schumann, S.; Selvaggi, M.; Shivaji, A.; Siodmok, A.; Skands, P.; Torrielli, P.; Tramontano, F.; Tsinikos, I.; Tweedie, B.; Vicini, A.; Westhoff, S.; Zaro, M.; Zeppenfeld, D.; CERN. Geneva. ATS Department

    2017-06-22

    This report summarises the properties of Standard Model processes at the 100 TeV pp collider. We document the production rates and typical distributions for a number of benchmark Standard Model processes, and discuss new dynamical phenomena arising at the highest energies available at this collider. We discuss the intrinsic physics interest in the measurement of these Standard Model processes, as well as their role as backgrounds for New Physics searches.

  4. 3D Printing of Molecular Models

    Science.gov (United States)

    Gardner, Adam; Olson, Arthur

    2016-01-01

    Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

  5. WWTP Process Tank Modelling

    DEFF Research Database (Denmark)

    Laursen, Jesper

    The present thesis considers numerical modeling of activated sludge tanks on municipal wastewater treatment plants. Focus is aimed at integrated modeling where the detailed microbiological model the Activated Sludge Model 3 (ASM3) is combined with a detailed hydrodynamic model based on a numerical...... solution of the Navier-Stokes equations in a multiphase scheme. After a general introduction to the activated sludge tank as a system, the activated sludge tank model is gradually setup in separate stages. The individual sub-processes that are often occurring in activated sludge tanks are initially...... hydrofoil shaped propellers. These two sub-processes deliver the main part of the supplied energy to the activated sludge tank, and for this reason they are important for the mixing conditions in the tank. For other important processes occurring in the activated sludge tank, existing models and measurements...

  6. Molecular scale modeling of polymer imprint nanolithography.

    Science.gov (United States)

    Chandross, Michael; Grest, Gary S

    2012-01-10

    We present the results of large-scale molecular dynamics simulations of two different nanolithographic processes, step-flash imprint lithography (SFIL), and hot embossing. We insert rigid stamps into an entangled bead-spring polymer melt above the glass transition temperature. After equilibration, the polymer is then hardened in one of two ways, depending on the specific process to be modeled. For SFIL, we cross-link the polymer chains by introducing bonds between neighboring beads. To model hot embossing, we instead cool the melt to below the glass transition temperature. We then study the ability of these methods to retain features by removing the stamps, both with a zero-stress removal process in which stamp atoms are instantaneously deleted from the system as well as a more physical process in which the stamp is pulled from the hardened polymer at fixed velocity. We find that it is necessary to coat the stamp with an antifriction coating to achieve clean removal of the stamp. We further find that a high density of cross-links is necessary for good feature retention in the SFIL process. The hot embossing process results in good feature retention at all length scales studied as long as coated, low surface energy stamps are used.

  7. Model Process Control Language

    Data.gov (United States)

    National Aeronautics and Space Administration — The MPC (Model Process Control) language enables the capture, communication and preservation of a simulation instance, with sufficient detail that it can be...

  8. Biosphere Process Model Report

    Energy Technology Data Exchange (ETDEWEB)

    J. Schmitt

    2000-05-25

    To evaluate the postclosure performance of a potential monitored geologic repository at Yucca Mountain, a Total System Performance Assessment (TSPA) will be conducted. Nine Process Model Reports (PMRs), including this document, are being developed to summarize the technical basis for each of the process models supporting the TSPA model. These reports cover the following areas: (1) Integrated Site Model; (2) Unsaturated Zone Flow and Transport; (3) Near Field Environment; (4) Engineered Barrier System Degradation, Flow, and Transport; (5) Waste Package Degradation; (6) Waste Form Degradation; (7) Saturated Zone Flow and Transport; (8) Biosphere; and (9) Disruptive Events. Analysis/Model Reports (AMRs) contain the more detailed technical information used to support TSPA and the PMRs. The AMRs consists of data, analyses, models, software, and supporting documentation that will be used to defend the applicability of each process model for evaluating the postclosure performance of the potential Yucca Mountain repository system. This documentation will ensure the traceability of information from its source through its ultimate use in the TSPA-Site Recommendation (SR) and in the National Environmental Policy Act (NEPA) analysis processes. The objective of the Biosphere PMR is to summarize (1) the development of the biosphere model, and (2) the Biosphere Dose Conversion Factors (BDCFs) developed for use in TSPA. The Biosphere PMR does not present or summarize estimates of potential radiation doses to human receptors. Dose calculations are performed as part of TSPA and will be presented in the TSPA documentation. The biosphere model is a component of the process to evaluate postclosure repository performance and regulatory compliance for a potential monitored geologic repository at Yucca Mountain, Nevada. The biosphere model describes those exposure pathways in the biosphere by which radionuclides released from a potential repository could reach a human receptor

  9. Biosphere Process Model Report

    International Nuclear Information System (INIS)

    Schmitt, J.

    2000-01-01

    To evaluate the postclosure performance of a potential monitored geologic repository at Yucca Mountain, a Total System Performance Assessment (TSPA) will be conducted. Nine Process Model Reports (PMRs), including this document, are being developed to summarize the technical basis for each of the process models supporting the TSPA model. These reports cover the following areas: (1) Integrated Site Model; (2) Unsaturated Zone Flow and Transport; (3) Near Field Environment; (4) Engineered Barrier System Degradation, Flow, and Transport; (5) Waste Package Degradation; (6) Waste Form Degradation; (7) Saturated Zone Flow and Transport; (8) Biosphere; and (9) Disruptive Events. Analysis/Model Reports (AMRs) contain the more detailed technical information used to support TSPA and the PMRs. The AMRs consists of data, analyses, models, software, and supporting documentation that will be used to defend the applicability of each process model for evaluating the postclosure performance of the potential Yucca Mountain repository system. This documentation will ensure the traceability of information from its source through its ultimate use in the TSPA-Site Recommendation (SR) and in the National Environmental Policy Act (NEPA) analysis processes. The objective of the Biosphere PMR is to summarize (1) the development of the biosphere model, and (2) the Biosphere Dose Conversion Factors (BDCFs) developed for use in TSPA. The Biosphere PMR does not present or summarize estimates of potential radiation doses to human receptors. Dose calculations are performed as part of TSPA and will be presented in the TSPA documentation. The biosphere model is a component of the process to evaluate postclosure repository performance and regulatory compliance for a potential monitored geologic repository at Yucca Mountain, Nevada. The biosphere model describes those exposure pathways in the biosphere by which radionuclides released from a potential repository could reach a human receptor

  10. Inferring Molecular Processes Heterogeneity from Transcriptional Data.

    Science.gov (United States)

    Gogolewski, Krzysztof; Wronowska, Weronika; Lech, Agnieszka; Lesyng, Bogdan; Gambin, Anna

    2017-01-01

    RNA microarrays and RNA-seq are nowadays standard technologies to study the transcriptional activity of cells. Most studies focus on tracking transcriptional changes caused by specific experimental conditions. Information referring to genes up- and downregulation is evaluated analyzing the behaviour of relatively large population of cells by averaging its properties. However, even assuming perfect sample homogeneity, different subpopulations of cells can exhibit diverse transcriptomic profiles, as they may follow different regulatory/signaling pathways. The purpose of this study is to provide a novel methodological scheme to account for possible internal, functional heterogeneity in homogeneous cell lines, including cancer ones. We propose a novel computational method to infer the proportion between subpopulations of cells that manifest various functional behaviour in a given sample. Our method was validated using two datasets from RNA microarray experiments. Both experiments aimed to examine cell viability in specific experimental conditions. The presented methodology can be easily extended to RNA-seq data as well as other molecular processes. Moreover, it complements standard tools to indicate most important networks from transcriptomic data and in particular could be useful in the analysis of cancer cell lines affected by biologically active compounds or drugs.

  11. Atomic and molecular processes in JT-60U divertor plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Takenaga, H.; Shimizu, K.; Itami, K. [Japan Atomic Energy Research Inst., Naka, Ibaraki (Japan). Naka Fusion Research Establishment] [and others

    1997-01-01

    Atomic and molecular data are indispensable for the understanding of the divertor characteristics, because behavior of particles in the divertor plasma is closely related to the atomic and molecular processes. In the divertor configuration, heat and particles escaping from the main plasma flow onto the divertor plate along the magnetic field lines. In the divertor region, helium ash must be effectively exhausted, and radiation must be enhanced for the reduction of the heat load onto the divertor plate. In order to exhaust helium ash effectively, the difference between behavior of neutral hydrogen (including deuterium and tritium) and helium in the divertor plasma should be understood. Radiation from the divertor plasma generally caused by the impurities which produced by the erosion of the divertor plate and/or injected by gas-puffing. Therefore, it is important to understand impurity behavior in the divertor plasma. The ions hitting the divertor plate recycle through the processes of neutralization, reflection, absorption and desorption at the divertor plates and molecular dissociation, charge-exchange reaction and ionization in the divertor plasma. Behavior of hydrogen, helium and impurities in the divertor plasmas can not be understood without the atomic and molecular data. In this report, recent results of the divertor study related to the atomic and molecular processes in JT-60U were summarized. Behavior of neural deuterium and helium was discussed in section 2. In section 3, the comparisons between the modelling of the carbon impurity transport and the measurements of C II and C IV were discussed. In section 4, characteristics of the radiative divertor using Ne puffing were reported. The new diagnostic method for the electron density and temperature in the divertor plasmas using the intensity ratios of He I lines was described in section 5. (author)

  12. The cognitive life of mechanical molecular models.

    Science.gov (United States)

    Charbonneau, Mathieu

    2013-12-01

    The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler's cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models' materiality contributing to the solving of the molecule's structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Aerospace Materials Process Modelling

    Science.gov (United States)

    1988-08-01

    Cooling Transformation diagram ( CCT diagram ) When a IT diagram is used in the heat process modelling, we suppose that a sudden cooling (instantaneous...processes. CE, chooses instead to study thermo-mechanical properties referring to a CCT diagram . This is thinked to be more reliable to give a true...k , mm-_____sml l ml A I 1 III 12.4 This determination is however based on the following approximations: i) A CCT diagram is valid only for the

  14. Deep Generative Models for Molecular Science

    DEFF Research Database (Denmark)

    Jørgensen, Peter Bjørn; Schmidt, Mikkel Nørgaard; Winther, Ole

    2018-01-01

    Generative deep machine learning models now rival traditional quantum-mechanical computations in predicting properties of new structures, and they come with a significantly lower computational cost, opening new avenues in computational molecular science. In the last few years, a variety of deep...... generative models have been proposed for modeling molecules, which differ in both their model structure and choice of input features. We review these recent advances within deep generative models for predicting molecular properties, with particular focus on models based on the probabilistic autoencoder (or...

  15. Application of statistical process control to qualitative molecular diagnostic assays

    LENUS (Irish Health Repository)

    O'Brien, Cathal P.

    2014-11-01

    Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data.

  16. 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

  17. Application of statistical process control to qualitative molecular diagnostic assays.

    Science.gov (United States)

    O'Brien, Cathal P; Finn, Stephen P

    2014-01-01

    Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data.

  18. Business Model Process Configurations

    DEFF Research Database (Denmark)

    Taran, Yariv; Nielsen, Christian; Thomsen, Peter

    2015-01-01

    , by developing (inductively) an ontological classification framework, in view of the BM process configurations typology developed. Design/methodology/approach – Given the inconsistencies found in the business model studies (e.g. definitions, configurations, classifications) we adopted the analytical induction...

  19. Business process model repositories : efficient process retrieval

    NARCIS (Netherlands)

    Yan, Z.

    2012-01-01

    As organizations increasingly work in process-oriented manner, the number of business process models that they develop and have to maintain increases. As a consequence, it has become common for organizations to have collections of hundreds or even thousands of business process models. When a

  20. Human butyrylcholinesterase polymorphism: Molecular modeling.

    Science.gov (United States)

    Lushchekina, S; Delacour, H; Lockridge, O; Masson, P

    2015-01-01

    Prolonged apnoea following injection of ester-containing myoralaxants was first described in 1953. Because a large part of administered succinylcholine is shortly hydrolyzed by plasma butyrylcholinesterase (BChE) under normal conditions, prolonged apnoea was attributed to deficiency in BChE. It was found that BChE deficiency was due to genetic variations. Human BChE gene shows a large polyallelism. About 75 natural mutations of the BCHE gene have been documented so far [1]. Most of them cause alteration in BChE activity through point mutation effect on catalytic activity. Frame shifts and stop codons may also affect expression, or cause truncations in the sequence. Recently, two novel BChE "silent" variants, Val204Asp [2] and Ala34Val [3], causing prolonged neuromuscular block after administration of mivacurium, were discovered. Mutations were genetically and kinetically characterized. The aim of the current study was to understand how these mutations determine "silent" phenotype. Molecular dynamics studies were carried out with NAMD 2.9 software at the Lomonosov supercomputer. Charmm 36 force field was used, periodical boundary conditions, 1 atm pressure, 298 K. 100 ns molecular dynamics runs were performed for the wild-type BChE and its mutants Val204Asp and Ala34Val. Unlike wild-type BChE, which retained its operative catalytic triad through the whole MD simulation, the catalytic triad of mutants was disrupted, making chemical step impossible. Val204Asp mutation leads to reorganization of hydrogen bonding network around the catalytic triad, which in turn increases the distance between catalytic residue main chains. Mutation Ala34Val, located on the protein surface, leads to increased fluctuations in the Ω-loop and subsequent disruption of the gorge structure, including disruption of the catalytic triad and formation of new hydrogen bonds involving catalytic center residues. Comparative study of the "silent" Ala328Asp mutant and the catalytically active mutant

  1. Process model repositories and PNML

    NARCIS (Netherlands)

    Hee, van K.M.; Post, R.D.J.; Somers, L.J.A.M.; Werf, van der J.M.E.M.; Kindler, E.

    2004-01-01

    Bringing system and process models together in repositories facilitates the interchange of model information between modelling tools, and allows the combination and interlinking of complementary models. Petriweb is a web application for managing such repositories. It supports hierarchical process

  2. Application of statistical process control to qualitative molecular diagnostic assays.

    Directory of Open Access Journals (Sweden)

    Cathal P O'brien

    2014-11-01

    Full Text Available Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control. Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply statistical process control to assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater samples with a resultant protracted time to detection. Modelled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of statistical process control to qualitative laboratory data.

  3. Limiting assumptions in molecular modeling: electrostatics.

    Science.gov (United States)

    Marshall, Garland R

    2013-02-01

    Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

  4. Genomic Signal Processing: Predicting Basic Molecular Biological Principles

    Science.gov (United States)

    Alter, Orly

    2005-03-01

    Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of

  5. Molecular dynamics modeling of polymer flammability

    International Nuclear Information System (INIS)

    Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

    1992-01-01

    Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

  6. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

  7. Failure of single electron descriptions of molecular orbital collision processes

    International Nuclear Information System (INIS)

    Elston, S.B.

    1978-01-01

    Inner-shell excitation occurring in low and moderate (keV range) energy collisions between light atomic and ionic systems is frequently describable in terms of molecular promotion mechanisms, which were extensively explored both theoretically and experimentally. The bulk of such studies have concentrated on processes understandable through the use of single- and independent-electron models. Nonetheless, it is possible to find cases of inner-shell excitation in relatively simple collision systems which involve nearly simultaneous multiple-electron transitions and transitions induced by inherently two-electron interactions. Evidence for these many- and nonindependent-electron phenomena in inner-shell excitation processes and the importance of considering such effects in the interpretation of collisionally induced excitation spectra is discussed. 13 references

  8. Molecular dynamics simulations of cluster fission and fusion processes

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...

  9. Exploring the boundaries of molecular modeling : a study of nanochannels and transmembrane proteins

    NARCIS (Netherlands)

    Spijker, P.

    2009-01-01

    Many interesting physical and biological phenomena can be investigated using molecular modeling techniques, either theoretically or by using computer simulation methods, such as molecular dynamics and Monte Carlo simulations. Due to the increasing power of computer processing units, these simulation

  10. Classical molecular dynamics simulation of electronically non-adiabatic processes.

    Science.gov (United States)

    Miller, William H; Cotton, Stephen J

    2016-12-22

    Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

  11. Modeling Complex Workflow in Molecular Diagnostics

    Science.gov (United States)

    Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

    2010-01-01

    One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

  12. Modeling styles in business process modeling

    NARCIS (Netherlands)

    Pinggera, J.; Soffer, P.; Zugal, S.; Weber, B.; Weidlich, M.; Fahland, D.; Reijers, H.A.; Mendling, J.; Bider, I.; Halpin, T.; Krogstie, J.; Nurcan, S.; Proper, E.; Schmidt, R.; Soffer, P.; Wrycza, S.

    2012-01-01

    Research on quality issues of business process models has recently begun to explore the process of creating process models. As a consequence, the question arises whether different ways of creating process models exist. In this vein, we observed 115 students engaged in the act of modeling, recording

  13. Medulloblastoma: Molecular Genetics and Animal Models

    Directory of Open Access Journals (Sweden)

    Corey Raffel

    2004-07-01

    Full Text Available Medulloblastoma is a primary brain tumor found in the cerebellum of children. The tumor occurs in association with two inherited cancer syndromes: Turcot syndrome and Gorlin syndrome. Insights into the molecular biology of the tumor have come from looking at alterations in the genes altered in these syndromes, PTC and APC, respectively. Murine models of medulloblastoma have been constructed based on these alterations. Additional murine models that, while mimicking the appearance of the human tumor, seem unrelated to the human tumor's molecular alterations have been made. In this review, the clinical picture, origin, molecular biology, murine models of medulloblastoma are discussed. Although a great deal has been discovered about this tumor, the genetic alterations responsible for tumor development in a majority of patients have yet to be described.

  14. Distillation modeling for a uranium refining process

    Energy Technology Data Exchange (ETDEWEB)

    Westphal, B.R.

    1996-03-01

    As part of the spent fuel treatment program at Argonne National Laboratory, a vacuum distillation process is being employed for the recovery of uranium following an electrorefining process. Distillation of a salt electrolyte, containing a eutectic mixture of lithium and potassium chlorides, from uranium is achieved by a simple batch operation and is termed {open_quotes}cathode processing{close_quotes}. The incremental distillation of electrolyte salt will be modeled by an equilibrium expression and on a molecular basis since the operation is conducted under moderate vacuum conditions. As processing continues, the two models will be compared and analyzed for correlation with actual operating results. Possible factors that may contribute to aberrations from the models include impurities at the vapor-liquid boundary, distillate reflux, anomalous pressure gradients, and mass transport phenomena at the evaporating surface. Ultimately, the purpose of either process model is to enable the parametric optimization of the process.

  15. On Atomistic Models for Molecular Oxygen

    DEFF Research Database (Denmark)

    Javanainen, Matti; Vattulainen, Ilpo; Monticelli, Luca

    2017-01-01

    Molecular oxygen (O2) is key to all life on earth, as it is constantly cycled via photosynthesis and cellular respiration. Substantial scientific effort has been devoted to understanding every part of this cycle. Classical molecular dynamics (MD) simulations have been used to study some of the key...... processes involved in cellular respiration: O2 permeation through alveolar monolayers and cellular membranes, its binding to hemoglobin during transport in the bloodstream, as well as its transport along optimal pathways toward its reduction sites in proteins. Moreover, MD simulations can help interpret...

  16. Grid computing in large pharmaceutical molecular modeling.

    Science.gov (United States)

    Claus, Brian L; Johnson, Stephen R

    2008-07-01

    Most major pharmaceutical companies have employed grid computing to expand their compute resources with the intention of minimizing additional financial expenditure. Historically, one of the issues restricting widespread utilization of the grid resources in molecular modeling is the limited set of suitable applications amenable to coarse-grained parallelization. Recent advances in grid infrastructure technology coupled with advances in application research and redesign will enable fine-grained parallel problems, such as quantum mechanics and molecular dynamics, which were previously inaccessible to the grid environment. This will enable new science as well as increase resource flexibility to load balance and schedule existing workloads.

  17. Modeling shockwave deformation via molecular dynamics

    International Nuclear Information System (INIS)

    Holian, B.L.

    1987-01-01

    Molecular dynamics (MD), where the equations of motion of up to thousands of interacting atoms are solved on the computer, has proven to be a powerful tool for investigating a wide variety of nonequilibrium processes from the atomistic viewpoint. Simulations of shock waves in three-dimensional (3D) solids and fluids have shown conclusively that shear-stress relaxation is achieved through atomic rearrangement. In the case of fluids, the transverse motion is viscous, and the constitutive model of Navier-Stokes hydrodynamics has been shown to be accurate - even on the time and distance scales of MD experiments. For strong shocks in solids, the plastic flow that leads to shear-stress relaxation in MD is highly localized near the shock front, involving a slippage along close-packed planes. For shocks of intermediate strength, MD calculations exhibit an elastic precursor running out in front of the steady plastic wave, where slippage similar in character to that in the very strong shocks leads to shear-stress relaxation. An interesting correlation between the maximum shear stress and the Hugoniot pressure jump is observed for both 3D and fluid shockwave calculations, which may have some utility in modeling applications. At low shock strengths, the MD simulations show only elastic compression, with no permanent transverse atomic strains. The result for perfect 3D crystals is also seen in calculations for 1D chains. It is speculated that, if it were practical, a very large MD system containing dislocations could be expected to exhibit more realistic plastic flow for weak shock waves, too

  18. Realistic molecular model of kerogen's nanostructure.

    Science.gov (United States)

    Bousige, Colin; Ghimbeu, Camélia Matei; Vix-Guterl, Cathie; Pomerantz, Andrew E; Suleimenova, Assiya; Vaughan, Gavin; Garbarino, Gaston; Feygenson, Mikhail; Wildgruber, Christoph; Ulm, Franz-Josef; Pellenq, Roland J-M; Coasne, Benoit

    2016-05-01

    Despite kerogen's importance as the organic backbone for hydrocarbon production from source rocks such as gas shale, the interplay between kerogen's chemistry, morphology and mechanics remains unexplored. As the environmental impact of shale gas rises, identifying functional relations between its geochemical, transport, elastic and fracture properties from realistic molecular models of kerogens becomes all the more important. Here, by using a hybrid experimental-simulation method, we propose a panel of realistic molecular models of mature and immature kerogens that provide a detailed picture of kerogen's nanostructure without considering the presence of clays and other minerals in shales. We probe the models' strengths and limitations, and show that they predict essential features amenable to experimental validation, including pore distribution, vibrational density of states and stiffness. We also show that kerogen's maturation, which manifests itself as an increase in the sp(2)/sp(3) hybridization ratio, entails a crossover from plastic-to-brittle rupture mechanisms.

  19. Distillation modeling for a uranium refining process

    International Nuclear Information System (INIS)

    Westphal, B.R.

    1996-01-01

    As part of the spent fuel treatment program at Argonne National Laboratory, a vacuum distillation process is being employed for the recovery of uranium following an electrorefining process. Distillation of a salt electrolyte, containing a eutectic mixture of lithium and potassium chlorides, from uranium is achieved by a simple batch operation and is termed open-quotes cathode processingclose quotes. The incremental distillation of electrolyte salt will be modeled by an equilibrium expression and on a molecular basis since the operation is conducted under moderate vacuum conditions. As processing continues, the two models will be compared and analyzed for correlation with actual operating results. Possible factors that may contribute to aberrations from the models include impurities at the vapor-liquid boundary, distillate reflux, anomalous pressure gradients, and mass transport phenomena at the evaporating surface. Ultimately, the purpose of either process model is to enable the parametric optimization of the process

  20. Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

    KAUST Repository

    Kadoura, Ahmad Salim

    2016-01-01

    This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method

  1. 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)

  2. Generating process model collections

    NARCIS (Netherlands)

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

    2017-01-01

    Business process management plays an important role in the management of organizations. More and more organizations describe their operations as business processes. It is common for organizations to have collections of thousands of business processes, but for reasons of confidentiality these

  3. What makes process models understandable?

    NARCIS (Netherlands)

    Mendling, J.; Reijers, H.A.; Cardoso, J.; Alonso, G.; Dadam, P.; Rosemann, M.

    2007-01-01

    Despite that formal and informal quality aspects are of significant importance to business process modeling, there is only little empirical work reported on process model quality and its impact factors. In this paper we investigate understandability as a proxy for quality of process models and focus

  4. Molecular models and simulations of layered materials

    International Nuclear Information System (INIS)

    Kalinichev, Andrey G.; Cygan, Randall Timothy; Heinz, Hendrik; Greathouse, Jeffery A.

    2008-01-01

    The micro- to nano-sized nature of layered materials, particularly characteristic of naturally occurring clay minerals, limits our ability to fully interrogate their atomic dispositions and crystal structures. The low symmetry, multicomponent compositions, defects, and disorder phenomena of clays and related phases necessitate the use of molecular models and modern simulation methods. Computational chemistry tools based on classical force fields and quantum-chemical methods of electronic structure calculations provide a practical approach to evaluate structure and dynamics of the materials on an atomic scale. Combined with classical energy minimization, molecular dynamics, and Monte Carlo techniques, quantum methods provide accurate models of layered materials such as clay minerals, layered double hydroxides, and clay-polymer nanocomposites

  5. Molecular Modeling of Interfacial Behaviors of Nanomaterials

    Science.gov (United States)

    2007-05-01

    potential was originally designed for the modeling of mixed covalent- ionic bonding and was successfully used to describe oxides in crystalline, glassy, and...is separates from the bulk liquid polymer, i.e., the structure of this layer, as influenced by that of the meatal surface, is significantly more...Striolo, J. Kieffer, and P. Cummings, ’Evaluation of Force- fields for molecular simulation of polyhedral oligomeric silsesquioxanes,’ J. Phys. Chem

  6. Applications of Molecular and Materials Modeling

    Science.gov (United States)

    2002-01-01

    Chimica Industriale Molecular modeling of solvation Prof. Jacopo Tomasi http://www.dcci.unipi.it/attivita /attivita.html; http://www.dcci.unipi.it...solutions/ cases/notes/scale.html BNFL Sorption of gases in zeolites Dr. Scott L. Owens http://www.bnfl.co.uk/ BAE (British Aerospace Engineering) Rare...permeation of gases ; adhesion and interfacial interactions of siloxane networks; chemical reactivity and catalysis; environmental and cosmetics

  7. 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.

  8. 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.

  9. AUTOMR: An automatic processing program system for the molecular replacement method

    International Nuclear Information System (INIS)

    Matsuura, Yoshiki

    1991-01-01

    An automatic processing program system of the molecular replacement method AUTMR is presented. The program solves the initial model of the target crystal structure using a homologous molecule as the search model. It processes the structure-factor calculation of the model molecule, the rotation function, the translation function and the rigid-group refinement successively in one computer job. Test calculations were performed for six protein crystals and the structures were solved in all of these cases. (orig.)

  10. Observational Constraints for Modeling Diffuse Molecular Clouds

    Science.gov (United States)

    Federman, S. R.

    2014-02-01

    Ground-based and space-borne observations of diffuse molecular clouds suggest a number of areas where further improvements to modeling efforts is warranted. I will highlight those that have the widest applicability. The range in CO fractionation caused by selective isotope photodissociation, in particular the large 12C16O/13C16O ratios observed toward stars in Ophiuchus, is not reproduced well by current models. Our ongoing laboratory measurements of oscillator strengths and predissociation rates for Rydberg transitions in CO isotopologues may help clarify the situtation. The CH+ abundance continues to draw attention. Small scale structure seen toward ζ Per may provide additional constraints on the possible synthesis routes. The connection between results from optical transitions and those from radio and sub-millimeter wave transitions requires further effort. A study of OH+ and OH toward background stars reveals that these species favor different environments. This brings to focus the need to model each cloud along the line of sight separately, and to allow the physical conditions to vary within an individual cloud, in order to gain further insight into the chemistry. Now that an extensive set of data on molecular excitation is available, the models should seek to reproduce these data to place further constraints on the modeling results.

  11. MULTI: a shared memory approach to cooperative molecular modeling.

    Science.gov (United States)

    Darden, T; Johnson, P; Smith, H

    1991-03-01

    A general purpose molecular modeling system, MULTI, based on the UNIX shared memory and semaphore facilities for interprocess communication is described. In addition to the normal querying or monitoring of geometric data, MULTI also provides processes for manipulating conformations, and for displaying peptide or nucleic acid ribbons, Connolly surfaces, close nonbonded contacts, crystal-symmetry related images, least-squares superpositions, and so forth. This paper outlines the basic techniques used in MULTI to ensure cooperation among these specialized processes, and then describes how they can work together to provide a flexible modeling environment.

  12. Neuroscientific Model of Motivational Process

    OpenAIRE

    Kim, Sung-il

    2013-01-01

    Considering the neuroscientific findings on reward, learning, value, decision-making, and cognitive control, motivation can be parsed into three sub processes, a process of generating motivation, a process of maintaining motivation, and a process of regulating motivation. I propose a tentative neuroscientific model of motivational processes which consists of three distinct but continuous sub processes, namely reward-driven approach, value-based decision-making, and goal-directed control. Rewa...

  13. Atomic and molecular processes with lithium in peripheral plasmas

    International Nuclear Information System (INIS)

    Murakami, I.; Kato, D.; Hirooka, Y.; Sawada, K.

    2010-01-01

    Atomic and molecular processes for Li chemistry are examined for low temperature plasma such as peripheral plasmas in fusion research laboratory devices. Particle abundances of Li, Li ions, LiH and LiH ion are calculated by solving rate equations in which all reactions of the Li chemistry are considered for low temperature plasma.

  14. 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

  15. 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.

  16. Molecular modeling of auxin transport inhibitors

    International Nuclear Information System (INIS)

    Gardner, G.; Black-Schaefer, C.; Bures, M.G.

    1990-01-01

    Molecular modeling techniques have been used to study the chemical and steric properties of auxin transport inhibitors. These bind to a specific site on the plant plasma membrane characterized by its affinity for N-1-naphthylphthalamic acid (NPA). A three-dimensional model was derived from critical features of ligands for the NPA receptor, and a suggested binding conformation is proposed. This model, along with three-dimensional structural searching techniques, was then used to search the Abbott corporate database of chemical structures. Of the 467 compounds that satisfied the search criteria, 77 representative molecules were evaluated for their ability to compete for [ 3 H]NPA binding to corn microsomal membranes. Nineteen showed activity that ranged from 16 to 85% of the maximum NPA binding. Four of the most active of these, from chemical classes not included in the original compound set, also inhibited polar auxin transport through corn coleoptile sections

  17. MOLECULAR VALIDATED MODEL FOR ADSORPTION OF PROTONATED DYE ON LDH

    Directory of Open Access Journals (Sweden)

    B. M. Braga

    Full Text Available Abstract Hydrotalcite-like compounds are anionic clays of scientific and technological interest for their use as ion exchange materials, catalysts and modified electrodes. Surface phenomenon are important for all these applications. Although conventional analytical methods have enabled progress in understanding the behavior of anionic clays in solution, an evaluation at the atomic scale of the dynamics of their ionic interactions has never been performed. Molecular simulation has become an extremely useful tool to provide this perspective. Our purpose is to validate a simplified model for the adsorption of 5-benzoyl-4-hydroxy-2-methoxy-benzenesulfonic acid (MBSA, a prototype molecule of anionic dyes, onto a hydrotalcite surface. Monte Carlo simulations were performed in the canonical ensemble with MBSA ions and a pore model of hydrotalcite using UFF and ClayFF force fields. The proposed molecular model has allowed us to reproduce experimental data of atomic force microscopy. Influences of protonation during the adsorption process are also presented.

  18. 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.

  19. Molecular processes from the AGB to the PN stage

    Science.gov (United States)

    García-Hernández, D. Anibal

    2012-08-01

    Many complex organic molecules and inorganic solid-state compounds have been observed in the circumstellar shell of stars (both C-rich and O-rich) in the transition phase between Asymptotic Giant Branch (AGB) stars and Planetary Nebulae (PNe). This short (~102-104 years) phase of stellar evolution represents a wonderful laboratory for astrochemistry and provides severe constraints on any model of gas-phase and solid-state chemistry. One of the major challenges of present day astrophysics and astrochemistry is to understand the formation pathways of these complex organic molecules and inorganic solid-state compounds (e.g., polycyclic aromatic hydrocarbons, fullerenes, and graphene in the case of a C-rich chemistry and oxides and crystalline silicates in O-rich environments) in space. In this review, I present an observational review of the molecular processes in the late stages of stellar evolution with a special emphasis on the first detections of fullerenes and graphene in PNe.

  20. Modeling of column apparatus processes

    CERN Document Server

    Boyadjiev, Christo; Boyadjiev, Boyan; Popova-Krumova, Petya

    2016-01-01

    This book presents a new approach for the modeling of chemical and interphase mass transfer processes in industrial column apparatuses, using convection-diffusion and average-concentration models. The convection-diffusion type models are used for a qualitative analysis of the processes and to assess the main, small and slight physical effects, and then reject the slight effects. As a result, the process mechanism can be identified. It also introduces average concentration models for quantitative analysis, which use the average values of the velocity and concentration over the cross-sectional area of the column. The new models are used to analyze different processes (simple and complex chemical reactions, absorption, adsorption and catalytic reactions), and make it possible to model the processes of gas purification with sulfur dioxide, which form the basis of several patents.

  1. Group Contribution Based Process Flowsheet Synthesis, Design and Modelling

    DEFF Research Database (Denmark)

    d'Anterroches, Loïc; Gani, Rafiqul

    2004-01-01

    This paper presents a process-group-contribution Method to model. simulate and synthesize a flowsheet. The process-group based representation of a flowsheet together with a process "property" model are presented. The process-group based synthesis method is developed on the basis of the computer...... aided molecular design methods and gives the ability to screen numerous process alternatives without the need to use the rigorous process simulation models. The process "property" model calculates the design targets for the generated flowsheet alternatives while a reverse modelling method (also...... developed) determines the design variables matching the target. A simple illustrative example highlighting the main features of the methodology is also presented....

  2. 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

  3. 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

  4. UML in business process modeling

    Directory of Open Access Journals (Sweden)

    Bartosz Marcinkowski

    2013-03-01

    Full Text Available Selection and proper application of business process modeling methods and techniques have a significant impact on organizational improvement capabilities as well as proper understanding of functionality of information systems that shall support activity of the organization. A number of business process modeling notations were popularized in practice in recent decades. Most significant of the notations include Business Process Modeling Notation (OMG BPMN and several Unified Modeling Language (OMG UML extensions. In this paper, the assessment whether one of the most flexible and strictly standardized contemporary business process modeling notations, i.e. Rational UML Profile for Business Modeling, enable business analysts to prepare business models that are all-embracing and understandable by all the stakeholders. After the introduction, methodology of research is discussed. Section 2 presents selected case study results. The paper is concluded with a summary.

  5. Modeling ion sensing in molecular electronics

    International Nuclear Information System (INIS)

    Chen, Caroline J.; Smeu, Manuel; Ratner, Mark A.

    2014-01-01

    We examine the ability of molecules to sense ions by measuring the change in molecular conductance in the presence of such charged species. The detection of protons (H + ), alkali metal cations (M + ), calcium ions (Ca 2+ ), and hydronium ions (H 3 O + ) is considered. Density functional theory (DFT) is used within the Keldysh non-equilibrium Green's function framework (NEGF) to model electron transport properties of quinolinedithiol (QDT, C 9 H 7 NS 2 ), bridging Al electrodes. The geometry of the transport region is relaxed with DFT. The transport properties of the device are modeled with NEGF-DFT to determine if this device can distinguish among the M + + QDT species containing monovalent cations, where M + = H + , Li + , Na + , or K + . Because of the asymmetry of QDT in between the two electrodes, both positive and negative biases are considered. The electron transmission function and conductance properties are simulated for electrode biases in the range from −0.5 V to 0.5 V at increments of 0.1 V. Scattering state analysis is used to determine the molecular orbitals that are the main contributors to the peaks in the transmission function near the Fermi level of the electrodes, and current-voltage relationships are obtained. The results show that QDT can be used as a proton detector by measuring transport through it and can conceivably act as a pH sensor in solutions. In addition, QDT may be able to distinguish among different monovalent species. This work suggests an approach to design modern molecular electronic conductance sensors with high sensitivity and specificity using well-established quantum chemistry

  6. Business Process Modeling: Perceived Benefits

    Science.gov (United States)

    Indulska, Marta; Green, Peter; Recker, Jan; Rosemann, Michael

    The process-centered design of organizations and information systems is globally seen as an appropriate response to the increased economic pressure on organizations. At the methodological core of process-centered management is process modeling. However, business process modeling in large initiatives can be a time-consuming and costly exercise, making it potentially difficult to convince executive management of its benefits. To date, and despite substantial interest and research in the area of process modeling, the understanding of the actual benefits of process modeling in academia and practice is limited. To address this gap, this paper explores the perception of benefits derived from process modeling initiatives, as reported through a global Delphi study. The study incorporates the views of three groups of stakeholders - academics, practitioners and vendors. Our findings lead to the first identification and ranking of 19 unique benefits associated with process modeling. The study in particular found that process modeling benefits vary significantly between practitioners and academics. We argue that the variations may point to a disconnect between research projects and practical demands.

  7. Molecular motors that digest their track to rectify Brownian motion: processive movement of exonuclease enzymes.

    Science.gov (United States)

    Xie, Ping

    2009-09-16

    A general model is presented for the processive movement of molecular motors such as λ-exonuclease, RecJ and exonuclease I that use digestion of a DNA track to rectify Brownian motion along this track. Using this model, the translocation dynamics of these molecular motors is studied. The sequence-dependent pausing of λ-exonuclease, which results from a site-specific high affinity DNA interaction, is also studied. The theoretical results are consistent with available experimental data. Moreover, the model is used to predict the lifetime distribution and force dependence of these paused states.

  8. Molecular motors that digest their track to rectify Brownian motion: processive movement of exonuclease enzymes

    International Nuclear Information System (INIS)

    Xie Ping

    2009-01-01

    A general model is presented for the processive movement of molecular motors such as λ-exonuclease, RecJ and exonuclease I that use digestion of a DNA track to rectify Brownian motion along this track. Using this model, the translocation dynamics of these molecular motors is studied. The sequence-dependent pausing of λ-exonuclease, which results from a site-specific high affinity DNA interaction, is also studied. The theoretical results are consistent with available experimental data. Moreover, the model is used to predict the lifetime distribution and force dependence of these paused states.

  9. Molecular Modeling: A Powerful Tool for Drug Design and Molecular ...

    Indian Academy of Sciences (India)

    eling studies is generally a two-dimensional drawing of a re- quired molecule. ... The most active area of theoretical research using molecular orbi tal theory has been in ... minimum energy structure for example, by using conjugated gradient algorithm .... QSARwas applied to understand how the structure might be modified ...

  10. 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.

  11. Conceptual models of information processing

    Science.gov (United States)

    Stewart, L. J.

    1983-01-01

    The conceptual information processing issues are examined. Human information processing is defined as an active cognitive process that is analogous to a system. It is the flow and transformation of information within a human. The human is viewed as an active information seeker who is constantly receiving, processing, and acting upon the surrounding environmental stimuli. Human information processing models are conceptual representations of cognitive behaviors. Models of information processing are useful in representing the different theoretical positions and in attempting to define the limits and capabilities of human memory. It is concluded that an understanding of conceptual human information processing models and their applications to systems design leads to a better human factors approach.

  12. Business process modeling in healthcare.

    Science.gov (United States)

    Ruiz, Francisco; Garcia, Felix; Calahorra, Luis; Llorente, César; Gonçalves, Luis; Daniel, Christel; Blobel, Bernd

    2012-01-01

    The importance of the process point of view is not restricted to a specific enterprise sector. In the field of health, as a result of the nature of the service offered, health institutions' processes are also the basis for decision making which is focused on achieving their objective of providing quality medical assistance. In this chapter the application of business process modelling - using the Business Process Modelling Notation (BPMN) standard is described. Main challenges of business process modelling in healthcare are the definition of healthcare processes, the multi-disciplinary nature of healthcare, the flexibility and variability of the activities involved in health care processes, the need of interoperability between multiple information systems, and the continuous updating of scientific knowledge in healthcare.

  13. Modeling nuclear processes by Simulink

    Energy Technology Data Exchange (ETDEWEB)

    Rashid, Nahrul Khair Alang Md, E-mail: nahrul@iium.edu.my [Faculty of Engineering, International Islamic University Malaysia, Jalan Gombak, Selangor (Malaysia)

    2015-04-29

    Modelling and simulation are essential parts in the study of dynamic systems behaviours. In nuclear engineering, modelling and simulation are important to assess the expected results of an experiment before the actual experiment is conducted or in the design of nuclear facilities. In education, modelling can give insight into the dynamic of systems and processes. Most nuclear processes can be described by ordinary or partial differential equations. Efforts expended to solve the equations using analytical or numerical solutions consume time and distract attention from the objectives of modelling itself. This paper presents the use of Simulink, a MATLAB toolbox software that is widely used in control engineering, as a modelling platform for the study of nuclear processes including nuclear reactor behaviours. Starting from the describing equations, Simulink models for heat transfer, radionuclide decay process, delayed neutrons effect, reactor point kinetic equations with delayed neutron groups, and the effect of temperature feedback are used as examples.

  14. Modeling nuclear processes by Simulink

    International Nuclear Information System (INIS)

    Rashid, Nahrul Khair Alang Md

    2015-01-01

    Modelling and simulation are essential parts in the study of dynamic systems behaviours. In nuclear engineering, modelling and simulation are important to assess the expected results of an experiment before the actual experiment is conducted or in the design of nuclear facilities. In education, modelling can give insight into the dynamic of systems and processes. Most nuclear processes can be described by ordinary or partial differential equations. Efforts expended to solve the equations using analytical or numerical solutions consume time and distract attention from the objectives of modelling itself. This paper presents the use of Simulink, a MATLAB toolbox software that is widely used in control engineering, as a modelling platform for the study of nuclear processes including nuclear reactor behaviours. Starting from the describing equations, Simulink models for heat transfer, radionuclide decay process, delayed neutrons effect, reactor point kinetic equations with delayed neutron groups, and the effect of temperature feedback are used as examples

  15. Homology modeling, docking studies and molecular dynamic simulations using graphical processing unit architecture to probe the type-11 phosphodiesterase catalytic site: a computational approach for the rational design of selective inhibitors.

    Science.gov (United States)

    Cichero, Elena; D'Ursi, Pasqualina; Moscatelli, Marco; Bruno, Olga; Orro, Alessandro; Rotolo, Chiara; Milanesi, Luciano; Fossa, Paola

    2013-12-01

    Phosphodiesterase 11 (PDE11) is the latest isoform of the PDEs family to be identified, acting on both cyclic adenosine monophosphate and cyclic guanosine monophosphate. The initial reports of PDE11 found evidence for PDE11 expression in skeletal muscle, prostate, testis, and salivary glands; however, the tissue distribution of PDE11 still remains a topic of active study and some controversy. Given the sequence similarity between PDE11 and PDE5, several PDE5 inhibitors have been shown to cross-react with PDE11. Accordingly, many non-selective inhibitors, such as IBMX, zaprinast, sildenafil, and dipyridamole, have been documented to inhibit PDE11. Only recently, a series of dihydrothieno[3,2-d]pyrimidin-4(3H)-one derivatives proved to be selective toward the PDE11 isoform. In the absence of experimental data about PDE11 X-ray structures, we found interesting to gain a better understanding of the enzyme-inhibitor interactions using in silico simulations. In this work, we describe a computational approach based on homology modeling, docking, and molecular dynamics simulation to derive a predictive 3D model of PDE11. Using a Graphical Processing Unit architecture, it is possible to perform long simulations, find stable interactions involved in the complex, and finally to suggest guideline for the identification and synthesis of potent and selective inhibitors. © 2013 John Wiley & Sons A/S.

  16. modeling grinding modeling grinding processes as micro processes

    African Journals Online (AJOL)

    eobe

    industrial precision grinding processes are cylindrical, center less and ... Several model shave been proposed and used to study grinding ..... grinding force for the two cases were 9.07237N/mm ..... International Journal of Machine Tools &.

  17. Molecular level in silico studies for oncology. Direct models review

    Science.gov (United States)

    Psakhie, S. G.; Tsukanov, A. A.

    2017-09-01

    The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented.

  18. Automated processing of data generated by molecular dynamics

    International Nuclear Information System (INIS)

    Lobato Hoyos, Ivan; Rojas Tapia, Justo; Instituto Peruano de Energia Nuclear, Lima

    2008-01-01

    A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)

  19. Accelerating Molecular Dynamic Simulation on Graphics Processing Units

    Science.gov (United States)

    Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.

    2009-01-01

    We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337

  20. Multi-enzyme Process Modeling

    DEFF Research Database (Denmark)

    Andrade Santacoloma, Paloma de Gracia

    are affected (in a positive or negative way) by the presence of the other enzymes and compounds in the media. In this thesis the concept of multi-enzyme in-pot term is adopted for processes that are carried out by the combination of enzymes in a single reactor and implemented at pilot or industrial scale...... features of the process and provides the information required to structure the process model by using a step-by-step procedure with the required tools and methods. In this way, this framework increases efficiency of the model development process with respect to time and resources needed (fast and effective....... In this way the model parameters that drives the main dynamic behavior can be identified and thus a better understanding of this type of processes. In order to develop, test and verify the methodology, three case studies were selected, specifically the bi-enzyme process for the production of lactobionic acid...

  1. Sato Processes in Default Modeling

    DEFF Research Database (Denmark)

    Kokholm, Thomas; Nicolato, Elisa

    -change of a homogeneous Levy process. While the processes in these two classes share the same average behavior over time, the associated intensities exhibit very different properties. Concrete specifications are calibrated to data on the single names included in the iTraxx Europe index. The performances are compared......In reduced form default models, the instantaneous default intensity is classically the modeling object. Survival probabilities are then given by the Laplace transform of the cumulative hazard defined as the integrated intensity process. Instead, recent literature has shown a tendency towards...... specifying the cumulative hazard process directly. Within this framework we present a new model class where cumulative hazards are described by self-similar additive processes, also known as Sato processes. Furthermore we also analyze specifications obtained via a simple deterministic time...

  2. From cellulose to kerogen: molecular simulation of a geological process.

    Science.gov (United States)

    Atmani, Lea; Bichara, Christophe; Pellenq, Roland J-M; Van Damme, Henri; van Duin, Adri C T; Raza, Zamaan; Truflandier, Lionel A; Obliger, Amaël; Kralert, Paul G; Ulm, Franz J; Leyssale, Jean-Marc

    2017-12-01

    The process by which organic matter decomposes deep underground to form petroleum and its underlying kerogen matrix has so far remained a no man's land to theoreticians, largely because of the geological (Myears) timescale associated with the process. Using reactive molecular dynamics and an accelerated simulation framework, the replica exchange molecular dynamics method, we simulate the full transformation of cellulose into kerogen and its associated fluid phase under prevailing geological conditions. We observe in sequence the fragmentation of the cellulose crystal and production of water, the development of an unsaturated aliphatic macromolecular phase and its aromatization. The composition of the solid residue along the maturation pathway strictly follows what is observed for natural type III kerogen and for artificially matured samples under confined conditions. After expulsion of the fluid phase, the obtained microporous kerogen possesses the structure, texture, density, porosity and stiffness observed for mature type III kerogen and a microporous carbon obtained by saccharose pyrolysis at low temperature. As expected for this variety of precursor, the main resulting hydrocarbon is methane. The present work thus demonstrates that molecular simulations can now be used to assess, almost quantitatively, such complex chemical processes as petrogenesis in fossil reservoirs and, more generally, the possible conversion of any natural product into bio-sourced materials and/or fuel.

  3. An Integrated Biochemistry Laboratory, Including Molecular Modeling

    Science.gov (United States)

    Hall, Adele J. Wolfson Mona L.; Branham, Thomas R.

    1996-11-01

    purity of the final preparation. Using mini-gels (BioRad Mini-Protean II apparatus), each group can pour, run, and stain their own 8 7.3-cm gel within the lab period; destaining can be carried out at any time afterward. The main contaminating band observed is ovalbumin, at a molecular weight of 46,000. Computer Modeling Using the program Quanta (MSI, Burlington, MA) on Indigo workstations (Silicon Graphics, Hudson, MA), the students retrieve coordinates from an MSI version of the Protein Data Bank, display the structure, and rationalize what changes would occur with a mutated form of the protein. Even for those who do not have Quanta or analogous programs, structural coordinates are available through the Internet. Students are prepared for their independent use of the molecular modeling workstations through a series of tutorials during the course of the semester. These exercises require that the students become familiar with specific applications of Quanta, including setting secondary conformation and hydrogen bonds, energy calculations, selectively displaying parts of molecules, measuring interatomic distances, and editing existing proteins. This introduction to macromolecular modeling is comparable to that suggested by Harvey and Tan (17) as a brief introduction to the field. Peer Review For each writing assignment (short paper and grant proposal), one week of lab is devoted to the peer review process. Students are to come to lab with a draft of their paper and a cover letter to their reviewers, which states how far they believe they are in the writing process; what they like and don't like about their work at this stage; and in what specific areas they need help (e.g., audience level, organization, use of references). They exchange papers, reading two or three during the course of the lab period. For each paper, they fill out a peer review form, which requires that they summarize the paper; look for clarity of presentation, appropriate citations, and use of others

  4. 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.

  5. Markov Decision Process Measurement Model.

    Science.gov (United States)

    LaMar, Michelle M

    2018-03-01

    Within-task actions can provide additional information on student competencies but are challenging to model. This paper explores the potential of using a cognitive model for decision making, the Markov decision process, to provide a mapping between within-task actions and latent traits of interest. Psychometric properties of the model are explored, and simulation studies report on parameter recovery within the context of a simple strategy game. The model is then applied to empirical data from an educational game. Estimates from the model are found to correlate more strongly with posttest results than a partial-credit IRT model based on outcome data alone.

  6. Social Models: Blueprints or Processes?

    Science.gov (United States)

    Little, Graham R.

    1981-01-01

    Discusses the nature and implications of two different models for societal planning: (1) the problem-solving process approach based on Karl Popper; and (2) the goal-setting "blueprint" approach based on Karl Marx. (DC)

  7. Simple Models for Process Control

    Czech Academy of Sciences Publication Activity Database

    Gorez, R.; Klán, Petr

    2011-01-01

    Roč. 22, č. 2 (2011), s. 58-62 ISSN 0929-2268 Institutional research plan: CEZ:AV0Z10300504 Keywords : process model s * PID control * second order dynamics Subject RIV: JB - Sensors, Measurment, Regulation

  8. Model feedstock supply processing plants

    Directory of Open Access Journals (Sweden)

    V. M. Bautin

    2013-01-01

    Full Text Available The model of raw providing the processing enterprises entering into vertically integrated structure on production and processing of dairy raw materials, differing by an orientation on achievement of cumulative effect by the integrated structure acting as criterion function which maximizing is reached by optimization of capacities, volumes of deliveries of raw materials and its qualitative characteristics, costs of industrial processing of raw materials and demand for dairy production is developed.

  9. Belowground Carbon Cycling Processes at the Molecular Scale: An EMSL Science Theme Advisory Panel Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Nancy J.; Brown, Gordon E.; Plata, Charity

    2014-02-21

    As part of the Belowground Carbon Cycling Processes at the Molecular Scale workshop, an EMSL Science Theme Advisory Panel meeting held in February 2013, attendees discussed critical biogeochemical processes that regulate carbon cycling in soil. The meeting attendees determined that as a national scientific user facility, EMSL can provide the tools and expertise needed to elucidate the molecular foundation that underlies mechanistic descriptions of biogeochemical processes that control carbon allocation and fluxes at the terrestrial/atmospheric interface in landscape and regional climate models. Consequently, the workshop's goal was to identify the science gaps that hinder either development of mechanistic description of critical processes or their accurate representation in climate models. In part, this report offers recommendations for future EMSL activities in this research area. The workshop was co-chaired by Dr. Nancy Hess (EMSL) and Dr. Gordon Brown (Stanford University).

  10. 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.

  11. 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.

  12. Sato Processes in Default Modeling

    DEFF Research Database (Denmark)

    Kokholm, Thomas; Nicolato, Elisa

    2010-01-01

    In reduced form default models, the instantaneous default intensity is the classical modeling object. Survival probabilities are then given by the Laplace transform of the cumulative hazard defined as the integrated intensity process. Instead, recent literature tends to specify the cumulative haz...

  13. Sato Processes in Default Modeling

    DEFF Research Database (Denmark)

    Kokholm, Thomas; Nicolato, Elisa

    In reduced form default models, the instantaneous default intensity is classically the modeling object. Survival probabilities are then given by the Laplace transform of the cumulative hazard defined as the integrated intensity process. Instead, recent literature has shown a tendency towards...

  14. Metrics for Business Process Models

    Science.gov (United States)

    Mendling, Jan

    Up until now, there has been little research on why people introduce errors in real-world business process models. In a more general context, Simon [404] points to the limitations of cognitive capabilities and concludes that humans act rationally only to a certain extent. Concerning modeling errors, this argument would imply that human modelers lose track of the interrelations of large and complex models due to their limited cognitive capabilities and introduce errors that they would not insert in a small model. A recent study by Mendling et al. [275] explores in how far certain complexity metrics of business process models have the potential to serve as error determinants. The authors conclude that complexity indeed appears to have an impact on error probability. Before we can test such a hypothesis in a more general setting, we have to establish an understanding of how we can define determinants that drive error probability and how we can measure them.

  15. 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)

  16. 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)

  17. Molecular Probes: An Innovative Technology for Monitoring Membrane Processes

    Science.gov (United States)

    Santoro, Sergio

    The ultimate objective of this study is to use molecular probes as an innovative and alternative technology contributing to the advance of membrane science by monitoring membrane processes in-situ, on-line and at sub-micron scale. An optical sensor for oxygen sensing was developed by the immobilization of tris (1,10-phenanthroline) ruthenium (II) (Ru(phen)3) in a dense polymeric membrane made of polystyrene (PS) or Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). The emission of the probe was quenched by both the temperature and by the oxygen. Moreover, the oxygen sensitivity was affected by the oxygen permeability of the membrane. The evaluation of the oxygen concentration is prone to errors since the emission of a single probe depends on several parameters (i.e. optical path, source intensity). The correction of these artefacts was obtained by the immobilization of a second luminescent molecule non-sensitive to the oxygen, Coumarin. The potential of the luminescent ratiometric sensor for the non-invasive monitoring of oxygen in food packaging using polymeric films with different oxygen permeability was evaluated. Emphasis was given to the efficiency of the optical sensor for the on-line, in-situ and non invasive monitoring of the oxygen by comparing the experimental data with a model which takes into account the oxygen permeability of the packaging materials evaluated independently. A nano-thermometer based on silica nano-particles doped with Ru(phen)3 was developed. A systematic study shows how it is possible to control the properties of the nano-particles as well as their temperature sensitivity. The nano-thermometer was immobilized on a membrane surface by dip-coating providing information about the temperature on the membrane surface. Hydrophobic porous membrane made of Poly(vinylidene fluoride) was prepared via electrospinning and employed in a direct contact membrane distillation process. Using a designed membrane module and a membrane doped with Ru

  18. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik; Szepessy, Anders

    2010-01-01

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  19. A stochastic phase-field model determined from molecular dynamics

    KAUST Repository

    von Schwerin, Erik

    2010-03-17

    The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

  20. Computer Modelling of Dynamic Processes

    Directory of Open Access Journals (Sweden)

    B. Rybakin

    2000-10-01

    Full Text Available Results of numerical modeling of dynamic problems are summed in the article up. These problems are characteristic for various areas of human activity, in particular for problem solving in ecology. The following problems are considered in the present work: computer modeling of dynamic effects on elastic-plastic bodies, calculation and determination of performances of gas streams in gas cleaning equipment, modeling of biogas formation processes.

  1. Modelling Hospital Materials Management Processes

    Directory of Open Access Journals (Sweden)

    Raffaele Iannone

    2013-06-01

    integrated and detailed analysis and description model for hospital materials management data and tasks, which is able to tackle information from patient requirements to usage, from replenishment requests to supplying and handling activities. The model takes account of medical risk reduction, traceability and streamlined processes perspectives. Second, the paper translates this information into a business process model and mathematical formalization.The study provides a useful guide to the various relevant technology‐related, management and business issues, laying the foundations of an efficient reengineering of the supply chain to reduce healthcare costs and improve the quality of care.

  2. Declarative modeling for process supervision

    International Nuclear Information System (INIS)

    Leyval, L.

    1989-01-01

    Our work is a contribution to computer aided supervision of continuous processes. It is inspired by an area of Artificial Intelligence: qualitative physics. Here, supervision is based on a model which continuously provides operators with a synthetic view of the process; but this model is founded on general principles of control theory rather than on physics. It involves concepts such as high gain or small time response. It helps in linking temporally the evolution of various variables. Moreover, the model provides predictions of the future behaviour of the process, which allows action advice and alarm filtering. This should greatly reduce the famous cognitive overload associated to any complex and dangerous evolution of the process

  3. The independent molecular interaction sites model. Pt. 1

    International Nuclear Information System (INIS)

    Naumann, K.H.; Lippert, E.

    1981-01-01

    A new reference system for the treatment of molecular fluids within the framework of thermodynamic perturbation theory is presented. The basic ingredient of our approach is a potential transformation which allows us to view molecular liquids and gases as mixtures of formally independent molecular interaction sites (IMIS model). Some relations between out method and the RAM theory are discussed. (orig.)

  4. Modeling of biopharmaceutical processes. Part 2: Process chromatography unit operation

    DEFF Research Database (Denmark)

    Kaltenbrunner, Oliver; McCue, Justin; Engel, Philip

    2008-01-01

    Process modeling can be a useful tool to aid in process development, process optimization, and process scale-up. When modeling a chromatography process, one must first select the appropriate models that describe the mass transfer and adsorption that occurs within the porous adsorbent. The theoret......Process modeling can be a useful tool to aid in process development, process optimization, and process scale-up. When modeling a chromatography process, one must first select the appropriate models that describe the mass transfer and adsorption that occurs within the porous adsorbent...

  5. Bayesian semiparametric regression models to characterize molecular evolution

    Directory of Open Access Journals (Sweden)

    Datta Saheli

    2012-10-01

    Full Text Available Abstract Background Statistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the molecular level typically do not take into account the correlations between such properties. We propose a Bayesian hierarchical regression model with a generalization of the Dirichlet process prior on the distribution of the regression coefficients that describes the relationship between the changes in amino acid distances and natural selection in protein-coding DNA sequence alignments. Results The Bayesian semiparametric approach is illustrated with simulated data and the abalone lysin sperm data. Our method identifies groups of properties which, for this particular dataset, have a similar effect on evolution. The model also provides nonparametric site-specific estimates for the strength of conservation of these properties. Conclusions The model described here is distinguished by its ability to handle a large number of amino acid properties simultaneously, while taking into account that such data can be correlated. The multi-level clustering ability of the model allows for appealing interpretations of the results in terms of properties that are roughly equivalent from the standpoint of molecular evolution.

  6. Neuroscientific Model of Motivational Process

    Science.gov (United States)

    Kim, Sung-il

    2013-01-01

    Considering the neuroscientific findings on reward, learning, value, decision-making, and cognitive control, motivation can be parsed into three sub processes, a process of generating motivation, a process of maintaining motivation, and a process of regulating motivation. I propose a tentative neuroscientific model of motivational processes which consists of three distinct but continuous sub processes, namely reward-driven approach, value-based decision-making, and goal-directed control. Reward-driven approach is the process in which motivation is generated by reward anticipation and selective approach behaviors toward reward. This process recruits the ventral striatum (reward area) in which basic stimulus-action association is formed, and is classified as an automatic motivation to which relatively less attention is assigned. By contrast, value-based decision-making is the process of evaluating various outcomes of actions, learning through positive prediction error, and calculating the value continuously. The striatum and the orbitofrontal cortex (valuation area) play crucial roles in sustaining motivation. Lastly, the goal-directed control is the process of regulating motivation through cognitive control to achieve goals. This consciously controlled motivation is associated with higher-level cognitive functions such as planning, retaining the goal, monitoring the performance, and regulating action. The anterior cingulate cortex (attention area) and the dorsolateral prefrontal cortex (cognitive control area) are the main neural circuits related to regulation of motivation. These three sub processes interact with each other by sending reward prediction error signals through dopaminergic pathway from the striatum and to the prefrontal cortex. The neuroscientific model of motivational process suggests several educational implications with regard to the generation, maintenance, and regulation of motivation to learn in the learning environment. PMID:23459598

  7. Neuroscientific model of motivational process.

    Science.gov (United States)

    Kim, Sung-Il

    2013-01-01

    Considering the neuroscientific findings on reward, learning, value, decision-making, and cognitive control, motivation can be parsed into three sub processes, a process of generating motivation, a process of maintaining motivation, and a process of regulating motivation. I propose a tentative neuroscientific model of motivational processes which consists of three distinct but continuous sub processes, namely reward-driven approach, value-based decision-making, and goal-directed control. Reward-driven approach is the process in which motivation is generated by reward anticipation and selective approach behaviors toward reward. This process recruits the ventral striatum (reward area) in which basic stimulus-action association is formed, and is classified as an automatic motivation to which relatively less attention is assigned. By contrast, value-based decision-making is the process of evaluating various outcomes of actions, learning through positive prediction error, and calculating the value continuously. The striatum and the orbitofrontal cortex (valuation area) play crucial roles in sustaining motivation. Lastly, the goal-directed control is the process of regulating motivation through cognitive control to achieve goals. This consciously controlled motivation is associated with higher-level cognitive functions such as planning, retaining the goal, monitoring the performance, and regulating action. The anterior cingulate cortex (attention area) and the dorsolateral prefrontal cortex (cognitive control area) are the main neural circuits related to regulation of motivation. These three sub processes interact with each other by sending reward prediction error signals through dopaminergic pathway from the striatum and to the prefrontal cortex. The neuroscientific model of motivational process suggests several educational implications with regard to the generation, maintenance, and regulation of motivation to learn in the learning environment.

  8. Molecular modeling and multiscaling issues for electronic material applications

    CERN Document Server

    Iwamoto, Nancy; Yuen, Matthew; Fan, Haibo

    Volume 1 : Molecular Modeling and Multiscaling Issues for Electronic Material Applications provides a snapshot on the progression of molecular modeling in the electronics industry and how molecular modeling is currently being used to understand material performance to solve relevant issues in this field. This book is intended to introduce the reader to the evolving role of molecular modeling, especially seen through the eyes of the IEEE community involved in material modeling for electronic applications.  Part I presents  the role that quantum mechanics can play in performance prediction, such as properties dependent upon electronic structure, but also shows examples how molecular models may be used in performance diagnostics, especially when chemistry is part of the performance issue.  Part II gives examples of large-scale atomistic methods in material failure and shows several examples of transitioning between grain boundary simulations (on the atomistic level)and large-scale models including an example ...

  9. ECONOMIC MODELING PROCESSES USING MATLAB

    Directory of Open Access Journals (Sweden)

    Anamaria G. MACOVEI

    2008-06-01

    Full Text Available To study economic phenomena and processes using mathem atical modeling, and to determine the approximatesolution to a problem we need to choose a method of calculation and a numerical computer program, namely thepackage of programs MatLab. Any economic process or phenomenon is a mathematical description of h is behavior,and thus draw up an economic and mathematical model that has the following stages: formulation of the problem, theanalysis process modeling, the production model and design verification, validation and implementation of the model.This article is presented an economic model and its modeling is using mathematical equations and software packageMatLab, which helps us approximation effective solution. As data entry is considered the net cost, the cost of direct andtotal cost and the link between them. I presented the basic formula for determining the total cost. Economic modelcalculations were made in MatLab software package and with graphic representation of its interpretation of the resultsachieved in terms of our specific problem.

  10. Path modeling and process control

    DEFF Research Database (Denmark)

    Høskuldsson, Agnar; Rodionova, O.; Pomerantsev, A.

    2007-01-01

    and having three or more stages. The methods are applied to a process control of a multi-stage production process having 25 variables and one output variable. When moving along the process, variables change their roles. It is shown how the methods of path modeling can be applied to estimate variables...... be performed regarding the foreseeable output property y, and with respect to an admissible range of correcting actions for the parameters of the next stage. In this paper the basic principles of path modeling is presented. The mathematics is presented for processes having only one stage, having two stages...... of the next stage with the purpose of obtaining optimal or almost optimal quality of the output variable. An important aspect of the methods presented is the possibility of extensive graphic analysis of data that can provide the engineer with a detailed view of the multi-variate variation in data....

  11. Diffusion in Liquids : Equilibrium Molecular Simulations and Predictive Engineering Models

    NARCIS (Netherlands)

    Liu, X.

    2013-01-01

    The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations.

  12. Process Models for Security Architectures

    Directory of Open Access Journals (Sweden)

    Floarea NASTASE

    2006-01-01

    Full Text Available This paper presents a model for an integrated security system, which can be implemented in any organization. It is based on security-specific standards and taxonomies as ISO 7498-2 and Common Criteria. The functionalities are derived from the classes proposed in the Common Criteria document. In the paper we present the process model for each functionality and also we focus on the specific components.

  13. 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.

  14. 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.

  15. Molecular-level insights into aging processes of skin elastin

    DEFF Research Database (Denmark)

    Mora Huertas, Angela C; Schmelzer, Christian E H; Hoehenwarter, Wolfgang

    2016-01-01

    Skin aging is characterized by different features including wrinkling, atrophy of the dermis and loss of elasticity associated with damage to the extracellular matrix protein elastin. The aim of this study was to investigate the aging process of skin elastin at the molecular level by evaluating...... the influence of intrinsic (chronological aging) and extrinsic factors (sun exposure) on the morphology and susceptibility of elastin towards enzymatic degradation. Elastin was isolated from biopsies derived from sun-protected or sun-exposed skin of differently aged individuals. The morphology of the elastin...... pronounced in sun-exposed tissue. Marker peptides were identified, which showed an age-related increase or decrease in their abundances and provide insights into the progression of the aging process of elastin fibers. Strong age-related cleavage occurs in hydrophobic tropoelastin domains 18, 20, 24 and 26...

  16. A consistent transported PDF model for treating differential molecular diffusion

    Science.gov (United States)

    Wang, Haifeng; Zhang, Pei

    2016-11-01

    Differential molecular diffusion is a fundamentally significant phenomenon in all multi-component turbulent reacting or non-reacting flows caused by the different rates of molecular diffusion of energy and species concentrations. In the transported probability density function (PDF) method, the differential molecular diffusion can be treated by using a mean drift model developed by McDermott and Pope. This model correctly accounts for the differential molecular diffusion in the scalar mean transport and yields a correct DNS limit of the scalar variance production. The model, however, misses the molecular diffusion term in the scalar variance transport equation, which yields an inconsistent prediction of the scalar variance in the transported PDF method. In this work, a new model is introduced to remedy this problem that can yield a consistent scalar variance prediction. The model formulation along with its numerical implementation is discussed, and the model validation is conducted in a turbulent mixing layer problem.

  17. Mathematical modelling in economic processes.

    Directory of Open Access Journals (Sweden)

    L.V. Kravtsova

    2008-06-01

    Full Text Available In article are considered a number of methods of mathematical modelling of economic processes and opportunities of use of spreadsheets Excel for reception of the optimum decision of tasks or calculation of financial operations with the help of the built-in functions.

  18. Fracture of Carbon Nanotube - Amorphous Carbon Composites: Molecular Modeling

    Science.gov (United States)

    Jensen, Benjamin D.; Wise, Kristopher E.; Odegard, Gregory M.

    2015-01-01

    Carbon nanotubes (CNTs) are promising candidates for use as reinforcements in next generation structural composite materials because of their extremely high specific stiffness and strength. They cannot, however, be viewed as simple replacements for carbon fibers because there are key differences between these materials in areas such as handling, processing, and matrix design. It is impossible to know for certain that CNT composites will represent a significant advance over carbon fiber composites before these various factors have been optimized, which is an extremely costly and time intensive process. This work attempts to place an upper bound on CNT composite mechanical properties by performing molecular dynamics simulations on idealized model systems with a reactive forcefield that permits modeling of both elastic deformations and fracture. Amorphous carbon (AC) was chosen for the matrix material in this work because of its structural simplicity and physical compatibility with the CNT fillers. It is also much stiffer and stronger than typical engineering polymer matrices. Three different arrangements of CNTs in the simulation cell have been investigated: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. The SWNT and MWNT array systems are clearly idealizations, but the SWNT bundle system is a step closer to real systems in which individual tubes aggregate into large assemblies. The effect of chemical crosslinking on composite properties is modeled by adding bonds between the CNTs and AC. The balance between weakening the CNTs and improving fiber-matrix load transfer is explored by systematically varying the extent of crosslinking. It is, of course, impossible to capture the full range of deformation and fracture processes that occur in real materials with even the largest atomistic molecular dynamics simulations. With this limitation in mind, the simulation results reported here provide a plausible upper limit on

  19. Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

    Science.gov (United States)

    Kulasiri, Don

    2011-01-01

    We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

  20. Visualizing the process of process modeling with PPMCharts

    NARCIS (Netherlands)

    Claes, J.; Vanderfeesten, I.T.P.; Pinggera, J.; Reijers, H.A.; Weber, B.; Poels, G.; La Rosa, M.; Soffer, P.

    2013-01-01

    In the quest for knowledge about how to make good process models, recent research focus is shifting from studying the quality of process models to studying the process of process modeling (often abbreviated as PPM) itself. This paper reports on our efforts to visualize this specific process in such

  1. Neuroscientific Model of Motivational Process

    Directory of Open Access Journals (Sweden)

    Sung-Il eKim

    2013-03-01

    Full Text Available Considering the neuroscientific findings on reward, learning, value, decision-making, and cognitive control, motivation can be parsed into three subprocesses, a process of generating motivation, a process of maintaining motivation, and a process of regulating motivation. I propose a tentative neuroscientific model of motivational processes which consists of three distinct but continuous subprocesses, namely reward-driven approach, value-based decision making, and goal-directed control. Reward-driven approach is the process in which motivation is generated by reward anticipation and selective approach behaviors toward reward. This process recruits the ventral striatum (reward area in which basic stimulus-action association is formed, and is classified as an automatic motivation to which relatively less attention is assigned. By contrast, value-based decision making is the process of evaluating various outcomes of actions, learning through positive prediction error, and calculating the value continuously. The striatum and the orbitofrontal cortex (valuation area play crucial roles in sustaining motivation. Lastly, the goal-directed control is the process of regulating motivation through cognitive control to achieve goals. This consciously controlled motivation is associated with higher-level cognitive functions such as planning, retaining the goal, monitoring the performance, and regulating action. The anterior cingulate cortex (attention area and the dorsolateral prefrontal cortex (cognitive control area are the main neural circuits related to regulation of motivation. These three subprocesses interact with each other by sending reward prediction error signals through dopaminergic pathway from the striatum and to the prefrontal cortex. The neuroscientific model of motivational process suggests several educational implications with regard to the generation, maintenance, and regulation of motivation to learn in the learning environment.

  2. Molecular Dynamic Modeling and Simulation for Polymers

    National Research Council Canada - National Science Library

    Harrell, Anthony

    2003-01-01

    ... the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity...

  3. Integrated Site Model Process Model Report

    International Nuclear Information System (INIS)

    Booth, T.

    2000-01-01

    The Integrated Site Model (ISM) provides a framework for discussing the geologic features and properties of Yucca Mountain, which is being evaluated as a potential site for a geologic repository for the disposal of nuclear waste. The ISM is important to the evaluation of the site because it provides 3-D portrayals of site geologic, rock property, and mineralogic characteristics and their spatial variabilities. The ISM is not a single discrete model; rather, it is a set of static representations that provide three-dimensional (3-D), computer representations of site geology, selected hydrologic and rock properties, and mineralogic-characteristics data. These representations are manifested in three separate model components of the ISM: the Geologic Framework Model (GFM), the Rock Properties Model (RPM), and the Mineralogic Model (MM). The GFM provides a representation of the 3-D stratigraphy and geologic structure. Based on the framework provided by the GFM, the RPM and MM provide spatial simulations of the rock and hydrologic properties, and mineralogy, respectively. Functional summaries of the component models and their respective output are provided in Section 1.4. Each of the component models of the ISM considers different specific aspects of the site geologic setting. Each model was developed using unique methodologies and inputs, and the determination of the modeled units for each of the components is dependent on the requirements of that component. Therefore, while the ISM represents the integration of the rock properties and mineralogy into a geologic framework, the discussion of ISM construction and results is most appropriately presented in terms of the three separate components. This Process Model Report (PMR) summarizes the individual component models of the ISM (the GFM, RPM, and MM) and describes how the three components are constructed and combined to form the ISM

  4. Viscoelasticity in Polymers: Phenomenological to Molecular Mathematical Modelling

    National Research Council Canada - National Science Library

    Banks, H. T; Luke, N. S

    2006-01-01

    We report on two recent advances in the modelling of viscoelastic polymers: (i) a new constitutive model which combines the virtual stick-slip continuum "molecular-based" ideas of Johnson and Stacer with the Rouse bead chain ideas; (ii...

  5. Investigating the Process of Process Modeling with Eye Movement Analysis

    OpenAIRE

    Pinggera, Jakob; Furtner, Marco; Martini, Markus; Sachse, Pierre; Reiter, Katharina; Zugal, Stefan; Weber, Barbara

    2015-01-01

    Research on quality issues of business process models has recently begun to explore the process of creating process models by analyzing the modeler's interactions with the modeling environment. In this paper we aim to complement previous insights on the modeler's modeling behavior with data gathered by tracking the modeler's eye movements when engaged in the act of modeling. We present preliminary results and outline directions for future research to triangulate toward a more comprehensive un...

  6. Welding process modelling and control

    Science.gov (United States)

    Romine, Peter L.; Adenwala, Jinen A.

    1993-01-01

    The research and analysis performed, and software developed, and hardware/software recommendations made during 1992 in development of the PC-based data acquisition system for support of Welding Process Modeling and Control is reported. A need was identified by the Metals Processing Branch of NASA Marshall Space Flight Center, for a mobile data aquisition and analysis system, customized for welding measurement and calibration. Several hardware configurations were evaluated and a PC-based system was chosen. The Welding Measurement System (WMS) is a dedicated instrument, strictly for the use of data aquisition and analysis. Although the WMS supports many of the functions associated with the process control, it is not the intention for this system to be used for welding process control.

  7. Application of Molecular Modeling to Urokinase Inhibitors Development

    Directory of Open Access Journals (Sweden)

    V. B. Sulimov

    2014-01-01

    Full Text Available Urokinase-type plasminogen activator (uPA plays an important role in the regulation of diverse physiologic and pathologic processes. Experimental research has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients, whereas suppression of proteolytic activity of uPA leads to evident decrease of metastasis. Therefore, uPA has been considered as a promising molecular target for development of anticancer drugs. The present study sets out to develop the new selective uPA inhibitors using computer-aided structural based drug design methods. Investigation involves the following stages: computer modeling of the protein active site, development and validation of computer molecular modeling methods: docking (SOL program, postprocessing (DISCORE program, direct generalized docking (FLM program, and the application of the quantum chemical calculations (MOPAC package, search of uPA inhibitors among molecules from databases of ready-made compounds to find new uPA inhibitors, and design of new chemical structures and their optimization and experimental examination. On the basis of known uPA inhibitors and modeling results, 18 new compounds have been designed, calculated using programs mentioned above, synthesized, and tested in vitro. Eight of them display inhibitory activity and two of them display activity about 10 μM.

  8. Graphics processing units accelerated semiclassical initial value representation molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Tamascelli, Dario; Dambrosio, Francesco Saverio [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Conte, Riccardo [Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States); Ceotto, Michele, E-mail: michele.ceotto@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)

    2014-05-07

    This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly.

  9. Advanced oxidation processes: overall models

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, M. [Univ. de los Andes, Escuela Basica de Ingenieria, La Hechicera, Merida (Venezuela); Curco, D.; Addardak, A.; Gimenez, J.; Esplugas, S. [Dept. de Ingenieria Quimica. Univ. de Barcelona, Barcelona (Spain)

    2003-07-01

    Modelling AOPs implies to consider all the steps included in the process, that means, mass transfer, kinetic (reaction) and luminic steps. In this way, recent works develop models which relate the global reaction rate to catalyst concentration and radiation absorption. However, the application of such models requires to know what is the controlling step for the overall process. In this paper, a simple method is explained which allows to determine the controlling step. Thus, it is assumed that reactor is divided in two hypothetical zones (dark and illuminated), and according to the experimental results, obtained by varying only the reaction volume, it can be decided if reaction occurs only in the illuminated zone or in the all reactor, including dark zone. The photocatalytic degradation of phenol, by using titania degussa P-25 as catalyst, is studied as reaction model. The preliminary results obtained are presented here, showing that it seems that, in this case, reaction only occurs in the illuminated zone of photoreactor. A model is developed to explain this behaviour. (orig.)

  10. Model for amorphous aggregation processes

    Science.gov (United States)

    Stranks, Samuel D.; Ecroyd, Heath; van Sluyter, Steven; Waters, Elizabeth J.; Carver, John A.; von Smekal, Lorenz

    2009-11-01

    The amorphous aggregation of proteins is associated with many phenomena, ranging from the formation of protein wine haze to the development of cataract in the eye lens and the precipitation of recombinant proteins during their expression and purification. While much literature exists describing models for linear protein aggregation, such as amyloid fibril formation, there are few reports of models which address amorphous aggregation. Here, we propose a model to describe the amorphous aggregation of proteins which is also more widely applicable to other situations where a similar process occurs, such as in the formation of colloids and nanoclusters. As first applications of the model, we have tested it against experimental turbidimetry data of three proteins relevant to the wine industry and biochemistry, namely, thaumatin, a thaumatinlike protein, and α -lactalbumin. The model is very robust and describes amorphous experimental data to a high degree of accuracy. Details about the aggregation process, such as shape parameters of the aggregates and rate constants, can also be extracted.

  11. 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.

  12. The VSEPR model of molecular geometry

    CERN Document Server

    Gillespie, Ronald J

    2012-01-01

    Valence Shell Electron Pair Repulsion (VSEPR) theory is a simple technique for predicting the geometry of atomic centers in small molecules and molecular ions. This authoritative reference was written by Istvan Hartiggai and the developer of VSEPR theory, Ronald J. Gillespie. In addition to its value as a text for courses in molecular geometry and chemistry, it constitutes a classic reference for professionals.Starting with coverage of the broader aspects of VSEPR, this volume narrows its focus to a succinct survey of the methods of structural determination. Additional topics include the appli

  13. Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

    KAUST Repository

    Kadoura, Ahmad

    2016-09-01

    This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method to replace correlations and equations of state in subsurface flow simulators. In order to accelerate MC simulations, a set of early rejection schemes (conservative, hybrid, and non-conservative) in addition to extrapolation methods through reweighting and reconstruction of pre-generated MC Markov chains were developed. Furthermore, an extensive study was conducted to investigate sorption and transport processes of methane, carbon dioxide, water, and their mixtures in the inorganic part of shale using both MC and MD simulations. These simulations covered a wide range of thermodynamic conditions, pore sizes, and fluid compositions shedding light on several interesting findings. For example, the possibility to have more carbon dioxide adsorbed with more preadsorbed water concentrations at relatively large basal spaces. The dissertation is divided into four chapters. The first chapter corresponds to the introductory part where a brief background about molecular simulation and motivations are given. The second chapter is devoted to discuss the theoretical aspects and methodology of the proposed MC speeding up techniques in addition to the corresponding results leading to the successful multi-scale simulation of the compressible single-phase flow scenario. In chapter 3, the results regarding our extensive study on shale gas at laboratory conditions are reported. At the fourth and last chapter, we end the dissertation with few concluding remarks highlighting the key findings and summarizing the future directions.

  14. Development and Evaluation of Amino Acid Molecular Models

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2007-05-01

    Full Text Available The comprehension of structure and function of proteins has a tight relationshipwith the development of structural biology. However, biochemistry students usuallyfind difficulty to visualize the structures when they use only schematic drawings ofdidactic books. The representation of three-dimensional structures of somebiomolecules with ludic models, built with representative units, have supplied tothe students and teachers a successfully experience to better visualize andcorrelate the structures to the real molecules. The present work shows thedeveloped models and the process to produce the representative units of the mainamino acids in industrial scale. The design and applicability of the representativeunits were discussed with many teachers and some suggestions wereimplemented to the models. The preliminary evaluation and perspective ofutilization by researchers show that the work is in the right direction. At the actualstage, the models are defined, prototypes were made and will be presented in thismeeting. The moulds for the units are at the final stage of construction and trial inspecialized tool facilities. The last term will consist of an effective evaluation of thedidactic tool for the teaching/learning process in Structural Molecular Biology. Theevaluation protocol is being elaborated containing simple and objective questions,similar to those used in research on science teaching.

  15. Probabilistic evaluation of process model matching techniques

    NARCIS (Netherlands)

    Kuss, Elena; Leopold, Henrik; van der Aa, Han; Stuckenschmidt, Heiner; Reijers, Hajo A.

    2016-01-01

    Process model matching refers to the automatic identification of corresponding activities between two process models. It represents the basis for many advanced process model analysis techniques such as the identification of similar process parts or process model search. A central problem is how to

  16. Mathematical modeling of biological processes

    CERN Document Server

    Friedman, Avner

    2014-01-01

    This book on mathematical modeling of biological processes includes a wide selection of biological topics that demonstrate the power of mathematics and computational codes in setting up biological processes with a rigorous and predictive framework. Topics include: enzyme dynamics, spread of disease, harvesting bacteria, competition among live species, neuronal oscillations, transport of neurofilaments in axon, cancer and cancer therapy, and granulomas. Complete with a description of the biological background and biological question that requires the use of mathematics, this book is developed for graduate students and advanced undergraduate students with only basic knowledge of ordinary differential equations and partial differential equations; background in biology is not required. Students will gain knowledge on how to program with MATLAB without previous programming experience and how to use codes in order to test biological hypothesis.

  17. Modeling pellet impact drilling process

    Science.gov (United States)

    Kovalyov, A. V.; Ryabchikov, S. Ya; Isaev, Ye D.; Ulyanova, O. S.

    2016-03-01

    The paper describes pellet impact drilling which could be used to increase the drilling speed and the rate of penetration when drilling hard rocks. Pellet impact drilling implies rock destruction by metal pellets with high kinetic energy in the immediate vicinity of the earth formation encountered. The pellets are circulated in the bottom hole by a high velocity fluid jet, which is the principle component of the ejector pellet impact drill bit. The experiments conducted has allowed modeling the process of pellet impact drilling, which creates the scientific and methodological basis for engineering design of drilling operations under different geo-technical conditions.

  18. Molecular models of zinc phthalocyanines: semi-empirical molecular orbital computations and physicochemical properties studied by molecular mechanics simulations

    International Nuclear Information System (INIS)

    Gantchev, Tsvetan G.; van Lier, Johan E.; Hunting, Darel J.

    2005-01-01

    To build 3D-molecular models of Zinc-phthalocyanines (ZnPc) and to study their diverse chemical and photosensitization properties, we performed quantum mechanical molecular orbital (MO) semi-empirical (AM1) computations of the ground, excited singlet and triplet states as well as free radical (ionic) species. RHF and UHF (open shell) geometry optimizations led to near-perfect symmetrical ZnPc. Predicted ionization potentials (IP), electron affinities (EA) and lowest electronic transitions of ZnPc are in good agreement with the published experimental and theoretical data. The computation-derived D 4h /D 2h -symmetry 3D-structures of ground and excited states and free radicals of ZnPc, together with the frontier orbital energies and Mulliken electron population analysis enabled us to build robust molecular models. These models were used to predict important chemical-reactivity entities such as global electronegativity (χ), hardness (η) and local softness based on Fukui-functions analysis. Examples of molecular mechanics (MM) applications of the 3D-molecular models are presented as approaches to evaluate solvation free energy (ΔG 0 ) solv and to estimate ground- and excited- state oxidation/reduction potentials as well as intermolecular interactions and stability of ground and excited state dimers (exciplexes) and radical ion-pairs

  19. Membrane dynamics of γ-secretase provides a molecular basis for Aβ binding and processing

    DEFF Research Database (Denmark)

    Somavarapu, Arun Kumar; Kepp, Kasper Planeta

    2017-01-01

    and explicit dynamics relevant to substrate processing remain unknown. We report a modeled structure utilizing the optimal multi-template information available, including loops and missing side chains, account of maturation cleavage, and explicit all-atom molecular dynamics in the membrane. We observe three...... interactions and induces shorter residence time and by inference releases Aβ peptides of longer lengths. Our simulations thus provide a molecular basis for substrate processing and changes in the Aβ42/Aβ40 ratio. Accordingly, selective binding to protect the semi-open “innocent” conformation provides......γ-secretase produces β-amyloid (Aβ) within its presenilin (PS1) subunit, mutations in which cause Alzheimer’s disease, and current therapies thus seek to modulate its activity. While the general structure is known from recent electron microscopy studies, direct loop- and membrane-interactions...

  20. Enhanced mechanical properties of graphene/copper nanocomposites using a molecular-level mixing process.

    Science.gov (United States)

    Hwang, Jaewon; Yoon, Taeshik; Jin, Sung Hwan; Lee, Jinsup; Kim, Taek-Soo; Hong, Soon Hyung; Jeon, Seokwoo

    2013-12-10

    RGO flakes are homogeneously dispersed in a Cu matrix through a molecular-level mixing process. This novel fabrication process prevents the agglomeration of the RGO and enhances adhesion between the RGO and the Cu. The yield strength of the 2.5 vol% RGO/Cu nanocomposite is 1.8 times higher than that of pure Cu. The strengthening mechanism of the RGO is investigated by a double cantilever beam test using the graphene/Cu model structure. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Molecular modelling of a chemodosimeter for the selective detection ...

    Indian Academy of Sciences (India)

    Wintec

    Molecular modelling of a chemodosimeter for the selective detection of. As(III) ion in water. † ... high levels of arsenic cause severe skin diseases in- cluding skin cancer ..... Special Attention to Groundwater in SE Asia (eds) D. Chakraborti, A ...

  2. Integrated modelling in materials and process technology

    DEFF Research Database (Denmark)

    Hattel, Jesper Henri

    2008-01-01

    Integrated modelling of entire process sequences and the subsequent in-service conditions, and multiphysics modelling of the single process steps are areas that increasingly support optimisation of manufactured parts. In the present paper, three different examples of modelling manufacturing...... processes from the viewpoint of combined materials and process modelling are presented: solidification of thin walled ductile cast iron, integrated modelling of spray forming and multiphysics modelling of friction stir welding. The fourth example describes integrated modelling applied to a failure analysis...

  3. Constructing Molecular Models with Low-Cost Toy Beads

    Science.gov (United States)

    Ng, Pun-hon; Wong, Siu-ling; Mak, Se-yuen

    2012-01-01

    In teaching the science of the nano world, ball-and-stick molecular models are frequently used as 3D representations of molecules. Unlike a chemical formula, a molecular model allows us to visualise the 3D shape of the molecule and the relative positions of its atoms, the bonds between atoms and why a pair of mirror isomers with the same atoms,…

  4. Molecular evolution across the Asteraceae: micro- and macroevolutionary processes.

    Science.gov (United States)

    Kane, Nolan C; Barker, Michael S; Zhan, Shing H; Rieseberg, Loren H

    2011-12-01

    The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.

  5. Collapse models and perceptual processes

    International Nuclear Information System (INIS)

    Ghirardi, Gian Carlo; Romano, Raffaele

    2014-01-01

    Theories including a collapse mechanism have been presented various years ago. They are based on a modification of standard quantum mechanics in which nonlinear and stochastic terms are added to the evolution equation. Their principal merits derive from the fact that they are mathematically precise schemes accounting, on the basis of a unique universal dynamical principle, both for the quantum behavior of microscopic systems as well as for the reduction associated to measurement processes and for the classical behavior of macroscopic objects. Since such theories qualify themselves not as new interpretations but as modifications of the standard theory they can be, in principle, tested against quantum mechanics. Recently, various investigations identifying possible crucial test have been discussed. In spite of the extreme difficulty to perform such tests it seems that recent technological developments allow at least to put precise limits on the parameters characterizing the modifications of the evolution equation. Here we will simply mention some of the recent investigations in this direction, while we will mainly concentrate our attention to the way in which collapse theories account for definite perceptual process. The differences between the case of reductions induced by perceptions and those related to measurement procedures by means of standard macroscopic devices will be discussed. On this basis, we suggest a precise experimental test of collapse theories involving conscious observers. We make plausible, by discussing in detail a toy model, that the modified dynamics can give rise to quite small but systematic errors in the visual perceptual process.

  6. Hillslope runoff processes and models

    Science.gov (United States)

    Kirkby, Mike

    1988-07-01

    Hillslope hydrology is concerned with the partition of precipitation as it passes through the vegetation and soil between overland flow and subsurface flow. Flow follows routes which attenuate and delay the flow to different extents, so that a knowledge of the relevant mechanisms is important. In the 1960s and 1970s, hillslope hydrology developed as a distinct topic through the application of new field observations to develop a generation of physically based forecasting models. In its short history, theory has continually been overturned by field observation. Thus the current tendency, particularly among temperate zone hydrologists, to dismiss all Hortonian overland flow as a myth, is now being corrected by a number of significant field studies which reveal the great range in both climatic and hillslope conditions. Some recent models have generally attempted to simplify the processes acting, for example including only vertical unsaturated flow and lateral saturated flows. Others explicitly forecast partial or contributing areas. With hindsight, the most complete and distributed models have generally shown little forecasting advantage over simpler approaches, perhaps trending towards reliable models which can run on desk top microcomputers. The variety now being recognised in hillslope hydrological responses should also lead to models which take account of more complex interactions, even if initially with a less secure physical and mathematical basis than the Richards equation. In particular, there is a need to respond to the variety of climatic responses, and to spatial variability on and beneath the surface, including the role of seepage macropores and pipes which call into question whether the hillside can be treated as a Darcian flow system.

  7. Molecular-level insights into aging processes of skin elastin.

    Science.gov (United States)

    Mora Huertas, Angela C; Schmelzer, Christian E H; Hoehenwarter, Wolfgang; Heyroth, Frank; Heinz, Andrea

    2016-01-01

    Skin aging is characterized by different features including wrinkling, atrophy of the dermis and loss of elasticity associated with damage to the extracellular matrix protein elastin. The aim of this study was to investigate the aging process of skin elastin at the molecular level by evaluating the influence of intrinsic (chronological aging) and extrinsic factors (sun exposure) on the morphology and susceptibility of elastin towards enzymatic degradation. Elastin was isolated from biopsies derived from sun-protected or sun-exposed skin of differently aged individuals. The morphology of the elastin fibers was characterized by scanning electron microscopy. Mass spectrometric analysis and label-free quantification allowed identifying differences in the cleavage patterns of the elastin samples after enzymatic digestion. Principal component analysis and hierarchical cluster analysis were used to visualize differences between the samples and to determine the contribution of extrinsic and intrinsic aging to the proteolytic susceptibility of elastin. Moreover, the release of potentially bioactive peptides was studied. Skin aging is associated with the decomposition of elastin fibers, which is more pronounced in sun-exposed tissue. Marker peptides were identified, which showed an age-related increase or decrease in their abundances and provide insights into the progression of the aging process of elastin fibers. Strong age-related cleavage occurs in hydrophobic tropoelastin domains 18, 20, 24 and 26. Photoaging makes the N-terminal and central parts of the tropoelastin molecules more susceptible towards enzymatic cleavage and, hence, accelerates the age-related degradation of elastin. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  8. Business Process Modelling for Measuring Quality

    NARCIS (Netherlands)

    Heidari, F.; Loucopoulos, P.; Brazier, F.M.

    2013-01-01

    Business process modelling languages facilitate presentation, communication and analysis of business processes with different stakeholders. This paper proposes an approach that drives specification and measurement of quality requirements and in doing so relies on business process models as

  9. Multifunctional multiscale composites: Processing, modeling and characterization

    Science.gov (United States)

    Qiu, Jingjing

    Carbon nanotubes (CNTs) demonstrate extraordinary properties and show great promise in enhancing out-of-plane properties of traditional polymer/fiber composites and enabling functionality. However, current manufacturing challenges hinder the realization of their potential. In the dissertation research, both experimental and computational efforts have been conducted to investigate effective manufacturing techniques of CNT integrated multiscale composites. The fabricated composites demonstrated significant improvements in physical properties, such as tensile strength, tensile modulus, inter-laminar shear strength, thermal dimension stability and electrical conductivity. Such multiscale composites were truly multifunctional with the addition of CNTs. Furthermore, a novel hierarchical multiscale modeling method was developed in this research. Molecular dynamic (MD) simulation offered reasonable explanation of CNTs dispersion and their motion in polymer solution. Bi-mode finite-extensible-nonlinear-elastic (FENE) dumbbell simulation was used to analyze the influence of CNT length distribution on the stress tensor and shear-rate-dependent viscosity. Based on the simulated viscosity profile and empirical equations from experiments, a macroscale flow simulation model on the finite element method (FEM) method was developed and validated to predict resin flow behavior in the processing of CNT-enhanced multiscale composites. The proposed multiscale modeling method provided a comprehensive understanding of micro/nano flow in both atomistic details and mesoscale. The simulation model can be used to optimize process design and control of the mold-filling process in multiscale composite manufacturing. This research provided systematic investigations into the CNT-based multiscale composites. The results from this study may be used to leverage the benefits of CNTs and open up new application opportunities for high-performance multifunctional multiscale composites. Keywords. Carbon

  10. Bayesian molecular design with a chemical language model

    Science.gov (United States)

    Ikebata, Hisaki; Hongo, Kenta; Isomura, Tetsu; Maezono, Ryo; Yoshida, Ryo

    2017-04-01

    The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.

  11. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  12. Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

    Science.gov (United States)

    Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

    2017-03-01

    Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

  13. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  14. Quantum simulation and quantum information processing with molecular dipolar crystals

    International Nuclear Information System (INIS)

    Ortner, M.

    2011-01-01

    In this thesis interactions between dipolar crystals and neutral atoms or separated molecules have been investigated. They were motivated to realize new kinds of lattice models in mixtures of atoms and polar molecules where an MDC functions as an underlying periodic lattice structure for the second species. Such models bring out the peculiar features of MDC's, that include a controllable, potentially sub-optical wavelength periodicity and strong particle phonon interactions. Only stable collisional configurations have been investigated, excluding chemical reactions between the substituents, and crystal distortions beyond the scope of perturbation theory. The system was treated in the polaron picture where particles of the second species are dressed by surrounding crystal phonons. To describe the competition between coherent and incoherent dynamics of the polarons, a master equation in the Brownian motion limit was used with phonons treated as a thermal heat bath. It was shown analytically that in a wide range of realistic parameters the corrections to the coherent time evolution are small, and that the dynamics of the dressed particles can be described by an effective extended Hubbard model with controllable system parameters. The last chapter of this thesis contains a proposal for QIP with cold polar molecules that, in contrast to previous works, uses an MDC as a quantum register. It was motivated by the unique features of dipolar molecules and to exploit the peculiar physical conditions in dipolar crystals. In this proposal the molecular dipole moments were tailored by non-local fields to include a small, switchable, state-dependent dipole moment in addition to the large internal state independent moment that stabilizes the crystal. It was shown analytically that a controllable, non-trivial phonon-mediated interaction can be generated that exceeds non-trivial, direct dipole-dipole couplings. The addressability problem due to high crystal densities was overcome by

  15. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

    Science.gov (United States)

    Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

    2017-06-28

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

  16. Properties of spatial Cox process models

    DEFF Research Database (Denmark)

    Møller, Jesper

    Probabilistic properties of Cox processes of relevance for statistical modelling and inference are studied. Particularly, we study the most important classes of Cox processes, including log Gaussian Cox processes, shot noise Cox processes, and permanent Cox processes. We consider moment properties...... and point process operations such as thinning, displacements, and superpositioning. We also discuss how to simulate specific Cox processes....

  17. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  18. Developing engineering processes through integrated modelling of product and process

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Bjerrum; Hvam, Lars

    2012-01-01

    This article aims at developing an operational tool for integrated modelling of product assortments and engineering processes in companies making customer specific products. Integrating a product model in the design of engineering processes will provide a deeper understanding of the engineering...... activities as well as insight into how product features affect the engineering processes. The article suggests possible ways of integrating models of products with models of engineering processes. The models have been tested and further developed in an action research study carried out in collaboration...... with a major international engineering company....

  19. Automatic extraction of process categories from process model collections

    NARCIS (Netherlands)

    Malinova, M.; Dijkman, R.M.; Mendling, J.; Lohmann, N.; Song, M.; Wohed, P.

    2014-01-01

    Many organizations build up their business process management activities in an incremental way. As a result, there is no overarching structure defined at the beginning. However, as business process modeling initiatives often yield hundreds to thousands of process models, there is a growing need for

  20. Radiation chemistry of polymer degradation processes: molecular weight distribution effects

    International Nuclear Information System (INIS)

    Viswanathan, N.S.

    1976-01-01

    The molecular weight distributions of poly(methyl methacrylate) irradiated at 15 and 25 MeV with electron beams were investigated. The experimental values for the effect of chain scissions on the dispersivity agreed well with theoretical predictions

  1. Assessing the Impact of Electrostatic Drag on Processive Molecular Motor Transport.

    Science.gov (United States)

    Smith, J Darby; McKinley, Scott A

    2018-06-04

    The bidirectional movement of intracellular cargo is usually described as a tug-of-war among opposite-directed families of molecular motors. While tug-of-war models have enjoyed some success, recent evidence suggests underlying motor interactions are more complex than previously understood. For example, these tug-of-war models fail to predict the counterintuitive phenomenon that inhibiting one family of motors can decrease the functionality of opposite-directed transport. In this paper, we use a stochastic differential equations modeling framework to explore one proposed physical mechanism, called microtubule tethering, that could play a role in this "co-dependence" among antagonistic motors. This hypothesis includes the possibility of a trade-off: weakly bound trailing molecular motors can serve as tethers for cargoes and processing motors, thereby enhancing motor-cargo run lengths along microtubules; however, this introduces a cost of processing at a lower mean velocity. By computing the small- and large-time mean-squared displacement of our theoretical model and comparing our results to experimental observations of dynein and its "helper protein" dynactin, we find some supporting evidence for microtubule tethering interactions. We extrapolate these findings to predict how dynein-dynactin might interact with the opposite-directed kinesin motors and introduce a criterion for when the trade-off is beneficial in simple systems.

  2. Modeling of ultrafast THz interactions in molecular crystals

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

    2014-01-01

    In this paper we present a numerical study of terahertz pulses interacting with crystals of cesium iodide. We model the molecular dynamics of the cesium iodide crystals with the Density Functional Theory software CASTEP, where ultrafast terahertz pulses are implemented to the CASTEP software...... to interact with molecular crystals. We investigate the molecular dynamics of cesium iodide crystals when interacting with realistic terahertz pulses of field strengths from 0 to 50 MV/cm. We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

  3. 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.

  4. Two-Dimensional Model of Scrolled Packings of Molecular Nanoribbons

    Science.gov (United States)

    Savin, A. V.; Mazo, M. A.

    2018-04-01

    A simplified model of the in-plane molecular chain, allowing the description of folded and scrolled packings of molecular nanoribbons of different structures, is proposed. Using this model, possible steady states of single-layer nanoribbons scrolls of graphene, graphane, fluorographene, and fluorographane (graphene hydrogenated on the one side and fluorinated on the other side) are obtained. Their stability is demonstrated and their energy is calculated as a function of the nanoribbon length. It is shown that the scrolled packing is the most energetically favorable nanoribbon conformation at long lengths. The existences of scrolled packings for fluorographene nanoribbons and the existence of two different scroll types corresponding to left- and right-hand Archimedean spirals for fluorographane nanoribbons in the chain model are shown for the first time. The simplicity of the proposed model makes it possible to consider the dynamics of scrolls of rather long molecular nanoribbons at long enough time intervals.

  5. Process mining using BPMN: relating event logs and process models

    NARCIS (Netherlands)

    Kalenkova, A.A.; van der Aalst, W.M.P.; Lomazova, I.A.; Rubin, V.A.

    2017-01-01

    Process-aware information systems (PAIS) are systems relying on processes, which involve human and software resources to achieve concrete goals. There is a need to develop approaches for modeling, analysis, improvement and monitoring processes within PAIS. These approaches include process mining

  6. Process mining using BPMN : relating event logs and process models

    NARCIS (Netherlands)

    Kalenkova, A.A.; Aalst, van der W.M.P.; Lomazova, I.A.; Rubin, V.A.

    2015-01-01

    Process-aware information systems (PAIS) are systems relying on processes, which involve human and software resources to achieve concrete goals. There is a need to develop approaches for modeling, analysis, improvement and monitoring processes within PAIS. These approaches include process mining

  7. Molecular models for DNA damaged by photoreaction

    International Nuclear Information System (INIS)

    Pearlman, D.A.; Holbrook, S.R.; Pirkle, D.H.; Kim, S.H.

    1985-01-01

    Structural models of a DNA molecule containing a radiation-induced psoralen cross-link and of a DNA containing a thymine photodimer were constructed by applying energy-minimization techniques and model-building procedures to data from x-ray crystallographic studies. The helical axes of the models show substantial kinking and unwinding at the sites of the damage, which may have long-range as well as local effects arising from the concomitant changes in the supercoiling and overall structure of the DNA. The damaged areas may also serve as recognition sites for repair enzymes. These results should help in understanding the biologic effects of radiation-induced damage on cells

  8. Toluene model for molecular dynamics simulations in the ranges 298

    NARCIS (Netherlands)

    Fioroni, M.; Vogt, D.

    2004-01-01

    An all-atom model for toluene is presented in the framework of classical molecular dynamics (MD). The model has been parametrized under the GROMOS96 force field to reproduce the physicochemical properties of the neat liquid. Four new atom types have been introduced, distinguishing between carbons

  9. Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

    DEFF Research Database (Denmark)

    Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing

    2007-01-01

    Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included...

  10. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  11. Corn Storage Protein - A Molecular Genetic Model

    Energy Technology Data Exchange (ETDEWEB)

    Messing, Joachim [Rutgers Univ., Piscataway, NJ (United States)

    2013-05-31

    Corn is the highest yielding crop on earth and probably the most valuable agricultural product of the United States. Because it converts sun energy through photosynthesis into starch and proteins, we addressed energy savings by focusing on protein quality. People and animals require essential amino acids derived from the digestion of proteins. If proteins are relatively low in certain essential amino acids, the crop becomes nutritionally defective and has to be supplemented. Such deficiency affects meat and fish production and countries where corn is a staple. Because corn seed proteins have relatively low levels of lysine and methionine, a diet has to be supplemented with soybeans for the missing lysine and with chemically synthesized methionine. We therefore have studied genes expressed during maize seed development and their chromosomal organization. A critical technical requirement for the understanding of the molecular structure of genes and their positional information was DNA sequencing. Because of the length of sequences, DNA sequencing methods themselves were insufficient for this type of analysis. We therefore developed the so-called “DNA shotgun sequencing” strategy, where overlapping DNA fragments were sequenced in parallel and used to reconstruct large DNA molecules via overlaps. Our publications became the most frequently cited ones during the decade of 1981-1990 and former Associate Director of Science for the Office of Basic Energy Sciences Patricia M. Dehmer presented our work as one of the great successes of this program. A major component of the sequencing strategy was the development of bacterial strains and vectors, which were also used to develop the first biotechnology crops. These crops possessed new traits thanks to the expression of foreign genes in plants. To enable such expression, chimeric genes had to be constructed using our materials and methods by the industry. Because we made our materials and methods freely available to

  12. Multiphysics modelling of manufacturing processes: A review

    DEFF Research Database (Denmark)

    Jabbari, Masoud; Baran, Ismet; Mohanty, Sankhya

    2018-01-01

    Numerical modelling is increasingly supporting the analysis and optimization of manufacturing processes in the production industry. Even if being mostly applied to multistep processes, single process steps may be so complex by nature that the needed models to describe them must include multiphysics...... the diversity in the field of modelling of manufacturing processes as regards process, materials, generic disciplines as well as length scales: (1) modelling of tape casting for thin ceramic layers, (2) modelling the flow of polymers in extrusion, (3) modelling the deformation process of flexible stamps...... for nanoimprint lithography, (4) modelling manufacturing of composite parts and (5) modelling the selective laser melting process. For all five examples, the emphasis is on modelling results as well as describing the models in brief mathematical details. Alongside with relevant references to the original work...

  13. Modeling Suspension and Continuation of a Process

    Directory of Open Access Journals (Sweden)

    Oleg Svatos

    2012-04-01

    Full Text Available This work focuses on difficulties an analyst encounters when modeling suspension and continuation of a process in contemporary process modeling languages. As a basis there is introduced general lifecycle of an activity which is then compared to activity lifecycles supported by individual process modeling languages. The comparison shows that the contemporary process modeling languages cover the defined general lifecycle of an activity only partially. There are picked two popular process modeling languages and there is modeled real example, which reviews how the modeling languages can get along with their lack of native support of suspension and continuation of an activity. Upon the unsatisfying results of the contemporary process modeling languages in the modeled example, there is presented a new process modeling language which, as demonstrated, is capable of capturing suspension and continuation of an activity in much simpler and precise way.

  14. Molecular modeling: An open invitation for applied mathematics

    Science.gov (United States)

    Mezey, Paul G.

    2013-10-01

    Molecular modeling methods provide a very wide range of challenges for innovative mathematical and computational techniques, where often high dimensionality, large sets of data, and complicated interrelations imply a multitude of iterative approximations. The physical and chemical basis of these methodologies involves quantum mechanics with several non-intuitive aspects, where classical interpretation and classical analogies are often misleading or outright wrong. Hence, instead of the everyday, common sense approaches which work so well in engineering, in molecular modeling one often needs to rely on rather abstract mathematical constraints and conditions, again emphasizing the high level of reliance on applied mathematics. Yet, the interdisciplinary aspects of the field of molecular modeling also generates some inertia and perhaps too conservative reliance on tried and tested methodologies, that is at least partially caused by the less than up-to-date involvement in the newest developments in applied mathematics. It is expected that as more applied mathematicians take up the challenge of employing the latest advances of their field in molecular modeling, important breakthroughs may follow. In this presentation some of the current challenges of molecular modeling are discussed.

  15. Computer Aided Continuous Time Stochastic Process Modelling

    DEFF Research Database (Denmark)

    Kristensen, N.R.; Madsen, Henrik; Jørgensen, Sten Bay

    2001-01-01

    A grey-box approach to process modelling that combines deterministic and stochastic modelling is advocated for identification of models for model-based control of batch and semi-batch processes. A computer-aided tool designed for supporting decision-making within the corresponding modelling cycle...

  16. Process modeling for Humanities: tracing and analyzing scientific processes

    OpenAIRE

    Hug , Charlotte; Salinesi , Camille; Deneckere , Rebecca; Lamasse , Stéphane

    2011-01-01

    International audience; This paper concerns epistemology and the understanding of research processes in Humanities, such as Archaeology. We believe that to properly understand research processes, it is essential to trace them. The collected traces depend on the process model established, which has to be as accurate as possible to exhaustively record the traces. In this paper, we briefly explain why the existing process models for Humanities are not sufficient to represent traces. We then pres...

  17. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

    Science.gov (United States)

    Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

    2015-03-01

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

  18. A fermionic molecular dynamics technique to model nuclear matter

    International Nuclear Information System (INIS)

    Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

    2009-01-01

    Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

  19. The emerging role of cloud computing in molecular modelling.

    Science.gov (United States)

    Ebejer, Jean-Paul; Fulle, Simone; Morris, Garrett M; Finn, Paul W

    2013-07-01

    There is a growing recognition of the importance of cloud computing for large-scale and data-intensive applications. The distinguishing features of cloud computing and their relationship to other distributed computing paradigms are described, as are the strengths and weaknesses of the approach. We review the use made to date of cloud computing for molecular modelling projects and the availability of front ends for molecular modelling applications. Although the use of cloud computing technologies for molecular modelling is still in its infancy, we demonstrate its potential by presenting several case studies. Rapid growth can be expected as more applications become available and costs continue to fall; cloud computing can make a major contribution not just in terms of the availability of on-demand computing power, but could also spur innovation in the development of novel approaches that utilize that capacity in more effective ways. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Business process modeling for processing classified documents using RFID technology

    Directory of Open Access Journals (Sweden)

    Koszela Jarosław

    2016-01-01

    Full Text Available The article outlines the application of the processing approach to the functional description of the designed IT system supporting the operations of the secret office, which processes classified documents. The article describes the application of the method of incremental modeling of business processes according to the BPMN model to the description of the processes currently implemented (“as is” in a manual manner and target processes (“to be”, using the RFID technology for the purpose of their automation. Additionally, the examples of applying the method of structural and dynamic analysis of the processes (process simulation to verify their correctness and efficiency were presented. The extension of the process analysis method is a possibility of applying the warehouse of processes and process mining methods.

  1. Process correlation analysis model for process improvement identification.

    Science.gov (United States)

    Choi, Su-jin; Kim, Dae-Kyoo; Park, Sooyong

    2014-01-01

    Software process improvement aims at improving the development process of software systems. It is initiated by process assessment identifying strengths and weaknesses and based on the findings, improvement plans are developed. In general, a process reference model (e.g., CMMI) is used throughout the process of software process improvement as the base. CMMI defines a set of process areas involved in software development and what to be carried out in process areas in terms of goals and practices. Process areas and their elements (goals and practices) are often correlated due to the iterative nature of software development process. However, in the current practice, correlations of process elements are often overlooked in the development of an improvement plan, which diminishes the efficiency of the plan. This is mainly attributed to significant efforts and the lack of required expertise. In this paper, we present a process correlation analysis model that helps identify correlations of process elements from the results of process assessment. This model is defined based on CMMI and empirical data of improvement practices. We evaluate the model using industrial data.

  2. Molecular Physiology of Root System Architecture in Model Grasses

    Science.gov (United States)

    Hixson, K.; Ahkami, A. H.; Anderton, C.; Veličković, D.; Myers, G. L.; Chrisler, W.; Lindenmaier, R.; Fang, Y.; Yabusaki, S.; Rosnow, J. J.; Farris, Y.; Khan, N. E.; Bernstein, H. C.; Jansson, C.

    2017-12-01

    Unraveling the molecular and physiological mechanisms involved in responses of Root System Architecture (RSA) to abiotic stresses and shifts in microbiome structure is critical to understand and engineer plant-microbe-soil interactions in the rhizosphere. In this study, accessions of Brachypodium distachyon Bd21 (C3 model grass) and Setaria viridis A10.1 (C4 model grass) were grown in phytotron chambers under current and elevated CO2 levels. Detailed growth stage-based phenotypic analysis revealed different above- and below-ground morphological and physiological responses in C3 and C4 grasses to enhanced CO2 levels. Based on our preliminary results and by screening values of total biomass, water use efficiency, root to shoot ratio, RSA parameters and net assimilation rates, we postulated a three-phase physiological mechanism, i.e. RootPlus, BiomassPlus and YieldPlus phases, for grass growth under elevated CO2 conditions. Moreover, this comprehensive set of morphological and process-based observations are currently in use to develop, test, and calibrate biophysical whole-plant models and in particular to simulate leaf-level photosynthesis at various developmental stages of C3 and C4 using the model BioCro. To further link the observed phenotypic traits at the organismal level to tissue and molecular levels, and to spatially resolve the origin and fate of key metabolites involved in primary carbohydrate metabolism in different root sections, we complement root phenotypic observations with spatial metabolomics data using mass spectrometry imaging (MSI) methods. Focusing on plant-microbe interactions in the rhizosphere, six bacterial strains with plant growth promoting features are currently in use in both gel-based and soil systems to screen root growth and development in Brachypodium. Using confocal microscopy, GFP-tagged bacterial systems are utilized to study the initiation of different root types of RSA, including primary root (PR), coleoptile node axile root (CNR

  3. Syntax highlighting in business process models

    NARCIS (Netherlands)

    Reijers, H.A.; Freytag, T.; Mendling, J.; Eckleder, A.

    2011-01-01

    Sense-making of process models is an important task in various phases of business process management initiatives. Despite this, there is currently hardly any support in business process modeling tools to adequately support model comprehension. In this paper we adapt the concept of syntax

  4. Configurable multi-perspective business process models

    NARCIS (Netherlands)

    La Rosa, M.; Dumas, M.; Hofstede, ter A.H.M.; Mendling, J.

    2011-01-01

    A configurable process model provides a consolidated view of a family of business processes. It promotes the reuse of proven practices by providing analysts with a generic modeling artifact from which to derive individual process models. Unfortunately, the scope of existing notations for

  5. Atmospheric processes on ice nanoparticles in molecular beams

    Czech Academy of Sciences Publication Activity Database

    Fárník, Michal; Poterya, Viktoriya

    2014-01-01

    Roč. 2, č. 2014 (2014), s. 4 ISSN 2296-2646 R&D Projects: GA ČR GA203/09/0422; GA ČR GAP208/11/0161 Institutional support: RVO:61388955 Keywords : molecular beams * photodissociation * water clusters Subject RIV: BL - Plasma and Gas Discharge Physics

  6. 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

  7. Models and algorithms for biomolecules and molecular networks

    CERN Document Server

    DasGupta, Bhaskar

    2016-01-01

    By providing expositions to modeling principles, theories, computational solutions, and open problems, this reference presents a full scope on relevant biological phenomena, modeling frameworks, technical challenges, and algorithms. * Up-to-date developments of structures of biomolecules, systems biology, advanced models, and algorithms * Sampling techniques for estimating evolutionary rates and generating molecular structures * Accurate computation of probability landscape of stochastic networks, solving discrete chemical master equations * End-of-chapter exercises

  8. Molecular Modeling of Prion Transmission to Humans

    Directory of Open Access Journals (Sweden)

    Etienne Levavasseur

    2014-10-01

    Full Text Available Using different prion strains, such as the variant Creutzfeldt-Jakob disease agent and the atypical bovine spongiform encephalopathy agents, and using transgenic mice expressing human or bovine prion protein, we assessed the reliability of protein misfolding cyclic amplification (PMCA to model interspecies and genetic barriers to prion transmission. We compared our PMCA results with in vivo transmission data characterized by attack rates, i.e., the percentage of inoculated mice that developed the disease. Using 19 seed/substrate combinations, we observed that a significant PMCA amplification was only obtained when the mouse line used as substrate is susceptible to the corresponding strain. Our results suggest that PMCA provides a useful tool to study genetic barriers to transmission and to study the zoonotic potential of emerging prion strains.

  9. User's manual for a process model code

    International Nuclear Information System (INIS)

    Kern, E.A.; Martinez, D.P.

    1981-03-01

    The MODEL code has been developed for computer modeling of materials processing facilities associated with the nuclear fuel cycle. However, it can also be used in other modeling applications. This report provides sufficient information for a potential user to apply the code to specific process modeling problems. Several examples that demonstrate most of the capabilities of the code are provided

  10. Repairing process models to reflect reality

    NARCIS (Netherlands)

    Fahland, D.; Aalst, van der W.M.P.; Barros, A.; Gal, A.; Kindler, E.

    2012-01-01

    Process mining techniques relate observed behavior (i.e., event logs) to modeled behavior (e.g., a BPMN model or a Petri net). Processes models can be discovered from event logs and conformance checking techniques can be used to detect and diagnose differences between observed and modeled behavior.

  11. Diffusion-controlled interface kinetics-inclusive system-theoretic propagation models for molecular communication systems

    Science.gov (United States)

    Chude-Okonkwo, Uche A. K.; Malekian, Reza; Maharaj, B. T.

    2015-12-01

    Inspired by biological systems, molecular communication has been proposed as a new communication paradigm that uses biochemical signals to transfer information from one nano device to another over a short distance. The biochemical nature of the information transfer process implies that for molecular communication purposes, the development of molecular channel models should take into consideration diffusion phenomenon as well as the physical/biochemical kinetic possibilities of the process. The physical and biochemical kinetics arise at the interfaces between the diffusion channel and the transmitter/receiver units. These interfaces are herein termed molecular antennas. In this paper, we present the deterministic propagation model of the molecular communication between an immobilized nanotransmitter and nanoreceiver, where the emission and reception kinetics are taken into consideration. Specifically, we derived closed-form system-theoretic models and expressions for configurations that represent different communication systems based on the type of molecular antennas used. The antennas considered are the nanopores at the transmitter and the surface receptor proteins/enzymes at the receiver. The developed models are simulated to show the influence of parameters such as the receiver radius, surface receptor protein/enzyme concentration, and various reaction rate constants. Results show that the effective receiver surface area and the rate constants are important to the system's output performance. Assuming high rate of catalysis, the analysis of the frequency behavior of the developed propagation channels in the form of transfer functions shows significant difference introduce by the inclusion of the molecular antennas into the diffusion-only model. It is also shown that for t > > 0 and with the information molecules' concentration greater than the Michaelis-Menten kinetic constant of the systems, the inclusion of surface receptors proteins and enzymes in the models

  12. The Jukes-Cantor Model of Molecular Evolution

    Science.gov (United States)

    Erickson, Keith

    2010-01-01

    The material in this module introduces students to some of the mathematical tools used to examine molecular evolution. This topic is standard fare in many mathematical biology or bioinformatics classes, but could also be suitable for classes in linear algebra or probability. While coursework in matrix algebra, Markov processes, Monte Carlo…

  13. Genetic Process Mining: Alignment-based Process Model Mutation

    NARCIS (Netherlands)

    Eck, van M.L.; Buijs, J.C.A.M.; Dongen, van B.F.; Fournier, F.; Mendling, J.

    2015-01-01

    The Evolutionary Tree Miner (ETM) is a genetic process discovery algorithm that enables the user to guide the discovery process based on preferences with respect to four process model quality dimensions: replay fitness, precision, generalization and simplicity. Traditionally, the ETM algorithm uses

  14. Molecular modeling of protein materials: case study of elastin

    International Nuclear Information System (INIS)

    Tarakanova, Anna; Buehler, Markus J

    2013-01-01

    Molecular modeling of protein materials is a quickly growing area of research that has produced numerous contributions in fields ranging from structural engineering to medicine and biology. We review here the history and methods commonly employed in molecular modeling of protein materials, emphasizing the advantages for using modeling as a complement to experimental work. We then consider a case study of the protein elastin, a critically important ‘mechanical protein’ to exemplify the approach in an area where molecular modeling has made a significant impact. We outline the progression of computational modeling studies that have considerably enhanced our understanding of this important protein which endows elasticity and recoil to the tissues it is found in, including the skin, lungs, arteries and the heart. A vast collection of literature has been directed at studying the structure and function of this protein for over half a century, the first molecular dynamics study of elastin being reported in the 1980s. We review the pivotal computational works that have considerably enhanced our fundamental understanding of elastin's atomistic structure and its extraordinary qualities—focusing on two in particular: elastin's superb elasticity and the inverse temperature transition—the remarkable ability of elastin to take on a more structured conformation at higher temperatures, suggesting its effectiveness as a biomolecular switch. Our hope is to showcase these methods as both complementary and enriching to experimental approaches that have thus far dominated the study of most protein-based materials. (topical review)

  15. Generalized kinetic model of reduction of molecular oxidant by metal containing redox

    International Nuclear Information System (INIS)

    Kravchenko, T.A.

    1986-01-01

    Present work is devoted to kinetics of reduction of molecular oxidant by metal containing redox. Constructed generalized kinetic model of redox process in the system solid redox - reagent solution allows to perform the general theoretical approach to research and to obtain new results on kinetics and mechanism of interaction of redox with oxidants.

  16. Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

    Science.gov (United States)

    Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

    2018-01-01

    A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…

  17. Production of nanostructured molecular liquids by supercritical CO2 processing

    Directory of Open Access Journals (Sweden)

    Sudhir Kumar Sharma

    2017-01-01

    Full Text Available Stable molecular clusters of ibuprofen and naproxen were prepared in dry ice, by supersonic jet expansion of their supercritical CO2 drug formulations into a liquid nitrogen cooled collection vessel, with up to 80% yield. Mixing the “dry ice” in water, resulted in the solubilization of the clusters and in the case of ibuprofen, we were able to create solutions, with concentrations of up to 6 mg/ml, a 300-fold increase over previously reported values. Drop casting and ambient drying of these solutions on silicon substrate resulted in a stable, viscous liquid film, referred to as nanostructured molecular liquids. These liquids exhibited a highly aligned, fine (self-assembled super lattice features. In vitro cancer cell viability studies of these formulations exhibited similar cytotoxicity to that of the original raw materials, thus retaining their original potency. Besides its scientific importance, this invention is expected to open up new drug delivery platforms.

  18. Composing Models of Geographic Physical Processes

    Science.gov (United States)

    Hofer, Barbara; Frank, Andrew U.

    Processes are central for geographic information science; yet geographic information systems (GIS) lack capabilities to represent process related information. A prerequisite to including processes in GIS software is a general method to describe geographic processes independently of application disciplines. This paper presents such a method, namely a process description language. The vocabulary of the process description language is derived formally from mathematical models. Physical processes in geography can be described in two equivalent languages: partial differential equations or partial difference equations, where the latter can be shown graphically and used as a method for application specialists to enter their process models. The vocabulary of the process description language comprises components for describing the general behavior of prototypical geographic physical processes. These process components can be composed by basic models of geographic physical processes, which is shown by means of an example.

  19. MORTALITY MODELING WITH LEVY PROCESSES

    Directory of Open Access Journals (Sweden)

    M. Serhat Yucel, FRM

    2012-07-01

    Full Text Available Mortality and longevity risk is usually one of the main risk components ineconomic capital models of insurance companies. Above all, future mortalityexpectations are an important input in the modeling and pricing of long termproducts. Deviations from the expectation can lead insurance company even todefault if sufficient reserves and capital is not held. Thus, Modeling of mortalitytime series accurately is a vital concern for the insurance industry. The aim of thisstudy is to perform distributional and spectral testing to the mortality data andpracticed discrete and continuous time modeling. We believe, the results and thetechniques used in this study will provide a basis for Value at Risk formula incase of mortality.

  20. Model-based software process improvement

    Science.gov (United States)

    Zettervall, Brenda T.

    1994-01-01

    The activities of a field test site for the Software Engineering Institute's software process definition project are discussed. Products tested included the improvement model itself, descriptive modeling techniques, the CMM level 2 framework document, and the use of process definition guidelines and templates. The software process improvement model represents a five stage cyclic approach for organizational process improvement. The cycles consist of the initiating, diagnosing, establishing, acting, and leveraging phases.

  1. Kopernik : modeling business processes for digital customers

    OpenAIRE

    Estañol Lamarca, Montserrat; Castro, Manuel; Díaz-Montenegro, Sylvia; Teniente López, Ernest

    2016-01-01

    This paper presents the Kopernik methodology for modeling business processes for digital customers. These processes require a high degree of flexibility in the execution of their tasks or actions. We achieve this by using the artifact-centric approach to process modeling and the use of condition-action rules. The processes modeled following Kopernik can then be implemented in an existing commercial tool, Balandra.

  2. The triconnected abstraction of process models

    OpenAIRE

    Polyvyanyy, Artem; Smirnov, Sergey; Weske, Mathias

    2009-01-01

    Contents: Artem Polyvanny, Sergey Smirnow, and Mathias Weske The Triconnected Abstraction of Process Models 1 Introduction 2 Business Process Model Abstraction 3 Preliminaries 4 Triconnected Decomposition 4.1 Basic Approach for Process Component Discovery 4.2 SPQR-Tree Decomposition 4.3 SPQR-Tree Fragments in the Context of Process Models 5 Triconnected Abstraction 5.1 Abstraction Rules 5.2 Abstraction Algorithm 6 Related Work and Conclusions

  3. Modelling of Batch Process Operations

    DEFF Research Database (Denmark)

    Abdul Samad, Noor Asma Fazli; Cameron, Ian; Gani, Rafiqul

    2011-01-01

    Here a batch cooling crystalliser is modelled and simulated as is a batch distillation system. In the batch crystalliser four operational modes of the crystalliser are considered, namely: initial cooling, nucleation, crystal growth and product removal. A model generation procedure is shown that s...

  4. Mathematical Modeling: A Structured Process

    Science.gov (United States)

    Anhalt, Cynthia Oropesa; Cortez, Ricardo

    2015-01-01

    Mathematical modeling, in which students use mathematics to explain or interpret physical, social, or scientific phenomena, is an essential component of the high school curriculum. The Common Core State Standards for Mathematics (CCSSM) classify modeling as a K-12 standard for mathematical practice and as a conceptual category for high school…

  5. Birth/death process model

    Science.gov (United States)

    Solloway, C. B.; Wakeland, W.

    1976-01-01

    First-order Markov model developed on digital computer for population with specific characteristics. System is user interactive, self-documenting, and does not require user to have complete understanding of underlying model details. Contains thorough error-checking algorithms on input and default capabilities.

  6. Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.

    Directory of Open Access Journals (Sweden)

    Tommi Aho

    2010-05-01

    Full Text Available Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is approximately 67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in approximately 590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our

  7. Molecular interaction of PCB153 to human serum albumin: Insights from spectroscopic and molecular modeling studies

    Energy Technology Data Exchange (ETDEWEB)

    Han, Chao; Fang, Senbiao; Cao, Huiming; Lu, Yan; Ma, Yaqiong [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Wei, Dongfeng [Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700 (China); Xie, Xiaoyun [College of Earth and Environmental Science, Lanzhou University, Lanzhou 730000 (China); Liu, Xiaohua [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Li, Xin [College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471003 (China); Fei, Dongqing [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Zhao, Chunyan, E-mail: zhaochy07@lzu.edu.cn [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China)

    2013-03-15

    Highlights: ► We identify the binding mode of PCB153 to human serum albumin (HSA). ► Spectroscopic and molecular modeling results reveal that PCB153 binds at the site II. ► The interaction is mainly governed by hydrophobic and hydrogen bond forces. ► The work helps to probe transporting, distribution and toxicity effect of PCBs. -- Abstract: Polychlorinated biphenyls (PCBs) possessed much potential hazard to environment because of its chemical stability and biological toxicity. Here, we identified the binding mode of a representative compound, PCB153, to human serum albumin (HSA) using fluorescence and molecular dynamics simulation methods. The fluorescence study showed that the intrinsic fluorescence of HSA was quenched by addition of PCB153 through a static quenching mechanism. The thermodynamic analysis proved the binding behavior was mainly governed by hydrophobic force. Furthermore, as evidenced by site marker displacement experiments using two probe compounds, it revealed that PCB153 acted exactly on subdomain IIIA (site II) of HSA. On the other hand, the molecular dynamics studies as well as free energy calculations made another important contribution to understand the conformational changes of HSA and the stability of HSA-PCB153 system. Molecular docking revealed PCB153 can bind in a large hydrophobic activity of subdomain IIIA by the hydrophobic interaction and hydrogen bond interactions between chlorine atoms and residue ASN391. The present work provided reasonable models helping us further understand the transporting, distribution and toxicity effect of PCBs when it spread into human blood serum.

  8. Transforming Collaborative Process Models into Interface Process Models by Applying an MDA Approach

    Science.gov (United States)

    Lazarte, Ivanna M.; Chiotti, Omar; Villarreal, Pablo D.

    Collaborative business models among enterprises require defining collaborative business processes. Enterprises implement B2B collaborations to execute these processes. In B2B collaborations the integration and interoperability of processes and systems of the enterprises are required to support the execution of collaborative processes. From a collaborative process model, which describes the global view of the enterprise interactions, each enterprise must define the interface process that represents the role it performs in the collaborative process in order to implement the process in a Business Process Management System. Hence, in this work we propose a method for the automatic generation of the interface process model of each enterprise from a collaborative process model. This method is based on a Model-Driven Architecture to transform collaborative process models into interface process models. By applying this method, interface processes are guaranteed to be interoperable and defined according to a collaborative process.

  9. The Use of Molecular Modeling Programs in Medicinal Chemistry Instruction.

    Science.gov (United States)

    Harrold, Marc W.

    1992-01-01

    This paper describes and evaluates the use of a molecular modeling computer program (Alchemy II) in a pharmaceutical education program. Provided are the hardware requirements and basic program features as well as several examples of how this program and its features have been applied in the classroom. (GLR)

  10. Metal cluster fission: jellium model and Molecular dynamics simulations

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18...

  11. Modeling the Thiophene HDS reaction on a molecular level

    NARCIS (Netherlands)

    Diemann, E.; Weber, T.; Müller, A.

    1994-01-01

    The structure of MoS2/Al2O3 catalyst and the initial step of the hydrodesulfurization (HDS) reaction using an experimental model have been studied by in situ Raman-, infrared emission (IRE)-, inelastic electron tunneling (IET)-spectroscopy and thermal desorption measurements accompanied by molecular

  12. Molecular modeling for the design of novel performance chemicals and materials

    CERN Document Server

    Rai, Beena

    2012-01-01

    Molecular modeling (MM) tools offer significant benefits in the design of industrial chemical plants and material processing operations. While the role of MM in biological fields is well established, in most cases MM works as an accessory in novel products/materials development rather than a tool for direct innovation. As a result, MM engineers and practitioners are often seized with the question: ""How do I leverage these tools to develop novel materials or chemicals in my industry?"" Molecular Modeling for the Design of Novel Performance Chemicals and Materials answers this important questio

  13. Modeling business processes: theoretical and practical aspects

    Directory of Open Access Journals (Sweden)

    V.V. Dubininа

    2015-06-01

    Full Text Available The essence of process-oriented enterprise management has been examined in the article. The content and types of information technology have been analyzed in the article, due to the complexity and differentiation of existing methods, as well as the specificity of language, terminology of the enterprise business processes modeling. The theoretical aspects of business processes modeling have been reviewed and the modern traditional modeling techniques received practical application in the visualization model of retailers activity have been studied in the article. In the process of theoretical analysis of the modeling methods found that UFO-toolkit method that has been developed by Ukrainian scientists due to it systemology integrated opportunities, is the most suitable for structural and object analysis of retailers business processes. It was designed visualized simulation model of the business process "sales" as is" of retailers using a combination UFO-elements with the aim of the further practical formalization and optimization of a given business process.

  14. Energetics and efficiency of a molecular motor model

    DEFF Research Database (Denmark)

    C. Fogedby, Hans; Svane, Axel

    2013-01-01

    The energetics and efficiency of a linear molecular motor model proposed by Mogilner et al. (Phys. Lett. 237, 297 (1998)) is analyzed from an analytical point of view. The model which is based on protein friction with a track is described by coupled Langevin equations for the motion in combination...... when incorporating the full motor dynamics, owing to the strong dissipation associated with the motor action....

  15. A Comparative of business process modelling techniques

    Science.gov (United States)

    Tangkawarow, I. R. H. T.; Waworuntu, J.

    2016-04-01

    In this era, there is a lot of business process modeling techniques. This article is the research about differences of business process modeling techniques. For each technique will explain about the definition and the structure. This paper presents a comparative analysis of some popular business process modelling techniques. The comparative framework is based on 2 criteria: notation and how it works when implemented in Somerleyton Animal Park. Each technique will end with the advantages and disadvantages. The final conclusion will give recommend of business process modeling techniques that easy to use and serve the basis for evaluating further modelling techniques.

  16. Information-Processing Models and Curriculum Design

    Science.gov (United States)

    Calfee, Robert C.

    1970-01-01

    "This paper consists of three sections--(a) the relation of theoretical analyses of learning to curriculum design, (b) the role of information-processing models in analyses of learning processes, and (c) selected examples of the application of information-processing models to curriculum design problems." (Author)

  17. How visual cognition influences process model comprehension

    NARCIS (Netherlands)

    Petrusel, Razvan; Mendling, Jan; Reijers, Hajo A.

    2017-01-01

    Process analysts and other professionals extensively use process models to analyze business processes and identify performance improvement opportunities. Therefore, it is important that such models can be easily and properly understood. Previous research has mainly focused on two types of factors

  18. Social software for business process modeling

    NARCIS (Netherlands)

    Koschmider, A.; Song, M.S.; Reijers, H.A.

    2010-01-01

    Formal models of business processes are used for a variety of purposes. But where the elicitation of the characteristics of a business process usually takes place in a collaborative fashion, the building of the final, formal process model is done mostly by a single person. This article presents the

  19. Failure of single electron descriptions of molecular orbital collision processes. [Electron promotion mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Elston, S.B.

    1978-01-01

    Inner-shell excitation occurring in low and moderate (keV range) energy collisions between light atomic and ionic systems is frequently describable in terms of molecular promotion mechanisms, which were extensively explored both theoretically and experimentally. The bulk of such studies have concentrated on processes understandable through the use of single- and independent-electron models. Nonetheless, it is possible to find cases of inner-shell excitation in relatively simple collision systems which involve nearly simultaneous multiple-electron transitions and transitions induced by inherently two-electron interactions. Evidence for these many- and nonindependent-electron phenomena in inner-shell excitation processes and the importance of considering such effects in the interpretation of collisionally induced excitation spectra is discussed. 13 references.

  20. Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities.

    Science.gov (United States)

    Bardhan, Jaydeep P

    2013-12-01

    In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

  1. Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities

    Science.gov (United States)

    Bardhan, Jaydeep P.

    2014-01-01

    In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics. PMID:25505358

  2. Gradient models in molecular biophysics: progress, challenges, opportunities

    Science.gov (United States)

    Bardhan, Jaydeep P.

    2013-12-01

    In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g., molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding nonlocal dielectric response. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain, and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost 40 years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The review concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

  3. Hydrophobic ampersand hydrophilic: Theoretical models of solvation for molecular biophysics

    International Nuclear Information System (INIS)

    Pratt, L.R.; Tawa, G.J.; Hummer, G.; Garcia, A.E.; Corcelli, S.A.

    1996-01-01

    Molecular statistical thermodynamic models of hydration for chemistry and biophysics have advanced abruptly in recent years. With liquid water as solvent, salvation phenomena are classified as either hydrophobic or hydrophilic effects. Recent progress in treatment of hydrophilic effects have been motivated by continuum dielectric models interpreted as a modelistic implementation of second order perturbation theory. New results testing that perturbation theory of hydrophilic effects are presented and discussed. Recent progress in treatment of hydrophobic effects has been achieved by applying information theory to discover models of packing effects in dense liquids. The simplest models to which those ideas lead are presented and discussed

  4. Measuring similarity between business process models

    NARCIS (Netherlands)

    Dongen, van B.F.; Dijkman, R.M.; Mendling, J.

    2007-01-01

    Quality aspects become increasingly important when business process modeling is used in a large-scale enterprise setting. In order to facilitate a storage without redundancy and an efficient retrieval of relevant process models in model databases it is required to develop a theoretical understanding

  5. Steady-State Process Modelling

    DEFF Research Database (Denmark)

    Cameron, Ian; Gani, Rafiqul

    2011-01-01

    illustrate the “equation oriented” approach as well as the “sequential modular” approach to solving complex flowsheets for steady state applications. The applications include the Williams-Otto plant, the hydrodealkylation (HDA) of toluene, conversion of ethylene to ethanol and a bio-ethanol process....

  6. Micro structure processing on plastics by accelerated hydrogen molecular ions

    Science.gov (United States)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  7. Modeling molecular boiling points using computed interaction energies.

    Science.gov (United States)

    Peterangelo, Stephen C; Seybold, Paul G

    2017-12-20

    The noncovalent van der Waals interactions between molecules in liquids are typically described in textbooks as occurring between the total molecular dipoles (permanent, induced, or transient) of the molecules. This notion was tested by examining the boiling points of 67 halogenated hydrocarbon liquids using quantum chemically calculated molecular dipole moments, ionization potentials, and polarizabilities obtained from semi-empirical (AM1 and PM3) and ab initio Hartree-Fock [HF 6-31G(d), HF 6-311G(d,p)], and density functional theory [B3LYP/6-311G(d,p)] methods. The calculated interaction energies and an empirical measure of hydrogen bonding were employed to model the boiling points of the halocarbons. It was found that only terms related to London dispersion energies and hydrogen bonding proved significant in the regression analyses, and the performances of the models generally improved at higher levels of quantum chemical computation. An empirical estimate for the molecular polarizabilities was also tested, and the best models for the boiling points were obtained using either this empirical polarizability itself or the polarizabilities calculated at the B3LYP/6-311G(d,p) level, along with the hydrogen-bonding parameter. The results suggest that the cohesive forces are more appropriately described as resulting from highly localized interactions rather than interactions between the global molecular dipoles.

  8. Multi-level molecular modelling for plasma medicine

    International Nuclear Information System (INIS)

    Bogaerts, Annemie; Khosravian, Narjes; Van der Paal, Jonas; Verlackt, Christof C W; Yusupov, Maksudbek; Kamaraj, Balu; Neyts, Erik C

    2016-01-01

    Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. (paper)

  9. The impact of working memory and the "process of process modelling" on model quality: Investigating experienced versus inexperienced modellers

    DEFF Research Database (Denmark)

    Martini, Markus; Pinggera, Jakob; Neurauter, Manuel

    2016-01-01

    of reconciliation phases was positively related to PM quality in experienced modellers. Our research reveals central cognitive mechanisms in process modelling and has potential practical implications for the development of modelling software and teaching the craft of process modelling....... the role of cognitive processes as well as modelling processes in creating a PM in experienced and inexperienced modellers. Specifically, two working memory (WM) functions (holding and processing of information and relational integration) and three process of process modelling phases (comprehension...

  10. Styles in business process modeling: an exploration and a model

    NARCIS (Netherlands)

    Pinggera, J.; Soffer, P.; Fahland, D.; Weidlich, M.; Zugal, S.; Weber, B.; Reijers, H.A.; Mendling, J.

    2015-01-01

    Business process models are an important means to design, analyze, implement, and control business processes. As with every type of conceptual model, a business process model has to meet certain syntactic, semantic, and pragmatic quality requirements to be of value. For many years, such quality

  11. 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.

  12. Process generalization in conceptual models

    NARCIS (Netherlands)

    Wieringa, Roelf J.

    In conceptual modeling, the universe of discourse (UoD) is divided into classes which have a taxonomic structure. The classes are usually defined in terms of attributes (all objects in a class share attribute names) and possibly of events. For enmple, the class of employees is the set of objects to

  13. Numerical modelling of reflood processes

    International Nuclear Information System (INIS)

    Glynn, D.R.; Rhodes, N.; Tatchell, D.G.

    1983-01-01

    The use of a detailed computer model to investigate the effects of grid size and the choice of wall-to-fluid heat-transfer correlations on the predictions obtained for reflooding of a vertical heated channel is described. The model employs equations for the momentum and enthalpy of vapour and liquid and hence accounts for both thermal non-equilibrium and slip between the phases. Empirical correlations are used to calculate interphase and wall-to-fluid friction and heat-transfer as functions of flow regime and local conditions. The empirical formulae have remained fixed with the exception of the wall-to-fluid heat-transfer correlations. These have been varied according to the practices adopted in other computer codes used to model reflood, namely REFLUX, RELAP and TRAC. Calculations have been performed to predict the CSNI standard problem number 7, and the results are compared with experiment. It is shown that the results are substantially grid-independent, and that the choice of correlation has a significant influence on the general flow behaviour, the rate of quenching and on the maximum cladding temperature predicted by the model. It is concluded that good predictions of reflooding rates can be obtained with particular correlation sets. (author)

  14. Branching process models of cancer

    CERN Document Server

    Durrett, Richard

    2015-01-01

    This volume develops results on continuous time branching processes and applies them to study rate of tumor growth, extending classic work on the Luria-Delbruck distribution. As a consequence, the authors calculate the probability that mutations that confer resistance to treatment are present at detection and quantify the extent of tumor heterogeneity. As applications, the authors evaluate ovarian cancer screening strategies and give rigorous proofs for results of Heano and Michor concerning tumor metastasis. These notes should be accessible to students who are familiar with Poisson processes and continuous time. Richard Durrett is mathematics professor at Duke University, USA. He is the author of 8 books, over 200 journal articles, and has supervised more than 40 Ph.D. students. Most of his current research concerns the applications of probability to biology: ecology, genetics, and most recently cancer.

  15. Plasma Processing of Model Residential Solid Waste

    Science.gov (United States)

    Messerle, V. E.; Mossé, A. L.; Nikonchuk, A. N.; Ustimenko, A. B.; Baimuldin, R. V.

    2017-09-01

    The authors have tested the technology of processing of model residential solid waste. They have developed and created a pilot plasma unit based on a plasma chamber incinerator. The waste processing technology has been tested and prepared for commercialization.

  16. Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

    DEFF Research Database (Denmark)

    Lonsdale, Richard; Fort, Rachel M; Rydberg, Patrik

    2016-01-01

    )-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP-D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers......The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear and is relevant to drug metabolism; previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R...... indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynamics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site...

  17. Hierarchical modeling of molecular energies using a deep neural network

    Science.gov (United States)

    Lubbers, Nicholas; Smith, Justin S.; Barros, Kipton

    2018-06-01

    We introduce the Hierarchically Interacting Particle Neural Network (HIP-NN) to model molecular properties from datasets of quantum calculations. Inspired by a many-body expansion, HIP-NN decomposes properties, such as energy, as a sum over hierarchical terms. These terms are generated from a neural network—a composition of many nonlinear transformations—acting on a representation of the molecule. HIP-NN achieves the state-of-the-art performance on a dataset of 131k ground state organic molecules and predicts energies with 0.26 kcal/mol mean absolute error. With minimal tuning, our model is also competitive on a dataset of molecular dynamics trajectories. In addition to enabling accurate energy predictions, the hierarchical structure of HIP-NN helps to identify regions of model uncertainty.

  18. Spherical convolutions and their application in molecular modelling

    DEFF Research Database (Denmark)

    Boomsma, Wouter; Frellsen, Jes

    2017-01-01

    Convolutional neural networks are increasingly used outside the domain of image analysis, in particular in various areas of the natural sciences concerned with spatial data. Such networks often work out-of-the box, and in some cases entire model architectures from image analysis can be carried over...... to other problem domains almost unaltered. Unfortunately, this convenience does not trivially extend to data in non-euclidean spaces, such as spherical data. In this paper, we introduce two strategies for conducting convolutions on the sphere, using either a spherical-polar grid or a grid based...... of spherical convolutions in the context of molecular modelling, by considering structural environments within proteins. We show that the models are capable of learning non-trivial functions in these molecular environments, and that our spherical convolutions generally outperform standard 3D convolutions...

  19. Modeling of nanotoxicity molecular interactions of nanomaterials with bionanomachines

    CERN Document Server

    Zhou, Ruhong

    2015-01-01

    This book provides a comprehensive overview of the fundamentals of nanotoxicity modeling and its implications for the development of novel nanomedicines. It lays out the fundamentals of nanotoxicity modeling for an array of nanomaterial systems, ranging from carbon-based nanoparticles to noble metals, metal oxides, and quantum dots. The author illustrates how molecular (classical mechanics) and atomic (quantum mechanics) modeling approaches can be applied to bolster our understanding of many important aspects of this critical nanotoxicity issue. Each chapter is organized by types of nanomaterials for practicality, making this an ideal book for senior undergraduate students, graduate students, and researchers in nanotechnology, chemistry, physics, molecular biology, and computer science. It is also of interest to academic and industry professionals who work on nanodrug delivery and related biomedical applications, and aids readers in their biocompatibility assessment efforts in the coming age of nanotechnology...

  20. Simulation Modeling of Software Development Processes

    Science.gov (United States)

    Calavaro, G. F.; Basili, V. R.; Iazeolla, G.

    1996-01-01

    A simulation modeling approach is proposed for the prediction of software process productivity indices, such as cost and time-to-market, and the sensitivity analysis of such indices to changes in the organization parameters and user requirements. The approach uses a timed Petri Net and Object Oriented top-down model specification. Results demonstrate the model representativeness, and its usefulness in verifying process conformance to expectations, and in performing continuous process improvement and optimization.

  1. Atmospheric processes on ice nanoparticles in molecular beams

    Directory of Open Access Journals (Sweden)

    Michal eFárník

    2014-02-01

    Full Text Available This review summarizes some recent experiments with ice nanoparticles (large water clusters in molecular beams and outlines their atmospheric relevance: (1 Investigation of mixed water–nitric acid particles by means of the electron ionization and sodium doping combined with photoionization revealed the prominent role of HNO3 molecule as the condensation nuclei. (2 The uptake of atmospheric molecules by water ice nanoparticles has been studied, and the pickup cross sections for some molecules exceed significantly the geometrical sizes of the ice nanoparticles. (3 Photodissociation of hydrogen halides on water ice particles has been shown to proceed via excitation of acidically dissociated ion pair and subsequent biradical generation and H3O dissociation. The photodissociation of CF2Cl2 molecule in clusters is also mentioned. Possible atmospheric consequences of all these results are briefly discussed.

  2. A molecular prognostic model predicts esophageal squamous cell carcinoma prognosis.

    Directory of Open Access Journals (Sweden)

    Hui-Hui Cao

    Full Text Available Esophageal squamous cell carcinoma (ESCC has the highest mortality rates in China. The 5-year survival rate of ESCC remains dismal despite improvements in treatments such as surgical resection and adjuvant chemoradiation, and current clinical staging approaches are limited in their ability to effectively stratify patients for treatment options. The aim of the present study, therefore, was to develop an immunohistochemistry-based prognostic model to improve clinical risk assessment for patients with ESCC.We developed a molecular prognostic model based on the combined expression of axis of epidermal growth factor receptor (EGFR, phosphorylated Specificity protein 1 (p-Sp1, and Fascin proteins. The presence of this prognostic model and associated clinical outcomes were analyzed for 130 formalin-fixed, paraffin-embedded esophageal curative resection specimens (generation dataset and validated using an independent cohort of 185 specimens (validation dataset.The expression of these three genes at the protein level was used to build a molecular prognostic model that was highly predictive of ESCC survival in both generation and validation datasets (P = 0.001. Regression analysis showed that this molecular prognostic model was strongly and independently predictive of overall survival (hazard ratio = 2.358 [95% CI, 1.391-3.996], P = 0.001 in generation dataset; hazard ratio = 1.990 [95% CI, 1.256-3.154], P = 0.003 in validation dataset. Furthermore, the predictive ability of these 3 biomarkers in combination was more robust than that of each individual biomarker.This technically simple immunohistochemistry-based molecular model accurately predicts ESCC patient survival and thus could serve as a complement to current clinical risk stratification approaches.

  3. Discovering Process Reference Models from Process Variants Using Clustering Techniques

    NARCIS (Netherlands)

    Li, C.; Reichert, M.U.; Wombacher, Andreas

    2008-01-01

    In today's dynamic business world, success of an enterprise increasingly depends on its ability to react to changes in a quick and flexible way. In response to this need, process-aware information systems (PAIS) emerged, which support the modeling, orchestration and monitoring of business processes

  4. Modelling and simulation of diffusive processes methods and applications

    CERN Document Server

    Basu, SK

    2014-01-01

    This book addresses the key issues in the modeling and simulation of diffusive processes from a wide spectrum of different applications across a broad range of disciplines. Features: discusses diffusion and molecular transport in living cells and suspended sediment in open channels; examines the modeling of peristaltic transport of nanofluids, and isotachophoretic separation of ionic samples in microfluidics; reviews thermal characterization of non-homogeneous media and scale-dependent porous dispersion resulting from velocity fluctuations; describes the modeling of nitrogen fate and transport

  5. Validation process of simulation model

    International Nuclear Information System (INIS)

    San Isidro, M. J.

    1998-01-01

    It is presented a methodology on empirical validation about any detailed simulation model. This king of validation it is always related with an experimental case. The empirical validation has a residual sense, because the conclusions are based on comparisons between simulated outputs and experimental measurements. This methodology will guide us to detect the fails of the simulation model. Furthermore, it can be used a guide in the design of posterior experiments. Three steps can be well differentiated: Sensitivity analysis. It can be made with a DSA, differential sensitivity analysis, and with a MCSA, Monte-Carlo sensitivity analysis. Looking the optimal domains of the input parameters. It has been developed a procedure based on the Monte-Carlo methods and Cluster techniques, to find the optimal domains of these parameters. Residual analysis. This analysis has been made on the time domain and on the frequency domain, it has been used the correlation analysis and spectral analysis. As application of this methodology, it is presented the validation carried out on a thermal simulation model on buildings, Esp., studying the behavior of building components on a Test Cell of LECE of CIEMAT. (Author) 17 refs

  6. Towards Model Checking Stochastic Process Algebra

    NARCIS (Netherlands)

    Hermanns, H.; Grieskamp, W.; Santen, T.; Katoen, Joost P.; Stoddart, B.; Meyer-Kayser, J.; Siegle, M.

    2000-01-01

    Stochastic process algebras have been proven useful because they allow behaviour-oriented performance and reliability modelling. As opposed to traditional performance modelling techniques, the behaviour- oriented style supports composition and abstraction in a natural way. However, analysis of

  7. Molecular Models for DSMC Simulations of Metal Vapor Deposition

    OpenAIRE

    Venkattraman, A; Alexeenko, Alina A

    2010-01-01

    The direct simulation Monte Carlo (DSMC) method is applied here to model the electron‐beam (e‐beam) physical vapor deposition of copper thin films. A suitable molecular model for copper‐copper interactions have been determined based on comparisons with experiments for a 2D slit source. The model for atomic copper vapor is then used in axi‐symmetric DSMC simulations for analysis of a typical e‐beam metal deposition system with a cup crucible. The dimensional and non‐dimensional mass fluxes obt...

  8. Parameter identification in multinomial processing tree models

    NARCIS (Netherlands)

    Schmittmann, V.D.; Dolan, C.V.; Raijmakers, M.E.J.; Batchelder, W.H.

    2010-01-01

    Multinomial processing tree models form a popular class of statistical models for categorical data that have applications in various areas of psychological research. As in all statistical models, establishing which parameters are identified is necessary for model inference and selection on the basis

  9. Modeling of molecular weight and molecular weight distribution in slurry polymerization of propylene by Ziegler-Natta catalysts

    International Nuclear Information System (INIS)

    Khorasani, R.; Pourmahdian, S.

    2007-01-01

    The Precise prediction of polypropylene synthesized by heterogeneous Ziegler-Natta catalysts needs good knowledge of parameters affecting on polymerization. molecular weight and molecular weight distribution are among important characteristics of a polymer determining physical-mechanical properties. broadening of molecular weight distribution is an important and well known characteristic of polypropylene synthesized by heterogeneous Ziegler-Natta catalysts, So it is important to understand the origin of broad molecular weight. Two main factors in broadening molecular weight, namely mass transfer resistances and multiplicity of active sites, are discussed in this paper and a model including these factors is presented. Then we calculate molecular weight and molecular weight distribution by the model and compare our results with

  10. Process modelling on a canonical basis[Process modelling; Canonical modelling

    Energy Technology Data Exchange (ETDEWEB)

    Siepmann, Volker

    2006-12-20

    Based on an equation oriented solving strategy, this thesis investigates a new approach to process modelling. Homogeneous thermodynamic state functions represent consistent mathematical models of thermodynamic properties. Such state functions of solely extensive canonical state variables are the basis of this work, as they are natural objective functions in optimisation nodes to calculate thermodynamic equilibrium regarding phase-interaction and chemical reactions. Analytical state function derivatives are utilised within the solution process as well as interpreted as physical properties. By this approach, only a limited range of imaginable process constraints are considered, namely linear balance equations of state variables. A second-order update of source contributions to these balance equations is obtained by an additional constitutive equation system. These equations are general dependent on state variables and first-order sensitivities, and cover therefore practically all potential process constraints. Symbolic computation technology efficiently provides sparsity and derivative information of active equations to avoid performance problems regarding robustness and computational effort. A benefit of detaching the constitutive equation system is that the structure of the main equation system remains unaffected by these constraints, and a priori information allows to implement an efficient solving strategy and a concise error diagnosis. A tailor-made linear algebra library handles the sparse recursive block structures efficiently. The optimisation principle for single modules of thermodynamic equilibrium is extended to host entire process models. State variables of different modules interact through balance equations, representing material flows from one module to the other. To account for reusability and encapsulation of process module details, modular process modelling is supported by a recursive module structure. The second-order solving algorithm makes it

  11. Post-processing interstitialcy diffusion from molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bhardwaj, U.; Bukkuru, S.; Warrier, M.

    2016-01-01

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:

  12. Post-processing interstitialcy diffusion from molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India); Bukkuru, S. [Nuclear Physics Dept., Andhra University, Visakhapatnam, 530003 (India); Warrier, M. [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India)

    2016-01-15

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.

  13. Integrated Process Modeling-A Process Validation Life Cycle Companion.

    Science.gov (United States)

    Zahel, Thomas; Hauer, Stefan; Mueller, Eric M; Murphy, Patrick; Abad, Sandra; Vasilieva, Elena; Maurer, Daniel; Brocard, Cécile; Reinisch, Daniela; Sagmeister, Patrick; Herwig, Christoph

    2017-10-17

    During the regulatory requested process validation of pharmaceutical manufacturing processes, companies aim to identify, control, and continuously monitor process variation and its impact on critical quality attributes (CQAs) of the final product. It is difficult to directly connect the impact of single process parameters (PPs) to final product CQAs, especially in biopharmaceutical process development and production, where multiple unit operations are stacked together and interact with each other. Therefore, we want to present the application of Monte Carlo (MC) simulation using an integrated process model (IPM) that enables estimation of process capability even in early stages of process validation. Once the IPM is established, its capability in risk and criticality assessment is furthermore demonstrated. IPMs can be used to enable holistic production control strategies that take interactions of process parameters of multiple unit operations into account. Moreover, IPMs can be trained with development data, refined with qualification runs, and maintained with routine manufacturing data which underlines the lifecycle concept. These applications will be shown by means of a process characterization study recently conducted at a world-leading contract manufacturing organization (CMO). The new IPM methodology therefore allows anticipation of out of specification (OOS) events, identify critical process parameters, and take risk-based decisions on counteractions that increase process robustness and decrease the likelihood of OOS events.

  14. Property Integration - A New Approach for Simultaneous Solution of Process and Molecular Design Problems

    DEFF Research Database (Denmark)

    The objective of this paper is to introduce the new concept of property integration. It is based on tracking and integrating properties throughout the process. This is made possible by exploiting the unique features at the interface of process and molecular design. Recently developed clustering...... concepts are employed to identify optimal properties without commitment to specific species. Subsequently, group contribution methods and molecular design techniques are employed to solve the reverse property prediction problem to design molecules possessing the optimal properties....

  15. Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

    Science.gov (United States)

    Palczynski, Karol; Wilke, Andreas; Paeschke, Manfred; Dzubiella, Joachim

    2017-09-01

    Linking the experimentally accessible macroscopic properties of thermoplastic polymers to their microscopic static and dynamic properties is a key requirement for targeted material design. Classical molecular dynamics simulations enable us to study the structural and dynamic behavior of molecules on microscopic scales, and statistical physics provides a framework for relating these properties to the macroscopic properties. We take a first step toward creating an automated workflow for the theoretical prediction of thermoplastic material properties by developing an expeditious method for parameterizing a simple yet surprisingly powerful coarse-grained bisphenol-A polycarbonate model which goes beyond previous coarse-grained models and successfully reproduces the thermal expansion behavior, the glass transition temperature as a function of the molecular weight, and several elastic properties.

  16. Models of charge transport and transfer in molecular switch tunnel junctions of bistable catenanes and rotaxanes

    International Nuclear Information System (INIS)

    Flood, Amar H.; Wong, Eric W.; Stoddart, J. Fraser

    2006-01-01

    The processes by which charge transfer can occur play a foundational role in molecular electronics. Here we consider simplified models of the transfer processes that could be present in bistable molecular switch tunnel junction (MSTJ) devices during one complete cycle of the device from its low- to high- and back to low-conductance state. The bistable molecular switches, which are composed of a monolayer of either switchable catenanes or rotaxanes, exist in either a ground-state co-conformation or a metastable one in which the conduction properties of the two co-conformations, when measured at small biases (+0.1 V), are significantly different irrespective of whether transport is dominated by tunneling or hopping. The voltage-driven generation (±2 V) of molecule-based redox states, which are sufficiently long-lived to allow the relative mechanical movements necessary to switch between the two co-conformations, rely upon unequal charge transfer rates on to and/or off of the molecules. Surface-enhanced Raman spectroscopy has been used to image the ground state of the bistable rotaxane in MSTJ-like devices. Consideration of these models provide new ways of looking at molecular electronic devices that rely, not only on nanoscale charge-transport, but also upon the bustling world of molecular motion in mechanically interlocked bistable molecules

  17. Revising process models through inductive learning

    NARCIS (Netherlands)

    Maggi, F.M.; Corapi, D.; Russo, A.; Lupu, E.; Visaggio, G.; Muehlen, zur M.; Su, J.

    2011-01-01

    Discovering the Business Process (BP) model underpinning existing practices through analysis of event logs, allows users to understand, analyse and modify the process. But, to be useful, the BP model must be kept in line with practice throughout its lifetime, as changes occur to the business

  18. Diagnosing differences between business process models

    NARCIS (Netherlands)

    Dijkman, R.M.; Dumas, M.; Reichert, M.; Shan, M.-C.

    2008-01-01

    This paper presents a technique to diagnose differences between business process models in the EPC notation. The diagnosis returns the exact position of a difference in the business process models and diagnoses the type of a difference, using a typology of differences developed in previous work.

  19. APROMORE : an advanced process model repository

    NARCIS (Netherlands)

    La Rosa, M.; Reijers, H.A.; Aalst, van der W.M.P.; Dijkman, R.M.; Mendling, J.; Dumas, M.; García-Bañuelos, L.

    2011-01-01

    Business process models are becoming available in large numbers due to their widespread use in many industrial applications such as enterprise and quality engineering projects. On the one hand, this raises a challenge as to their proper management: how can it be ensured that the proper process model

  20. Efficient querying of large process model repositories

    NARCIS (Netherlands)

    Jin, Tao; Wang, Jianmin; La Rosa, M.; Hofstede, ter A.H.M.; Wen, Lijie

    2013-01-01

    Recent years have seen an increased uptake of business process management technology in industries. This has resulted in organizations trying to manage large collections of business process models. One of the challenges facing these organizations concerns the retrieval of models from large business

  1. Jacobian elliptic wave solutions in an anharmonic molecular crystal model

    International Nuclear Information System (INIS)

    Teh, C.G.R.; Lee, B.S.; Koo, W.K.

    1997-07-01

    Explicit Jacobian elliptic wave solutions are found in the anharmonic molecular crystal model for both the continuum limit and discrete modes. This class of wave solutions include the famous pulse-like and kink-like solitary modes. We would also like to report on the existence of some highly discrete staggered solitary wave modes not found in the continuum limit. (author). 9 refs, 1 fig

  2. Molecular Analysis of Phr Peptide Processing in Bacillus subtilis†

    Science.gov (United States)

    Stephenson, Sophie; Mueller, Christian; Jiang, Min; Perego, Marta

    2003-01-01

    In Bacillus subtilis, an export-import pathway regulates production of the Phr pentapeptide inhibitors of Rap proteins. Processing of the Phr precursor proteins into the active pentapeptide form is a key event in the initiation of sporulation and competence development. The PhrA (ARNQT) and PhrE (SRNVT) peptides inhibit the RapA and RapE phosphatases, respectively, whose activity is directed toward the Spo0F∼P intermediate response regulator of the sporulation phosphorelay. The PhrC (ERGMT) peptide inhibits the RapC protein acting on the ComA response regulator for competence with regard to DNA transformation. The structural organization of PhrA, PhrE, and PhrC suggested a role for type I signal peptidases in the processing of the Phr preinhibitor, encoded by the phr genes, into the proinhibitor form. The proinhibitor was then postulated to be cleaved to the active pentapeptide inhibitor by an additional enzyme. In this report, we provide evidence that Phr preinhibitor proteins are subject to only one processing event at the peptide bond on the amino-terminal end of the pentapeptide. This processing event is most likely independent of type I signal peptidase activity. In vivo and in vitro analyses indicate that none of the five signal peptidases of B. subtilis (SipS, SipT, SipU, SipV, and SipW) are indispensable for Phr processing. However, we show that SipV and SipT have a previously undescribed role in sporulation, competence, and cell growth. PMID:12897006

  3. Molecular analysis of Phr peptide processing in Bacillus subtilis.

    Science.gov (United States)

    Stephenson, Sophie; Mueller, Christian; Jiang, Min; Perego, Marta

    2003-08-01

    In Bacillus subtilis, an export-import pathway regulates production of the Phr pentapeptide inhibitors of Rap proteins. Processing of the Phr precursor proteins into the active pentapeptide form is a key event in the initiation of sporulation and competence development. The PhrA (ARNQT) and PhrE (SRNVT) peptides inhibit the RapA and RapE phosphatases, respectively, whose activity is directed toward the Spo0F approximately P intermediate response regulator of the sporulation phosphorelay. The PhrC (ERGMT) peptide inhibits the RapC protein acting on the ComA response regulator for competence with regard to DNA transformation. The structural organization of PhrA, PhrE, and PhrC suggested a role for type I signal peptidases in the processing of the Phr preinhibitor, encoded by the phr genes, into the proinhibitor form. The proinhibitor was then postulated to be cleaved to the active pentapeptide inhibitor by an additional enzyme. In this report, we provide evidence that Phr preinhibitor proteins are subject to only one processing event at the peptide bond on the amino-terminal end of the pentapeptide. This processing event is most likely independent of type I signal peptidase activity. In vivo and in vitro analyses indicate that none of the five signal peptidases of B. subtilis (SipS, SipT, SipU, SipV, and SipW) are indispensable for Phr processing. However, we show that SipV and SipT have a previously undescribed role in sporulation, competence, and cell growth.

  4. Coffee husk composting: an investigation of the process using molecular and non-molecular tools.

    Science.gov (United States)

    Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

    2014-03-01

    Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Coffee husk composting: An investigation of the process using molecular and non-molecular tools

    Science.gov (United States)

    Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H.; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

    2014-01-01

    Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. PMID:24369846

  6. Improved model management with aggregated business process models

    NARCIS (Netherlands)

    Reijers, H.A.; Mans, R.S.; Toorn, van der R.A.

    2009-01-01

    Contemporary organizations invest much efforts in creating models of their business processes. This raises the issue of how to deal with large sets of process models that become available over time. This paper proposes an extension of Event-driven Process Chains, called the aggregate EPC (aEPC),

  7. Molecular modeling in the development of metal radiopharmaceuticals

    International Nuclear Information System (INIS)

    Green, M.A.

    1993-10-01

    We began this project with a compilation of a structural library to serve as a data base containing descriptions of the molecular features of metal-labeled radiopharmaceuticals known to efficiently cross the blood-brain barrier. Such a data base is needed in order to identify structural features (size, shape, molecular surface areas and volumes) that are critical in allowing blood-brain barrier penetration. Nine metal complexes have been added to this structural library. We have completed a detailed comparison of four molecular mechanics computer programs QUANTA, SYBYL, BOYD, and MM2DREW to assess their applicability to modeling the structures of low molecular weight metal complexes. We tested the ability of each program to reproduce the crystallographic structures of 38 complexes between nickel(II) and saturated N-donor ligands. The programs were evaluated in terns of their ability to reproduce structural features such as bond lengths, bond angles, and torsion angles. Recently, we investigated the synthesis and characterization of lipophilic cationic gallium complexes with hexadentate bis(salicylaldimine) ligands. This work identified the first gallium-68 radiopharrnaceuticals that can be injected intravenously and that subsequently exhibit significant myocardial uptake followed by prolonged myocardial retention of 68 Ga radioactivity. Tracers of this type remain under investigation as agents for evaluation of myocardial perfusion with positron emission tomography

  8. Two Models of Magnetic Support for Photoevaporated Molecular Clouds

    International Nuclear Information System (INIS)

    Ryutov, D; Kane, J; Mizuta, A; Pound, M; Remington, B

    2004-01-01

    The thermal pressure inside molecular clouds is insufficient for maintaining the pressure balance at an ablation front at the cloud surface illuminated by nearby UV stars. Most probably, the required stiffness is provided by the magnetic pressure. After surveying existing models of this type, we concentrate on two of them: the model of a quasi-homogeneous magnetic field and the recently proposed model of a ''magnetostatic turbulence''. We discuss observational consequences of the two models, in particular, the structure and the strength of the magnetic field inside the cloud and in the ionized outflow. We comment on the possible role of reconnection events and their observational signatures. We mention laboratory experiments where the most significant features of the models can be tested

  9. Molecular model for solubility of gases in flexible polymers

    DEFF Research Database (Denmark)

    Neergaard, Jesper; Hassager, Ole; Szabo, Peter

    1999-01-01

    We propose a model for a priori prediction of the solubility of gases in flexible polymers. The model is based on the concept of ideal solubility of gases in liquids. According to this concept, the mole fraction of gases in liquids is given by Raoult's law with the total pressure and the vapor...... pressure of the gas, where the latter may have to be extrapolated. However, instead of considering each polymer molecule as a rigid structure, we estimate the effective number of degrees of freedom from an equivalent freely jointed bead-rod model for the flexible polymer. In this model, we associate...... the length of the rods with the molecular weight corresponding to a Kuhn step. The model provides a tool for crude estimation of the gas solubility on the basis of only the monomer unit of the polymer and properties of the gas. A comparison with the solubility data for several gases in poly...

  10. Conceptual modelling of human resource evaluation process

    Directory of Open Access Journals (Sweden)

    Negoiţă Doina Olivia

    2017-01-01

    Full Text Available Taking into account the highly diverse tasks which employees have to fulfil due to complex requirements of nowadays consumers, the human resource within an enterprise has become a strategic element for developing and exploiting products which meet the market expectations. Therefore, organizations encounter difficulties when approaching the human resource evaluation process. Hence, the aim of the current paper is to design a conceptual model of the aforementioned process, which allows the enterprises to develop a specific methodology. In order to design the conceptual model, Business Process Modelling instruments were employed - Adonis Community Edition Business Process Management Toolkit using the ADONIS BPMS Notation. The conceptual model was developed based on an in-depth secondary research regarding the human resource evaluation process. The proposed conceptual model represents a generic workflow (sequential and/ or simultaneously activities, which can be extended considering the enterprise’s needs regarding their requirements when conducting a human resource evaluation process. Enterprises can benefit from using software instruments for business process modelling as they enable process analysis and evaluation (predefined / specific queries and also model optimization (simulations.

  11. Measures of Quality in Business Process Modelling

    Directory of Open Access Journals (Sweden)

    Radek Hronza

    2015-06-01

    Full Text Available Business process modelling and analysing is undoubtedly one of the most important parts of Applied (Business Informatics. Quality of business process models (diagrams is crucial for any purpose in this area. The goal of a process analyst’s work is to create generally understandable, explicit and error free models. If a process is properly described, created models can be used as an input into deep analysis and optimization. It can be assumed that properly designed business process models (similarly as in the case of correctly written algorithms contain characteristics that can be mathematically described. Besides it will be possible to create a tool that will help process analysts to design proper models. As part of this review will be conducted systematic literature review in order to find and analyse business process model’s design and business process model’s quality measures. It was found that mentioned area had already been the subject of research investigation in the past. Thirty-three suitable scietific publications and twenty-two quality measures were found. Analysed scientific publications and existing quality measures do not reflect all important attributes of business process model’s clarity, simplicity and completeness. Therefore it would be appropriate to add new measures of quality.

  12. Online Rule Generation Software Process Model

    OpenAIRE

    Sudeep Marwaha; Alka Aroa; Satma M C; Rajni Jain; R C Goyal

    2013-01-01

    For production systems like expert systems, a rule generation software can facilitate the faster deployment. The software process model for rule generation using decision tree classifier refers to the various steps required to be executed for the development of a web based software model for decision rule generation. The Royce’s final waterfall model has been used in this paper to explain the software development process. The paper presents the specific output of various steps of modified wat...

  13. Molecular Biomarkers for Detecting, Monitoring and Quantifying Reductive Microbial Processes

    Science.gov (United States)

    2013-07-01

    Bagley ,   1998...77–92.  doi:10.1016/j.jconhyd.2010.02.004.   Bagley ,   D.M.   1998.   Systematic   approach   for  modeling   tetrachloroethene...biodegradation.   J.   Environ.   Eng.,  124:  1076–1086.   Bagley ,  D.M.,  Gossett,   J.M.,   1990.  

  14. Influence of the Molecular Adhesion Force on the Indentation Depth of a Particle into the Wafer Surface in the CMP Process

    Directory of Open Access Journals (Sweden)

    Zhou Jianhua

    2014-01-01

    Full Text Available By theoretical calculation, the external force on the particle conveyed by pad asperities and the molecular adhesion force between particle and wafer are compared and analyzed quantitatively. It is confirmed that the molecular adhesion force between particle and wafer has a great influence on the chemical mechanical polishing (CMP material removal process. Considering the molecular adhesion force between particle and wafer, a more precise model for the indentation of a particle into the wafer surface is developed in this paper, and the new model is compared with the former model which neglected the molecular adhesion force. Through theoretical analyses, an approach and corresponding critical values are applied to estimate whether the molecular adhesion force in CMP can be neglected. These methods can improve the precision of the material removal model of CMP.

  15. Evaluation of Models of the Reading Process.

    Science.gov (United States)

    Balajthy, Ernest

    A variety of reading process models have been proposed and evaluated in reading research. Traditional approaches to model evaluation specify the workings of a system in a simplified fashion to enable organized, systematic study of the system's components. Following are several statistical methods of model evaluation: (1) empirical research on…

  16. Edgar Schein's Process versus Content Consultation Models.

    Science.gov (United States)

    Rockwood, Gary F.

    1993-01-01

    Describes Schein's three models of consultation based on assumptions inherent in different helping styles: purchase of expertise and doctor-patient models, which focus on content of organization problems; and process consultation model, which focuses on how organizational problems are solved. Notes that Schein has suggested that consultants begin…

  17. Multiscale simulation of molecular processes in cellular environments.

    Science.gov (United States)

    Chiricotto, Mara; Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone

    2016-11-13

    We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

  18. Theoretical model for calculation of molecular stopping power

    International Nuclear Information System (INIS)

    Xu, Y.J.

    1984-01-01

    A modified local plasma model based on the work of Linhard-Winther, Bethe, Brown, and Walske is established. The Gordon-Kim's molecular charged density model is employed to obtain a formula to evaluate the stopping power of many useful molecular systems. The stopping power of H 2 and He gas was calculated for incident proton energy ranging from 100 KeV to 2.5 MeV. The stopping power of O 2 , N 2 , and water vapor was also calculated for incident proton energy ranging from 40 keV to 2.5 MeV. Good agreement with experimental data was obtained. A discussion of molecular effects leading to departure from Bragg's rule is presented. The equipartition rule and the effect of nuclear momentum recoiling in stopping power are also discussed in the appendix. The calculation procedure presented hopefully can easily be extended to include the most useful organic systems such as the molecules composed of carbon, nitrogen, hydrogen and oxygen which are useful in radiation protection field

  19. Naumovozyma castellii: an alternative model for budding yeast molecular biology.

    Science.gov (United States)

    Karademir Andersson, Ahu; Cohn, Marita

    2017-03-01

    Naumovozyma castellii (Saccharomyces castellii) is a member of the budding yeast family Saccharomycetaceae. It has been extensively used as a model organism for telomere biology research and has gained increasing interest as a budding yeast model for functional analyses owing to its amenability to genetic modifications. Owing to the suitable phylogenetic distance to S. cerevisiae, the whole genome sequence of N. castellii has provided unique data for comparative genomic studies, and it played a key role in the establishment of the timing of the whole genome duplication and the evolutionary events that took place in the subsequent genomic evolution of the Saccharomyces lineage. Here we summarize the historical background of its establishment as a laboratory yeast species, and the development of genetic and molecular tools and strains. We review the research performed on N. castellii, focusing on areas where it has significantly contributed to the discovery of new features of molecular biology and to the advancement of our understanding of molecular evolution. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Piecewise deterministic processes in biological models

    CERN Document Server

    Rudnicki, Ryszard

    2017-01-01

    This book presents a concise introduction to piecewise deterministic Markov processes (PDMPs), with particular emphasis on their applications to biological models. Further, it presents examples of biological phenomena, such as gene activity and population growth, where different types of PDMPs appear: continuous time Markov chains, deterministic processes with jumps, processes with switching dynamics, and point processes. Subsequent chapters present the necessary tools from the theory of stochastic processes and semigroups of linear operators, as well as theoretical results concerning the long-time behaviour of stochastic semigroups induced by PDMPs and their applications to biological models. As such, the book offers a valuable resource for mathematicians and biologists alike. The first group will find new biological models that lead to interesting and often new mathematical questions, while the second can observe how to include seemingly disparate biological processes into a unified mathematical theory, and...

  1. Modeling closed nuclear fuel cycles processes

    Energy Technology Data Exchange (ETDEWEB)

    Shmidt, O.V. [A.A. Bochvar All-Russian Scientific Research Institute for Inorganic Materials, Rogova, 5a street, Moscow, 123098 (Russian Federation); Makeeva, I.R. [Zababakhin All-Russian Scientific Research Institute of Technical Physics, Vasiliev street 13, Snezhinsk, Chelyabinsk region, 456770 (Russian Federation); Liventsov, S.N. [Tomsk Polytechnic University, Tomsk, Lenin Avenue, 30, 634050 (Russian Federation)

    2016-07-01

    Computer models of processes are necessary for determination of optimal operating conditions for closed nuclear fuel cycle (NFC) processes. Computer models can be quickly changed in accordance with new and fresh data from experimental research. 3 kinds of process simulation are necessary. First, the VIZART software package is a balance model development used for calculating the material flow in technological processes. VIZART involves taking into account of equipment capacity, transport lines and storage volumes. Secondly, it is necessary to simulate the physico-chemical processes that are involved in the closure of NFC. The third kind of simulation is the development of software that allows the optimization, diagnostics and control of the processes which implies real-time simulation of product flows on the whole plant or on separate lines of the plant. (A.C.)

  2. Fermentation process diagnosis using a mathematical model

    Energy Technology Data Exchange (ETDEWEB)

    Yerushalmi, L; Volesky, B; Votruba, J

    1988-09-01

    Intriguing physiology of a solvent-producing strain of Clostridium acetobutylicum led to the synthesis of a mathematical model of the acetone-butanol fermentation process. The model presented is capable of describing the process dynamics and the culture behavior during a standard and a substandard acetone-butanol fermentation. In addition to the process kinetic parameters, the model includes the culture physiological parameters, such as the cellular membrane permeability and the number of membrane sites for active transport of sugar. Computer process simulation studies for different culture conditions used the model, and quantitatively pointed out the importance of selected culture parameters that characterize the cell membrane behaviour and play an important role in the control of solvent synthesis by the cell. The theoretical predictions by the new model were confirmed by experimental determination of the cellular membrane permeability.

  3. Advances in molecular modeling of human cytochrome P450 polymorphism.

    Science.gov (United States)

    Martiny, Virginie Y; Miteva, Maria A

    2013-11-01

    Cytochrome P450 (CYP) is a supergene family of metabolizing enzymes involved in the phase I metabolism of drugs and endogenous compounds. CYP oxidation often leads to inactive drug metabolites or to highly toxic or carcinogenic metabolites involved in adverse drug reactions (ADR). During the last decade, the impact of CYP polymorphism in various drug responses and ADR has been demonstrated. Of the drugs involved in ADR, 56% are metabolized by polymorphic phase I metabolizing enzymes, 86% among them being CYP. Here, we review the major CYP polymorphic forms, their impact for drug response and current advances in molecular modeling of CYP polymorphism. We focus on recent studies exploring CYP polymorphism performed by the use of sequence-based and/or protein-structure-based computational approaches. The importance of understanding the molecular mechanisms related to CYP polymorphism and drug response at the atomic level is outlined. © 2013.

  4. Towards structural models of molecular recognition in olfactory receptors.

    Science.gov (United States)

    Afshar, M; Hubbard, R E; Demaille, J

    1998-02-01

    The G protein coupled receptors (GPCR) are an important class of proteins that act as signal transducers through the cytoplasmic membrane. Understanding the structure and activation mechanism of these proteins is crucial for understanding many different aspects of cellular signalling. The olfactory receptors correspond to the largest family of GPCRs. Very little is known about how the structures of the receptors govern the specificity of interaction which enables identification of particular odorant molecules. In this paper, we review recent developments in two areas of molecular modelling: methods for modelling the configuration of trans-membrane helices and methods for automatic docking of ligands into receptor structures. We then show how a subset of these methods can be combined to construct a model of a rat odorant receptor interacting with lyral for which experimental data are available. This modelling can help us make progress towards elucidating the specificity of interactions between receptors and odorant molecules.

  5. Software-Engineering Process Simulation (SEPS) model

    Science.gov (United States)

    Lin, C. Y.; Abdel-Hamid, T.; Sherif, J. S.

    1992-01-01

    The Software Engineering Process Simulation (SEPS) model is described which was developed at JPL. SEPS is a dynamic simulation model of the software project development process. It uses the feedback principles of system dynamics to simulate the dynamic interactions among various software life cycle development activities and management decision making processes. The model is designed to be a planning tool to examine tradeoffs of cost, schedule, and functionality, and to test the implications of different managerial policies on a project's outcome. Furthermore, SEPS will enable software managers to gain a better understanding of the dynamics of software project development and perform postmodern assessments.

  6. Model of diffusers / permeators for hydrogen processing

    International Nuclear Information System (INIS)

    Jacobs, W. D.; Hang, T.

    2008-01-01

    Palladium-silver (Pd-Ag) diffusers are mainstays of hydrogen processing. Diffusers separate hydrogen from inert species such as nitrogen, argon or helium. The tubing becomes permeable to hydrogen when heated to more than 250 C and a differential pressure is created across the membrane. The hydrogen diffuses better at higher temperatures. Experimental or experiential results have been the basis for determining or predicting a diffuser's performance. However, the process can be mathematically modeled, and comparison to experimental or other operating data can be utilized to improve the fit of the model. A reliable model-based diffuser system design is the goal which will have impacts on tritium and hydrogen processing. A computer model has been developed to solve the differential equations for diffusion given the operating boundary conditions. The model was compared to operating data for a low pressure diffuser system. The modeling approach and the results are presented in this paper. (authors)

  7. Modeling Business Processes in Public Administration

    Science.gov (United States)

    Repa, Vaclav

    During more than 10 years of its existence business process modeling became a regular part of organization management practice. It is mostly regarded. as a part of information system development or even as a way to implement some supporting technology (for instance workflow system). Although I do not agree with such reduction of the real meaning of a business process, it is necessary to admit that information technologies play an essential role in business processes (see [1] for more information), Consequently, an information system is inseparable from a business process itself because it is a cornerstone of the general basic infrastructure of a business. This fact impacts on all dimensions of business process management. One of these dimensions is the methodology that postulates that the information systems development provide the business process management with exact methods and tools for modeling business processes. Also the methodology underlying the approach presented in this paper has its roots in the information systems development methodology.

  8. Mathematical model of seed germination process

    International Nuclear Information System (INIS)

    Gładyszewska, B.; Koper, R.; Kornarzyński, K.

    1999-01-01

    An analytical model of seed germination process was described. The model based on proposed working hypothesis leads - by analogy - to a law corresponding with Verhulst-Pearl's law, known from the theory of population kinetics. The model was applied to describe the germination kinetics of tomato seeds, Promyk field cultivar, biostimulated by laser treatment. Close agreement of experimental and model data was obtained [pl

  9. Ontological Model of Business Process Management Systems

    Science.gov (United States)

    Manoilov, G.; Deliiska, B.

    2008-10-01

    The activities which constitute business process management (BPM) can be grouped into five categories: design, modeling, execution, monitoring and optimization. Dedicated software packets for business process management system (BPMS) are available on the market. But the efficiency of its exploitation depends on used ontological model in the development time and run time of the system. In the article an ontological model of BPMS in area of software industry is investigated. The model building is preceded by conceptualization of the domain and taxonomy of BPMS development. On the base of the taxonomy an simple online thesaurus is created.

  10. Molecular Dynamics Simulation of Mahkota Dewa (Phaleria Macrocarpa) Extract in Subcritical Water Extraction Process

    Science.gov (United States)

    Hashim, N. A.; Mudalip, S. K. Abdul; Harun, N.; Che Man, R.; Sulaiman, S. Z.; Arshad, Z. I. M.; Shaarani, S. M.

    2018-05-01

    Mahkota Dewa (Phaleria Macrocarpa), a good source of saponin, flavanoid, polyphenol, alkaloid, and mangiferin has an extensive range of medicinal effects. The intermolecular interactions between solute and solvents such as hydrogen bonding considered as an important factor that affect the extraction of bioactive compounds. In this work, molecular dynamics simulation was performed to elucidate the hydrogen bonding exists between Mahkota Dewa extracts and water during subcritical extraction process. A bioactive compound in the Mahkota Dewa extract, namely mangiferin was selected as a model compound. The simulation was performed at 373 K and 4.0 MPa using COMPASS force field and Ewald summation method available in Material Studio 7.0 simulation package. The radial distribution functions (RDF) between mangiferin and water signify the presence of hydrogen bonding in the extraction process. The simulation of the binary mixture of mangiferin:water shows that strong hydrogen bonding was formed. It is suggested that, the intermolecular interaction between OH2O••HMR4(OH1) has been identified to be responsible for the mangiferin extraction process.

  11. Towards a universal competitive intelligence process model

    Directory of Open Access Journals (Sweden)

    Rene Pellissier

    2013-08-01

    Full Text Available Background: Competitive intelligence (CI provides actionable intelligence, which provides a competitive edge in enterprises. However, without proper process, it is difficult to develop actionable intelligence. There are disagreements about how the CI process should be structured. For CI professionals to focus on producing actionable intelligence, and to do so with simplicity, they need a common CI process model.Objectives: The purpose of this research is to review the current literature on CI, to look at the aims of identifying and analysing CI process models, and finally to propose a universal CI process model.Method: The study was qualitative in nature and content analysis was conducted on all identified sources establishing and analysing CI process models. To identify relevant literature, academic databases and search engines were used. Moreover, a review of references in related studies led to more relevant sources, the references of which were further reviewed and analysed. To ensure reliability, only peer-reviewed articles were used.Results: The findings reveal that the majority of scholars view the CI process as a cycle of interrelated phases. The output of one phase is the input of the next phase.Conclusion: The CI process is a cycle of interrelated phases. The output of one phase is the input of the next phase. These phases are influenced by the following factors: decision makers, process and structure, organisational awareness and culture, and feedback.

  12. Transient Changes in Molecular Geometries and How to Model Them

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard

    Light-induced chemical processes are accompanied by molecular motion on the femtosecond time scale. Uncovering this dynamical motion is central to understanding the chemical reaction on a fundamental level. This thesis focuses on the aspects of excess excitation energy dissipation via dynamic...... observe how the wide distribution of ground state geometries is responsible for decoherence, and that the solvent cage actually facilitates coherent motion, by blocking the newly discovered vibrational mode. We furthermore observe a non-specific, rotational solvent response to the excitation. The second...

  13. Validating clustering of molecular dynamics simulations using polymer models

    Directory of Open Access Journals (Sweden)

    Phillips Joshua L

    2011-11-01

    Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

  14. Three-dimensional model analysis and processing

    CERN Document Server

    Yu, Faxin; Luo, Hao; Wang, Pinghui

    2011-01-01

    This book focuses on five hot research directions in 3D model analysis and processing in computer science:  compression, feature extraction, content-based retrieval, irreversible watermarking and reversible watermarking.

  15. Fusion Plasma Modelling Using Atomic and Molecular Data. Summary report of a Joint ICTP-IAEA Workshop

    International Nuclear Information System (INIS)

    Braams, B.J.

    2012-03-01

    The Joint ICTP-IAEA Workshop on Fusion Plasma Modelling using Atomic and Molecular Data was held from 23-27 January 2012 at Abdus Salam International Centre for Theoretical Physics in Trieste, Italy. Ten lecturers presented tutorials and reviews on topics in fusion plasma modelling and atomic, molecular and plasma-material interaction processes. There were 20 participants, generally early-career researchers in the area of A+M+PMI processes and also plasma modellers. The participants presented their work in short talks and a poster session. The proceedings of the workshop are summarized here. (author)

  16. Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

    OpenAIRE

    Kishimoto, Toshihiko; Ying, Bei-Wen; Tsuru, Saburo; Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya

    2015-01-01

    The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution e...

  17. CGDM: collaborative genomic data model for molecular profiling data using NoSQL.

    Science.gov (United States)

    Wang, Shicai; Mares, Mihaela A; Guo, Yi-Ke

    2016-12-01

    High-throughput molecular profiling has greatly improved patient stratification and mechanistic understanding of diseases. With the increasing amount of data used in translational medicine studies in recent years, there is a need to improve the performance of data warehouses in terms of data retrieval and statistical processing. Both relational and Key Value models have been used for managing molecular profiling data. Key Value models such as SeqWare have been shown to be particularly advantageous in terms of query processing speed for large datasets. However, more improvement can be achieved, particularly through better indexing techniques of the Key Value models, taking advantage of the types of queries which are specific for the high-throughput molecular profiling data. In this article, we introduce a Collaborative Genomic Data Model (CGDM), aimed at significantly increasing the query processing speed for the main classes of queries on genomic databases. CGDM creates three Collaborative Global Clustering Index Tables (CGCITs) to solve the velocity and variety issues at the cost of limited extra volume. Several benchmarking experiments were carried out, comparing CGDM implemented on HBase to the traditional SQL data model (TDM) implemented on both HBase and MySQL Cluster, using large publicly available molecular profiling datasets taken from NCBI and HapMap. In the microarray case, CGDM on HBase performed up to 246 times faster than TDM on HBase and 7 times faster than TDM on MySQL Cluster. In single nucleotide polymorphism case, CGDM on HBase outperformed TDM on HBase by up to 351 times and TDM on MySQL Cluster by up to 9 times. The CGDM source code is available at https://github.com/evanswang/CGDM. y.guo@imperial.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Modeling of Dielectric Heating within Lyophilization Process

    Directory of Open Access Journals (Sweden)

    Jan Kyncl

    2014-01-01

    Full Text Available A process of lyophilization of paper books is modeled. The process of drying is controlled by a dielectric heating system. From the physical viewpoint, the task represents a 2D coupled problem described by two partial differential equations for the electric and temperature fields. The material parameters are supposed to be temperature-dependent functions. The continuous mathematical model is solved numerically. The methodology is illustrated with some examples whose results are discussed.

  19. Cost Models for MMC Manufacturing Processes

    Science.gov (United States)

    Elzey, Dana M.; Wadley, Haydn N. G.

    1996-01-01

    Processes for the manufacture of advanced metal matrix composites are rapidly approaching maturity in the research laboratory and there is growing interest in their transition to industrial production. However, research conducted to date has almost exclusively focused on overcoming the technical barriers to producing high-quality material and little attention has been given to the economical feasibility of these laboratory approaches and process cost issues. A quantitative cost modeling (QCM) approach was developed to address these issues. QCM are cost analysis tools based on predictive process models relating process conditions to the attributes of the final product. An important attribute, of the QCM approach is the ability to predict the sensitivity of material production costs to product quality and to quantitatively explore trade-offs between cost and quality. Applications of the cost models allow more efficient direction of future MMC process technology development and a more accurate assessment of MMC market potential. Cost models were developed for two state-of-the art metal matrix composite (MMC) manufacturing processes: tape casting and plasma spray deposition. Quality and Cost models are presented for both processes and the resulting predicted quality-cost curves are presented and discussed.

  20. A molecular-thermodynamic model for polyelectrolyte solutions

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, J.; Liu, H.; Hu, Y. [Thermodynamics Research Laboratory, East China University of Science and Technology, Shanghai 200237 (China); Prausnitz, J.M. [Department of Chemical Engineering, University of California, Berkeley, and Chemical Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, California 94720 (United States)

    1998-01-01

    Polyelectrolyte solutions are modeled as freely tangent-jointed, charged hard-sphere chains and corresponding counterions in a continuum medium with permitivity {var_epsilon}. By adopting the sticky-point model, the Helmholtz function for polyelectrolyte solutions is derived through the r-particle cavity-correlation function (CCF) for chains of sticky, charged hard spheres. The r-CCF is approximated by a product of effective nearest-neighbor two-particle CCFs; these are determined from the hypernetted-chain and mean-spherical closures (HNC/MSA) inside and outside the hard core, respectively, for the integral equation theory for electrolytes. The colligative properties are given as explicit functions of a scaling parameter {Gamma} that can be estimated by a simple iteration procedure. Osmotic pressures, osmotic coefficients, and activity coefficients are calculated for model solutions with various chain lengths. They are in good agreement with molecular simulation and experimental results. {copyright} {ital 1998 American Institute of Physics.}

  1. Structural and Molecular Modeling Features of P2X Receptors

    Directory of Open Access Journals (Sweden)

    Luiz Anastacio Alves

    2014-03-01

    Full Text Available Currently, adenosine 5'-triphosphate (ATP is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors.

  2. In Vivo Molecular Imaging of Cathepsin and Matrix Metalloproteinase Activity Discriminates between Arthritic and Osteoarthritic Processes in Mice

    Directory of Open Access Journals (Sweden)

    Eline A. Vermeij

    2014-01-01

    Full Text Available Rheumatoid arthritis (RA and osteoarthritis (OA are serologically and clinically distinctive, but at the local level, both diseases have many molecular pathways in common. In vivo molecular imaging can unravel the local pathologic processes involved in both diseases. In this study, we investigated matrix metalloproteinase (MMP and cathepsin activity during cartilage destruction, in an RA and an OA mouse model, using biophotonic imaging of substrate-based probes. Mice with collagen-induced arthritis (CIA or destabilization of the medial meniscus (DMM were imaged using near-infrared fluorescent probes, activated by several cathepsins or MMPs. Fluorescence signal intensity was compared to synovial gene expression, histology, and cartilage staining of a neoepitope of aggrecan cleaved by MMPs with the amino acids DIPEN. Increased cathepsin and MMP activity was seen during CIA, whereas the DMM model only showed increased MMP activity. DIPEN expression was seen only during CIA. A possible explanation can be differences in gene expressions; MMP3 and -13, known to produce DIPEN neoepitopes, were upregulated in the CIA model, whereas MMP12, known to be involved in elastin degradation and chemokine inhibition, was upregulated in the DMM model. Thus, molecular imaging showed no cathepsin activity at the time of cartilage damage in the DMM model, whereas both cathepsins and MMPs are active in the CIA model during disease progression.

  3. Model visualization for evaluation of biocatalytic processes

    DEFF Research Database (Denmark)

    Law, HEM; Lewis, DJ; McRobbie, I

    2008-01-01

    Biocatalysis offers great potential as an additional, and in some cases as an alternative, synthetic tool for organic chemists, especially as a route to introduce chirality. However, the implementation of scalable biocatalytic processes nearly always requires the introduction of process and/or bi......,S-EDDS), a biodegradable chelant, and is characterised by the use of model visualization using `windows of operation"....

  4. Business process modeling using Petri nets

    NARCIS (Netherlands)

    Hee, van K.M.; Sidorova, N.; Werf, van der J.M.E.M.; Jensen, K.; Aalst, van der W.M.P.; Balbo, G.; Koutny, M.; Wolf, K.

    2013-01-01

    Business process modeling has become a standard activity in many organizations. We start with going back into the history and explain why this activity appeared and became of such importance for organizations to achieve their business targets. We discuss the context in which business process

  5. Business Process Modeling Notation - An Overview

    Directory of Open Access Journals (Sweden)

    Alexandra Fortiş

    2006-01-01

    Full Text Available BPMN represents an industrial standard created to offer a common and user friendly notation to all the participants to a business process. The present paper aims to briefly present the main features of this notation as well as an interpretation of some of the main patterns characterizing a business process modeled by the working fluxes.

  6. Workflow Patterns for Business Process Modeling

    NARCIS (Netherlands)

    Thom, Lucineia Heloisa; Lochpe, Cirano; Reichert, M.U.

    For its reuse advantages, workflow patterns (e.g., control flow patterns, data patterns, resource patterns) are increasingly attracting the interest of both researchers and vendors. Frequently, business process or workflow models can be assembeled out of a set of recurrent process fragments (or

  7. Physical and mathematical modelling of extrusion processes

    DEFF Research Database (Denmark)

    Arentoft, Mogens; Gronostajski, Z.; Niechajowics, A.

    2000-01-01

    The main objective of the work is to study the extrusion process using physical modelling and to compare the findings of the study with finite element predictions. The possibilities and advantages of the simultaneous application of both of these methods for the analysis of metal forming processes...

  8. Cross-link guided molecular modeling with ROSETTA.

    Directory of Open Access Journals (Sweden)

    Abdullah Kahraman

    Full Text Available Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.

  9. Qualitative simulation in formal process modelling

    International Nuclear Information System (INIS)

    Sivertsen, Elin R.

    1999-01-01

    In relation to several different research activities at the OECD Halden Reactor Project, the usefulness of formal process models has been identified. Being represented in some appropriate representation language, the purpose of these models is to model process plants and plant automatics in a unified way to allow verification and computer aided design of control strategies. The present report discusses qualitative simulation and the tool QSIM as one approach to formal process models. In particular, the report aims at investigating how recent improvements of the tool facilitate the use of the approach in areas like process system analysis, procedure verification, and control software safety analysis. An important long term goal is to provide a basis for using qualitative reasoning in combination with other techniques to facilitate the treatment of embedded programmable systems in Probabilistic Safety Analysis (PSA). This is motivated from the potential of such a combination in safety analysis based on models comprising both software, hardware, and operator. It is anticipated that the research results from this activity will benefit V and V in a wide variety of applications where formal process models can be utilized. Examples are operator procedures, intelligent decision support systems, and common model repositories (author) (ml)

  10. New models and molecular markers in evaluation of developmental toxicity

    International Nuclear Information System (INIS)

    Huuskonen, Hannele

    2005-01-01

    Mammalian and non-mammalian embryos and embryonic stem cells may be used as models in mechanistic studies and in testing embryotoxicity of compounds. In addition to conventional culture methods, genetic modifications and use of molecular markers offer significant advantages in mechanistic studies as well as in developing new test methods for embryotoxicity. Zebrafish model has been used for a long time and at present several applications are available. It is an easy vertebral non-mammalian model, whose genome is largely known and several genetic modifications are easily constructed to study gene expression or knocked down genes. Fluorescent marker proteins can be used also in zebrafish to indicate gene activation in transgenic models. Chemical genetics approach has been developed using zebrafish model. This is a new approach to screen small molecules that regulate signaling pathways. Embryonic stem cells have been used in mechanistic studies and mouse embryonic stem cell test has been validated to study embryotoxicity in vitro. This method has been improved using quantitative measurements of molecular endpoints by real-time RT-PCR or fluorescent activated cell sorting methods (FACS). Methods facilitating differentiation to several different cell types are available. We have studied preimplantation mouse embryos as a possible model for in vitro testing. In this method, superovulated and in vivo fertilized preimplantation embryos were collected at morula stage and cultured up to blastocysts. The mouse preimplantation culture test was improved by quantitative gene expression measurement using two-step real-time RT-PCR methods. New endpoints improve the tests of in vitro embryotoxicity because subjective assessments are replaced by objective measurements. In addition, automation is possible and less time is needed for analysis. Thus, high throughput screening will come possible to test large numbers of compounds

  11. Multiphysics modelling of the spray forming process

    International Nuclear Information System (INIS)

    Mi, J.; Grant, P.S.; Fritsching, U.; Belkessam, O.; Garmendia, I.; Landaberea, A.

    2008-01-01

    An integrated, multiphysics numerical model has been developed through the joint efforts of the University of Oxford (UK), University of Bremen (Germany) and Inasmet (Spain) to simulate the spray forming process. The integrated model consisted of four sub-models: (1) an atomization model simulating the fragmentation of a continuous liquid metal stream into droplet spray during gas atomization; (2) a droplet spray model simulating the droplet spray mass and enthalpy evolution in the gas flow field prior to deposition; (3) a droplet deposition model simulating droplet deposition, splashing and re-deposition behavior and the resulting preform shape and heat flow; and (4) a porosity model simulating the porosity distribution inside a spray formed ring preform. The model has been validated against experiments of the spray forming of large diameter IN718 Ni superalloy rings. The modelled preform shape, surface temperature and final porosity distribution showed good agreement with experimental measurements

  12. Molecular modeling of human neutral sphingomyelinase provides insight into its molecular interactions.

    Science.gov (United States)

    Dinesh; Goswami, Angshumala; Suresh, Panneer Selvam; Thirunavukkarasu, Chinnasamy; Weiergräber, Oliver H; Kumar, Muthuvel Suresh

    2011-01-01

    The neutral sphingomyelinase (N-SMase) is considered a major candidate for mediating the stress-induced production of ceramide, and it plays an important role in cell-cycle arrest, apoptosis, inflammation, and eukaryotic stress responses. Recent studies have identified a small region at the very N-terminus of the 55 kDa tumour necrosis factor receptor (TNF-R55), designated the neutral sphingomyelinase activating domain (NSD) that is responsible for the TNF-induced activation of N-SMase. There is no direct association between TNF-R55 NSD and N-SMase; instead, a protein named factor associated with N-SMase activation (FAN) has been reported to couple the TNF-R55 NSD to N-SMase. Since the three-dimensional fold of N-SMase is still unknown, we have modeled the structure using the protein fold recognition and threading method. Moreover, we propose models for the TNF-R55 NSD as well as the FAN protein in order to study the structural basis of N-SMase activation and regulation. Protein-protein interaction studies suggest that FAN is crucially involved in mediating TNF-induced activation of the N-SMase pathway, which in turn regulates mitogenic and proinflammatory responses. Inhibition of N-SMase may lead to reduction of ceramide levels and hence may provide a novel therapeutic strategy for inflammation and autoimmune diseases. Molecular dynamics (MD) simulations were performed to check the stability of the predicted model and protein-protein complex; indeed, stable RMS deviations were obtained throughout the simulation. Furthermore, in silico docking of low molecular mass ligands into the active site of N-SMase suggests that His135, Glu48, Asp177, and Asn179 residues play crucial roles in this interaction. Based on our results, these ligands are proposed to be potent and selective N-SMase inhibitors, which may ultimately prove useful as lead compounds for drug development.

  13. The (Mathematical) Modeling Process in Biosciences.

    Science.gov (United States)

    Torres, Nestor V; Santos, Guido

    2015-01-01

    In this communication, we introduce a general framework and discussion on the role of models and the modeling process in the field of biosciences. The objective is to sum up the common procedures during the formalization and analysis of a biological problem from the perspective of Systems Biology, which approaches the study of biological systems as a whole. We begin by presenting the definitions of (biological) system and model. Particular attention is given to the meaning of mathematical model within the context of biology. Then, we present the process of modeling and analysis of biological systems. Three stages are described in detail: conceptualization of the biological system into a model, mathematical formalization of the previous conceptual model and optimization and system management derived from the analysis of the mathematical model. All along this work the main features and shortcomings of the process are analyzed and a set of rules that could help in the task of modeling any biological system are presented. Special regard is given to the formative requirements and the interdisciplinary nature of this approach. We conclude with some general considerations on the challenges that modeling is posing to current biology.

  14. The semantics of hybrid process models

    NARCIS (Netherlands)

    Slaats, T.; Schunselaar, D.M.M.; Maggi, F.M.; Reijers, H.A.; Debruyne, C.; Panetto, H.; Meersman, R.; Dillon, T.; Kuhn, E.; O'Sullivan, D.; Agostino Ardagna, C.

    2016-01-01

    In the area of business process modelling, declarative notations have been proposed as alternatives to notations that follow the dominant, imperative paradigm. Yet, the choice between an imperative or declarative style of modelling is not always easy to make. Instead, a mixture of these styles is

  15. Modeling biochemical transformation processes and information processing with Narrator

    Directory of Open Access Journals (Sweden)

    Palfreyman Niall M

    2007-03-01

    Full Text Available Abstract Background Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs, which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Results Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Conclusion Narrator is a

  16. Modeling biochemical transformation processes and information processing with Narrator.

    Science.gov (United States)

    Mandel, Johannes J; Fuss, Hendrik; Palfreyman, Niall M; Dubitzky, Werner

    2007-03-27

    Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Narrator is a flexible and intuitive systems biology tool. It is

  17. HOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDY OF MYCOBACTERIUM TUBERCULOSIS UREASE

    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.

    2017-10-01

    Full Text Available Introduction. M. tuberculosis urease (MTU is an attractive target for chemotherapeutic intervention in tuberculosis by designing new safe and efficient enzyme inhibitors. A prerequisite for designing such inhibitors is an understanding of urease's three-dimensional (3D structure organization. 3D structure of M. tuberculosis urease is unknown. When experimental three-dimensional structure of a protein is not known, homology modeling, the most commonly used computational structure prediction method, is the technique of choice. This paper aimed to build a 3D-structure of M. tuberculosis urease by homology modeling and to study its stability by molecular dynamics simulations. Materials and methods. To build MTU model, five high-resolution X-ray structures of bacterial ureases with three-subunit composition (2KAU, 5G4H, 4UBP, 4СEU, and 4EPB have been selected as templates. For each template five stochastic alignments were created and for each alignment, a three-dimensional model was built. Then, each model was energy minimized and the models were ranked by quality Z-score. The MTU model with highest quality estimation amongst 25 potential models was selected. To further improve structure quality the model was refined by short molecular dynamics simulation that resulted in 20 snapshots which were rated according to their energy and the quality Z-score. The best scoring model having minimum energy was chosen as a final homology model of 3D structure for M. tuberculosis. The final model of MTU was also validated by using PDBsum and QMEAN servers. These checks confirmed good quality of MTU homology model. Results and discussion. Homology model of MTU is a nonamer (homotrimer of heterotrimers, (αβγ3 consisting of 2349 residues. In MTU heterotrimer, sub-units α, β, and γ tightly interact with each other at a surface of approximately 3000 Å2. Sub-unit α contains the enzyme active site with two Ni atoms coordinated by amino acid residues His347, His

  18. Capturing molecular multimode relaxation processes in excitable gases based on decomposition of acoustic relaxation spectra

    Science.gov (United States)

    Zhu, Ming; Liu, Tingting; Wang, Shu; Zhang, Kesheng

    2017-08-01

    Existing two-frequency reconstructive methods can only capture primary (single) molecular relaxation processes in excitable gases. In this paper, we present a reconstructive method based on the novel decomposition of frequency-dependent acoustic relaxation spectra to capture the entire molecular multimode relaxation process. This decomposition of acoustic relaxation spectra is developed from the frequency-dependent effective specific heat, indicating that a multi-relaxation process is the sum of the interior single-relaxation processes. Based on this decomposition, we can reconstruct the entire multi-relaxation process by capturing the relaxation times and relaxation strengths of N interior single-relaxation processes, using the measurements of acoustic absorption and sound speed at 2N frequencies. Experimental data for the gas mixtures CO2-N2 and CO2-O2 validate our decomposition and reconstruction approach.

  19. Model morphing and sequence assignment after molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States); Read, Randy J. [University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY (United Kingdom); Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Brunger, Axel T. [Stanford University, 318 Campus Drive West, Stanford, CA 94305 (United States); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Hung, Li-Wei [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States)

    2013-11-01

    A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

  20. Model morphing and sequence assignment after molecular replacement

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.; Brunger, Axel T.; Afonine, Pavel V.; Hung, Li-Wei

    2013-01-01

    A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package

  1. Process modeling of a HLA research lab

    Science.gov (United States)

    Ribeiro, Bruna G. C.; Sena, Alexandre C.; Silva, Dilson; Marzulo, Leandro A. J.

    2017-11-01

    Bioinformatics has provided tremendous breakthroughs in the field of molecular biology. All this evolution has generated a large volume of biological data that increasingly require the use of computing for analysis and storage of this information. The identification of the human leukocyte antigen (HLA) genotypes is critical to the success of organ transplants in humans. HLA typing involves not only laboratory tests but also DNA sequencing, with the participation of several professionals responsible for different stages of the process. Thus, the objective of this paper is to map the main steps in HLA typing in a laboratory specialized in performing such procedures, analyzing each process and proposing solutions to speed up the these steps, avoiding mistakes.

  2. The Automation of Nowcast Model Assessment Processes

    Science.gov (United States)

    2016-09-01

    secondly, provide modelers with the information needed to understand the model errors and how their algorithm changes might mitigate these errors. In...by ARL modelers. 2. Development Environment The automation of Point-Stat processes (i.e., PSA) was developed using Python 3.5.* Python was selected...because it is easy to use, widely used for scripting, and satisfies all the requirements to automate the implementation of the Point-Stat tool. In

  3. Inclusion Complexes of Sunscreen Agents with β-Cyclodextrin: Spectroscopic and Molecular Modeling Studies

    Directory of Open Access Journals (Sweden)

    Nathir A. F. Al-Rawashdeh

    2013-01-01

    Full Text Available The inclusion complexes of selected sunscreen agents, namely, oxybenzone (Oxy, octocrylene (Oct, and ethylhexyl-methoxycinnamate (Cin with β-cyclodextrin (β-CD were studied by UV-Vis spectroscopy, differential scanning calorimetry (DSC, 13C NMR techniques, and molecular mechanics (MM calculations and modeling. Molecular modeling (MM study of the entire process of the formation of 1 : 1 stoichiometry sunscreen agent/β-cyclodextrin structures has been used to contribute to the understanding and rationalization of the experimental results. Molecular mechanics calculations, together with 13C NMR measurements, for the complex with β-CD have been used to describe details of the structural, energetic, and dynamic features of host-guest complex. Accurate structures of CD inclusion complexes have been derived from molecular mechanics (MM calculations and modeling. The photodegradation reaction of the sunscreen agents' molecules in lotion was explored using UV-Vis spectroscopy. It has been demonstrated that the photostability of these selected sunscreen agents has been enhanced upon forming inclusion complexes with β-CD in lotion. The results of this study demonstrate that β-CD can be utilized as photostabilizer additive for enhancing the photostability of the selected sunscreen agents' molecules.

  4. Applying the Business Process and Practice Alignment Meta-model: Daily Practices and Process Modelling

    Directory of Open Access Journals (Sweden)

    Ventura Martins Paula

    2017-03-01

    Full Text Available Background: Business Process Modelling (BPM is one of the most important phases of information system design. Business Process (BP meta-models allow capturing informational and behavioural aspects of business processes. Unfortunately, standard BP meta-modelling approaches focus just on process description, providing different BP models. It is not possible to compare and identify related daily practices in order to improve BP models. This lack of information implies that further research in BP meta-models is needed to reflect the evolution/change in BP. Considering this limitation, this paper introduces a new BP meta-model designed by Business Process and Practice Alignment Meta-model (BPPAMeta-model. Our intention is to present a meta-model that addresses features related to the alignment between daily work practices and BP descriptions. Objectives: This paper intends to present a metamodel which is going to integrate daily work information into coherent and sound process definitions. Methods/Approach: The methodology employed in the research follows a design-science approach. Results: The results of the case study are related to the application of the proposed meta-model to align the specification of a BP model with work practices models. Conclusions: This meta-model can be used within the BPPAM methodology to specify or improve business processes models based on work practice descriptions.

  5. Thermochemical equilibrium modelling of a gasifying process

    International Nuclear Information System (INIS)

    Melgar, Andres; Perez, Juan F.; Laget, Hannes; Horillo, Alfonso

    2007-01-01

    This article discusses a mathematical model for the thermochemical processes in a downdraft biomass gasifier. The model combines the chemical equilibrium and the thermodynamic equilibrium of the global reaction, predicting the final composition of the producer gas as well as its reaction temperature. Once the composition of the producer gas is obtained, a range of parameters can be derived, such as the cold gas efficiency of the gasifier, the amount of dissociated water in the process and the heating value and engine fuel quality of the gas. The model has been validated experimentally. This work includes a parametric study of the influence of the gasifying relative fuel/air ratio and the moisture content of the biomass on the characteristics of the process and the producer gas composition. The model helps to predict the behaviour of different biomass types and is a useful tool for optimizing the design and operation of downdraft biomass gasifiers

  6. Process modeling study of the CIF incinerator

    International Nuclear Information System (INIS)

    Hang, T.

    1995-01-01

    The Savannah River Site (SRS) plans to begin operating the Consolidated Incineration Facility (CIF) in 1996. The CIF will treat liquid and solid low-level radioactive, mixed and RCRA hazardous wastes generated at SRS. In addition to experimental test programs, process modeling was applied to provide guidance in areas of safety, environmental regulation compliances, process improvement and optimization. A steady-state flowsheet model was used to calculate material/energy balances and to track key chemical constituents throughout the process units. Dynamic models were developed to predict the CIF transient characteristics in normal and abnormal operation scenarios. Predictions include the rotary kiln heat transfer, dynamic responses of the CIF to fluctuations in the solid waste feed or upsets in the system equipments, performance of the control system, air inleakage in the kiln, etc. This paper reviews the modeling study performed to assist in the deflagration risk assessment

  7. Deterministic geologic processes and stochastic modeling

    International Nuclear Information System (INIS)

    Rautman, C.A.; Flint, A.L.

    1992-01-01

    This paper reports that recent outcrop sampling at Yucca Mountain, Nevada, has produced significant new information regarding the distribution of physical properties at the site of a potential high-level nuclear waste repository. consideration of the spatial variability indicates that her are a number of widespread deterministic geologic features at the site that have important implications for numerical modeling of such performance aspects as ground water flow and radionuclide transport. Because the geologic processes responsible for formation of Yucca Mountain are relatively well understood and operate on a more-or-less regional scale, understanding of these processes can be used in modeling the physical properties and performance of the site. Information reflecting these deterministic geologic processes may be incorporated into the modeling program explicitly using geostatistical concepts such as soft information, or implicitly, through the adoption of a particular approach to modeling

  8. Modeling and simulation of heterogeneous catalytic processes

    CERN Document Server

    Dixon, Anthony

    2014-01-01

    Heterogeneous catalysis and mathematical modeling are essential components of the continuing search for better utilization of raw materials and energy, with reduced impact on the environment. Numerical modeling of chemical systems has progressed rapidly due to increases in computer power, and is used extensively for analysis, design and development of catalytic reactors and processes. This book presents reviews of the state-of-the-art in modeling of heterogeneous catalytic reactors and processes. Reviews by leading authorities in the respective areas Up-to-date reviews of latest techniques in modeling of catalytic processes Mix of US and European authors, as well as academic/industrial/research institute perspectives Connections between computation and experimental methods in some of the chapters.

  9. Modeling Aspects of Activated Sludge Processes Part l l: Mathematical Process Modeling and Biokinetics of Activated Sludge Processes

    Energy Technology Data Exchange (ETDEWEB)

    AbdElHaleem, H S [Cairo Univ.-CivlI Eng. Dept., Giza (Egypt); EI-Ahwany, A H [CairoUlmrsity- Faculty ofEngincering - Chemical Engineering Department, Giza (Egypt); Ibrahim, H I [Helwan University- Faculty of Engineering - Biomedical Engineering Department, Helwan (Egypt); Ibrahim, G [Menofia University- Faculty of Engineering Sbebin EI Kom- Basic Eng. Sc. Dept., Menofia (Egypt)

    2004-07-01

    Mathematical process modeling and biokinetics of activated sludge process were reviewed considering different types of models. It has been evaluated the task group models of ASMI. and 2, and 3 versioned by Henze et al considering the conditions of each model and the different processes of which every model consists. It is revealed that ASMI contains some defects avoided in ASM3. Relied on homogeneity, Models can be classified into homogenous models characterized by taking the activated sludge process as one phase. In this type of models, the internal mass transfer inside the floes was neglected.. Hence, the kinetic parameter produces can be considered inaccurate. The other type of models is the heterogeneous model This type considers the mass transfer operations in addition to the biochemical reaction processes; hence, the resulted kinetic parameters can be considered more accurate than that of homogenous type.

  10. Modeling Aspects of Activated Sludge Processes Part l l: Mathematical Process Modeling and Biokinetics of Activated Sludge Processes

    International Nuclear Information System (INIS)

    AbdElHaleem, H.S.; EI-Ahwany, A. H.; Ibrahim, H.I.; Ibrahim, G.

    2004-01-01

    Mathematical process modeling and biokinetics of activated sludge process were reviewed considering different types of models. It has been evaluated the task group models of ASMI. and 2, and 3 versioned by Henze et al considering the conditions of each model and the different processes of which every model consists. It is revealed that ASMI contains some defects avoided in ASM3. Relied on homogeneity, Models can be classified into homogenous models characterized by taking the activated sludge process as one phase. In this type of models, the internal mass transfer inside the floes was neglected.. Hence, the kinetic parameter produces can be considered inaccurate. The other type of models is the heterogeneous model This type considers the mass transfer operations in addition to the biochemical reaction processes; hence, the resulted kinetic parameters can be considered more accurate than that of homogenous type

  11. Pedagogic process modeling: Humanistic-integrative approach

    Directory of Open Access Journals (Sweden)

    Boritko Nikolaj M.

    2007-01-01

    Full Text Available The paper deals with some current problems of modeling the dynamics of the subject-features development of the individual. The term "process" is considered in the context of the humanistic-integrative approach, in which the principles of self education are regarded as criteria for efficient pedagogic activity. Four basic characteristics of the pedagogic process are pointed out: intentionality reflects logicality and regularity of the development of the process; discreteness (stageability in dicates qualitative stages through which the pedagogic phenomenon passes; nonlinearity explains the crisis character of pedagogic processes and reveals inner factors of self-development; situationality requires a selection of pedagogic conditions in accordance with the inner factors, which would enable steering the pedagogic process. Offered are two steps for singling out a particular stage and the algorithm for developing an integrative model for it. The suggested conclusions might be of use for further theoretic research, analyses of educational practices and for realistic predicting of pedagogical phenomena. .

  12. Statistical molecular design of balanced compound libraries for QSAR modeling.

    Science.gov (United States)

    Linusson, A; Elofsson, M; Andersson, I E; Dahlgren, M K

    2010-01-01

    A fundamental step in preclinical drug development is the computation of quantitative structure-activity relationship (QSAR) models, i.e. models that link chemical features of compounds with activities towards a target macromolecule associated with the initiation or progression of a disease. QSAR models are computed by combining information on the physicochemical and structural features of a library of congeneric compounds, typically assembled from two or more building blocks, and biological data from one or more in vitro assays. Since the models provide information on features affecting the compounds' biological activity they can be used as guides for further optimization. However, in order for a QSAR model to be relevant to the targeted disease, and drug development in general, the compound library used must contain molecules with balanced variation of the features spanning the chemical space believed to be important for interaction with the biological target. In addition, the assays used must be robust and deliver high quality data that are directly related to the function of the biological target and the associated disease state. In this review, we discuss and exemplify the concept of statistical molecular design (SMD) in the selection of building blocks and final synthetic targets (i.e. compounds to synthesize) to generate information-rich, balanced libraries for biological testing and computation of QSAR models.

  13. Numerical modeling of atmospheric washout processes

    International Nuclear Information System (INIS)

    Bayer, D.; Beheng, K.D.; Herbert, F.

    1987-01-01

    For the washout of particles from the atmosphere by clouds and rain one has to distinguish between processes which work in the first phase of cloud development, when condensation nuclei build up in saturated air (Nucleation Aerosol Scavenging, NAS) and those processes which work at the following cloud development. In the second case particles are taken off by cloud droplets or by falling rain drops via collision (Collision Aerosol Scavenging, CAS). The physics of both processes is described. For the CAS process a numerical model is presented. The report contains a documentation of the mathematical equations and the computer programs (FORTRAN). (KW) [de

  14. Various Models for Reading Comprehension Process

    Directory of Open Access Journals (Sweden)

    Parastoo Babashamsi

    2013-11-01

    Full Text Available In recent years reading can be viewed as a process, as a form of thinking, as a true experience, and as a tool subject. As a process, reading includes visual discrimination, independent recognition of word, rhythmic progression along a line of print, precision in the return sweep of the eyes, and adjustment of rate. In the same line, the present paper aims at considering the various models of reading process. Moreover, the paper will take a look at various factors such as schema and vocabulary knowledge which affect reading comprehension process.

  15. Mathematical modeling of biomass fuels formation process

    International Nuclear Information System (INIS)

    Gaska, Krzysztof; Wandrasz, Andrzej J.

    2008-01-01

    The increasing demand for thermal and electric energy in many branches of industry and municipal management accounts for a drastic diminishing of natural resources (fossil fuels). Meanwhile, in numerous technical processes, a huge mass of wastes is produced. A segregated and converted combustible fraction of the wastes, with relatively high calorific value, may be used as a component of formed fuels. The utilization of the formed fuel components from segregated groups of waste in associated processes of co-combustion with conventional fuels causes significant savings resulting from partial replacement of fossil fuels, and reduction of environmental pollution resulting directly from the limitation of waste migration to the environment (soil, atmospheric air, surface and underground water). The realization of technological processes with the utilization of formed fuel in associated thermal systems should be qualified by technical criteria, which means that elementary processes as well as factors of sustainable development, from a global viewpoint, must not be disturbed. The utilization of post-process waste should be preceded by detailed technical, ecological and economic analyses. In order to optimize the mixing process of fuel components, a mathematical model of the forming process was created. The model is defined as a group of data structures which uniquely identify a real process and conversion of this data in algorithms based on a problem of linear programming. The paper also presents the optimization of parameters in the process of forming fuels using a modified simplex algorithm with a polynomial worktime. This model is a datum-point in the numerical modeling of real processes, allowing a precise determination of the optimal elementary composition of formed fuels components, with assumed constraints and decision variables of the task

  16. Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

    Science.gov (United States)

    Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

    2018-04-01

    Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.

  17. 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.

  18. 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

  19. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    CERN Document Server

    2014-01-01

    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  20. Interactive display of molecular models using a microcomputer system

    Science.gov (United States)

    Egan, J. T.; Macelroy, R. D.

    1980-01-01

    A simple, microcomputer-based, interactive graphics display system has been developed for the presentation of perspective views of wire frame molecular models. The display system is based on a TERAK 8510a graphics computer system with a display unit consisting of microprocessor, television display and keyboard subsystems. The operating system includes a screen editor, file manager, PASCAL and BASIC compilers and command options for linking and executing programs. The graphics program, written in USCD PASCAL, involves the centering of the coordinate system, the transformation of centered model coordinates into homogeneous coordinates, the construction of a viewing transformation matrix to operate on the coordinates, clipping invisible points, perspective transformation and scaling to screen coordinates; commands available include ZOOM, ROTATE, RESET, and CHANGEVIEW. Data file structure was chosen to minimize the amount of disk storage space. Despite the inherent slowness of the system, its low cost and flexibility suggests general applicability.

  1. Energetics and efficiency of a molecular motor model

    International Nuclear Information System (INIS)

    Fogedby, Hans C; Svane, Axel

    2013-01-01

    The energetics and efficiency of a linear molecular motor model proposed by Mogilner et al are analyzed from an analytical point of view. The model, which is based on protein friction with a track, is described by coupled Langevin equations for the motion in combination with coupled master equations for the ATP hydrolysis. Here the energetics and efficiency of the motor are addressed using a many body scheme with focus on the efficiency at maximum power (EMP). It is found that the EMP is reduced from about 10% in a heuristic description of the motor to about 1 per mille when incorporating the full motor dynamics, owing to the strong dissipation associated with the motor action. (paper)

  2. Applications of neural networks to real-time data processing at the Environmental and Molecular Sciences Laboratory (EMSL)

    International Nuclear Information System (INIS)

    Keller, P.E.; Kouzes, R.T.; Kangas, L.J.

    1993-06-01

    Detailed design of the Environmental and Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory (PNL) is nearing completion and construction is scheduled to begin later this year. This facility will assist in the environmental restoration and waste management mission at the Hanford Site. This paper identifies several real-time data processing applications within the EMSL where neural networks can potentially be beneficial. These applications include real-time sensor data acquisition and analysis, spectral analysis, process control, theoretical modeling, and data compression

  3. Purex process modelling - do we really need speciation data?

    International Nuclear Information System (INIS)

    Taylor, R.J.; May, I.

    2001-01-01

    The design of reprocessing flowsheets has become a complex process requiring sophisticated simulation models, containing both chemical and engineering features. Probably the most basic chemical data needed is the distribution of process species between solvent and aqueous phases at equilibrium, which is described by mathematical algorithms. These algorithms have been constructed from experimentally determined distribution coefficients over a wide range of conditions. Distribution algorithms can either be empirical fits of the data or semi-empirical equations, which describe extraction as functions of process variables such as temperature, activity coefficients, uranium loading, etc. Speciation data is not strictly needed in the accumulation of distribution coefficients, which are simple ratios of analyte concentration in the solvent phase to that in the aqueous phase. However, as we construct process models of increasing complexity, speciation data becomes much more important both to raise confidence in the model and to understand the process chemistry at a more fundamental level. UV/vis/NIR spectrophotometry has been our most commonly used speciation method since it is a well-established method for the analysis of actinide ion oxidation states in solution at typical process concentrations. However, with the increasing availability to actinide science of more sophisticated techniques (e.g. NMR; EXAFS) complementary structural information can often be obtained. This paper will, through examples, show how we have used spectrophotometry as a primary tool in distribution and kinetic experiments to obtain data for process models, which are then validated through counter-current flowsheet trials. It will also discuss how spectrophotometry and other speciation methods are allowing us to study the link between molecular structure and extraction behaviour, showing how speciation data really is important in PUREX process modelling. (authors)

  4. Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands.

    Science.gov (United States)

    Barboiu, Mihail; Stadler, Adrian-Mihail; Lehn, Jean-Marie

    2016-03-18

    General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Spectrally selective molecular doped solids: spectroscopy, photophysics and their application to ultrafast optical pulse processing

    International Nuclear Information System (INIS)

    Galaup, Jean-Pierre

    2005-01-01

    The persistent spectral hole-burning (PSHB) phenomenon observed in molecular doped polymers cooled down to liquid helium temperatures allows the engraving of spectral structures in the inhomogeneous absorption profile of the material. This phenomenon known since 1974 has became a fruitful field for the study of the intimacy of complex molecular systems in the solid state, revealing high-resolution spectroscopy, photophysics, photochemistry and dynamics of molecular doped amorphous media, organic as well as inorganic. A PSHB molecular doped solid can be programmed in spectral domain and therefore, it can be converted in an optical processor capable to achieve user-defined optical functions. Some aspects of this field are illustrated in the present paper. An application is presented where a naphthalocyanine doped polymer film is used in a demonstrative experiment to prove that temporal aberration free re-compression of ultra-short light pulses is feasible. Perspectives for the coherent control of light fields or photochemical processes are also evoked

  6. Quantum mechanical Hamiltonian models of discrete processes

    International Nuclear Information System (INIS)

    Benioff, P.

    1981-01-01

    Here the results of other work on quantum mechanical Hamiltonian models of Turing machines are extended to include any discrete process T on a countably infinite set A. The models are constructed here by use of scattering phase shifts from successive scatterers to turn on successive step interactions. Also a locality requirement is imposed. The construction is done by first associating with each process T a model quantum system M with associated Hilbert space H/sub M/ and step operator U/sub T/. Since U/sub T/ is not unitary in general, M, H/sub M/, and U/sub T/ are extended into a (continuous time) Hamiltonian model on a larger space which satisfies the locality requirement. The construction is compared with the minimal unitary dilation of U/sub T/. It is seen that the model constructed here is larger than the minimal one. However, the minimal one does not satisfy the locality requirement

  7. A review of molecular modelling of electric double layer capacitors.

    Science.gov (United States)

    Burt, Ryan; Birkett, Greg; Zhao, X S

    2014-04-14

    Electric double-layer capacitors are a family of electrochemical energy storage devices that offer a number of advantages, such as high power density and long cyclability. In recent years, research and development of electric double-layer capacitor technology has been growing rapidly, in response to the increasing demand for energy storage devices from emerging industries, such as hybrid and electric vehicles, renewable energy, and smart grid management. The past few years have witnessed a number of significant research breakthroughs in terms of novel electrodes, new electrolytes, and fabrication of devices, thanks to the discovery of innovative materials (e.g. graphene, carbide-derived carbon, and templated carbon) and the availability of advanced experimental and computational tools. However, some experimental observations could not be clearly understood and interpreted due to limitations of traditional theories, some of which were developed more than one hundred years ago. This has led to significant research efforts in computational simulation and modelling, aimed at developing new theories, or improving the existing ones to help interpret experimental results. This review article provides a summary of research progress in molecular modelling of the physical phenomena taking place in electric double-layer capacitors. An introduction to electric double-layer capacitors and their applications, alongside a brief description of electric double layer theories, is presented first. Second, molecular modelling of ion behaviours of various electrolytes interacting with electrodes under different conditions is reviewed. Finally, key conclusions and outlooks are given. Simulations on comparing electric double-layer structure at planar and porous electrode surfaces under equilibrium conditions have revealed significant structural differences between the two electrode types, and porous electrodes have been shown to store charge more efficiently. Accurate electrolyte and

  8. Modeling nonhomogeneous Markov processes via time transformation.

    Science.gov (United States)

    Hubbard, R A; Inoue, L Y T; Fann, J R

    2008-09-01

    Longitudinal studies are a powerful tool for characterizing the course of chronic disease. These studies are usually carried out with subjects observed at periodic visits giving rise to panel data. Under this observation scheme the exact times of disease state transitions and sequence of disease states visited are unknown and Markov process models are often used to describe disease progression. Most applications of Markov process models rely on the assumption of time homogeneity, that is, that the transition rates are constant over time. This assumption is not satisfied when transition rates depend on time from the process origin. However, limited statistical tools are available for dealing with nonhomogeneity. We propose models in which the time scale of a nonhomogeneous Markov process is transformed to an operational time scale on which the process is homogeneous. We develop a method for jointly estimating the time transformation and the transition intensity matrix for the time transformed homogeneous process. We assess maximum likelihood estimation using the Fisher scoring algorithm via simulation studies and compare performance of our method to homogeneous and piecewise homogeneous models. We apply our methodology to a study of delirium progression in a cohort of stem cell transplantation recipients and show that our method identifies temporal trends in delirium incidence and recovery.

  9. Software Engineering Laboratory (SEL) cleanroom process model

    Science.gov (United States)

    Green, Scott; Basili, Victor; Godfrey, Sally; Mcgarry, Frank; Pajerski, Rose; Waligora, Sharon

    1991-01-01

    The Software Engineering Laboratory (SEL) cleanroom process model is described. The term 'cleanroom' originates in the integrated circuit (IC) production process, where IC's are assembled in dust free 'clean rooms' to prevent the destructive effects of dust. When applying the clean room methodology to the development of software systems, the primary focus is on software defect prevention rather than defect removal. The model is based on data and analysis from previous cleanroom efforts within the SEL and is tailored to serve as a guideline in applying the methodology to future production software efforts. The phases that are part of the process model life cycle from the delivery of requirements to the start of acceptance testing are described. For each defined phase, a set of specific activities is discussed, and the appropriate data flow is described. Pertinent managerial issues, key similarities and differences between the SEL's cleanroom process model and the standard development approach used on SEL projects, and significant lessons learned from prior cleanroom projects are presented. It is intended that the process model described here will be further tailored as additional SEL cleanroom projects are analyzed.

  10. Molecular and multiscale modeling: review on the theories and applications in chemical engineering

    International Nuclear Information System (INIS)

    Morales M, Giovanni; Martinez R, Ramiro

    2010-01-01

    We call molecular modeling to the application of suitable laws in the analysis of phenomena occurred at scales less than those accounted for by the macroscopic world. Such different scales (including micro-, meso- and macro scales), can be linked and integrated in order to improve understanding and predictions of complex physical chemistry phenomena, thus originating a global or multi scale analysis. A considerable amount of chemical engineering phenomena are complex due to the interrelation among these different realms of length and time. Multi scale modeling rises as an alternative for an outstanding mathematical and conceptual representation of such phenomena. This adequate representation may help to design and optimize chemical and petrochemical processes from a microscopic point of view. Herein we present a brief introduction to both molecular and multi scale modeling methods. We also comment and examine opportunities for applying the different levels of modeling to the analysis of industrial problems. The fundamental mathematical machinery of the molecular modelling theories is presented in order to motivate the study of these new engineering tools. Finally, we show a classification of different strategies for applying multilevel analysis, illustrating various examples of each methodology.

  11. A n-vector model for charge transport in molecular semiconductors.

    Science.gov (United States)

    Jackson, Nicholas E; Kohlstedt, Kevin L; Chen, Lin X; Ratner, Mark A

    2016-11-28

    We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topology-dependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors.

  12. Causally nonseparable processes admitting a causal model

    International Nuclear Information System (INIS)

    Feix, Adrien; Araújo, Mateus; Brukner, Caslav

    2016-01-01

    A recent framework of quantum theory with no global causal order predicts the existence of ‘causally nonseparable’ processes. Some of these processes produce correlations incompatible with any causal order (they violate so-called ‘causal inequalities’ analogous to Bell inequalities ) while others do not (they admit a ‘causal model’ analogous to a local model ). Here we show for the first time that bipartite causally nonseparable processes with a causal model exist, and give evidence that they have no clear physical interpretation. We also provide an algorithm to generate processes of this kind and show that they have nonzero measure in the set of all processes. We demonstrate the existence of processes which stop violating causal inequalities but are still causally nonseparable when mixed with a certain amount of ‘white noise’. This is reminiscent of the behavior of Werner states in the context of entanglement and nonlocality. Finally, we provide numerical evidence for the existence of causally nonseparable processes which have a causal model even when extended with an entangled state shared among the parties. (paper)

  13. Stochastic differential equation model to Prendiville processes

    Energy Technology Data Exchange (ETDEWEB)

    Granita, E-mail: granitafc@gmail.com [Dept. of Mathematical Science, Universiti Teknologi Malaysia, 81310, Johor Malaysia (Malaysia); Bahar, Arifah [Dept. of Mathematical Science, Universiti Teknologi Malaysia, 81310, Johor Malaysia (Malaysia); UTM Center for Industrial & Applied Mathematics (UTM-CIAM) (Malaysia)

    2015-10-22

    The Prendiville process is another variation of the logistic model which assumes linearly decreasing population growth rate. It is a continuous time Markov chain (CTMC) taking integer values in the finite interval. The continuous time Markov chain can be approximated by stochastic differential equation (SDE). This paper discusses the stochastic differential equation of Prendiville process. The work started with the forward Kolmogorov equation in continuous time Markov chain of Prendiville process. Then it was formulated in the form of a central-difference approximation. The approximation was then used in Fokker-Planck equation in relation to the stochastic differential equation of the Prendiville process. The explicit solution of the Prendiville process was obtained from the stochastic differential equation. Therefore, the mean and variance function of the Prendiville process could be easily found from the explicit solution.

  14. Stochastic differential equation model to Prendiville processes

    International Nuclear Information System (INIS)

    Granita; Bahar, Arifah

    2015-01-01

    The Prendiville process is another variation of the logistic model which assumes linearly decreasing population growth rate. It is a continuous time Markov chain (CTMC) taking integer values in the finite interval. The continuous time Markov chain can be approximated by stochastic differential equation (SDE). This paper discusses the stochastic differential equation of Prendiville process. The work started with the forward Kolmogorov equation in continuous time Markov chain of Prendiville process. Then it was formulated in the form of a central-difference approximation. The approximation was then used in Fokker-Planck equation in relation to the stochastic differential equation of the Prendiville process. The explicit solution of the Prendiville process was obtained from the stochastic differential equation. Therefore, the mean and variance function of the Prendiville process could be easily found from the explicit solution

  15. Modelling a uranium ore bioleaching process

    International Nuclear Information System (INIS)

    Chien, D.C.H.; Douglas, P.L.; Herman, D.H.; Marchbank, A.

    1990-01-01

    A dynamic simulation model for the bioleaching of uranium ore in a stope leaching process has been developed. The model incorporates design and operating conditions, reaction kinetics enhanced by Thiobacillus ferroxidans present in the leaching solution and transport properties. Model predictions agree well with experimental data with an average deviation of about ± 3%. The model is sensitive to small errors in the estimates of fragment size and ore grade. Because accurate estimates are difficult to obtain a parameter estimation approach was developed to update the value of fragment size and ore grade using on-line plant information

  16. Chain binomial models and binomial autoregressive processes.

    Science.gov (United States)

    Weiss, Christian H; Pollett, Philip K

    2012-09-01

    We establish a connection between a class of chain-binomial models of use in ecology and epidemiology and binomial autoregressive (AR) processes. New results are obtained for the latter, including expressions for the lag-conditional distribution and related quantities. We focus on two types of chain-binomial model, extinction-colonization and colonization-extinction models, and present two approaches to parameter estimation. The asymptotic distributions of the resulting estimators are studied, as well as their finite-sample performance, and we give an application to real data. A connection is made with standard AR models, which also has implications for parameter estimation. © 2011, The International Biometric Society.

  17. The Probability Model of Expectation Disconfirmation Process

    Directory of Open Access Journals (Sweden)

    Hui-Hsin HUANG

    2015-06-01

    Full Text Available This paper proposes a probability model to explore the dynamic process of customer’s satisfaction. Bases on expectation disconfirmation theory, the satisfaction is constructed with customer’s expectation before buying behavior and the perceived performance after purchase. The experiment method is designed to measure expectation disconfirmation effects and we also use the collection data to estimate the overall satisfaction and model calibration. The results show good fitness between the model and the real data. This model has application for business marketing areas in order to manage relationship satisfaction.

  18. Implementation of the Business Process Modelling Notation (BPMN) in the modelling of anatomic pathology processes.

    Science.gov (United States)

    Rojo, Marcial García; Rolón, Elvira; Calahorra, Luis; García, Felix Oscar; Sánchez, Rosario Paloma; Ruiz, Francisco; Ballester, Nieves; Armenteros, María; Rodríguez, Teresa; Espartero, Rafael Martín

    2008-07-15

    Process orientation is one of the essential elements of quality management systems, including those in use in healthcare. Business processes in hospitals are very complex and variable. BPMN (Business Process Modelling Notation) is a user-oriented language specifically designed for the modelling of business (organizational) processes. Previous experiences of the use of this notation in the processes modelling within the Pathology in Spain or another country are not known. We present our experience in the elaboration of the conceptual models of Pathology processes, as part of a global programmed surgical patient process, using BPMN. With the objective of analyzing the use of BPMN notation in real cases, a multidisciplinary work group was created, including software engineers from the Dep. of Technologies and Information Systems from the University of Castilla-La Mancha and health professionals and administrative staff from the Hospital General de Ciudad Real. The work in collaboration was carried out in six phases: informative meetings, intensive training, process selection, definition of the work method, process describing by hospital experts, and process modelling. The modelling of the processes of Anatomic Pathology is presented using BPMN. The presented subprocesses are those corresponding to the surgical pathology examination of the samples coming from operating theatre, including the planning and realization of frozen studies. The modelling of Anatomic Pathology subprocesses has allowed the creation of an understandable graphical model, where management and improvements are more easily implemented by health professionals.

  19. Multi input single output model predictive control of non-linear bio-polymerization process

    Energy Technology Data Exchange (ETDEWEB)

    Arumugasamy, Senthil Kumar; Ahmad, Z. [School of Chemical Engineering, Univerisiti Sains Malaysia, Engineering Campus, Seri Ampangan,14300 Nibong Tebal, Seberang Perai Selatan, Pulau Pinang (Malaysia)

    2015-05-15

    This paper focuses on Multi Input Single Output (MISO) Model Predictive Control of bio-polymerization process in which mechanistic model is developed and linked with the feedforward neural network model to obtain a hybrid model (Mechanistic-FANN) of lipase-catalyzed ring-opening polymerization of ε-caprolactone (ε-CL) for Poly (ε-caprolactone) production. In this research, state space model was used, in which the input to the model were the reactor temperatures and reactor impeller speeds and the output were the molecular weight of polymer (M{sub n}) and polymer polydispersity index. State space model for MISO created using System identification tool box of Matlab™. This state space model is used in MISO MPC. Model predictive control (MPC) has been applied to predict the molecular weight of the biopolymer and consequently control the molecular weight of biopolymer. The result shows that MPC is able to track reference trajectory and give optimum movement of manipulated variable.

  20. Interaction of sucralose with whey protein: Experimental and molecular modeling studies

    Science.gov (United States)

    Zhang, Hongmei; Sun, Shixin; Wang, Yanqing; Cao, Jian

    2017-12-01

    The objective of this research was to study the interactions of sucralose with whey protein isolate (WPI) by using the three-dimensional fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling. The results showed that the peptide strands structure of WPI had been changed by sucralose. Sucralose binding induced the secondary structural changes and increased content of aperiodic structure of WPI. Sucralose decreased the thermal stability of WPI and acted as a structure destabilizer during the thermal unfolding process of protein. In addition, the existence of sucralose decreased the reversibility of the unfolding of WPI. Nonetheless, sucralose-WPI complex was less stable than protein alone. The molecular modeling result showed that van der Waals and hydrogen bonding interactions contribute to the complexation free binding energy. There are more than one possible binding sites of WPI with sucralose by surface binding mode.

  1. Determinantal point process models on the sphere

    DEFF Research Database (Denmark)

    Møller, Jesper; Nielsen, Morten; Porcu, Emilio

    defined on Sd × Sd . We review the appealing properties of such processes, including their specific moment properties, density expressions and simulation procedures. Particularly, we characterize and construct isotropic DPPs models on Sd , where it becomes essential to specify the eigenvalues......We consider determinantal point processes on the d-dimensional unit sphere Sd . These are finite point processes exhibiting repulsiveness and with moment properties determined by a certain determinant whose entries are specified by a so-called kernel which we assume is a complex covariance function...... and eigenfunctions in a spectral representation for the kernel, and we figure out how repulsive isotropic DPPs can be. Moreover, we discuss the shortcomings of adapting existing models for isotropic covariance functions and consider strategies for developing new models, including a useful spectral approach....

  2. Quantitative Modeling of Earth Surface Processes

    Science.gov (United States)

    Pelletier, Jon D.

    This textbook describes some of the most effective and straightforward quantitative techniques for modeling Earth surface processes. By emphasizing a core set of equations and solution techniques, the book presents state-of-the-art models currently employed in Earth surface process research, as well as a set of simple but practical research tools. Detailed case studies demonstrate application of the methods to a wide variety of processes including hillslope, fluvial, aeolian, glacial, tectonic, and climatic systems. Exercises at the end of each chapter begin with simple calculations and then progress to more sophisticated problems that require computer programming. All the necessary computer codes are available online at www.cambridge.org/9780521855976. Assuming some knowledge of calculus and basic programming experience, this quantitative textbook is designed for advanced geomorphology courses and as a reference book for professional researchers in Earth and planetary science looking for a quantitative approach to Earth surface processes. More details...

  3. Hydrothermal processing of Hanford tank wastes: Process modeling and control

    International Nuclear Information System (INIS)

    Currier, R.P.

    1994-01-01

    In the Los Alamos National Laboratory (LANL) hydrothermal process, waste streams are first pressurized and heated as they pass through a continuous flow tubular reactor vessel. The waste is maintained at reaction temperature of 300--550 C where organic destruction and sludge reformation occur. This report documents LANL activities in process modeling and control undertaken in FY94 to support hydrothermal process development. Key issues discussed include non-ideal flow patterns (e.g. axial dispersion) and their effect on reactor performance, the use and interpretation of inert tracer experiments, and the use of computational fluid mechanics to evaluate novel hydrothermal reactor designs. In addition, the effects of axial dispersion (and simplifications to rate expressions) on the estimated kinetic parameters are explored by non-linear regression to experimental data. Safety-related calculations are reported which estimate the explosion limits of effluent gases and the fate of hydrogen as it passes through the reactor. Development and numerical solution of a generalized one-dimensional mathematical model is also summarized. The difficulties encountered in using commercially available software to correlate the behavior of high temperature, high pressure aqueous electrolyte mixtures are summarized. Finally, details of the control system and experiments conducted to empirically determine the system response are reported

  4. A process algebra model of QED

    International Nuclear Information System (INIS)

    Sulis, William

    2016-01-01

    The process algebra approach to quantum mechanics posits a finite, discrete, determinate ontology of primitive events which are generated by processes (in the sense of Whitehead). In this ontology, primitive events serve as elements of an emergent space-time and of emergent fundamental particles and fields. Each process generates a set of primitive elements, using only local information, causally propagated as a discrete wave, forming a causal space termed a causal tapestry. Each causal tapestry forms a discrete and finite sampling of an emergent causal manifold (space-time) M and emergent wave function. Interactions between processes are described by a process algebra which possesses 8 commutative operations (sums and products) together with a non-commutative concatenation operator (transitions). The process algebra possesses a representation via nondeterministic combinatorial games. The process algebra connects to quantum mechanics through the set valued process and configuration space covering maps, which associate each causal tapestry with sets of wave functions over M. Probabilities emerge from interactions between processes. The process algebra model has been shown to reproduce many features of the theory of non-relativistic scalar particles to a high degree of accuracy, without paradox or divergences. This paper extends the approach to a semi-classical form of quantum electrodynamics. (paper)

  5. An End-to-End Model of Plant Pheromone Channel for Long Range Molecular Communication.

    Science.gov (United States)

    Unluturk, Bige D; Akyildiz, Ian F

    2017-01-01

    A new track in molecular communication is using pheromones which can scale up the range of diffusion-based communication from μm meters to meters and enable new applications requiring long range. Pheromone communication is the emission of molecules in the air which trigger behavioral or physiological responses in receiving organisms. The objective of this paper is to introduce a new end-to-end model which incorporates pheromone behavior with communication theory for plants. The proposed model includes both the transmission and reception processes as well as the propagation channel. The transmission process is the emission of pheromones from the leaves of plants. The dispersion of pheromones by the flow of wind constitutes the propagation process. The reception process is the sensing of pheromones by the pheromone receptors of plants. The major difference of pheromone communication from other molecular communication techniques is the dispersion channel acting under the laws of turbulent diffusion. In this paper, the pheromone channel is modeled as a Gaussian puff, i.e., a cloud of pheromone released instantaneously from the source whose dispersion follows a Gaussian distribution. Numerical results on the performance of the overall end-to-end pheromone channel in terms of normalized gain and delay are provided.

  6. Molecular modeling used to evaluate CYP2C9-dependent metabolism: homology modeling, molecular dynamics and docking simulations.

    Science.gov (United States)

    Mendieta-Wejebe, Jessica E; Correa-Basurto, José; García-Segovia, Erika M; Ceballos-Cancino, Gisela; Rosales-Hernández, Martha C

    2011-07-01

    Cytochrome P450 (CYP) 2C9 is the principal isoform of the CYP2C subfamily in the human liver and is involved in the oxidation of several endogenous and xenobiotic compounds, including many therapeutic drugs. The metabolism of drugs by CYP2C9 can yield either safe or toxic products, which may be related to the recognition and binding modes of the substrates to this isoform. These interactions can be studied using in silico methods such as quantum chemistry, molecular dynamics and docking simulations, which can also be useful for predicting the structure of metabolites. In these types of studies, the ligand and the protein must be tridimensional models; thus, the protein can be built by homology modeling or retrieved from the Protein Data Bank. Therefore, the current review emphasizes the importance of using in silico methods to predict the metabolism of CYP2C9 because these computational tools have allowed the description of the principal characteristics of the active site of this isoform at the molecular level and the chemical properties of its ligands.

  7. Modeling Adsorption-Desorption Processes at the Intermolecular Interactions Level

    Science.gov (United States)

    Varfolomeeva, Vera V.; Terentev, Alexey V.

    2018-01-01

    Modeling of the surface adsorption and desorption processes, as well as the diffusion, are of considerable interest for the physical phenomenon under study in ground tests conditions. When imitating physical processes and phenomena, it is important to choose the correct parameters to describe the adsorption of gases and the formation of films on the structural materials surface. In the present research the adsorption-desorption processes on the gas-solid interface are modeled with allowance for diffusion. Approaches are proposed to describe the adsorbate distribution on the solid body surface at the intermolecular interactions level. The potentials of the intermolecular interaction of water-water, water-methane and methane-methane were used to adequately modeling the real physical and chemical processes. The energies calculated by the B3LYP/aug-cc-pVDZ method. Computational algorithms for determining the average molecule area in a dense monolayer, are considered here. Differences in modeling approaches are also given: that of the proposed in this work and the previously approved probabilistic cellular automaton (PCA) method. It has been shown that the main difference is due to certain limitations of the PCA method. The importance of accounting the intermolecular interactions via hydrogen bonding has been indicated. Further development of the adsorption-desorption processes modeling will allow to find the conditions for of surface processes regulation by means of quantity adsorbed molecules control. The proposed approach to representing the molecular system significantly shortens the calculation time in comparison with the use of atom-atom potentials. In the future, this will allow to modeling the multilayer adsorption at a reasonable computational cost.

  8. Fundamentals of Numerical Modelling of Casting Processes

    DEFF Research Database (Denmark)

    Hattel, Jesper Henri; Pryds, Nini; Thorborg, Jesper

    Fundamentals of Numerical Modelling of Casting Processes comprises a thorough presentation of the basic phenomena that need to be addressed in numerical simulation of casting processes. The main philosophy of the book is to present the topics in view of their physical meaning, whenever possible......, rather than relying strictly on mathematical formalism. The book, aimed both at the researcher and the practicing engineer, as well as the student, is naturally divided into four parts. Part I (Chapters 1-3) introduces the fundamentals of modelling in a 1-dimensional framework. Part II (Chapter 4...

  9. Process and Context in Choice Models

    DEFF Research Database (Denmark)

    Ben-Akiva, Moshe; Palma, André de; McFadden, Daniel

    2012-01-01

    . The extended choice framework includes more behavioral richness through the explicit representation of the planning process preceding an action and its dynamics and the effects of context (family, friends, and market) on the process leading to a choice, as well as the inclusion of new types of subjective data...... in choice models. We discuss the key issues involved in applying the extended framework, focusing on richer data requirements, theories, and models, and present three partial demonstrations of the proposed framework. Future research challenges include the development of more comprehensive empirical tests...

  10. Performance assessment modeling of pyrometallurgical process wasteforms

    International Nuclear Information System (INIS)

    Nutt, W.M.; Hill, R.N.; Bullen, D.B.

    1995-01-01

    Performance assessment analyses have been completed to estimate the behavior of high-level nuclear wasteforms generated from the pyrometallurgical processing of liquid metal reactor (LMR) and light water reactor (LWR) spent nuclear fuel. Waste emplaced in the proposed repository at Yucca Mountain is investigated as the basis for the study. The resulting cumulative actinide and fission product releases to the accessible environment within a 100,000 year period from the various pyrometallurgical process wasteforms are compared to those of directly disposed LWR spent fuel using the same total repository system model. The impact of differing radionuclide transport models on the overall release characteristics is investigated

  11. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method

    Science.gov (United States)

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-01

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔHθ) and entropy change (ΔSθ) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  12. Models of transport processes in concrete

    International Nuclear Information System (INIS)

    Pommersheim, J.M.; Clifton, J.R.

    1991-01-01

    An approach being considered by the US Nuclear Regulatory Commission for disposal of low-level radioactive waste is to place the waste forms in concrete vaults buried underground. The vaults would need a service life of 500 years. Approaches for predicting the service life of concrete of such vaults include the use of mathematical models. Mathematical models are presented in this report for the major degradation processes anticipated for the concrete vaults, which are corrosion of steel reinforcement, sulfate attack, acid attack, and leaching. The models mathematically represent rate controlling processes including diffusion, convection, and reaction and sorption of chemical species. These models can form the basis for predicting the life of concrete under in-service conditions. 33 refs., 6 figs., 7 tabs

  13. Retort process modelling for Indian traditional foods.

    Science.gov (United States)

    Gokhale, S V; Lele, S S

    2014-11-01

    Indian traditional staple and snack food is typically a heterogeneous recipe that incorporates varieties of vegetables, lentils and other ingredients. Modelling the retorting process of multilayer pouch packed Indian food was achieved using lumped-parameter approach. A unified model is proposed to estimate cold point temperature. Initial process conditions, retort temperature and % solid content were the significantly affecting independent variables. A model was developed using combination of vegetable solids and water, which was then validated using four traditional Indian vegetarian products: Pulav (steamed rice with vegetables), Sambar (south Indian style curry containing mixed vegetables and lentils), Gajar Halawa (carrot based sweet product) and Upama (wheat based snack product). The predicted and experimental values of temperature profile matched with ±10 % error which is a good match considering the food was a multi component system. Thus the model will be useful as a tool to reduce number of trials required to optimize retorting of various Indian traditional vegetarian foods.

  14. Towards a universal competitive intelligence process model

    Directory of Open Access Journals (Sweden)

    Rene Pellissier

    2013-08-01

    Objectives: The purpose of this research is to review the current literature on CI, to look at the aims of identifying and analysing CI process models, and finally to propose a universal CI process model. Method: The study was qualitative in nature and content analysis was conducted on all identified sources establishing and analysing CI process models. To identify relevant literature, academic databases and search engines were used. Moreover, a review of references in related studies led to more relevant sources, the references of which were further reviewed and analysed. To ensure reliability, only peer-reviewed articles were used. Results: The findings reveal that the majority of scholars view the CI process as a cycle of interrelated phases. The output of one phase is the input of the next phase. Conclusion: The CI process is a cycle of interrelated phases. The output of one phase is the input of the next phase. These phases are influenced by the following factors: decision makers, process and structure, organisational awareness and culture, and feedback.

  15. Modeling of Reaction Processes Controlled by Diffusion

    International Nuclear Information System (INIS)

    Revelli, Jorge

    2003-01-01

    Stochastic modeling is quite powerful in science and technology.The technics derived from this process have been used with great success in laser theory, biological systems and chemical reactions.Besides, they provide a theoretical framework for the analysis of experimental results on the field of particle's diffusion in ordered and disordered materials.In this work we analyze transport processes in one-dimensional fluctuating media, which are media that change their state in time.This fact induces changes in the movements of the particles giving rise to different phenomena and dynamics that will be described and analyzed in this work.We present some random walk models to describe these fluctuating media.These models include state transitions governed by different dynamical processes.We also analyze the trapping problem in a lattice by means of a simple model which predicts a resonance-like phenomenon.Also we study effective diffusion processes over surfaces due to random walks in the bulk.We consider different boundary conditions and transitions movements.We derive expressions that describe diffusion behaviors constrained to bulk restrictions and the dynamic of the particles.Finally it is important to mention that the theoretical results obtained from the models proposed in this work are compared with Monte Carlo simulations.We find, in general, excellent agreements between the theory and the simulations

  16. Model morphing and sequence assignment after molecular replacement.

    Science.gov (United States)

    Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Brunger, Axel T; Afonine, Pavel V; Hung, Li-Wei

    2013-11-01

    A procedure termed `morphing' for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

  17. Insights into channel dysfunction from modelling and molecular dynamics simulations.

    Science.gov (United States)

    Musgaard, Maria; Paramo, Teresa; Domicevica, Laura; Andersen, Ole Juul; Biggin, Philip C

    2018-04-01

    Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.' Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  18. Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

    Science.gov (United States)

    Clancy, Thomas C.; Gates, Thomas S.

    2005-01-01

    The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

  19. Spin models for the single molecular magnet Mn12-AC

    Science.gov (United States)

    Al-Saqer, Mohamad A.

    2005-11-01

    The single molecular magnet (SMM) Mn12-AC attracted the attention of scientists since the discovery of its magnetic hystereses which are accompanied by sudden jumps in magnetic moments at low temperature. Unlike conventional bulk magnets, hysteresis in SMMs is of molecular origin. This qualifies them as candidates for next generation of high density storage media where a molecule which is at most few nanometers in size can be used to store a bit of information. However, the jumps in these hystereses, due to spin tunneling, can lead to undesired loss of information. Mn12-AC molecule contains twelve magnetic ions antiferromagnetically coupled by exchanges leading to S = 10 ground state manifold. The magnetic ions are surrounded by ligands which isolate them magnetically from neighboring molecules. The lowest state of S = 9 manifold is believed to lie at about 40 K above the ground state. Therefore, at low temperatures, the molecule is considered as a single uncoupled moment of spin S = 10. Such model has been used widely to understand phenomena exhibited by the molecule at low temperatures including the tunneling of its spin, while a little attention has been paid for the multi-spin nature of the molecule. Using the 8-spin model, we demonstrate that in order to understand the phenomena of tunneling, a full spin description of the molecule is required. We utilized a calculation scheme where a fraction of energy levels are used in the calculations and the influence of levels having higher energy is neglected. From the dependence of tunnel splittings on the number of states include, we conclude that models based on restricting the number of energy levels (single-spin and 8-spin models) lead to unreliable results of tunnel splitting calculations. To attack the full 12-spin model, we employed the Davidson algorithm to calculated lowest energy levels produced by exchange interactions and single ion anisotropies. The model reproduces the anisotropy properties at low

  20. Multi-scale modelling of supercapacitors: From molecular simulations to a transmission line model

    Science.gov (United States)

    Pean, C.; Rotenberg, B.; Simon, P.; Salanne, M.

    2016-09-01

    We perform molecular dynamics simulations of a typical nanoporous-carbon based supercapacitor. The organic electrolyte consists in 1-ethyl-3-methylimidazolium and hexafluorophosphate ions dissolved in acetonitrile. We simulate systems at equilibrium, for various applied voltages. This allows us to determine the relevant thermodynamic (capacitance) and transport (in-pore resistivities) properties. These quantities are then injected in a transmission line model for testing its ability to predict the charging properties of the device. The results from this macroscopic model are in good agreement with non-equilibrium molecular dynamics simulations, which validates its use for interpreting electrochemical impedance experiments.

  1. Functional porous composites by blending with solution-processable molecular pores.

    Science.gov (United States)

    Jiang, S; Chen, L; Briggs, M E; Hasell, T; Cooper, A I

    2016-05-25

    We present a simple method for rendering non-porous materials porous by solution co-processing with organic cage molecules. This method can be used both for small functional molecules and for polymers, thus creating porous composites by molecular blending, rather than the more traditional approach of supporting functional molecules on pre-frabricated porous supports.

  2. Multiplicity of Mathematical Modeling Strategies to Search for Molecular and Cellular Insights into Bacteria Lung Infection.

    Science.gov (United States)

    Cantone, Martina; Santos, Guido; Wentker, Pia; Lai, Xin; Vera, Julio

    2017-01-01

    Even today two bacterial lung infections, namely pneumonia and tuberculosis, are among the 10 most frequent causes of death worldwide. These infections still lack effective treatments in many developing countries and in immunocompromised populations like infants, elderly people and transplanted patients. The interaction between bacteria and the host is a complex system of interlinked intercellular and the intracellular processes, enriched in regulatory structures like positive and negative feedback loops. Severe pathological condition can emerge when the immune system of the host fails to neutralize the infection. This failure can result in systemic spreading of pathogens or overwhelming immune response followed by a systemic inflammatory response. Mathematical modeling is a promising tool to dissect the complexity underlying pathogenesis of bacterial lung infection at the molecular, cellular and tissue levels, and also at the interfaces among levels. In this article, we introduce mathematical and computational modeling frameworks that can be used for investigating molecular and cellular mechanisms underlying bacterial lung infection. Then, we compile and discuss published results on the modeling of regulatory pathways and cell populations relevant for lung infection and inflammation. Finally, we discuss how to make use of this multiplicity of modeling approaches to open new avenues in the search of the molecular and cellular mechanisms underlying bacterial infection in the lung.

  3. Molecular dynamics studies of fluid/oil interfaces for improved oil recovery processes.

    Science.gov (United States)

    de Lara, Lucas S; Michelon, Mateus F; Miranda, Caetano R

    2012-12-20

    In our paper, we study the interface wettability, diffusivity, and molecular orientation between crude oil and different fluids for applications in improved oil recovery (IOR) processes through atomistic molecular dynamics (MD). The salt concentration, temperature, and pressure effects on the physical chemistry properties of different interfaces between IOR agents [brine (H(2)O + % NaCl), CO(2), N(2), and CH(4)] and crude oil have been determined. From the interfacial density profiles, an accumulation of aromatic molecules near the interface has been observed. In the case of brine interfaced with crude oil, our calculations indicate an increase in the interfacial tension with increasing pressure and salt concentration, which favors oil displacement. On the other hand, with the other fluids studied (CO(2), N(2), and CH(4)), the interfacial tension decreases with increasing pressure and temperature. With interfacial tension reduction, an increase in fluid diffusivity in the oil phase is observed. We also studied the molecular orientation properties of the hydrocarbon and fluids molecules in the interface region. We perceived that the molecular orientation could be affected by changes in the interfacial tension and diffusivity of the molecules in the interface region with the increased pressure and temperature: pressure (increasing) → interfacial tension (decreasing) → diffusion (increasing) → molecular ordering. From a molecular point of view, the combination of low interfacial tension and high diffusion of molecules in the oil phase gives the CO(2) molecules unique properties as an IOR fluid compared with other fluids studied here.

  4. IAEA technical meeting on 'Technical aspects of atomic and molecular data processing and exchange'. Summary report

    International Nuclear Information System (INIS)

    Humbert, Denis

    2004-03-01

    The proceedings of the IAEA Advisory Group Meeting on 'Technical Aspects of Atomic and Molecular Data Processing and Exchange' (17th Meeting of A+M Data Centres and ALADDIN Network), held on 6-7 October, 2003 in Vienna, Austria are briefly described. The meeting conclusions and recommendations on the priorities in A+M data compilation and evaluation, and on the technical aspects of data processing, exchange, and distribution are also presented. (author)

  5. Integrating textual and model-based process descriptions for comprehensive process search

    NARCIS (Netherlands)

    Leopold, Henrik; van der Aa, Han; Pittke, Fabian; Raffel, Manuel; Mendling, Jan; Reijers, Hajo A.

    2016-01-01

    Documenting business processes using process models is common practice in many organizations. However, not all process information is best captured in process models. Hence, many organizations complement these models with textual descriptions that specify additional details. The problem with this

  6. Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

    Science.gov (United States)

    Plimpton, Steve

    Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.

  7. First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations

    CERN Document Server

    Kastner, Oliver

    2012-01-01

    Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and  covers  thermodynamical, micro-mechanical  and crystallographical aspects. It addresses scientists in these research fields and thei...

  8. A simplified tether model for molecular motor transporting cargo

    International Nuclear Information System (INIS)

    Fang-Zhen, Li; Li-Chun, Jiang

    2010-01-01

    Molecular motors are proteins or protein complexes which function as transporting engines in biological cells. This paper models the tether between motor and its cargo as a symmetric linear potential. Different from Elston and Peskin's work for which performance of the system was discussed only in some limiting cases, this study produces analytic solutions of the problem for general cases by simplifying the transport system into two physical states, which makes it possible to discuss the dynamics of the motor–cargo system in detail. It turns out that the tether strength between motor and cargo should be greater than a threshold or the motor will fail to transport the cargo, which was not discussed by former researchers yet. Value of the threshold depends on the diffusion coefficients of cargo and motor and also on the strength of the Brownian ratchets dragging the system. The threshold approaches a finite constant when the strength of the ratchet tends to infinity. (general)

  9. A Generic Modeling Process to Support Functional Fault Model Development

    Science.gov (United States)

    Maul, William A.; Hemminger, Joseph A.; Oostdyk, Rebecca; Bis, Rachael A.

    2016-01-01

    Functional fault models (FFMs) are qualitative representations of a system's failure space that are used to provide a diagnostic of the modeled system. An FFM simulates the failure effect propagation paths within a system between failure modes and observation points. These models contain a significant amount of information about the system including the design, operation and off nominal behavior. The development and verification of the models can be costly in both time and resources. In addition, models depicting similar components can be distinct, both in appearance and function, when created individually, because there are numerous ways of representing the failure space within each component. Generic application of FFMs has the advantages of software code reuse: reduction of time and resources in both development and verification, and a standard set of component models from which future system models can be generated with common appearance and diagnostic performance. This paper outlines the motivation to develop a generic modeling process for FFMs at the component level and the effort to implement that process through modeling conventions and a software tool. The implementation of this generic modeling process within a fault isolation demonstration for NASA's Advanced Ground System Maintenance (AGSM) Integrated Health Management (IHM) project is presented and the impact discussed.

  10. Hencky's model for elastomer forming process

    Science.gov (United States)

    Oleinikov, A. A.; Oleinikov, A. I.

    2016-08-01

    In the numerical simulation of elastomer forming process, Henckys isotropic hyperelastic material model can guarantee relatively accurate prediction of strain range in terms of large deformations. It is shown, that this material model prolongate Hooke's law from the area of infinitesimal strains to the area of moderate ones. New representation of the fourth-order elasticity tensor for Hencky's hyperelastic isotropic material is obtained, it possesses both minor symmetries, and the major symmetry. Constitutive relations of considered model is implemented into MSC.Marc code. By calculating and fitting curves, the polyurethane elastomer material constants are selected. Simulation of equipment for elastomer sheet forming are considered.

  11. Model-based internal wave processing

    Energy Technology Data Exchange (ETDEWEB)

    Candy, J.V.; Chambers, D.H.

    1995-06-09

    A model-based approach is proposed to solve the oceanic internal wave signal processing problem that is based on state-space representations of the normal-mode vertical velocity and plane wave horizontal velocity propagation models. It is shown that these representations can be utilized to spatially propagate the modal (dept) vertical velocity functions given the basic parameters (wave numbers, Brunt-Vaisala frequency profile etc.) developed from the solution of the associated boundary value problem as well as the horizontal velocity components. Based on this framework, investigations are made of model-based solutions to the signal enhancement problem for internal waves.

  12. Laboratory and modeling studies of chemistry in dense molecular clouds

    Science.gov (United States)

    Huntress, W. T., Jr.; Prasad, S. S.; Mitchell, G. F.

    1980-01-01

    A chemical evolutionary model with a large number of species and a large chemical library is used to examine the principal chemical processes in interstellar clouds. Simple chemical equilibrium arguments show the potential for synthesis of very complex organic species by ion-molecule radiative association reactions.

  13. Temperature Effect on Micelle Formation: Molecular Thermodynamic Model Revisited.

    Science.gov (United States)

    Khoshnood, Atefeh; Lukanov, Boris; Firoozabadi, Abbas

    2016-03-08

    Temperature affects the aggregation of macromolecules such as surfactants, polymers, and proteins in aqueous solutions. The effect on the critical micelle concentration (CMC) is often nonmonotonic. In this work, the effect of temperature on the micellization of ionic and nonionic surfactants in aqueous solutions is studied using a molecular thermodynamic model. Previous studies based on this technique have predicted monotonic behavior for ionic surfactants. Our investigation shows that the choice of tail transfer energy to describe the hydrophobic effect between the surfactant tails and the polar solvent molecules plays a key role in the predicted CMC. We modify the tail transfer energy by taking into account the effect of the surfactant head on the neighboring methylene group. The modification improves the description of the CMC and the predicted micellar size for aqueous solutions of sodium n-alkyl sulfate, dodecyl trimethylammonium bromide (DTAB), and n-alkyl polyoxyethylene. The new tail transfer energy describes the nonmonotonic behavior of CMC versus temperature. In the DTAB-water system, we redefine the head size by including the methylene group, next to the nitrogen, in the head. The change in the head size along with our modified tail transfer energy improves the CMC and aggregation size prediction significantly. Tail transfer is a dominant energy contribution in micellar and microemulsion systems. It also promotes the adsorption of surfactants at fluid-fluid interfaces and affects the formation of adsorbed layer at fluid-solid interfaces. Our proposed modifications have direct applications in the thermodynamic modeling of the effect of temperature on molecular aggregation, both in the bulk and at the interfaces.

  14. 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

  15. Model Identification of Integrated ARMA Processes

    Science.gov (United States)

    Stadnytska, Tetiana; Braun, Simone; Werner, Joachim

    2008-01-01

    This article evaluates the Smallest Canonical Correlation Method (SCAN) and the Extended Sample Autocorrelation Function (ESACF), automated methods for the Autoregressive Integrated Moving-Average (ARIMA) model selection commonly available in current versions of SAS for Windows, as identification tools for integrated processes. SCAN and ESACF can…

  16. Kinetics and modeling of anaerobic digestion process

    DEFF Research Database (Denmark)

    Gavala, Hariklia N.; Angelidaki, Irini; Ahring, Birgitte Kiær

    2003-01-01

    Anaerobic digestion modeling started in the early 1970s when the need for design and efficient operation of anaerobic systems became evident. At that time not only was the knowledge about the complex process of anaerobic digestion inadequate but also there were computational limitations. Thus...

  17. Designing equivalent semantic models for process creation

    NARCIS (Netherlands)

    P.H.M. America (Pierre); J.W. de Bakker (Jaco)

    1986-01-01

    textabstractOperational and denotational semantic models are designed for languages with process creation, and the relationships between the two semantics are investigated. The presentation is organized in four sections dealing with a uniform and static, a uniform and dynamic, a nonuniform and

  18. Modeling as a Decision-Making Process

    Science.gov (United States)

    Bleiler-Baxter, Sarah K.; Stephens, D. Christopher; Baxter, Wesley A.; Barlow, Angela T.

    2017-01-01

    The goal in this article is to support teachers in better understanding what it means to model with mathematics by focusing on three key decision-making processes: Simplification, Relationship Mapping, and Situation Analysis. The authors use the Theme Park task to help teachers develop a vision of how students engage in these three decision-making…

  19. Mathematical Modelling of Continuous Biotechnological Processes

    Science.gov (United States)

    Pencheva, T.; Hristozov, I.; Shannon, A. G.

    2003-01-01

    Biotechnological processes (BTP) are characterized by a complicated structure of organization and interdependent characteristics. Partial differential equations or systems of partial differential equations are used for their behavioural description as objects with distributed parameters. Modelling of substrate without regard to dispersion…

  20. Aligning Grammatical Theories and Language Processing Models

    Science.gov (United States)

    Lewis, Shevaun; Phillips, Colin

    2015-01-01

    We address two important questions about the relationship between theoretical linguistics and psycholinguistics. First, do grammatical theories and language processing models describe separate cognitive systems, or are they accounts of different aspects of the same system? We argue that most evidence is consistent with the one-system view. Second,…

  1. Computational Process Modeling for Additive Manufacturing (OSU)

    Science.gov (United States)

    Bagg, Stacey; Zhang, Wei

    2015-01-01

    Powder-Bed Additive Manufacturing (AM) through Direct Metal Laser Sintering (DMLS) or Selective Laser Melting (SLM) is being used by NASA and the Aerospace industry to "print" parts that traditionally are very complex, high cost, or long schedule lead items. The process spreads a thin layer of metal powder over a build platform, then melts the powder in a series of welds in a desired shape. The next layer of powder is applied, and the process is repeated until layer-by-layer, a very complex part can be built. This reduces cost and schedule by eliminating very complex tooling and processes traditionally used in aerospace component manufacturing. To use the process to print end-use items, NASA seeks to understand SLM material well enough to develop a method of qualifying parts for space flight operation. Traditionally, a new material process takes many years and high investment to generate statistical databases and experiential knowledge, but computational modeling can truncate the schedule and cost -many experiments can be run quickly in a model, which would take years and a high material cost to run empirically. This project seeks to optimize material build parameters with reduced time and cost through modeling.

  2. Fuzzy model for Laser Assisted Bending Process

    Directory of Open Access Journals (Sweden)

    Giannini Oliviero

    2016-01-01

    Full Text Available In the present study, a fuzzy model was developed to predict the residual bending in a conventional metal bending process assisted by a high power diode laser. The study was focused on AA6082T6 aluminium thin sheets. In most dynamic sheet metal forming operations, the highly nonlinear deformation processes cause large amounts of elastic strain energy stored in the formed material. The novel hybrid forming process was thus aimed at inducing the local heating of the mechanically bent workpiece in order to decrease or eliminate the related springback phenomena. In particular, the influence on the extent of springback phenomena of laser process parameters such as source power, scan speed and starting elastic deformation of mechanically bent sheets, was experimentally assessed. Consistent trends in experimental response according to operational parameters were found. Accordingly, 3D process maps of the extent of the springback phenomena according to operational parameters were constructed. The effect of the inherent uncertainties on the predicted residual bending caused by the approximation in the model parameters was evaluated. In particular, a fuzzy-logic based approach was used to describe the model uncertainties and the transformation method was applied to propagate their effect on the residual bending.

  3. Computer aided molecular design with combined molecular modeling and group contribution

    DEFF Research Database (Denmark)

    Harper, Peter Mathias; Gani, Rafiqul; Kolar, Petr

    1999-01-01

    Computer-aided molecular design (CAMD) provides a means for determining molecules or mixtures of molecules (CAMMD) having a desirable set of physicochemical properties. The application range of CAMD is restricted due to limitations on the complexity of the generated molecular structures and on th......Computer-aided molecular design (CAMD) provides a means for determining molecules or mixtures of molecules (CAMMD) having a desirable set of physicochemical properties. The application range of CAMD is restricted due to limitations on the complexity of the generated molecular structures...

  4. Process Model for Friction Stir Welding

    Science.gov (United States)

    Adams, Glynn

    1996-01-01

    Friction stir welding (FSW) is a relatively new process being applied for joining of metal alloys. The process was initially developed by The Welding Institute (TWI) in Cambridge, UK. The FSW process is being investigated at NASA/MSEC as a repair/initial weld procedure for fabrication of the super-light-weight aluminum-lithium shuttle external tank. The FSW investigations at MSFC were conducted on a horizontal mill to produce butt welds of flat plate material. The weldment plates are butted together and fixed to a backing plate on the mill bed. A pin tool is placed into the tool holder of the mill spindle and rotated at approximately 400 rpm. The pin tool is then plunged into the plates such that the center of the probe lies at, one end of the line of contact, between the plates and the shoulder of the pin tool penetrates the top surface of the weldment. The weld is produced by traversing the tool along the line of contact between the plates. A lead angle allows the leading edge of the shoulder to remain above the top surface of the plate. The work presented here is the first attempt at modeling a complex phenomenon. The mechanical aspects of conducting the weld process are easily defined and the process itself is controlled by relatively few input parameters. However, in the region of the weld, plasticizing and forging of the parent material occurs. These are difficult processes to model. The model presented here addresses only variations in the radial dimension outward from the pin tool axis. Examinations of the grain structure of the weld reveal that a considerable amount of material deformation also occurs in the direction parallel to the pin tool axis of rotation, through the material thickness. In addition, measurements of the axial load on the pin tool demonstrate that the forging affect of the pin tool shoulder is an important process phenomenon. Therefore, the model needs to be expanded to account for the deformations through the material thickness and the

  5. Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: a model for "active" disease.

    Science.gov (United States)

    Peng, Ruoqi; Sridhar, Sriram; Tyagi, Gaurav; Phillips, Jonathan E; Garrido, Rosario; Harris, Paul; Burns, Lisa; Renteria, Lorena; Woods, John; Chen, Leena; Allard, John; Ravindran, Palanikumar; Bitter, Hans; Liang, Zhenmin; Hogaboam, Cory M; Kitson, Chris; Budd, David C; Fine, Jay S; Bauer, Carla M T; Stevenson, Christopher S

    2013-01-01

    The preclinical model of bleomycin-induced lung fibrosis, used to investigate mechanisms related to idiopathic pulmonary fibrosis (IPF), has incorrectly predicted efficacy for several candidate compounds suggesting that it may be of limited value. As an attempt to improve the predictive nature of this model, integrative bioinformatic approaches were used to compare molecular alterations in the lungs of bleomycin-treated mice and patients with IPF. Using gene set enrichment analysis we show for the first time that genes differentially expressed during the fibrotic phase of the single challenge bleomycin model were significantly enriched in the expression profiles of IPF patients. The genes that contributed most to the enrichment were largely involved in mitosis, growth factor, and matrix signaling. Interestingly, these same mitotic processes were increased in the expression profiles of fibroblasts isolated from rapidly progressing, but not slowly progressing, IPF patients relative to control subjects. The data also indicated that TGFβ was not the sole mediator responsible for the changes observed in this model since the ALK-5 inhibitor SB525334 effectively attenuated some but not all of the fibrosis associated with this model. Although some would suggest that repetitive bleomycin injuries may more effectively model IPF-like changes, our data do not support this conclusion. Together, these data highlight that a single bleomycin instillation effectively replicates several of the specific pathogenic molecular changes associated with IPF, and may be best used as a model for patients with active disease.

  6. Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: a model for "active" disease.

    Directory of Open Access Journals (Sweden)

    Ruoqi Peng

    Full Text Available The preclinical model of bleomycin-induced lung fibrosis, used to investigate mechanisms related to idiopathic pulmonary fibrosis (IPF, has incorrectly predicted efficacy for several candidate compounds suggesting that it may be of limited value. As an attempt to improve the predictive nature of this model, integrative bioinformatic approaches were used to compare molecular alterations in the lungs of bleomycin-treated mice and patients with IPF. Using gene set enrichment analysis we show for the first time that genes differentially expressed during the fibrotic phase of the single challenge bleomycin model were significantly enriched in the expression profiles of IPF patients. The genes that contributed most to the enrichment were largely involved in mitosis, growth factor, and matrix signaling. Interestingly, these same mitotic processes were increased in the expression profiles of fibroblasts isolated from rapidly progressing, but not slowly progressing, IPF patients relative to control subjects. The data also indicated that TGFβ was not the sole mediator responsible for the changes observed in this model since the ALK-5 inhibitor SB525334 effectively attenuated some but not all of the fibrosis associated with this model. Although some would suggest that repetitive bleomycin injuries may more effectively model IPF-like changes, our data do not support this conclusion. Together, these data highlight that a single bleomycin instillation effectively replicates several of the specific pathogenic molecular changes associated with IPF, and may be best used as a model for patients with active disease.

  7. Quantitative computational models of molecular self-assembly in systems biology.

    Science.gov (United States)

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  8. Modelling and control of a flotation process

    International Nuclear Information System (INIS)

    Ding, L.; Gustafsson, T.

    1999-01-01

    A general description of a flotation process is given. The dynamic model of a MIMO nonlinear subprocess in flotation, i. e. the pulp levels in five compartments in series is developed and the model is verified with real data from a production plant. In order to reject constant disturbances five extra states are introduced and the model is modified. An exact linearization has been made for the non-linear model and a linear quadratic gaussian controller is proposed based on the linearized model. The simulation result shows an improved performance of the pulp level control when the set points are changed or a disturbance occur. In future the controller will be tested in production. (author)

  9. Learning Markov Decision Processes for Model Checking

    DEFF Research Database (Denmark)

    Mao, Hua; Chen, Yingke; Jaeger, Manfred

    2012-01-01

    . The proposed learning algorithm is adapted from algorithms for learning deterministic probabilistic finite automata, and extended to include both probabilistic and nondeterministic transitions. The algorithm is empirically analyzed and evaluated by learning system models of slot machines. The evaluation......Constructing an accurate system model for formal model verification can be both resource demanding and time-consuming. To alleviate this shortcoming, algorithms have been proposed for automatically learning system models based on observed system behaviors. In this paper we extend the algorithm...... on learning probabilistic automata to reactive systems, where the observed system behavior is in the form of alternating sequences of inputs and outputs. We propose an algorithm for automatically learning a deterministic labeled Markov decision process model from the observed behavior of a reactive system...

  10. Advances in modeling plastic waste pyrolysis processes

    Energy Technology Data Exchange (ETDEWEB)

    Safadi, Y. [Department of Mechanical Engineering, American University of Beirut, PO Box 11-0236, Beirut (Lebanon); Zeaiter, J. [Chemical Engineering Program, American University of Beirut, PO Box 11-0236, Beirut (Lebanon)

    2013-07-01

    The tertiary recycling of plastics via pyrolysis is recently gaining momentum due to promising economic returns from the generated products that can be used as a chemical feedstock or fuel. The need for prediction models to simulate such processes is essential in understanding in depth the mechanisms that take place during the thermal or catalytic degradation of the waste polymer. This paper presents key different models used successfully in literature so far. Three modeling schemes are identified: Power-Law, Lumped-Empirical, and Population-Balance based equations. The categorization is based mainly on the level of detail and prediction capability from each modeling scheme. The data shows that the reliability of these modeling approaches vary with the degree of details the experimental work and product analysis are trying to achieve.

  11. A model evaluation checklist for process-based environmental models

    Science.gov (United States)

    Jackson-Blake, Leah

    2015-04-01

    Mechanistic catchment-scale phosphorus models appear to perform poorly where diffuse sources dominate. The reasons for this were investigated for one commonly-applied model, the INtegrated model of CAtchment Phosphorus (INCA-P). Model output was compared to 18 months of daily water quality monitoring data in a small agricultural catchment in Scotland, and model structure, key model processes and internal model responses were examined. Although the model broadly reproduced dissolved phosphorus dynamics, it struggled with particulates. The reasons for poor performance were explored, together with ways in which improvements could be made. The process of critiquing and assessing model performance was then generalised to provide a broadly-applicable model evaluation checklist, incorporating: (1) Calibration challenges, relating to difficulties in thoroughly searching a high-dimensional parameter space and in selecting appropriate means of evaluating model performance. In this study, for example, model simplification was identified as a necessary improvement to reduce the number of parameters requiring calibration, whilst the traditionally-used Nash Sutcliffe model performance statistic was not able to discriminate between realistic and unrealistic model simulations, and alternative statistics were needed. (2) Data limitations, relating to a lack of (or uncertainty in) input data, data to constrain model parameters, data for model calibration and testing, and data to test internal model processes. In this study, model reliability could be improved by addressing all four kinds of data limitation. For example, there was insufficient surface water monitoring data for model testing against an independent dataset to that used in calibration, whilst additional monitoring of groundwater and effluent phosphorus inputs would help distinguish between alternative plausible model parameterisations. (3) Model structural inadequacies, whereby model structure may inadequately represent

  12. Molecular dynamics study of dual-phase microstructure of Titanium and Zirconium metals during the quenching process

    Science.gov (United States)

    Miyazaki, Narumasa; Sato, Kazunori; Shibutani, Yoji

    Dual-phase (DP) transformation, which is composed of felite- and/or martensite- multicomponent microstructural phases, is one of the most effective tools to product functional alloys. To obtain this DP structure such as DP steels and other materials, we usually apply thermal processes such as quenching, tempering and annealing. As the transformation dynamics of DP microstructure depends on conditions of temperature, annealing time, and quenching rate, physical properties of materials are able to be tuned by controlling microstructure type, size, their interfaces and so on. In this study, to understand the behavior of DP transformation and to control physical properties of materials by tuning DP microstructures, we analyze the atomistic dynamics of DP transformation during the quenching process and the detail of DP microstructures by using the molecular dynamics simulations. As target metals of DP transformation, we focus on group 4 transition metals, such as Ti and Zr described by EAM interatomic potentials. For Ti and Zr models we perform molecular dynamics simulations by assuming melt-quenching process from 3000 K to 0 K under the isothermal-isobaric ensemble. During the process for each material, we observe liquid to HCP like transition around the melting temperature, and continuously HCP-BCC like transition around martensitic transformation temperature. Furthermore, we clearly distinguish DP microstructure for each quenched model.

  13. An ecological process model of systems change.

    Science.gov (United States)

    Peirson, Leslea J; Boydell, Katherine M; Ferguson, H Bruce; Ferris, Lorraine E

    2011-06-01

    In June 2007 the American Journal of Community Psychology published a special issue focused on theories, methods and interventions for systems change which included calls from the editors and authors for theoretical advancement in this field. We propose a conceptual model of systems change that integrates familiar and fundamental community psychology principles (succession, interdependence, cycling of resources, adaptation) and accentuates a process orientation. To situate our framework we offer a definition of systems change and a brief review of the ecological perspective and principles. The Ecological Process Model of Systems Change is depicted, described and applied to a case example of policy driven systems level change in publicly funded social programs. We conclude by identifying salient implications for thinking and action which flow from the Model.

  14. Modeling veterans healthcare administration disclosure processes :

    Energy Technology Data Exchange (ETDEWEB)

    Beyeler, Walter E; DeMenno, Mercy B.; Finley, Patrick D.

    2013-09-01

    As with other large healthcare organizations, medical adverse events at the Department of Veterans Affairs (VA) facilities can expose patients to unforeseen negative risks. VHA leadership recognizes that properly handled disclosure of adverse events can minimize potential harm to patients and negative consequences for the effective functioning of the organization. The work documented here seeks to help improve the disclosure process by situating it within the broader theoretical framework of issues management, and to identify opportunities for process improvement through modeling disclosure and reactions to disclosure. The computational model will allow a variety of disclosure actions to be tested across a range of incident scenarios. Our conceptual model will be refined in collaboration with domain experts, especially by continuing to draw on insights from VA Study of the Communication of Adverse Large-Scale Events (SCALE) project researchers.

  15. Deciphering spreading mechanisms in amyotrophic lateral sclerosis: clinical evidence and potential molecular processes.

    Science.gov (United States)

    Pradat, Pierre-François; Kabashi, Edor; Desnuelle, Claude

    2015-10-01

    The aim of this review is to refer to recent arguments supporting the existence of specific propagation mechanisms associated with spreading of neuron injury in amyotrophic lateral sclerosis (ALS). Misfolded ALS-linked protein accumulation can induce aggregation of their native equivalent isoforms through a mechanism analogous to the infectious prion proteins initiation and its propagation. Although ALS is clinically heterogeneous, a shared characteristic is the focal onset and the progressive extension to all body regions. Being viewed until now as just summation of the increased number of affected neurons, dispersion is now rather considered as the result of a seeded self-propagating process. A sequential regional spreading pattern is supported by the distribution of TDP-43 aggregates in ALS autopsy cases. Electrophysiology and advanced neuroimaging methods also recently provided some evidence for propagation of lesions both in the brain and spinal cord, more longitudinal studies being still needed. Lesions are supposed to spread cell-to-cell regionally or through connected neuronal pathway. At the molecular level, the prion-like spreading is an emerging mechanism hypothesis, but other machineries such as those that are in charge of dealing with misfolded proteins and secretion of deleterious peptides may be involved in the propagation of neuron loss. Deciphering the mechanisms underlying spreading of ALS symptoms is of crucial importance to better understand this neurodegenerative disease, build new and appropriate animal models and to define novel therapeutic targets.

  16. Warm and cold molecular gas conditions modeled in 87 galaxies observed by the Herschel SPIRE FTS

    Science.gov (United States)

    Kamenetzky, Julia; Rangwala, Naseem; Glenn, Jason

    2018-01-01

    Molecular gas is the raw material for star formation, and like the interstellar medium (ISM) in general, it can exist in regions of higher and lower excitation. Rotational transitions of the CO molecule are bright and sensitive to cold molecular gas. While the majority of the molecular gas exists in the very cold component traced by CO J=1-0, the higher-J lines trace the highly excited gas that may be more indicative of star formation processes. The atmosphere is opaque to these lines, but the launch of the Herschel Space Observatory made them accessible for study of Galactic and extragalactic sources. We have conducted two-component, non-local thermodynamic equilibrium (non-LTE) modeling of the CO lines from J=1‑0 through J=13‑12 in 87 galaxies observed by the Herschel SPIRE Fourier Transform Spectrometer (FTS). We used the nested sampling algorithm Multinest to compare the measured CO spectral line energy distributions (SLEDs) to the ones produced by a custom version of the non-LTE code RADEX. This allowed us to fully examine the degeneracies in parameter space for kinetic temperature, molecular gas density, CO column density, and area filling factor.Here we discuss the major findings of our study, as well as the important implications of two-component molecular gas modeling. The average pressure of the warm gas is slightly correlated with galaxy LFIR, but that of the cold gas is not. A high-J (such as J=11-10) to J=1-0 line ratio is diagnostic of warm component pressure. We find a very large spread in our derived values of "alpha-CO," with no discernable trend with LFIR, and average molecular gas depletion times that decrease with LFIR. If only a few molecular lines are available in a galaxy's SLED, the limited ability to model only one component will change the results. A one-component fit often underestimates the flux of carbon monoxide (CO) J=1‑0 and the mass. If low-J lines are not included, mass is underestimated by an order of magnitude. Even when

  17. Status of Safeguards and Separations Model Development at Plant and Molecular Levels

    Energy Technology Data Exchange (ETDEWEB)

    de Almeida, Valmor F [ORNL; Hay, Benjamin [ORNL; DePaoli, David W [ORNL

    2009-10-01

    A primary goal of the Safeguards and Separations IPSC effort is the development of process modeling tools that allow dynamic simulations of separations plant operations under various configurations and conditions, and integration of relevant safeguards analyses. A requirement of the effort is to develop codes on modern, expandable architectures, with flexibility to explore and evaluate a wide range of process options. During FY09, efforts at ORNL have been focused on two priority tasks toward achieving the IPSC goal: (1) a top-down exploration of architecture - Subtask 1: Explore framework for code development and integration for plant-level simulation; and (2) a bottom-up fundamental modeling effort - Subtask 2: Development of molecular-level agent design code. Subtask 1 is important because definition and development of architecture is a key issue for the overall effort, as selection of an overall approach and code/data requirements is a necessary first step in the organization, design and development of separations and safeguards codes that will be incorporated. The agent design effort of Subtask 2 is a molecular-level modeling effort that has a direct impact on a near-term issue of the Separations and Waste Forms Campaign. A current focus of experimental efforts is the development of robust agents and processes for separation of Am/Cm. Development of enhanced agent-design codes will greatly accelerate discovery and experimental testing.

  18. Status of Safeguards and Separations Model Development at Plant and Molecular Levels

    International Nuclear Information System (INIS)

    de Almeida, Valmor F.; Hay, Benjamin; DePaoli, David W.

    2009-01-01

    A primary goal of the Safeguards and Separations IPSC effort is the development of process modeling tools that allow dynamic simulations of separations plant operations under various configurations and conditions, and integration of relevant safeguards analyses. A requirement of the effort is to develop codes on modern, expandable architectures, with flexibility to explore and evaluate a wide range of process options. During FY09, efforts at ORNL have been focused on two priority tasks toward achieving the IPSC goal: (1) a top-down exploration of architecture - Subtask 1: Explore framework for code development and integration for plant-level simulation; and (2) a bottom-up fundamental modeling effort - Subtask 2: Development of molecular-level agent design code. Subtask 1 is important because definition and development of architecture is a key issue for the overall effort, as selection of an overall approach and code/data requirements is a necessary first step in the organization, design and development of separations and safeguards codes that will be incorporated. The agent design effort of Subtask 2 is a molecular-level modeling effort that has a direct impact on a near-term issue of the Separations and Waste Forms Campaign. A current focus of experimental efforts is the development of robust agents and processes for separation of Am/Cm. Development of enhanced agent-design codes will greatly accelerate discovery and experimental testing.

  19. Probing the RAFT process using a model reaction between alkoxyamine and dithioester

    NARCIS (Netherlands)

    Zhou, Y.

    2012-01-01

    A small-molecular model reaction was designed to probe the reversible addition–fragmentation chain transfer (RAFT) process. In this reaction, alkoxyamine releases radicals that react in situ with dithioester through the RAFT process, generating new radicals through the fragmentation of the

  20. Dimensional modeling: beyond data processing constraints.

    Science.gov (United States)

    Bunardzic, A

    1995-01-01

    The focus of information processing requirements is shifting from the on-line transaction processing (OLTP) issues to the on-line analytical processing (OLAP) issues. While the former serves to ensure the feasibility of the real-time on-line transaction processing (which has already exceeded a level of up to 1,000 transactions per second under normal conditions), the latter aims at enabling more sophisticated analytical manipulation of data. The OLTP requirements, or how to efficiently get data into the system, have been solved by applying the Relational theory in the form of Entity-Relation model. There is presently no theory related to OLAP that would resolve the analytical processing requirements as efficiently as Relational theory provided for the transaction processing. The "relational dogma" also provides the mathematical foundation for the Centralized Data Processing paradigm in which mission-critical information is incorporated as 'one and only one instance' of data, thus ensuring data integrity. In such surroundings, the information that supports business analysis and decision support activities is obtained by running predefined reports and queries that are provided by the IS department. In today's intensified competitive climate, businesses are finding that this traditional approach is not good enough. The only way to stay on top of things, and to survive and prosper, is to decentralize the IS services. The newly emerging Distributed Data Processing, with its increased emphasis on empowering the end user, does not seem to find enough merit in the relational database model to justify relying upon it. Relational theory proved too rigid and complex to accommodate the analytical processing needs. In order to satisfy the OLAP requirements, or how to efficiently get the data out of the system, different models, metaphors, and theories have been devised. All of them are pointing to the need for simplifying the highly non-intuitive mathematical constraints found

  1. A tight-binding model of the transmission probability through a molecular junction; a single molecule vs. a molecular layer

    International Nuclear Information System (INIS)

    Landau, A.; Nitzan, A.

    2006-01-01

    Full Text: Molecular electronics, one of the major fields of the current effort in nano-science, may be de ed as the study of electronic behaviors, devices and applications that depend on the properties of matter at the molecular scale. If the miniaturization trend of microelectronic devices is to continue, elements such as transistors and contacts will soon shrink to single molecules. The promise of these new technological breakthroughs has been major driving force in this ld. Moreover, the consideration of molecular systems as electronic devices has raised new fundamental questions. In particular, while traditional quantum chemistry deals with electronically closed systems, we now face problems involving molecular systems that are open to their electronic environment, moreover, function in far from equilibrium situations. A generic molecular junction is made of two electrodes connected by a molecular spacer that takes the form of a molecular chain of varying length or a molecular layer of varying thickness. We use a simple nearest-neighbors tight-biding model with the non-equilibrium Green's function (NEGF) method to investigate and compare between a self-assembled monolayer (SAM), finite molecular layer (FML), and single molecule (SM) chemisorption to a surface of a metal substrate. In addition, we examine the difference in the transmission probability through a SAM, FML and SM sandwiched between two metallic electrodes. Dramatic differences are observed between the SM, FML and SAM density of electronic states and transmission functions. In addition, we analyze the effects of changing different physical parameters such as molecule-substrate interaction, molecule-molecule interactions, etc; interesting effects that pertain to the conduction properties of single molecules and molecular layers are observed. Intriguing results are attained when we investigate the commensurability of the SAM with the metallic surface

  2. Effect of low molecular fraction of thymus humoral factor on blood formation processes of irradiated mice

    International Nuclear Information System (INIS)

    Stolyarova, T.V.; Skobel'tsyna, E.S.; Grinberg, S.M.; Kruglikov, I.L.; Korotaev, G.K.; Tepelina, O.M.; Il'ina, T.I.

    1982-01-01

    The effect of low-molecular fraction of thymus humoral factor on blood formation in mice irradiated at 4 Gy was studied. It is shown that injection of low-molecular fraction of thymus hymoral factor to irradiated animals affects proliferative processes in spleen and bone marrow, however the degree of the effect depends on the injection scheme of the preparation. Application of mathematical planning methods of the experiment enables to analyze various injection schemes of low-molecular fraction of thymus humoral factor on the investigated indices. The optimal scheme of preparation injection is determined: 1st injection with the dose of 10 mkg/kg following 4 hour after irradiation, 2d injection - with the same dose in 7-21 days

  3. 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

  4. Mathematical modeling of the flash converting process

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, H.Y.; Perez-Tello, M.; Riihilahti, K.M. [Utah Univ., Salt Lake City, UT (United States)

    1996-12-31

    An axisymmetric mathematical model for the Kennecott-Outokumpu flash converting process for converting solid copper matte to copper is presented. The model is an adaptation of the comprehensive mathematical model formerly developed at the University of Utah for the flash smelting of copper concentrates. The model incorporates the transport of momentum, heat, mass, and reaction kinetics between gas and particles in a particle-laden turbulent gas jet. The standard k-{epsilon} model is used to describe gas-phase turbulence in an Eulerian framework. The particle-phase is treated from a Lagrangian viewpoint which is coupled to the gas-phase via the source terms in the Eulerian gas-phase governing equations. Matte particles were represented as Cu{sub 2}S yFeS, and assumed to undergo homogeneous oxidation to Cu{sub 2}O, Fe{sub 3}O{sub 4}, and SO{sub 2}. A reaction kinetics mechanism involving both external mass transfer of oxygen gas to the particle surface and diffusion of oxygen through the porous oxide layer is proposed to estimate the particle oxidation rate Predictions of the mathematical model were compared with the experimental data collected in a bench-scale flash converting facility. Good agreement between the model predictions and the measurements was obtained. The model was used to study the effect of different gas-injection configurations on the overall fluid dynamics in a commercial size flash converting shaft. (author)

  5. Mathematical modeling of the flash converting process

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, H Y; Perez-Tello, M; Riihilahti, K M [Utah Univ., Salt Lake City, UT (United States)

    1997-12-31

    An axisymmetric mathematical model for the Kennecott-Outokumpu flash converting process for converting solid copper matte to copper is presented. The model is an adaptation of the comprehensive mathematical model formerly developed at the University of Utah for the flash smelting of copper concentrates. The model incorporates the transport of momentum, heat, mass, and reaction kinetics between gas and particles in a particle-laden turbulent gas jet. The standard k-{epsilon} model is used to describe gas-phase turbulence in an Eulerian framework. The particle-phase is treated from a Lagrangian viewpoint which is coupled to the gas-phase via the source terms in the Eulerian gas-phase governing equations. Matte particles were represented as Cu{sub 2}S yFeS, and assumed to undergo homogeneous oxidation to Cu{sub 2}O, Fe{sub 3}O{sub 4}, and SO{sub 2}. A reaction kinetics mechanism involving both external mass transfer of oxygen gas to the particle surface and diffusion of oxygen through the porous oxide layer is proposed to estimate the particle oxidation rate Predictions of the mathematical model were compared with the experimental data collected in a bench-scale flash converting facility. Good agreement between the model predictions and the measurements was obtained. The model was used to study the effect of different gas-injection configurations on the overall fluid dynamics in a commercial size flash converting shaft. (author)

  6. Process models and model-data fusion in dendroecology

    Directory of Open Access Journals (Sweden)

    Joel eGuiot

    2014-08-01

    Full Text Available Dendrochronology (i.e. the study of annually dated tree-ring time series has proved to be a powerful technique to understand tree-growth. This paper intends to show the interest of using ecophysiological modeling not only to understand and predict tree-growth (dendroecology but also to reconstruct past climates (dendroclimatology. Process models have been used for several decades in dendroclimatology, but it is only recently that methods of model-data fusion have led to significant progress in modeling tree-growth as a function of climate and in reconstructing past climates. These model-data fusion (MDF methods, mainly based on the Bayesian paradigm, have been shown to be powerful for both model calibration and model inversion. After a rapid survey of tree-growth modeling, we illustrate MDF with examples based on series of Southern France Aleppo pines and Central France oaks. These examples show that if plants experienced CO2 fertilization, this would have a significant effect on tree-growth which in turn would bias the climate reconstructions. This bias could be extended to other environmental non-climatic factors directly or indirectly affecting annual ring formation and not taken into account in classical empirical models, which supports the use of more complex process-based models. Finally, we conclude by showing the interest of the data assimilation methods applied in climatology to produce climate re-analyses.

  7. Reversibility in Quantum Models of Stochastic Processes

    Science.gov (United States)

    Gier, David; Crutchfield, James; Mahoney, John; James, Ryan

    Natural phenomena such as time series of neural firing, orientation of layers in crystal stacking and successive measurements in spin-systems are inherently probabilistic. The provably minimal classical models of such stochastic processes are ɛ-machines, which consist of internal states, transition probabilities between states and output values. The topological properties of the ɛ-machine for a given process characterize the structure, memory and patterns of that process. However ɛ-machines are often not ideal because their statistical complexity (Cμ) is demonstrably greater than the excess entropy (E) of the processes they represent. Quantum models (q-machines) of the same processes can do better in that their statistical complexity (Cq) obeys the relation Cμ >= Cq >= E. q-machines can be constructed to consider longer lengths of strings, resulting in greater compression. With code-words of sufficiently long length, the statistical complexity becomes time-symmetric - a feature apparently novel to this quantum representation. This result has ramifications for compression of classical information in quantum computing and quantum communication technology.

  8. Hidden Markov models and other machine learning approaches in computational molecular biology

    Energy Technology Data Exchange (ETDEWEB)

    Baldi, P. [California Inst. of Tech., Pasadena, CA (United States)

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Computational tools are increasingly needed to process the massive amounts of data, to organize and classify sequences, to detect weak similarities, to separate coding from non-coding regions, and reconstruct the underlying evolutionary history. The fundamental problem in machine learning is the same as in scientific reasoning in general, as well as statistical modeling: to come up with a good model for the data. In this tutorial four classes of models are reviewed. They are: Hidden Markov models; artificial Neural Networks; Belief Networks; and Stochastic Grammars. When dealing with DNA and protein primary sequences, Hidden Markov models are one of the most flexible and powerful alignments and data base searches. In this tutorial, attention is focused on the theory of Hidden Markov Models, and how to apply them to problems in molecular biology.

  9. Dual elaboration models in attitude change processes

    Directory of Open Access Journals (Sweden)

    Žeželj Iris

    2005-01-01

    Full Text Available This article examines empirical and theoretical developments in research on attitude change in the past 50 years. It focuses the period from 1980 till present as well as cognitive response theories as the dominant theoretical approach in the field. The postulates of Elaboration Likelihood Model, as most-researched representative of dual process theories are studied, based on review of accumulated research evidence. Main research findings are grouped in four basic factors: message source, message content, message recipient and its context. Most influential criticisms of the theory are then presented regarding its empirical base and dual process assumption. Some possible applications and further research perspectives are discussed at the end.

  10. Temperature Modelling of the Biomass Pretreatment Process

    DEFF Research Database (Denmark)

    Prunescu, Remus Mihail; Blanke, Mogens; Jensen, Jakob M.

    2012-01-01

    In a second generation biorefinery, the biomass pretreatment stage has an important contribution to the efficiency of the downstream processing units involved in biofuel production. Most of the pretreatment process occurs in a large pressurized thermal reactor that presents an irregular temperature...... that captures the environmental temperature differences inside the reactor using distributed parameters. A Kalman filter is then added to account for any missing dynamics and the overall model is embedded into a temperature soft sensor. The operator of the plant will be able to observe the temperature in any...

  11. Modelling the Molecular Transportation of Subcutaneously Injected Salubrinal

    Directory of Open Access Journals (Sweden)

    Andy Chen

    2011-01-01

    Full Text Available For the subcutaneous administration of a chemical agent (salubrinal, we constructed a mathematical model of molecule transportation and subsequently evaluated the kinetics of diffusion, convection, and molecular turnover. Salubrinal is a potential therapeutic agent that can reduce cellular damage and death. The understanding of its temporal profiles in local tissue as well as in a whole body is important to develop a proper strategy for its administration. Here, the diffusion and convection kinetics was formulated using partial and ordinary differential equations in one- and three-dimensional (semi-spherical coordinates. Several key parameters including an injection velocity, a diffusion coefficient, thickness of subcutaneous tissue, and a permeability factor at the tissue-blood boundary were estimated from experimental data in rats. With reference to analytical solutions in a simplified model without convection, numerical solutions revealed that the diffusion coefficient and thickness of subcutaneous tissue determined the timing of the peak concentration in the plasma, and its magnitude was dictated by the permeability factor. Furthermore, the initial velocity, induced by needle injection, elevated an immediate transport of salubrinal at t < 1h. The described analysis with a combination of partial and ordinary differential equations contributes to the prediction of local and systemic effects and the understanding of the transportation mechanism of salubrinal and other agents.

  12. Theoretical modelling of carbon deposition processes

    International Nuclear Information System (INIS)

    Marsh, G.R.; Norfolk, D.J.; Skinner, R.F.

    1985-01-01

    Work based on capsule experiments in the BNL Gamma Facility, aimed at elucidating the chemistry involved in the formation of carbonaceous deposit on CAGR fuel pin surfaces is described. Using a data-base derived from capsule experiments together with literature values for the kinetics of the fundamental reactions, a chemical model of the gas-phase processes has been developed. This model successfully reproduces the capsule results, whilst preliminary application to the WAGR coolant circuit indicates the likely concentration profiles of various radical species within the fuel channels. (author)

  13. Theoretical Modelling of Intercultural Communication Process

    Directory of Open Access Journals (Sweden)

    Mariia Soter

    2016-08-01

    Full Text Available The definition of the concepts of “communication”, “intercultural communication”, “model of communication” are analyzed in the article. The basic components of the communication process are singled out. The model of intercultural communication is developed. Communicative, behavioral and complex skills for optimal organization of intercultural communication, establishment of productive contact with a foreign partner to achieve mutual understanding, searching for acceptable ways of organizing interaction and cooperation for both communicants are highlighted in the article. It is noted that intercultural communication through interaction between people affects the development of different cultures’ aspects.

  14. 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

  15. Symmetry Breaking in NMR Spectroscopy: The Elucidation of Hidden Molecular Rearrangement Processes

    Directory of Open Access Journals (Sweden)

    Michael J. McGlinchey

    2014-08-01

    Full Text Available Variable-temperature NMR spectroscopy is probably the most convenient and sensitive technique to monitor changes in molecular structure in solution. Rearrangements that are rapid on the NMR time-scale exhibit simplified spectra, whereby non-equivalent nuclear environments yield time-averaged resonances. At lower temperatures, when the rate of exchange is sufficiently reduced, these degeneracies are split and the underlying “static” molecular symmetry, as seen by X-ray crystallography, becomes apparent. Frequently, however, such rearrangement processes are hidden, even when they become slow on the NMR time-scale, because the molecular point group remains unchanged. Judicious symmetry breaking, such as by substitution of a molecular fragment by a similar, but not identical moiety, or by the incorporation of potentially diastereotopic (chemically non-equivalent nuclei, allows the elucidation of the kinetics and energetics of such processes. Examples are chosen that include a wide range of rotations, migrations and other rearrangements in organic, inorganic and organometallic chemistry.

  16. Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching

    Science.gov (United States)

    Engstrom, James R.; Kummel, Andrew C.

    2017-02-01

    Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.

  17. Symmetries and modelling functions for diffusion processes

    International Nuclear Information System (INIS)

    Nikitin, A G; Spichak, S V; Vedula, Yu S; Naumovets, A G

    2009-01-01

    A constructive approach to the theory of diffusion processes is proposed, which is based on application of both symmetry analysis and the method of modelling functions. An algorithm for construction of the modelling functions is suggested. This algorithm is based on the error function expansion (ERFEX) of experimental concentration profiles. The high-accuracy analytical description of the profiles provided by ERFEX approximation allows a convenient extraction of the concentration dependence of diffusivity from experimental data and prediction of the diffusion process. Our analysis is exemplified by its employment in experimental results obtained for surface diffusion of lithium on the molybdenum (1 1 2) surface precovered with dysprosium. The ERFEX approximation can be directly extended to many other diffusion systems.

  18. Modeling of processes in the tourism sector

    Directory of Open Access Journals (Sweden)

    Salamatina Victoriya, S.

    2015-06-01

    Full Text Available In modern conditions for a number of Russian regions tourism is becoming budget. In this regard, it is of interest to the simulation of processes occurring in the tourism business, because they are affected by many random parameters, due to various economic, political, geographic, and other aspects. For improvement and development of systems for the management of tourism business systematically embeds economic mathematical apparatus in this area, because increased competitiveness requires continuous and constructive changes. Results of application of the economic mathematical apparatus allow a more systematic and internal unity to analyze and evaluate the applicability of further processes in tourism. For some economic processes typical tourist activities is that a certain effect and result from exposure to any of the factors on the indicators of the processes is not immediately but gradually, after some certain time, with a certain lag. With the necessity of accounting for this delay has to face when developing mathematical models of tourist business processes. In this case, the simulation of such processes it is advisable to apply economic-mathematical formalism of optimal control, called game theory.

  19. Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

    Science.gov (United States)

    Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

    2016-01-01

    Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

  20. Deep inelastic processes and the parton model

    International Nuclear Information System (INIS)

    Altarelli, G.

    The lecture was intended as an elementary introduction to the physics of deep inelastic phenomena from the point of view of theory. General formulae and facts concerning inclusive deep inelastic processes in the form: l+N→l'+hadrons (electroproduction, neutrino scattering) are first recalled. The deep inelastic annihilation e + e - →hadrons is then envisaged. The light cone approach, the parton model and their relation are mainly emphasized