WorldWideScience

Sample records for modeling molecular processes

  1. A model for processivity of molecular motors

    Institute of Scientific and Technical Information of China (English)

    Xie Ping; Dou Shuo-Xing; Wang Peng-Ye

    2004-01-01

    We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. Theoretical results on the distributions of the run length and dwell time at a given adenosine triphosphate (ATP) concentration, the dependences of mean run length, mean dwell time and mean velocity on ATP concentration and load are in good agreement with the previous experimental results.

  2. Machine learning for molecular scattering dynamics: Gaussian Process models for improved predictions of molecular collision observables

    Science.gov (United States)

    Krems, Roman; Cui, Jie; Li, Zhiying

    2016-05-01

    We show how statistical learning techniques based on kriging (Gaussian Process regression) can be used for improving the predictions of classical and/or quantum scattering theory. In particular, we show how Gaussian Process models can be used for: (i) efficient non-parametric fitting of multi-dimensional potential energy surfaces without the need to fit ab initio data with analytical functions; (ii) obtaining scattering observables as functions of individual PES parameters; (iii) using classical trajectories to interpolate quantum results; (iv) extrapolation of scattering observables from one molecule to another; (v) obtaining scattering observables with error bars reflecting the inherent inaccuracy of the underlying potential energy surfaces. We argue that the application of Gaussian Process models to quantum scattering calculations may potentially elevate the theoretical predictions to the same level of certainty as the experimental measurements and can be used to identify the role of individual atoms in determining the outcome of collisions of complex molecules. We will show examples and discuss the applications of Gaussian Process models to improving the predictions of scattering theory relevant for the cold molecules research field. Work supported by NSERC of Canada.

  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. 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.

  5. Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

    Science.gov (United States)

    Biswal, Debasmita; Kusalik, Peter G.

    2017-07-01

    Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

  6. 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.

  7. 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.

  8. Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model

    CERN Document Server

    Erdmann, Thorsten; Schwarz, Ulrich S

    2013-01-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of th...

  9. A non-Markov ratchet model of molecular motors: processive movement of single-headed kinesin KIF1A

    Institute of Scientific and Technical Information of China (English)

    Xie Ping; Dou Shuo-Xing; Wang Peng-Ye

    2006-01-01

    A fluctuating ratchet model of non-Markov process is presented to describe the processive movement of molecular motors of single-headed kinesin KIF1A, where the fluctuation perturbation to the local potential is introduced and the detailed ATPase pathway of the motor is included. The theoretical results show good quantitative agreement with the previous experimental ones.

  10. Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model.

    Science.gov (United States)

    Erdmann, Thorsten; Albert, Philipp J; Schwarz, Ulrich S

    2013-11-07

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  11. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    Science.gov (United States)

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  12. Towards better modelling of drug-loading in solid lipid nanoparticles: Molecular dynamics, docking experiments and Gaussian Processes machine learning.

    Science.gov (United States)

    Hathout, Rania M; Metwally, Abdelkader A

    2016-11-01

    This study represents one of the series applying computer-oriented processes and tools in digging for information, analysing data and finally extracting correlations and meaningful outcomes. In this context, binding energies could be used to model and predict the mass of loaded drugs in solid lipid nanoparticles after molecular docking of literature-gathered drugs using MOE® software package on molecularly simulated tripalmitin matrices using GROMACS®. Consequently, Gaussian processes as a supervised machine learning artificial intelligence technique were used to correlate the drugs' descriptors (e.g. M.W., xLogP, TPSA and fragment complexity) with their molecular docking binding energies. Lower percentage bias was obtained compared to previous studies which allows the accurate estimation of the loaded mass of any drug in the investigated solid lipid nanoparticles by just projecting its chemical structure to its main features (descriptors). Copyright © 2016 Elsevier B.V. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Parsons, Neal, E-mail: neal.parsons@cd-adapco.com; Levin, Deborah A., E-mail: deblevin@illinois.edu [Department of Aerospace Engineering, The Pennsylvania State University, 233 Hammond Building, University Park, Pennsylvania 16802 (United States); Duin, Adri C. T. van, E-mail: acv13@engr.psu.edu [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, 136 Research East, University Park, Pennsylvania 16802 (United States); Zhu, Tong, E-mail: tvz5037@psu.edu [Department of Aerospace Engineering, The Pennsylvania State University, 136 Research East, University Park, Pennsylvania 16802 (United States)

    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 N{sub 2}({sup 1}Σ{sub g}{sup +})-N{sub 2}({sup 1}Σ{sub g}{sup +}) 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.

  14. Challenges in modelling homogeneous catalysis: new answers from ab initio molecular dynamics to the controversy over the Wacker process.

    Science.gov (United States)

    Stirling, András; Nair, Nisanth N; Lledós, Agustí; Ujaque, Gregori

    2014-07-21

    We present here a review of the mechanistic studies of the Wacker process stressing the long controversy about the key reaction steps. We give an overview of the previous experimental and theoretical studies on the topic. Then we describe the importance of the most recent Ab Initio Molecular Dynamics (AIMD) calculations in modelling organometallic reactivity in water. As a prototypical example of homogeneous catalytic reactions, the Wacker process poses serious challenges to modelling. The adequate description of the multiple role of the water solvent is very difficult by using static quantum chemical approaches including cluster and continuum solvent models. In contrast, such reaction systems are suitable for AIMD, and by combining with rare event sampling techniques, the method provides reaction mechanisms and the corresponding free energy profiles. The review also highlights how AIMD has helped to obtain a novel understanding of the mechanism and kinetics of the Wacker process.

  15. Theoretical Modeling of Molecular and Electron Kinetic Processes. Volume I. Theoretical Formulation of Analysis and Description of Computer Program.

    Science.gov (United States)

    1979-01-01

    to motivate the form of the results for inelastic binary collisions characterized by an isotropic scattering cross section. For an inelastic...which are excited or ionized by the e -beam . Strictly speaking , the reverse process for reaction (101. 1) should also be included, although its...ETC F/S 20/5 THEORETICAL MODELING OF MOLECULAR AND ELECTRON KINETIC PROCESS~— efl ~ (rj)JAN 79 W B LACINA NO OO i~—78—C—Ofl9UNCLASSIFIED NRTC—79—7R

  16. 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.

  17. The Curing Process of Epoxy/Amino-Functionalized MWCNTs: Calorimetry, Molecular Modelling, and Electron Microscopy

    Directory of Open Access Journals (Sweden)

    S. G. Prolongo

    2010-01-01

    Full Text Available Curing kinetic of an epoxy resin reinforced with amino-functionalized MWCNTs has been studied by DSC and the obtained results were explained through morphological studies carried out by SEM, TEM, FEG-SEM, and molecular simulation tools. The presence of MWCNTs in the curing reaction induces a retardation effect of curing reaction and a decrease of the reaction heat. Both are associated with the adsorption of curing agent molecules inside carbon nanotubes, which was proved through the application of electron microscopic techniques and molecular simulation tools. It has been also demonstrated that there is a chemical reaction between amine groups anchored to the nanotubes and oxirane rings of epoxy monomer, which improves the nanoreinforcement/matrix interfacial adhesion, appearing a chemical interphase. The glass transition temperature (Tg of epoxy matrix increases by the addition of MWCNTs due to the restriction of its mobility.

  18. 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.

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

    Science.gov (United States)

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

    2015-05-01

    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.

  20. Coupled molecular dynamics-Monte Carlo model to study the role of chemical processes during laser ablation of polymeric materials.

    Science.gov (United States)

    Prasad, Manish; Conforti, Patrick F; Garrison, Barbara J

    2007-08-28

    The coarse grained chemical reaction model is enhanced to build a molecular dynamics (MD) simulation framework with an embedded Monte Carlo (MC) based reaction scheme. The MC scheme utilizes predetermined reaction chemistry, energetics, and rate kinetics of materials to incorporate chemical reactions occurring in a substrate into the MD simulation. The kinetics information is utilized to set the probabilities for the types of reactions to perform based on radical survival times and reaction rates. Implementing a reaction involves changing the reactants species types which alters their interaction potentials and thus produces the required energy change. We discuss the application of this method to study the initiation of ultraviolet laser ablation in poly(methyl methacrylate). The use of this scheme enables the modeling of all possible photoexcitation pathways in the polymer. It also permits a direct study of the role of thermal, mechanical, and chemical processes that can set off ablation. We demonstrate that the role of laser induced heating, thermomechanical stresses, pressure wave formation and relaxation, and thermochemical decomposition of the polymer substrate can be investigated directly by suitably choosing the potential energy and chemical reaction energy landscape. The results highlight the usefulness of such a modeling approach by showing that various processes in polymer ablation are intricately linked leading to the transformation of the substrate and its ejection. The method, in principle, can be utilized to study systems where chemical reactions are expected to play a dominant role or interact strongly with other physical processes.

  1. 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.

  2. Modeling of molecular properties

    CERN Document Server

    Comba, Peter

    2011-01-01

    Molecular modeling encompasses applied theoretical approaches and computational techniques to model structures and properties of molecular compounds and materials in order to predict and / or interpret their properties. The modeling covered in this book ranges from methods for small chemical to large biological molecules and materials. With its comprehensive coverage of important research fields in molecular and materials science, this is a must-have for all organic, inorganic and biochemists as well as materials scientists interested in applied theoretical and computational chemistry. The 28

  3. Molecular Processes in Biological Thermosensation

    Directory of Open Access Journals (Sweden)

    I. Digel

    2008-01-01

    Full Text Available Since thermal gradients are almost everywhere, thermosensation could represent one of the oldest sensory transduction processes that evolved in organisms. There are many examples of temperature changes affecting the physiology of living cells. Almost all classes of biological macromolecules in a cell (nucleic acids, lipids, proteins can present a target of the temperature-related stimuli. This review discusses some features of different classes of temperature-sensing molecules as well as molecular and biological processes that involve thermosensation. Biochemical, structural, and thermodynamic approaches are applied in the paper to organize the existing knowledge on molecular mechanisms of thermosensation. Special attention is paid to the fact that thermosensitive function cannot be assigned to any particular functional group or spatial structure but is rather of universal nature. For instance, the complex of thermodynamic, structural, and functional features of hemoglobin family proteins suggests their possible accessory role as “molecular thermometers”.

  4. 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

  5. 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

  6. Multi-scale continuum modeling of biological processes: from molecular electro-diffusion to sub-cellular signaling transduction

    Science.gov (United States)

    Cheng, Y.; Kekenes-Huskey, P.; Hake, J. E.; Holst, M. J.; McCammon, J. A.; Michailova, A. P.

    2012-01-01

    This paper presents a brief review of multi-scale modeling at the molecular to cellular scale, with new results for heart muscle cells. A finite element-based simulation package (SMOL) was used to investigate the signaling transduction at molecular and sub-cellular scales (http://mccammon.ucsd.edu/smol/, http://FETK.org) by numerical solution of the time-dependent Smoluchowski equations and a reaction-diffusion system. At the molecular scale, SMOL has yielded experimentally validated estimates of the diffusion-limited association rates for the binding of acetylcholine to mouse acetylcholinesterase using crystallographic structural data. The predicted rate constants exhibit increasingly delayed steady-state times, with increasing ionic strength, and demonstrate the role of an enzyme's electrostatic potential in influencing ligand binding. At the sub-cellular scale, an extension of SMOL solves a nonlinear, reaction-diffusion system describing Ca2+ ligand buffering and diffusion in experimentally derived rodent ventricular myocyte geometries. Results reveal the important role of mobile and stationary Ca2+ buffers, including Ca2+ indicator dye. We found that alterations in Ca2+-binding and dissociation rates of troponin C (TnC) and total TnC concentration modulate sub-cellular Ca2+ signals. The model predicts that reduced off-rate in the whole troponin complex (TnC, TnI, TnT) versus reconstructed thin filaments (Tn, Tm, actin) alters cytosolic Ca2+ dynamics under control conditions or in disease-linked TnC mutations. The ultimate goal of these studies is to develop scalable methods and theories for the integration of molecular-scale information into simulations of cellular-scale systems.

  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. Estimating reaction constants by ab initio molecular modeling: a study on the oxidation of phenol to catechol and hydroquinone in advanced oxidation processes

    Directory of Open Access Journals (Sweden)

    B. Ramos

    2012-03-01

    Full Text Available Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.

  9. Molecular modeling of heterogeneous catalysis

    Science.gov (United States)

    Gislason, Jason Joseph

    A novel method for modeling heterogeneous catalysis was developed to further facilitate the understanding of catalytic reactor mechanisms. The method employs molecular dynamics simulations, statistical mechanical, and Unity Bond Index - Quadratic Exponential Potential (UBI-QEP) calculations to calculate the rate constants for reactions on metal surfaces. The primary difficulty of molecular dynamics simulations on metal surfaces has been the lack of reliable reactive potential energy surfaces. We have overcome this through the development of the Normalized Bond Index - Reactive Potential Function (NBI-RPF), which can accurately describe the reaction of adsorbates on metal surfaces. The first calculations of rate constants for a reaction on a metal surface using molecular dynamics simulations are presented. This method is applied to the determination of the mechanism for selective hydrogenation of acetylene in an ethylene rich flow. It was determined that the selectivity for acetylene hydrogenation is attributable to the higher reactivity of acetylene versus ethylene with respect to hydrogenation by molecular hydrogen. It was shown that hydrogen transfer from the carbonaceous layer to acetylene or ethylene is insignificant in the hydrogenation process. Molecular dynamics simulations and molecular mechanics calculations were used to determine the diffusion rate constants for dimethylnaphthalene isomers is mordenite. 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene were found to have similar diffusion rate constants. Grand canonical Monte Carlo calculations were performed on the competitive adsorption of 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene in type X zeolites exchanged individually with barium, calcium, potassium, and rubidium ions, calcium exchanged MCM-22, and hydrogen form mordenite (MOR), X zeolite, Y zeolite, hypBEB, ZSM- 12, and MCM-22. These calculations showed that barium exchanged X zeolite was the most selective toward 2

  10. 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.

  11. Molecular modelling and molecular dynamics of CFTR.

    Science.gov (United States)

    Callebaut, Isabelle; Hoffmann, Brice; Lehn, Pierre; Mornon, Jean-Paul

    2017-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic disease cystic fibrosis (CF). This review provides a global overview of the theoretical studies that have been performed so far, especially molecular modelling and molecular dynamics (MD) simulations. A special emphasis is placed on the CFTR-specific evolution of an ABC transporter framework towards a channel function, as well as on the understanding of the effects of disease-causing mutations and their specific modulation. This in silico work should help structure-based drug discovery and design, with a view to develop CFTR-specific pharmacotherapeutic approaches for the treatment of CF in the context of precision medicine.

  12. 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

  13. Thermal Characteristic Of Waste-Derived Hydroxyapatite (HA) Reinforced Ultra High Molecular Weight Polyethylene (UHMWPE) Composites For Fused Deposition Modeling (FDM) Process

    Science.gov (United States)

    Ansari, Mohamad Helmi Bin Md; Ibrahim, Mohd Halim Irwan Bin

    2017-01-01

    The present study provides a hydrothermal synthesis to obtain Hydroxyapatite (HA) powder from waste eggshells. This waste-derived HA has been characterized by X-ray diffraction, scanning electron microscopy and energy dispersive spectroscopy analysis. Waste-derived HA will be reinforced the Ultra-High Molecular Weight Polyethylene (UHMWPE) to develop a material composite for biomedical applications because of impressive mechanical properties owned by UHMWPE. Main challenger is UHMWPE has an ultra-high viscosity that renders continuous melt- state processes including one of the additive manufacturing processes which is Fused Deposition Modeling (FDM). To develop this material as feedstock in FDM process, it has been overcome by blending UHMWPE with waste-derived HA as filler. It exhibit the inclusion of 50wt% HA has reduced the degradation temperature in TGA and DSC thus enhances the processability in FDM process.

  14. 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.

  15. The investigation of nucleation rate and Johnson–Mehl–Avrami model of Pt–Pd alloy using molecular dynamics simulation during heat treatment processes

    Energy Technology Data Exchange (ETDEWEB)

    Celik, Fatih Ahmet, E-mail: facelik@beu.edu.tr

    2015-05-25

    Highlights: • The Avrami exponent increases with increasing annealing temperature. • Recrystallization occurrence is most likely at low temperatures. • Heat of fusion and critical nucleus radius are evaluated from the MD calculations. - Abstract: In this work, molecular dynamics simulation is carried out to investigate the crystallization kinetics at low cooling rate during solidification and at different annealing temperature from amorphous phase during annealing of Pt–Pd (Pt{sub 50}–Pd{sub 50}) model alloy system. The interfacial free energies, critical nucleus radius, total free energy from high temperatures to low temperatures during solidification of alloy system are also determined by molecular dynamics. At the same time, in order to define the nucleation rate, it is suggested a model based on nucleation theory. The local atomic bonded pairs and short range order properties in the model alloy have been analyzed using Honeycutt–Andersen (HA) method. The kinetic of the crystallization is described by Johnson, Mehl and Avrami (JMA) model, which has been analyzed with MD method by using the crystalline-type bonded pairs during annealing process. The results demonstrated that the crystal kinetics is very important to understand the process of homogenous nucleation formation and also, the results are consistent with the classical nucleation theory.

  16. Asphaltenes molecular modeling of Boscan crude oil

    Energy Technology Data Exchange (ETDEWEB)

    Kowalewski, I.; Vandenbroucke, M.; Behar, F.; Huc, A.Y. [Institut Francais du Petrole (IFP), 92 - Rueil-Malmaison (France); Faulon, J.L. [Sandia National Labs., Albuquerque, NM (United States); Taylor, M.J.

    1996-01-01

    The asphaltenes presence in the petrochemical feedstocks can disturb a lot some refining processes. In this context, some molecular models have been carried out to better understand the chemical structures of these asphaltenes molecules. The aim of this work is to estimate for the asphaltenes molecules the molecular models potentialities by the use of crystal structure elucidation programs (XMOL and SIGNATURE softwares) and by molecular simulation (INSIGHT II/DISCOVER softwares). In particular, two models of Boscan asphaltenes covalent molecules with intense reticulation degrees are discussed. (O.L.). 29 refs., 6 figs., 6 tabs.

  17. New Trends in Inspecting GPCR-ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova.

    Science.gov (United States)

    Ciancetta, Antonella; Cuzzolin, Alberto; Deganutti, Giuseppe; Sturlese, Mattia; Salmaso, Veronica; Cristiani, Andrea; Sabbadin, Davide; Moro, Stefano

    2016-09-01

    In this review, we present a survey of the recent advances carried out by our research groups in the field of ligand-GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand-protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.

  18. 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.

  19. Modeling the diffraction process of molecular crystals: computation of X-ray scattering intensities from ab initio electron densities

    NARCIS (Netherlands)

    Bruning, W.; Feil, D.

    1992-01-01

    An algorithm for calculating the scattering factors of atomic fragments in molecules as defined by the Stockholder recipe is presented. This method allows the calculation, from ab initio molecular wave functions, of structure factors including individual anisotropic atomic temperature factors. These

  20. 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 orde

  1. 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)

  2. Modelling the molecular mechanisms of aging

    Science.gov (United States)

    Mc Auley, Mark T.; Guimera, Alvaro Martinez; Hodgson, David; Mcdonald, Neil; Mooney, Kathleen M.; Morgan, Amy E.

    2017-01-01

    The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field. PMID:28096317

  3. Modelling the molecular mechanisms of aging.

    Science.gov (United States)

    Mc Auley, Mark T; Guimera, Alvaro Martinez; Hodgson, David; Mcdonald, Neil; Mooney, Kathleen M; Morgan, Amy E; Proctor, Carole J

    2017-02-28

    The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field.

  4. Statistical kinetics of processive molecular motors

    Science.gov (United States)

    Schnitzer, Mark Jacob

    1999-10-01

    We describe new theoretical and experimental tools for studying biological motor proteins at the single molecule scale. These tools enable measurements of molecular fuel economies, thereby providing insight into the pathways for conversion of biochemical energy into mechanical work. Kinesin is an ATP-dependent motor that moves processively along microtubules in discrete steps of 8 nm. How many molecules of ATP are hydrolysed per step? To determine this coupling ratio, we develop a fluctuation analysis, which relates the variance in records of mechanical displacement to the number of rate-limiting biochemical transitions in the engine cycle. Using fluctuation analysis and optical trapping interferometry, we determine that near zero load, single molecules of kinesin hydrolyse one ATP nucleotide per 8-nm step. To study kinesin behavior under load, we use a molecular force clamp, capable of maintaining constant loads on single kinesin motors moving processively. Analysis of records of motion under variable ATP concentrations and loads reveals that kinesin is a `tightly- coupled' motor, maintaining the 1:1 coupling ratio up to loads of ~ 5 pN. Moreover, a Michaelis-Menten analysis of velocity shows that the kinesin cycle contains at least two load- dependent transitions. The rate of one of these transitions affects ATP affinity, while the other does not. Therefore, the kinesin stall force must depend on the ATP concentration, as is demonstrated experimentally. These findings rule out existing theoretical models of kinesin motility. We develop a simple theoretical formalism describing a tightly-coupled mechanism for movement. This `energy-landscape' formalism quantitatively accounts for motile properties of RNA polymerase (RNAP), the enzyme that transcribes DNA into RNA. The shapes of RNAP force-velocity curves indicate that biochemical steps limiting transcription rates at low loads do not generate movement. Modeling suggests that high loads may halt RNAP by promoting a

  5. Molecular Modeling of the Chain Structures of Polybenzoxazines

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structures and properties of benzoxazines were investigated by virtue of molecular modeling at a molecular level. By means of Cerius software(version 4.0) supplied by Molecular Simulations Inc., the molecular mechanics and the molecular dynamics were performed under a PCFF force field. Five kinds of the polymeric chains of benzoxazines were created by using polymer builder and energy minimization. The relaxation process was conducted with both energy minimization and molecular dynamics.

  6. A Process Calculus for Molecular Interaction Maps

    Directory of Open Access Journals (Sweden)

    Roberto Barbuti

    2009-11-01

    Full Text Available We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs, a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks.

  7. A Process Calculus for Molecular Interaction Maps

    CERN Document Server

    Barbuti, Roberto; Milazzo, Paolo; Pardini, Giovanni; Rama, Aureliano; 10.4204/EPTCS.11.3

    2009-01-01

    We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs), a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks.

  8. 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.

  9. 1984 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.; Howard, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    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.

  10. 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.

  11. 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.

  12. Modeling hybrid perovskites by molecular dynamics.

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  13. Modeling hybrid perovskites by molecular dynamics

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  14. 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

  15. Product Development Process Modeling

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The use of Concurrent Engineering and other modern methods of product development and maintenance require that a large number of time-overlapped "processes" be performed by many people. However, successfully describing and optimizing these processes are becoming even more difficult to achieve. The perspective of industrial process theory (the definition of process) and the perspective of process implementation (process transition, accumulation, and inter-operations between processes) are used to survey the method used to build one base model (multi-view) process model.

  16. 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.

  17. Trends in Substitution Models of Molecular Evolution

    Directory of Open Access Journals (Sweden)

    Miguel eArenas

    2015-10-01

    Full Text Available Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost forty years after the development of first substitution models, highly sophisticated and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis.

  18. 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

  19. Product and Process Modelling

    DEFF Research Database (Denmark)

    Cameron, Ian T.; Gani, Rafiqul

    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. These ...

  20. Molecular modelling and drug design.

    Science.gov (United States)

    Meyer, E F; Swanson, S M; Williams, J A

    2000-03-01

    Drug design is a creative act of the same magnitude as composing, sculpting, or writing. The results can touch the lives of millions, but the creator is rarely one scientist and the rewards are distributed differently in the arts than in the sciences. The mechanisms of creativity are the same, i.e., incremental (plodding from darkness to dawn) or sudden (the "Eureka" effect) realization, but both are poorly understood. Creativity remains a human characteristic, but it is directly related to the tools available, especially computer software and hardware. While modelling software continues to mature, very little new has evolved in terms of hardware. Here, we discuss the history of molecular modelling and describe two novel modelling tools, a haptic device and a program, SCULPT, to generate solid molecular models at atomic resolution.

  1. Product and Process Modelling

    DEFF Research Database (Denmark)

    Cameron, Ian T.; Gani, Rafiqul

    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....... 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...... 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....

  2. Standard Model processes

    CERN Document Server

    Mangano, M.L.; Aguilar Saavedra, J.A.; 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.

  3. Molecular model for chirality phenomena.

    Science.gov (United States)

    Latinwo, Folarin; Stillinger, Frank H; Debenedetti, Pablo G

    2016-10-21

    Chirality is a hallmark feature for molecular recognition in biology and chemical physics. We present a three-dimensional continuum model for studying chirality phenomena in condensed phases using molecular simulations. Our model system is based upon a simple four-site molecule and incorporates non-trivial kinetic behavior, including the ability to switch chirality or racemize, as well as thermodynamics arising from an energetic preference for specific chiral interactions. In particular, we introduce a chiral renormalization parameter that can locally favor either homochiral or heterochiral configurations. Using this model, we explore a range of chirality-specific phenomena, including the kinetics of chiral inversion, the mechanism of spontaneous chiral symmetry breaking in the liquid, chirally driven liquid-liquid phase separation, and chiral crystal structures.

  4. Business Process Modeling: Blueprinting

    OpenAIRE

    Al-Fedaghi, Sabah

    2017-01-01

    This paper presents a flow-based methodology for capturing processes specified in business process modeling. The proposed methodology is demonstrated through re-modeling of an IBM Blueworks case study. While the Blueworks approach offers a well-proven tool in the field, this should not discourage workers from exploring other ways of thinking about effectively capturing processes. The diagrammatic representation presented here demonstrates a viable methodology in this context. It is hoped this...

  5. 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...... in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding...

  6. Optical models of the molecular atmosphere

    Science.gov (United States)

    Zuev, V. E.; Makushkin, Y. S.; Mitsel, A. A.; Ponomarev, Y. N.; Rudenko, V. P.; Firsov, K. M.

    1986-01-01

    The use of optical and laser methods for performing atmospheric investigations has stimulated the development of the optical models of the atmosphere. The principles of constructing the optical models of molecular atmosphere for radiation with different spectral composition (wideband, narrowband, and monochromatic) are considered in the case of linear and nonlinear absorptions. The example of the development of a system which provides for the modeling of the processes of optical-wave energy transfer in the atmosphere is presented. Its physical foundations, structure, programming software, and functioning were considered.

  7. Business Model Process Configurations

    DEFF Research Database (Denmark)

    Taran, Yariv; Nielsen, Christian; Thomsen, Peter

    2015-01-01

    Purpose – The paper aims: 1) To develop systematically a structural list of various business model process configuration and to group (deductively) these selected configurations in a structured typological categorization list. 2) To facilitate companies in the process of BM innovation......, 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...... method of data analysis. Findings - A comprehensive literature review and analysis resulted in a list of business model process configurations systematically organized under five classification groups, namely, revenue model; value proposition; value configuration; target customers, and strategic...

  8. WWTP Process Tank Modelling

    DEFF Research Database (Denmark)

    Laursen, Jesper

    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...

  9. 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...

  10. 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

  11. 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.

  12. Interactive Modelling of Molecular Structures

    Science.gov (United States)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  13. Simple model of a coherent molecular photocell

    Science.gov (United States)

    Ernzerhof, Matthias; Bélanger, Marc-André; Mayou, Didier; Nemati Aram, Tahereh

    2016-04-01

    Electron transport in molecular electronic devices is often dominated by a coherent mechanism in which the wave function extends from the left contact over the molecule to the right contact. If the device is exposed to light, photon absorption in the molecule might occur, turning the device into a molecular photocell. The photon absorption promotes an electron to higher energy levels and thus modifies the electron transmission probability through the device. A model for such a molecular photocell is presented that minimizes the complexity of the problem while providing a non-trivial description of the device mechanism. In particular, the role of the molecule in the photocell is investigated. It is described within the Hückel method and the source-sink potential approach [F. Goyer, M. Ernzerhof, and M. Zhuang, J. Chem. Phys. 126, 144104 (2007)] is used to eliminate the contacts in favor of complex-valued potentials. Furthermore, the photons are explicitly incorporated into the model through a second-quantized field. This facilitates the description of the photon absorption process with a stationary state calculation, where eigenvalues and eigenvectors are determined. The model developed is applied to various generic molecular photocells.

  14. Plasma detachment with molecular processes in divertor plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Ohno, N.; Ezumi, N.; Nishijima, D.; Takamura, S. [Dept. of Energy Engineering and Science, Graduate School of Engineering, Nagoya Univ., Nagoya, Aichi (Japan); Krasheninnikov, S.I.; Pigarov, A.Yu. [MIT Plasma Science and Fusion Center, Cambridge, MA (United States)

    2000-01-01

    Molecular processes in detached recombining plasmas are briefly reviewed. Several reactions with vibrationally excited hydrogen molecule related to recombination processes are described. Experimental evidence of molecular activated recombination observed in a linear divertor plasma simulator is also shown. (author)

  15. Molecular contamination modeling with CTSP

    Science.gov (United States)

    Brieda, Lubos

    2016-11-01

    Spacecraft instruments and thermal control surfaces are generally highly sensitive to molecular and particulate contamination. Despite best efforts taken during assembly, integration, and test, it is impossible to completely eliminate all sources of contaminants. Contamination transport analysis then becomes of critical importance. It can be used to predict the end of life accumulation on critical surfaces from prescribed source rates. Conversely, given allowable deposition levels, contamination modeling can be used to determine the cleanliness requirements to be met prior to launch. This paper describes a recently developed code for modeling contamination transport. Unlike other tools used by the community, CTSP concurrently traces many simulation particles through small time steps. This allows the code to visualize contaminant partial pressures, and to also include aerodynamic, gravitation, or electrostatic forces. The code is demonstrated by simulating an outgassing characterization test in a bell jar.

  16. Foam process models.

    Energy Technology Data Exchange (ETDEWEB)

    Moffat, Harry K.; Noble, David R.; Baer, Thomas A. (Procter & Gamble Co., West Chester, OH); Adolf, Douglas Brian; Rao, Rekha Ranjana; Mondy, Lisa Ann

    2008-09-01

    In this report, we summarize our work on developing a production level foam processing computational model suitable for predicting the self-expansion of foam in complex geometries. The model is based on a finite element representation of the equations of motion, with the movement of the free surface represented using the level set method, and has been implemented in SIERRA/ARIA. An empirically based time- and temperature-dependent density model is used to encapsulate the complex physics of foam nucleation and growth in a numerically tractable model. The change in density with time is at the heart of the foam self-expansion as it creates the motion of the foam. This continuum-level model uses an homogenized description of foam, which does not include the gas explicitly. Results from the model are compared to temperature-instrumented flow visualization experiments giving the location of the foam front as a function of time for our EFAR model system.

  17. Refactoring Process Models in Large Process Repositories.

    NARCIS (Netherlands)

    Weber, B.; Reichert, M.U.

    2008-01-01

    With the increasing adoption of process-aware information systems (PAIS), large process model repositories have emerged. Over time respective models have to be re-aligned to the real-world business processes through customization or adaptation. This bears the risk that model redundancies are introdu

  18. Refactoring Process Models in Large Process Repositories.

    NARCIS (Netherlands)

    Weber, B.; Reichert, M.U.

    With the increasing adoption of process-aware information systems (PAIS), large process model repositories have emerged. Over time respective models have to be re-aligned to the real-world business processes through customization or adaptation. This bears the risk that model redundancies are

  19. Informing mechanistic toxicology with computational molecular models.

    Science.gov (United States)

    Goldsmith, Michael R; Peterson, Shane D; Chang, Daniel T; Transue, Thomas R; Tornero-Velez, Rogelio; Tan, Yu-Mei; Dary, Curtis C

    2012-01-01

    Computational molecular models of chemicals interacting with biomolecular targets provides toxicologists a valuable, affordable, and sustainable source of in silico molecular level information that augments, enriches, and complements in vitro and in vivo efforts. From a molecular biophysical ansatz, we describe how 3D molecular modeling methods used to numerically evaluate the classical pair-wise potential at the chemical/biological interface can inform mechanism of action and the dose-response paradigm of modern toxicology. With an emphasis on molecular docking, 3D-QSAR and pharmacophore/toxicophore approaches, we demonstrate how these methods can be integrated with chemoinformatic and toxicogenomic efforts into a tiered computational toxicology workflow. We describe generalized protocols in which 3D computational molecular modeling is used to enhance our ability to predict and model the most relevant toxicokinetic, metabolic, and molecular toxicological endpoints, thereby accelerating the computational toxicology-driven basis of modern risk assessment while providing a starting point for rational sustainable molecular design.

  20. Molecular modeling of fluoropropene refrigerants.

    Science.gov (United States)

    Raabe, Gabriele

    2012-05-17

    Different fluoropropenes are currently considered as refrigerants, either as pure compounds or as components in low GWP (global warming potential) refrigerant mixtures. Due to their limited commercial production, experimental data for the thermophysical properties of fluoropropenes and their mixtures are in general rare, which hampers the exploration of their performance in technical applications. In principle, molecular simulation can be used to predict the relevant properties of refrigerants and refrigerant blends, provided that adequate intermolecular potential functions ("force fields") are available. In our earlier work (Raabe, G.; Maginn, E. J., J. Phys. Chem. B2010, 114, 10133-10142), we introduced a transferable force field for fluoropropenes comprising the compounds 3,3,3-trifluoro-1-propene (HFO-1243zf), 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), and hexafluoro-1-propene (HFO-1216). In this paper, we provide an extension of the force field model to the trans- and cis-1,3,3,3-tetrafluoro-1-propene (HFO-1234ze(E), HFO-1234ze) and the cis-1,2,3,3,3-pentafluoro-1-propene (HFO-1225ye(Z)) as well as revised simulation results for HFO-1216. We present Gibbs ensemble simulation results on the vapor pressures, saturated densities, and heats of vaporization of these compounds in comparison with experimental results. The simulation results show that the force field model enables reliable predictions of the properties of the different fluoropropenes and also reproduces well the differing vapor-liquid coexistence and vapor pressure curve of the cis- and trans-isomers of 1,3,3,3-tetrafluoro-1-propene, HFO-1234ze and HFO-1234ze(E). For these two isomers, we also present molecular dynamics simulation studies on their local structure.

  1. Molecular and dust scattering processes in astrophysical environments

    Science.gov (United States)

    Lupu, Roxana-Elena

    2009-06-01

    Understanding the formation and evolution of structure in the universe requires knowledge of the stellar energy output and its processing by gas and dust, evaluating the abundances of atomic and molecular species, and constraining thermodynamic parameters. Molecules, with molecular hydrogen and carbon monoxide being the most abundant, are a major component of the interstellar medium, and play an essential role in structure formation, by participating in gas cooling. Molecular fluorescence studies aim to provide a better interpretation of far-ultraviolet observations, constraining the molecular abundances and their interaction with the radiation field. The fluorescent emission lines offer a set of diagnostics for molecules complementary to absorption line spectroscopy and to observations at infrared and radio wavelengths, but are often poorly reproduced by models. In this work, I have developed and expanded fluorescence models for molecular hydrogen and carbon monoxide, and employed them in determining the spatial distribution of CO in cometary comae, in characterizing the effects of partial frequency redistribution for emission line scattering in planetary atmospheres and reflection nebulae, and in abundance determinations from Bowen fluorescence lines of H 2 in planetary nebulae. Follow-up optical and infrared observations were used in addition to UV data to diagnose molecular excitation, temperature, and spatial distribution in planetary nebula M27. Knowledge of the spectral energy distribution of the exciting stars in the far- ultraviolet is essential in constraining both the fluorescence models and understanding the scattering properties of nebular gas and dust. Sounding rocket observations of the Trifid and Orion nebulae, performed as part of this work, provided the necessary dynamic range and spatial resolution to measure simultaneously the nebular scattered light and the spectral energy distribution of the illuminating stars. These low extinction sight lines

  2. Platelet-rich plasma and skeletal muscle healing: a molecular analysis of the early phases of the regeneration process in an experimental animal model.

    Directory of Open Access Journals (Sweden)

    Ivan Dimauro

    Full Text Available Platelet-rich plasma (PRP has received increasing interest in applied medicine, being widely used in clinical practice with the aim of stimulating tissue healing. Despite the reported clinical success, there is still a lack of knowledge when considering the biological mechanisms at the base of the activity of PRP during the process of muscle healing. The aim of the present study was to verify whether the local delivery of PRP modulates specific molecular events involved in the early stages of the muscle regeneration process. The right flexor sublimis muscle of anesthetized Wistar rats was mechanically injured and either treated with PRP or received no treatment. At day 2 and 5 after surgery, the animals were sacrificed and the muscle samples evaluated at molecular levels. PRP treatment increased significantly the mRNA level of the pro-inflammatory cytokines IL-1β, and TGF-β1. This phenomenon induced an increased expression at mRNA and/or protein levels of several myogenic regulatory factors such as MyoD1, Myf5 and Pax7, as well as the muscular isoform of insulin-like growth factor1 (IGF-1Eb. No effect was detected with respect to VEGF-A expression. In addition, PRP application modulated the expression of miR-133a together with its known target serum response factor (SRF; increased the phosphorylation of αB-cristallin, with a significant improvement in several apoptotic parameters (NF-κB-p65 and caspase 3, indexes of augmented cell survival. The results of the present study indicates that the effect of PRP in skeletal muscle injury repair is due both to the modulation of the molecular mediators of the inflammatory and myogenic pathways, and to the control of secondary pathways such as those regulated by myomiRNAs and heat shock proteins, which contribute to proper and effective tissue regeneration.

  3. Platelet-rich plasma and skeletal muscle healing: a molecular analysis of the early phases of the regeneration process in an experimental animal model.

    Science.gov (United States)

    Dimauro, Ivan; Grasso, Loredana; Fittipaldi, Simona; Fantini, Cristina; Mercatelli, Neri; Racca, Silvia; Geuna, Stefano; Di Gianfrancesco, Alessia; Caporossi, Daniela; Pigozzi, Fabio; Borrione, Paolo

    2014-01-01

    Platelet-rich plasma (PRP) has received increasing interest in applied medicine, being widely used in clinical practice with the aim of stimulating tissue healing. Despite the reported clinical success, there is still a lack of knowledge when considering the biological mechanisms at the base of the activity of PRP during the process of muscle healing. The aim of the present study was to verify whether the local delivery of PRP modulates specific molecular events involved in the early stages of the muscle regeneration process. The right flexor sublimis muscle of anesthetized Wistar rats was mechanically injured and either treated with PRP or received no treatment. At day 2 and 5 after surgery, the animals were sacrificed and the muscle samples evaluated at molecular levels. PRP treatment increased significantly the mRNA level of the pro-inflammatory cytokines IL-1β, and TGF-β1. This phenomenon induced an increased expression at mRNA and/or protein levels of several myogenic regulatory factors such as MyoD1, Myf5 and Pax7, as well as the muscular isoform of insulin-like growth factor1 (IGF-1Eb). No effect was detected with respect to VEGF-A expression. In addition, PRP application modulated the expression of miR-133a together with its known target serum response factor (SRF); increased the phosphorylation of αB-cristallin, with a significant improvement in several apoptotic parameters (NF-κB-p65 and caspase 3), indexes of augmented cell survival. The results of the present study indicates that the effect of PRP in skeletal muscle injury repair is due both to the modulation of the molecular mediators of the inflammatory and myogenic pathways, and to the control of secondary pathways such as those regulated by myomiRNAs and heat shock proteins, which contribute to proper and effective tissue regeneration.

  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. 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,…

  6. Modeling and simulation of membrane process

    Science.gov (United States)

    Staszak, Maciej

    2017-06-01

    The article presents the different approaches to polymer membrane mathematical modeling. Traditional models based on experimental physicochemical correlations and balance models are presented in the first part. Quantum and molecular mechanics models are presented as they are more popular for polymer membranes in fuel cells. The initial part is enclosed by neural network models which found their use for different types of processes in polymer membranes. The second part is devoted to models of fluid dynamics. The computational fluid dynamics technique can be divided into solving of Navier-Stokes equations and into Boltzmann lattice models. Both approaches are presented focusing on membrane processes.

  7. 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)

  8. Molecular Modeling of Cardiac Troponin

    Science.gov (United States)

    Manning, Edward P.

    The cardiac thin filament regulates interactions of actin and myosin, the force-generating elements of muscular contraction. Over the past several decades many details have been discovered regarding the structure and function of the cardiac thin filament and its components, including cardiac troponin (cTn). My hypothesis is that signal propagation occurs between distant ends of the cardiac troponin complex through calcium-dependent alterations in the dynamics of cTn and tropomyosin (Tm). I propose a model of the thin filament that encompasses known structures of cTn, Tm and actin to gain insight into cardiac troponin's allosteric regulation of thin filament dynamics. By performing molecular dynamics simulations of cTn in conjunction with overlapping Tm in two conditions, with and without calcium bound to site II of cardiac troponin C (cTnC), I found a combination of calcium-dependent changes in secondary structure and dynamics throughout the cTn-Tm complex. I then applied this model to investigate familial hypertrophic cardiomyopathy (FHC), a disease of the sarcomere that is one of the most commonly occurring genetic causes of heart disease. Approximately 15% of known FHC-related mutations are found in cardiac troponin T (cTnT), most of which are in or flank the alpha-helical N-tail domain TNT1. TNT1 directly interacts with overlapping Tm coiled coils. Using this model I identified effects of TNT1 mutations that propagate to the cTn core where site II of cTnC, the regulatory site of calcium binding in the thin filament, is located. Specifically, I found that mutations in TNT1 alter the flexibility of TNT1 and that the flexibility of TNT1 is inversely proportional to the cooperativity of calcium activation of the thin filament. Further, I identified a pathway of propagation of structural and dynamic changes linking TNT1 to site II of cTnC. Mutation-induced changes at site II cTnC alter calcium coordination which corresponds to biophysical measurements of calcium

  9. Molecular Processing of Polymers with Cyclodextrins

    Science.gov (United States)

    Tonelli, Alan E.

    We summarize our recent studies employing the cyclic starch derivatives called cyclodextrins (CDs) to both nanostructure and functionalize polymers. Two important structural characteristics of CDs are taken advantage of to achieve these goals. First the ability of CDs to form noncovalent inclusion complexes (ICs) with a variety of guest molecules, including many polymers, by threading and inclusion into their relatively hydrophobic interior cavities, which are roughly cylindrical with diameters of ˜ 0.5 - 1.0 nm. α-, β-, and γ-CD contain six, seven, and eight α-1,4-linked glucose units, respectively. Warm water washing of polymer-CD-ICs containing polymer guests insoluble in water or treatment with amylase enzymes serves to remove the host CDs and results in the coalescence of the guest polymers into solid samples. When guest polymers are coalesced from the CD-ICs by removing their host CDs, they are observed to solidify with structures, morphologies, and even conformations that are distinct from bulk samples made from their solutions and melts. Molecularly mixed, intimate blends of two or more polymers that are normally immiscible can be obtained from their common CD-ICs, and the phase segregation of incompatible blocks can be controlled (suppressed or increased) in CD-IC coalesced block copolymers. In addition, additives may be more effectively delivered to polymers in the form of their crystalline CD-ICs or soluble CD-rotaxanes. Secondly, the many hydroxyl groups attached to the exterior rims of CDs, in addition to conferring water solubility, provide an opportunity to covalently bond them to polymers either during their syntheses or via postpolymerization reactions. Polymers containing CDs in their backbones or attached to their side chains are observed to more readily accept and retain additives, such as dyes and fragrances. Processing with CDs can serve to both nanostructure and functionalize polymers, leading to greater understanding of their behaviors

  10. Computerized molecular modeling of carbohydrates

    Science.gov (United States)

    Computerized molecular modleing continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to carbohydrate-inexperienced computational chemists. Its comments on various methods and studi...

  11. Modular process modeling for OPC

    Science.gov (United States)

    Keck, M. C.; Bodendorf, C.; Schmidtling, T.; Schlief, R.; Wildfeuer, R.; Zumpe, S.; Niehoff, M.

    2007-03-01

    Modular OPC modeling, describing mask, optics, resist and etch processes separately is an approach to keep efforts for OPC manageable. By exchanging single modules of a modular OPC model, a fast response to process changes during process development is possible. At the same time efforts can be reduced, since only single modular process steps have to be re-characterized as input for OPC modeling as the process is adjusted and optimized. Commercially available OPC tools for full chip processing typically make use of semi-empirical models. The goal of our work is to investigate to what extent these OPC tools can be applied for modeling of single process steps as separate modules. For an advanced gate level process we analyze the modeling accuracy over different process conditions (focus and dose) when combining models for each process step - optics, resist and etch - for differing single processes to a model describing the total process.

  12. 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.

  13. Molecular processes and turbulent magnetic fields in the solar atmosphere

    Science.gov (United States)

    Shapiro, A. I.

    2008-08-01

    Coherent scattering in the solar atmosphere leads to the formation of the linearly polarized solar spectrum, just like Rayleigh scattering leads to the polarization of the blue sky. One of the most prominent features of the linearly polarized solar spectrum is the CN violet system as it is also in the unpolarized spectrum. This thesis is devoted to the modeling and interpretation of this system in both spectra and developing it into a very sensitive tool for studying the magnetic fields and the temperature structure of the solar atmosphere. The understanding of the solar magnetic field structure is very important as it is connected with and even controls most of the solar activity phenomena. Zeeman effect diagnostics allows to measure strong directed magnetic fields which only cover about 1% of the solar atmosphere. The remaining part is occupied by weak entangled magnetic fields with mixed polarity, which might significantly contribute to the overall solar magnetic energy. These fields are invisible to the Zeeman effect due to signal cancellation. Therefore the discovery of the linearly polarized solar spectrum opened a new epoch in solar physics. The polarization due to the scattering processes is modified by weak entangled magnetic fields via the Hanle effect and thus, provides us with a unique possibility to access and study such "hidden" magnetic fields. Molecular lines are very useful for probing magnetic fields as, due to their strong temperature sensitivity, different molecules sample different, narrow layers of the solar atmosphere. Therefore the extension of the atomic Hanle effect to molecular lines can provide the 3D structure of the solar turbulent magnetic field. Moreover, due to the broad range of magnetic sensitivities within narrow spectral regions molecular lines can be used for employing the differential Hanle effect technique, which allows dramatically reduced model dependence of the obtained magnetic field. This thesis consists of two main

  14. Molecular collision processes in the presence of picosecond laser pulses

    Science.gov (United States)

    Lee, H. W.; George, T. F.

    1979-01-01

    Radiative transitions in molecular collision processes taking place in the presence of picosecond pulses are studied within a semiclassical formalism. An expression for adiabatic potential surfaces in the electronic-field representation is obtained, which directly leads to the evaluation of transition probabilities. Calculations with a Landau-Zener-type model indicate that picosecond pulses can be much more effective in inducing transitions than a single long pulse of the same intensity and the same total energy, if the intensity is sufficiently high that the perturbation treatment is not valid.

  15. The pig as a model for excisional skin wound healing: characterization of the molecular and cellular biology, and bacteriology of the healing process.

    Science.gov (United States)

    Wang, J F; Olson, M E; Reno, C R; Wright, J B; Hart, D A

    2001-08-01

    A pig model of wound healing was developed by excision of 2-cm-diameter full thickness skin in young Yorkshire pigs. The results indicated that wound re-epithelialization in this animal model took an average of 20 days. Analysis of cellular change was assessed by use of DNA quantification and determination of apoptotic cells in tissue sections. The results indicate that RNA and DNA contents paralleled each other throughout the healing process, and observed changes in the pattern of RNA and DNA content of the scar tissues were consistent with cell loss due to apoptosis in this model. Expression of mRNA for relevant genes was assessed by use of semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis, using porcine specific primer sets and RNA isolated from normal skin and specimens obtained at various times after wounding. The mRNA values for tumor necrosis factor-alpha (TNF-alpha), connective tissue growth factor (CTGF), insulin-like growth factor II (IGF-II), and decorin were significantly high at specific times after wounding, but mRNA values for the transcription factors (c-fos and c-jun) were significantly decreased. Quantitative bacteriologic results indicated that the total bacterial count in this animal model reached 10(9) colony-forming units (CFU)/g, with the highest value at post-wounding day 7, and Pseudomonas aeruginosa and Staphylocococci aureus were the most common bacteria detected in this model. Further definition of this model should identify unique points in the healing process, and such information could lead to development of therapeutic interventions to improve skin wound healing.

  16. Molecular Modeling of Estrogen Receptor Using Molecular Operating Environment

    Science.gov (United States)

    Roy, Urmi; Luck, Linda A.

    2007-01-01

    Molecular modeling is pervasive in the pharmaceutical industry that employs many of our students from Biology, Chemistry and the interdisciplinary majors. To expose our students to this important aspect of their education we have incorporated a set of tutorials in our Biochemistry class. The present article describes one of our tutorials where…

  17. 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.

  18. Wiped-Film Molecular Distillation Process

    Institute of Scientific and Technical Information of China (English)

    LI Guobing; ZHANG Xubin; XU Chunjian; ZHOU Ming

    2005-01-01

    Based on the Bhatnagar-Gross-Krook equation, a new scheme of wiped-film molecular distillation for two components in the presenceof inert gas is developed. The equations in the scheme are solved numerically by the method of finite difference and iteration. The new scheme is used to simulate the molecular distillation of dibutyl phthalate and dibutyl sebacate (DBP-DBS) mixture. The effects of the inert gas pressure, the distance between the evaporation surface and condensation surface, the rotation rate of blade, and the number of blades on the distillation rate and separation factor are discussed.

  19. Molecular processes in plasmas collisions of charged particles with molecules

    CERN Document Server

    Itikawa, Yukikazu

    2007-01-01

    Molecular Processes in Plasmas describes elementary collision processes in plasmas, particularly those involving molecules or molecular ions. Those collision processes (called molecular processes) maintain plasmas, produce reactive species and emissions, and play a key role in energy balance in plasmas or more specifically in determining the energy distribution of plasma particles. Many books on plasma physics mention the elementary processes, but normally rather briefly. They only touch upon the general feature or fundamental concept of the collision processes. On the other hand, there are many books on atomic and molecular physics, but most of them are too general or too detailed to be useful to people in the application fields. The present book enumerates all the possible processes in the collisions of electrons, as well as ions, with molecules. For each process, a compact but informative description of its characteristics is given together with illustrative examples. Since the author has much experience a...

  20. Extended master equation models for molecular communication networks

    CERN Document Server

    Chou, Chun Tung

    2012-01-01

    We consider molecular communication networks consisting of transmitters and receivers distributed in a fluidic medium. In such networks, a transmitter sends one or more signalling molecules, which are diffused over the medium, to the receiver to realise the communication. In order to be able to engineer synthetic molecular communication networks, mathematical models for these networks are required. This paper proposes a new stochastic model for molecular communication networks called reaction-diffusion master equation with exogenous input (RDMEX). The key idea behind RDMEX is to model the transmitters as time sequences specify the emission patterns of signalling molecules, while diffusion in the medium and chemical reactions at the receivers are modelled as Markov processes using master equation. An advantage of RDMEX is that it can readily be used to model molecular communication networks with multiple transmitters and receivers. For the case where the reaction kinetics at the receivers is linear, we show ho...

  1. Molecular modeling of inelastic electron transport in molecular junctions

    Science.gov (United States)

    Jiang, Jun; Kula, Mathias; Luo, Yi

    2008-09-01

    A quantum chemical approach for the modeling of inelastic electron tunneling spectroscopy of molecular junctions based on scattering theory is presented. Within a harmonic approximation, the proposed method allows us to calculate the electron-vibration coupling strength analytically, which makes it applicable to many different systems. The calculated inelastic electron transport spectra are often in very good agreement with their experimental counterparts, allowing the revelation of detailed information about molecular conformations inside the junction, molecule-metal contact structures, and intermolecular interaction that is largely inaccessible experimentally.

  2. Molecular modeling of inelastic electron transport in molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Jun; Kula, Mathias; Luo Yi [Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm (Sweden)], E-mail: luo@kth.se

    2008-09-17

    A quantum chemical approach for the modeling of inelastic electron tunneling spectroscopy of molecular junctions based on scattering theory is presented. Within a harmonic approximation, the proposed method allows us to calculate the electron-vibration coupling strength analytically, which makes it applicable to many different systems. The calculated inelastic electron transport spectra are often in very good agreement with their experimental counterparts, allowing the revelation of detailed information about molecular conformations inside the junction, molecule-metal contact structures, and intermolecular interaction that is largely inaccessible experimentally.

  3. Modeling the Hydrogen Bond within Molecular Dynamics

    Science.gov (United States)

    Lykos, Peter

    2004-01-01

    The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.

  4. On Activity modelling in process modeling

    Directory of Open Access Journals (Sweden)

    Dorel Aiordachioaie

    2001-12-01

    Full Text Available The paper is looking to the dynamic feature of the meta-models of the process modelling process, the time. Some principles are considered and discussed as main dimensions of any modelling activity: the compatibility of the substances, the equipresence of phenomena and the solvability of the model. The activity models are considered and represented at meta-level.

  5. 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.

  6. Auditory processing models

    DEFF Research Database (Denmark)

    Dau, Torsten

    2008-01-01

    The Handbook of Signal Processing in Acoustics will compile the techniques and applications of signal processing as they are used in the many varied areas of Acoustics. The Handbook will emphasize the interdisciplinary nature of signal processing in acoustics. Each Section of the Handbook will pr...

  7. 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...... 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...... 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...

  8. 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

  9. 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).

  10. Acetylcholine molecular arrays enable quantum information processing

    Science.gov (United States)

    Tamulis, Arvydas; Majauskaite, Kristina; Talaikis, Martynas; Zborowski, Krzysztof; Kairys, Visvaldas

    2017-09-01

    We have found self-assembly of four neurotransmitter acetylcholine (ACh) molecular complexes in a water molecules environment by using geometry optimization with DFT B97d method. These complexes organizes to regular arrays of ACh molecules possessing electronic spins, i.e. quantum information bits. These spin arrays could potentially be controlled by the application of a non-uniform external magnetic field. The proper sequence of resonant electromagnetic pulses would then drive all the spin groups into the 3-spin entangled state and proceed large scale quantum information bits.

  11. Molecular Thermodynamic Model for Associated Polymers

    Institute of Scientific and Technical Information of China (English)

    PENG,Chang-Jun(彭昌军); LIU,Hong-Lai(刘洪来); HU,Ying(胡英)

    2001-01-01

    A molecular thermedynmnic model for homopolyrner and copolymer systems with association segments was establishedby adopting the molecular thermodynamic model for hard-sphere-chain fluid as a reference,a perturbation term contributed by the square-well potential and a contribution of as sociation terms.The latter considers the multi-associated-seg-ments in a chain-like molecule based on the shield-sticky model of chemical association.The model can be used to correlate the pVT of melten homopolymer and copolymer.Good agree-ments with experimental data have been obtained.

  12. Propagation Modeling and Analysis of Molecular Motors in Molecular Communication.

    Science.gov (United States)

    Chahibi, Youssef; Akyildiz, Ian F; Balasingham, Ilangko

    2016-12-01

    Molecular motor networks (MMNs) are networks constructed from molecular motors to enable nanomachines to perform coordinated tasks of sensing, computing, and actuation at the nano- and micro- scales. Living cells are naturally enabled with this same mechanism to establish point-to-point communication between different locations inside the cell. Similar to a railway system, the cytoplasm contains an intricate infrastructure of tracks, named microtubules, interconnecting different internal components of the cell. Motor proteins, such as kinesin and dynein, are able to travel along these tracks directionally, carrying with them large molecules that would otherwise be unreliably transported across the cytoplasm using free diffusion. Molecular communication has been previously proposed for the design and study of MMNs. However, the topological aspects of MMNs, including the effects of branches, have been ignored in the existing studies. In this paper, a physical end-to-end model for MMNs is developed, considering the location of the transmitter node, the network topology, and the receiver nodes. The end-to-end gain and group delay are considered as the performance measures, and analytical expressions for them are derived. The analytical model is validated by Monte-Carlo simulations and the performance of MMNs is analyzed numerically. It is shown that, depending on their nature and position, MMN nodes create impedance effects that are critical for the overall performance. This model could be applied to assist the design of artificial MMNs and to study cargo transport in neurofilaments to elucidate brain diseases related to microtubule jamming.

  13. Structures in Molecular Clouds: Modeling

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-04-20

    We attempt to predict the observed morphology, column density and velocity gradient of Pillar II of the Eagle Nebula, using Rayleigh Taylor (RT) models in which growth is seeded by an initial perturbation in density or in shape of the illuminated surface, and cometary models in which structure is arises from a initially spherical cloud with a dense core. Attempting to mitigate suppression of RT growth by recombination, we use a large cylindrical model volume containing the illuminating source and the self-consistently evolving ablated outflow and the photon flux field, and use initial clouds with finite lateral extent. An RT model shows no growth, while a cometary model appears to be more successful at reproducing observations.

  14. Molecular Thermodynamics for Chemical Process Design

    Science.gov (United States)

    Prausnitz, J. M.

    1976-01-01

    Discusses that aspect of thermodynamics which is particularly important in chemical process design: the calculation of the equilibrium properties of fluid mixtures, especially as required in phase-separation operations. (MLH)

  15. GREAT Process Modeller user manual

    OpenAIRE

    Rueda, Urko; España, Sergio; Ruiz, Marcela

    2015-01-01

    This report contains instructions to install, uninstall and use GREAT Process Modeller, a tool that supports Communication Analysis, a communication-oriented business process modelling method. GREAT allows creating communicative event diagrams (i.e. business process models), specifying message structures (which describe the messages associated to each communicative event), and automatically generating a class diagram (representing the data model of an information system that would support suc...

  16. INNOVATION PROCESS MODELLING

    Directory of Open Access Journals (Sweden)

    JANUSZ K. GRABARA

    2011-01-01

    Full Text Available Modelling phenomena in accordance with the structural approach enables one to simplify the observed relations and to present the classification grounds. An example may be a model of organisational structure identifying the logical relations between particular units and presenting the division of authority, work.

  17. Adaptive modelling of structured molecular representations for toxicity prediction

    Science.gov (United States)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  18. 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.

  19. Exploring Organic Mechanistic Puzzles with Molecular Modeling

    Science.gov (United States)

    Horowitz, Gail; Schwartz, Gary

    2004-01-01

    The molecular modeling was used to reinforce more general skills such as deducing and drawing reaction mechanisms, analyzing reaction kinetics and thermodynamics and drawing reaction coordinate energy diagrams. This modeling was done through the design of mechanistic puzzles, involving reactions not familiar to the students.

  20. Learning generative models of molecular dynamics.

    Science.gov (United States)

    Razavian, Narges Sharif; Kamisetty, Hetunandan; Langmead, Christopher J

    2012-01-01

    We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 regularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories.

  1. Modeling molecular hyperfine line emission

    CERN Document Server

    Keto, Eric

    2010-01-01

    In this paper we discuss two approximate methods previously suggested for modeling hyperfine spectral line emission for molecules whose collisional transitions rates between hyperfine levels are unknown. Hyperfine structure is seen in the rotational spectra of many commonly observed molecules such as HCN, HNC, NH3, N2H+, and C17O. The intensities of these spectral lines can be modeled by numerical techniques such as Lambda-iteration that alternately solve the equations of statistical equilibrium and the equation of radiative transfer. However, these calculations require knowledge of both the radiative and collisional rates for all transitions. For most commonly observed radio frequency spectral lines, only the net collisional rates between rotational levels are known. For such cases, two approximate methods have been suggested. The first method, hyperfine statistical equilibrium (HSE), distributes the hyperfine level populations according to their statistical weight, but allows the population of the rotationa...

  2. BPMN Impact on Process Modeling

    OpenAIRE

    Polak, Przemyslaw

    2013-01-01

    Recent years have seen huge rise in popularity of BPMN in the area of business process modeling, especially among business analysts. This notation has characteristics that distinguish it significantly from the previously popular process modeling notations, such as EPC. The article contains the analysis of some important characteristics of BPMN and provides author’s conclusions on the impact that the popularity and specificity of BPMN can have on the practice of process modeling. Author's obse...

  3. 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.

  4. Radiolysis Process Model

    Energy Technology Data Exchange (ETDEWEB)

    Buck, Edgar C.; Wittman, Richard S.; Skomurski, Frances N.; Cantrell, Kirk J.; McNamara, Bruce K.; Soderquist, Chuck Z.

    2012-07-17

    Assessing the performance of spent (used) nuclear fuel in geological repository requires quantification of time-dependent phenomena that may influence its behavior on a time-scale up to millions of years. A high-level waste repository environment will be a dynamic redox system because of the time-dependent generation of radiolytic oxidants and reductants and the corrosion of Fe-bearing canister materials. One major difference between used fuel and natural analogues, including unirradiated UO2, is the intense radiolytic field. The radiation emitted by used fuel can produce radiolysis products in the presence of water vapor or a thin-film of water (including OH• and H• radicals, O2-, eaq, H2O2, H2, and O2) that may increase the waste form degradation rate and change radionuclide behavior. H2O2 is the dominant oxidant for spent nuclear fuel in an O2 depleted water environment, the most sensitive parameters have been identified with respect to predictions of a radiolysis model under typical conditions. As compared with the full model with about 100 reactions it was found that only 30-40 of the reactions are required to determine [H2O2] to one part in 10–5 and to preserve most of the predictions for major species. This allows a systematic approach for model simplification and offers guidance in designing experiments for validation.

  5. 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.

  6. 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.

  7. Modeling Software Processes and Artifacts

    NARCIS (Netherlands)

    van den Berg, Klaas; Bosch, Jan; Mitchell, Stuart

    1997-01-01

    The workshop on Modeling Software Processes and Artifacts explored the application of object technology in process modeling. After the introduction and the invited lecture, a number of participants presented their position papers. First, an overview is given on some background work, and the aims, as

  8. Molecular recognition effects in atomistic models of imprinted polymers.

    Science.gov (United States)

    Dourado, Eduardo M A; Herdes, Carmelo; van Tassel, Paul R; Sarkisov, Lev

    2011-01-01

    In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  9. Molecular Recognition Effects in Atomistic Models of Imprinted Polymers

    Directory of Open Access Journals (Sweden)

    Carmelo Herdes

    2011-07-01

    Full Text Available In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  10. Multi-enzyme Process Modeling

    DEFF Research Database (Denmark)

    Andrade Santacoloma, Paloma de Gracia

    . 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......The subject of this thesis is to develop a methodological framework that can systematically guide mathematical model building for better understanding of multi-enzyme processes. In this way, opportunities for process improvements can be identified by analyzing simulations of either existing...... in the scientific literature. Reliable mathematical models of such multi-catalytic schemes can exploit the potential benefit of these processes. In this way, the best outcome of the process can be obtained understanding the types of modification that are required for process optimization. An effective evaluation...

  11. 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.

  12. Molecular Modeling of Interfacial Behaviors of Nanomaterials

    Science.gov (United States)

    2007-05-01

    15 L. Huang, and J. Kieffer, ’Molecular Dynamics Study of Cristobalite Silica Using a Charge Transfer Three- Body Potential Model,’ J. Chem. Phys...8217 Nano Letters in preparation (2006). 20 J. Zhou, and J. Kieffer, ’Simulation of Hexane-Functionalized Polyhedral Oligomeric Silses- quioxanes,’ J

  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

    Science.gov (United States)

    Rashid, Nahrul Khair Alang Md

    2015-04-01

    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. 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. Molecular simulation and modeling of complex I.

    Science.gov (United States)

    Hummer, Gerhard; Wikström, Mårten

    2016-07-01

    Molecular modeling and molecular dynamics simulations play an important role in the functional characterization of complex I. With its large size and complicated function, linking quinone reduction to proton pumping across a membrane, complex I poses unique modeling challenges. Nonetheless, simulations have already helped in the identification of possible proton transfer pathways. Simulations have also shed light on the coupling between electron and proton transfer, thus pointing the way in the search for the mechanistic principles underlying the proton pump. In addition to reviewing what has already been achieved in complex I modeling, we aim here to identify pressing issues and to provide guidance for future research to harness the power of modeling in the functional characterization of complex I. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Molecular dynamics model of dimethyl ether

    Energy Technology Data Exchange (ETDEWEB)

    Lin, B.; Halley, W.J. [Univ. of Minnesota, Minneapolis, MN (United States)

    1995-11-02

    We report a molecular dynamics model of the monomeric liquid dimethyl ether. The united atom approach is used to treat CH{sub 3} groups as point source centers. Partial charges are derived from the experimental dipole moment. Harmonic force constants are used for intramolecular interactions, and their values are so chosen that the model`s fundamental frequencies agree with experimental results. Because we are interested in solvation properties, the model contains flexible molecules, allowing molecular distortion and internal dynamical quantities. We report radial distribution functions and the static structure factors as well as some dynamical quantities such as the dynamical structure factor, infrared absorption, and Raman scattering spectra. Calculated results agree reasonably well with experimental and other simulation results. 25 refs., 8 figs., 1 tab.

  18. Molecular Models for Conductance in Junctions and Electrochemical Electron Transfer

    Science.gov (United States)

    Mazinani, Shobeir Khezr Seddigh

    This thesis develops molecular models for electron transport in molecular junctions and intra-molecular electron transfer. The goal is to identify molecular descriptors that afford a substantial simplification of these electronic processes. First, the connection between static molecular polarizability and the molecular conductance is examined. A correlation emerges whereby the measured conductance of a tunneling junction decreases as a function of the calculated molecular polarizability for several systems, a result consistent with the idea of a molecule as a polarizable dielectric. A model based on a macroscopic extension of the Clausius-Mossotti equation to the molecular domain and Simmon's tunneling model is developed to explain this correlation. Despite the simplicity of the theory, it paves the way for further experimental, conceptual and theoretical developments in the use of molecular descriptors to describe both conductance and electron transfer. Second, the conductance of several biologically relevant, weakly bonded, hydrogen-bonded systems is systematically investigated. While there is no correlation between hydrogen bond strength and conductance, the results indicate a relation between the conductance and atomic polarizability of the hydrogen bond acceptor atom. The relevance of these results to electron transfer in biological systems is discussed. Hydrogen production and oxidation using catalysts inspired by hydrogenases provides a more sustainable alternative to the use of precious metals. To understand electrochemical and spectroscopic properties of a collection of Fe and Ni mimics of hydrogenases, high-level density functional theory calculations are described. The results, based on a detailed analysis of the energies, charges and molecular orbitals of these metal complexes, indicate the importance of geometric constraints imposed by the ligand on molecular properties such as acidity and electrocatalytic activity. Based on model calculations of

  19. Molecular Modeling of Solid Fluid Phase Behavior

    Energy Technology Data Exchange (ETDEWEB)

    Peter A. Monson

    2007-12-20

    This report gives a summary of the achievements under DOE contract No. DOE/ER/14150 during the period September 1, 1990 to December 31, 2007. This project was concerned with the molecular modeling of solid-fluid equilibrium. The focus was on understanding how solid-fluid and solid-solid phase behavior are related to molecular structure, and the research program made a seminal contribution in this area. The project led to 34 journal articles, including a comprehensive review article published in Advances in Chemical Physics. The DOE funding supported the work of 5 Ph.D. students, 2 M.S. students and 5 postdoctoral researchers.

  20. 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...... 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......-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...

  1. 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...... 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 analyze specifications obtained via a simple deterministic time-change of a homogeneous Lévy 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 all the single names included in the iTraxx Europe index. The performances are compared with those of the classical CIR...

  2. Integrated Multiscale Modeling of Molecular Computing Devices

    Energy Technology Data Exchange (ETDEWEB)

    Jerzy Bernholc

    2011-02-03

    photolithography will some day reach a miniaturization limit, forcing designers of Si-based electronics to pursue increased performance by other means. Any other alternative approach would have the unenviable task of matching the ability of Si technology to pack more than a billion interconnected and addressable devices on a chip the size of a thumbnail. Nevertheless, the prospects of developing alternative approaches to fabricate electronic devices have spurred an ever-increasing pace of fundamental research. One of the promising possibilities is molecular electronics (ME), self-assembled molecular-based electronic systems composed of single-molecule devices in ultra dense, ultra fast molecular-sized components. This project focused on developing accurate, reliable theoretical modeling capabilities for describing molecular electronics devices. The participants in the project are given in Table 1. The primary outcomes of this fundamental computational science grant are publications in the open scientific literature. As listed below, 62 papers have been published from this project. In addition, the research has also been the subject of more than 100 invited talks at conferences, including several plenary or keynote lectures. Many of the goals of the original proposal were completed. Specifically, the multi-disciplinary group developed a unique set of capabilities and tools for investigating electron transport in fabricated and self-assembled nanostructures at multiple length and time scales.

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

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard

    changes in molecular structure, vibrations and solvation. In this thesis, we employ our recently developed Quantum-/Molecular -Mechanical Direct Dynamics method to do simulations of transition metal complexes in solution, to uncover their energy dissipation channels, and how they are affected...... quantum mechanic descriptions, to ascertain the accuracy of the quantum model in the Direct Dynamics simulations. We then test - and improve - the framework for calculating the experimental X-ray Diffuse Scattering Difference signal from (any kind of) Molecular Dynamics (MD) simulations. Comparisons......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...

  4. Extended master equation models for molecular communication networks.

    Science.gov (United States)

    Chou, Chun Tung

    2013-06-01

    We consider molecular communication networks consisting of transmitters and receivers distributed in a fluidic medium. In such networks, a transmitter sends one or more signaling molecules, which are diffused over the medium, to the receiver to realize the communication. In order to be able to engineer synthetic molecular communication networks, mathematical models for these networks are required. This paper proposes a new stochastic model for molecular communication networks called reaction-diffusion master equation with exogenous input (RDMEX). The key idea behind RDMEX is to model the transmitters as time series of signaling molecule counts, while diffusion in the medium and chemical reactions at the receivers are modeled as Markov processes using master equation. An advantage of RDMEX is that it can readily be used to model molecular communication networks with multiple transmitters and receivers. For the case where the reaction kinetics at the receivers is linear, we show how RDMEX can be used to determine the mean and covariance of the receiver output signals, and derive closed-form expressions for the mean receiver output signal of the RDMEX model. These closed-form expressions reveal that the output signal of a receiver can be affected by the presence of other receivers. Numerical examples are provided to demonstrate the properties of the model.

  5. 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 sp2/sp3 hybridization ratio, entails a crossover from plastic-to-brittle rupture mechanisms.

  6. 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.

  7. Molecular model of the neural dopamine transporter

    Science.gov (United States)

    Ravna, Aina Westrheim; Sylte, Ingebrigt; Dahl, Svein G.

    2003-05-01

    The dopamine transporter (DAT) regulates the action of dopamine by reuptake of the neurotransmitter into presynaptic neurons, and is the main molecular target of amphetamines and cocaine. DAT and the Na+/H+ antiporter (NhaA) are secondary transporter proteins that carry small molecules across a cell membrane against a concentration gradient, using ion gradients as energy source. A 3-dimensional projection map of the E. coli NhaA has confirmed a topology of 12 membrane spanning domains, and was previously used to construct a 3-dimensional NhaA model with 12 trans-membrane α-helices (TMHs). The NhaA model, and site directed mutagenesis data on DAT, were used to construct a detailed 3-dimensional DAT model using interactive molecular graphics and empiric force field calculations. The model proposes a dopamine transport mechanism involving TMHs 1, 3, 4, 5, 7 and 11. Asp79, Tyr252 and Tyr274 were the primary cocaine binding residues. Binding of cocaine or its analogue, (-)-2β-carbomethoxy-3β-(4-fluorophenyl)tropane (CFT), seemed to lock the transporter in an inactive state, and thus inhibit dopamine transport. The present model may be used to design further experimental studies of the molecular structure and mechanisms of DAT and other secondary transporter proteins.

  8. Modelling of CWS combustion process

    Science.gov (United States)

    Rybenko, I. A.; Ermakova, L. A.

    2016-10-01

    The paper considers the combustion process of coal water slurry (CWS) drops. The physico-chemical process scheme consisting of several independent parallel-sequential stages is offered. This scheme of drops combustion process is proved by the particle size distribution test and research stereomicroscopic analysis of combustion products. The results of mathematical modelling and optimization of stationary regimes of CWS combustion are provided. During modeling the problem of defining possible equilibrium composition of products, which can be obtained as a result of CWS combustion processes at different temperatures, is solved.

  9. 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.

  10. 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.

  11. Molecular Dynamics Modeling of Hydrated Calcium-Silicate-Hydrate (CSH) Cement Molecular Structure

    Science.gov (United States)

    2014-08-30

    properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown...public release; distribution is unlimited. Molecular Dynamics Modeling of Hydrated Calcium-Silicate- Hydrate (CSH) Cement Molecular Structure The views... Cement Molecular Structure Report Title Multi-scale modeling of complex material systems requires starting from fundamental building blocks to

  12. 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)

  13. A Stochastic Markov Model for Coordinated Molecular Motors

    CERN Document Server

    Materassi, Donatello; Salapaka, Murti V

    2010-01-01

    Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such proteins is quite well understood when there is only one of them moving a cargo particle. Indeed, numerous in vitro experiments have been performed to derive accurate models for a single molecular motor. However, in vivo macromolecules are often carried by multiple motors. The main focus of this paper is to provide an analysis of the behavior of more molecular motors interacting together in order to improve the understanding of their actual physiological behavior. Previous studies provide analyses based on results obtained from Monte Carlo simulations. Different from these studies, we derive an equipollent probabilistic model to describe the dynamics of multiple proteins coupled together and provide an exact theoretical analysis. We are capable of obtaining the probability den...

  14. 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.

  15. Molecular modeling of PMR-15 polyimide

    Science.gov (United States)

    Kokkada Ravindranath, Pruthul

    PMR-15 polyimide is a polymer that is used as a matrix in composites. These composites with PMR-15 matrices are called advanced polymer matrix composite that is abundantly used in the aerospace and electronics industries because of its high temperature resistivity. Apart from having high temperature sustainability, PMR-15 composites also display good thermal-oxidative stability, mechanical properties, processability and low costs, which makes it a suitable material for manufacturing aircraft structures. PMR-15 uses the reverse Diels-Alder (RDA) method for crosslinking which provides it with the groundwork for its distinctive thermal stability and a range of 280--300°C use temperature. Regardless of such desirable properties, this material has a number of limitations that compromises its application on a large scale basis. PMR-15 composites has been known to be very vulnerable to micro-cracking at inter and intra-laminar cracking. But the major factor that hinders its demand is PMR-15's carcinogenic constituent, methylene dianilineme (MDA), also a liver toxin. The necessity of providing a safe working environment during its production adds up to the cost of this material. In this study, Molecular Dynamics and Energy Minimization techniques are utilized to simulate a structure of PMR-15 at a given density of 1.324 g/cc and an attempt to recreate the polyimide to reduce the number of experimental testing and hence subdue the health hazards as well as the cost involved in its production. Even though this study does not involve in validating any mechanical properties of the model, it could be used in future for the validation of its properties and further testing for different properties like aging, microcracking, creep etc.

  16. Model Checking of Boolean Process Models

    CERN Document Server

    Schneider, Christoph

    2011-01-01

    In the field of Business Process Management formal models for the control flow of business processes have been designed since more than 15 years. Which methods are best suited to verify the bulk of these models? The first step is to select a formal language which fixes the semantics of the models. We adopt the language of Boolean systems as reference language for Boolean process models. Boolean systems form a simple subclass of coloured Petri nets. Their characteristics are low tokens to model explicitly states with a subsequent skipping of activations and arbitrary logical rules of type AND, XOR, OR etc. to model the split and join of the control flow. We apply model checking as a verification method for the safeness and liveness of Boolean systems. Model checking of Boolean systems uses the elementary theory of propositional logic, no modal operators are needed. Our verification builds on a finite complete prefix of a certain T-system attached to the Boolean system. It splits the processes of the Boolean sy...

  17. Molecular dynamics modelling of solidification in metals

    Energy Technology Data Exchange (ETDEWEB)

    Boercker, D.B.; Belak, J.; Glosli, J. [Lawrence Livermore National Lab., CA (United States)

    1997-12-31

    Molecular dynamics modeling is used to study the solidification of metals at high pressure and temperature. Constant pressure MD is applied to a simulation cell initially filled with both solid and molten metal. The solid/liquid interface is tracked as a function of time, and the data are used to estimate growth rates of crystallites at high pressure and temperature in Ta and Mg.

  18. Molecular Composites: Processing, Post-Treatment and Mechanics

    Science.gov (United States)

    1987-07-01

    Mechanical Analyzer was used. 3.2 Articulated Matricies Several isotropic solutions (2.5, 3.0, and 3.2 wt%) were made from PBT36 and ABPBI in MSA at a fixed...built to address this problem. 22 3.3 Thermoplastic Matricies Thermoplastic matrix molecular composites could potentially be melt processed. This would...provide obvious advantages over PBT which is, of course, limited to solution processing. Several candidates were considered for matricies . The only re

  19. 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.

  20. Command Process Modeling & Risk Analysis

    Science.gov (United States)

    Meshkat, Leila

    2011-01-01

    Commanding Errors may be caused by a variety of root causes. It's important to understand the relative significance of each of these causes for making institutional investment decisions. One of these causes is the lack of standardized processes and procedures for command and control. We mitigate this problem by building periodic tables and models corresponding to key functions within it. These models include simulation analysis and probabilistic risk assessment models.

  1. 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...... 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.......Many production processes are carried out in stages. At the end of each stage, the production engineer can analyze the intermediate results and correct process parameters (variables) of the next stage. Both analysis of the process and correction to process parameters at next stage should...

  2. Computational molecular basis for improved silica surface complexation models

    Energy Technology Data Exchange (ETDEWEB)

    Sahai, Nita; Rosso, Kevin M.

    2006-06-06

    The acidity and reactivity of surface sites on amorphous and crystalline polymorphs of silica and other oxides control their thermodynamic stability and kinetic reactivity towards reactants in surface-controlled processes of environmental, industrial, biomedical and technological relevance. Recent advances in computational methodologies such as CPMD and increasing computer power combined with spectroscopic measurements are now making it possible to link, with an impressive degree of accuracy, the molecular-level description of these processes to phenomenological, surface complexation models The future challenge now lies in linking mesoscale properties at the nanometer scale to phenomenological models that will afford a more intuitive understanding of the systems under consideration.

  3. 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.

  4. Stochastic simulations of cargo transport by processive molecular motors.

    Science.gov (United States)

    Korn, Christian B; Klumpp, Stefan; Lipowsky, Reinhard; Schwarz, Ulrich S

    2009-12-28

    We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.

  5. Molecular processes from the AGB to the PN stage

    CERN Document Server

    Garcia-Hernandez, D A

    2011-01-01

    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 (~100-10.000 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.

  6. Computational molecular engineering as an emerging technology in process engineering

    CERN Document Server

    Horsch, Martin; Vrabec, Jadran; Hasse, Hans

    2013-01-01

    The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline of Computational Molecular Engineering (CME) which makes basic research in soft matter physics fruitful for industrial applications. Within the coming decade, major breakthroughs can be reached if a research focus is placed on processes at interfaces, combining aspects where an increase in the accessible length and time scales due to massively parallel high-performance computing will lead to particularly significant improvements.

  7. Molecular model with quantum mechanical bonding information.

    Science.gov (United States)

    Bohórquez, Hugo J; Boyd, Russell J; Matta, Chérif F

    2011-11-17

    The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.

  8. 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.

  9. 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.

  10. 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.

  11. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.

    Science.gov (United States)

    Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem

    2015-02-13

    Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  12. Modeling molecular mechanisms in the axon

    Science.gov (United States)

    de Rooij, R.; Miller, K. E.; Kuhl, E.

    2017-03-01

    Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that interprets cellular-level characteristics as emergent properties from molecular-level events. We create an axon model of discrete microtubules, which are connected to neighboring microtubules via discrete crosslinking mechanisms that obey a set of simple rules. We explore two types of mechanisms: passive and active crosslinking. Our passive and active simulations suggest that the stiffness and viscosity of the axon increase linearly with the crosslink density, and that both are highly sensitive to the crosslink detachment and reattachment times. Our model explains how active crosslinking with dynein motors generates internal stresses and actively drives axon elongation. We anticipate that our model will allow us to probe a wide variety of molecular phenomena—both in isolation and in interaction—to explore emergent cellular-level features under physiological and pathological conditions.

  13. A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

    Science.gov (United States)

    Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

    2010-01-01

    As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

  14. A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

    Science.gov (United States)

    Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

    2010-01-01

    As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

  15. Modeling of the Hydroentanglement Process

    Directory of Open Access Journals (Sweden)

    Ping Xiang

    2006-11-01

    Full Text Available Mechanical performance of hydroentangled nonwovens is determined by the degree of the fiber entanglement, which depends on parameters of the fibers, fiberweb, forming surface, water jet and the process speed. This paper develops a computational fluid dynamics model of the hydroentanglement process. Extensive comparison with experimental data showed that the degree of fiber entanglement is linearly related to flow vorticity in the fiberweb, which is induced by impinging water jets. The fiberweb is modeled as a porous material of uniform porosity and the actual geometry of forming wires is accounted for in the model. Simulation results are compared with experimental data for a Perfojet ® sleeve and four woven forming surfaces. Additionally, the model is used to predict the effect of fiberweb thickness on the degree of fiber entanglement for different forming surfaces.

  16. 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.

  17. Modified Claus process probabilistic model

    Energy Technology Data Exchange (ETDEWEB)

    Larraz Mora, R. [Chemical Engineering Dept., Univ. of La Laguna (Spain)

    2006-03-15

    A model is proposed for the simulation of an industrial Claus unit with a straight-through configuration and two catalytic reactors. Process plant design evaluations based on deterministic calculations does not take into account the uncertainties that are associated with the different input variables. A probabilistic simulation method was applied in the Claus model to obtain an impression of how some of these inaccuracies influences plant performance. (orig.)

  18. 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.

  19. Multi-enzyme Process Modeling

    DEFF Research Database (Denmark)

    Andrade Santacoloma, Paloma de Gracia

    The subject of this thesis is to develop a methodological framework that can systematically guide mathematical model building for better understanding of multi-enzyme processes. In this way, opportunities for process improvements can be identified by analyzing simulations of either existing...... 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...

  20. 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...

  1. Network Model Building (Process Mapping)

    OpenAIRE

    Blau, Gary; Yih, Yuehwern

    2004-01-01

    12 slides Provider Notes:See Project Planning Video (Windows Media) Posted at the bottom are Gary Blau's slides. Before watching, please note that "process mapping" and "modeling" are mentioned in the video and notes. Here they are meant to refer to the NSCORT "project plan"

  2. Modeling of the reburning process

    Energy Technology Data Exchange (ETDEWEB)

    Rota, R.; Bonini, F.; Servida, A.; Morbidelli, M.; Carra, S. [Politecnico di Milano, Milano (Italy). Dip. di Chimica Fisica Applicata

    1997-07-01

    Reburning has become a popular method of abating NO{sub x} emission in power plants. Its effectiveness is strongly affected by the interaction between gas phase chemistry and combustion chamber fluid dynamics. Both the mixing of the reactant streams and the elementary reactions in the gas phase control the overall kinetics of the process. This work developed a model coupling a detailed kinetic mechanism to a simplified description of the fluid dynamics of the reburning chamber. The model was checked with reference to experimental data from the literature. Detailed kinetic modeling was found to be essential to describe the reburning process, since the fluid dynamics of the reactor have a strong influence on reactions within. 20 refs., 9 figs., 3 tabs.

  3. Ultrafast molecular processes at the short-wavelength regime

    Science.gov (United States)

    Picon, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Rolles, D.; Marinelli, A.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-05-01

    Fundamental molecular processes that underlie chemical reactivity and biological processes typically involve intramolecular dynamics consisting of nuclear motion and the flow of charge and energy across atomic sites. Examples include photosynthesis, electron transfer in biomolecules, and molecular fragmentation. Molecular phenomena initiated by the absorption of an XUV/x-ray photon is one of the most challenging questions for the new generation of XUV/x-ray sources. New capabilities at accelerator-based are continuously being developed, being possible to nowadays generate two-color XUV/x-ray pulses with controlled time delay. The site-specificity of those photons allow the excitation of inner-shell electrons in a particular site of the molecule and, with a controlled time delay, the probing of the induced intramolecular dynamics in another site of the same molecule, opening the door to the unexplored field of intramolecular processes initiated by short-wavelength photons. Also, novel XUV/x-ray sources allow the generation of two-color pulses with a high spatio-temporal degree of coherence, suitable for quantum control schemes involving inner-shell electrons. In this talk, we present new theoretical and experimental results towards this direction. This work is funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division, under Contract No. DE-AC02-06CH11357.

  4. Modeling ion sensing in molecular electronics

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Caroline J.; Smeu, Manuel, E-mail: manuel.smeu@northwestern.edu; Ratner, Mark A., E-mail: ratner@northwestern.edu [Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 (United States)

    2014-02-07

    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{sup +}), alkali metal cations (M{sup +}), calcium ions (Ca{sup 2+}), and hydronium ions (H{sub 3}O{sup +}) 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{sub 9}H{sub 7}NS{sub 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{sup +} + QDT species containing monovalent cations, where M{sup +} = H{sup +}, Li{sup +}, Na{sup +}, or K{sup +}. 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.

  5. Molecular model and ReaxFF molecular dynamics simulation of coal vitrinite pyrolysis.

    Science.gov (United States)

    Li, Wu; Zhu, Yan-ming; Wang, Geoff; Wang, Yang; Liu, Yu

    2015-08-01

    Vitrinite in coal, the mainly generating methane maceral, plays an important role in hydrocarbon generation of coal. This study aims at obtaining products formation mechanism of vitrinite pyrolysis, and hence determining the chemical bond, molecular liquefaction activity, and reactions mechanism of methane and C2-4 during pyrolysis. The ReaxFF molecular dynamics (MD) simulation was carried out at temperature of 1500 K in order to investigate the mechanism of vitrinite pyrolysis. Initially, a minimum energy conformational structure model was constrained by a combination of elemental and carbon-13 nuclear magnetic resonance ((13)C NMR) literature data. The model analysis shows the chemical and physical parameters of vitrinite pyrolysis are broadly consistent with the experimental data. Based on the molecular model, ReaxFF MD simulations further provide information of unimolecule such as bond length, and chemical shift, and hence the total population and energy of main products. Molecules bond and pyrolysis fragments, based on active bond analyzed, revealed pyrolysis products of single vitrinite molecule with aliphatic C-C bond, especially ring and chain aliphatic as liquefaction activity. The molecular cell whose density is 0.9 g/cm(3) with lowest energy accords with the experimental density 1.33 g/cm(3). The content of main products after pyrolysis, classifying as CH4, H2O, and H2, was changed along with the increasing temperature. The gas molecule, fragments and generation pathways of CO2, H2, CH4, and C2H6 were also elucidated. These results show agreement with experimental observations, implying that MD simulation can provide reasonable explanation for the reaction processes involved in coal vitrinite pyrolysis. Thus the mechanism of coal hydrocarbon generation was revealed at the molecular level.

  6. RNA processing-associated molecular mechanisms of neurodegenerative diseases.

    Science.gov (United States)

    Tang, Anna Y

    2016-08-01

    Dysfunctions of RNA processing and mutations of RNA binding proteins (RBPs) play a fundamental role in the pathogenesis of many neurodegenerative diseases. To elucidate the function of RNA processing and RBPs mutations in neuronal cells and to increase our understanding on the pathogenic mechanisms of neurodegeneration, I have reviewed recent advances on RNA processing-associated molecular mechanisms of neurodegenerative diseases, including RBPs-mediated dysfunction of RNA processing, dysfunctional microRNA (miRNA)-based regulation of gene expression, and oxidative RNA modification. I have focused on neurodegeneration induced by RBPs mutations, by dysfunction of miRNA regulation, and by the oxidized RNAs within neurons, and discuss how these dysfunctions have pathologically contributed to neurodegenerative diseases. The advances overviewed above will be valuable to basic investigation and clinical application of target diagnostic tests and therapies.

  7. Natural language processing and visualization in the molecular imaging domain.

    Science.gov (United States)

    Tulipano, P Karina; Tao, Ying; Millar, William S; Zanzonico, Pat; Kolbert, Katherine; Xu, Hua; Yu, Hong; Chen, Lifeng; Lussier, Yves A; Friedman, Carol

    2007-06-01

    Molecular imaging is at the crossroads of genomic sciences and medical imaging. Information within the molecular imaging literature could be used to link to genomic and imaging information resources and to organize and index images in a way that is potentially useful to researchers. A number of natural language processing (NLP) systems are available to automatically extract information from genomic literature. One existing NLP system, known as BioMedLEE, automatically extracts biological information consisting of biomolecular substances and phenotypic data. This paper focuses on the adaptation, evaluation, and application of BioMedLEE to the molecular imaging domain. In order to adapt BioMedLEE for this domain, we extend an existing molecular imaging terminology and incorporate it into BioMedLEE. BioMedLEE's performance is assessed with a formal evaluation study. The system's performance, measured as recall and precision, is 0.74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information.

  8. A Molecular Model for Chiral Symmetry Breaking

    Science.gov (United States)

    Latinwo, Folarin; Stillinger, Frank; Debenedetti, Pablo

    In this work, we present a new class of molecular models for chiral phenomena in condensed matter systems. A key feature of these models is the ability of the four-site (tetramer) ``molecules'' to inter-convert between two distinct chiral forms (enantiomers). Given this feature, we use analytical theory and computer simulations to investigate the emergent chiral properties (including symmetry breaking) over a range of conditions. In particular, we consider the single-molecule level and condensed-phase behavior of our model system. Interestingly, we find that our liquid-phase predictions are in excellent agreement with recent experimental reports on chiral self-sorting in isotropic liquids. From this perspective, our model demonstrates accurate predictive capabilities, as well as a platform for understanding the microscopic origins of a variety of chiral phenomena. In a broader context, we anticipate that this class of models will be relevant to chirality-dominated areas such as the pharmaceutical industry and pre-biotic geochemistry.

  9. Animal models and conserved processes

    Directory of Open Access Journals (Sweden)

    Greek Ray

    2012-09-01

    Full Text Available Abstract Background The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation? Methods We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes. Results Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes. Conclusion We conclude that even the presence of conserved processes is

  10. 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).

  11. 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.)

  12. 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.

  13. Face Processing: Models For Recognition

    Science.gov (United States)

    Turk, Matthew A.; Pentland, Alexander P.

    1990-03-01

    The human ability to process faces is remarkable. We can identify perhaps thousands of faces learned throughout our lifetime and read facial expression to understand such subtle qualities as emotion. These skills are quite robust, despite sometimes large changes in the visual stimulus due to expression, aging, and distractions such as glasses or changes in hairstyle or facial hair. Computers which model and recognize faces will be useful in a variety of applications, including criminal identification, human-computer interface, and animation. We discuss models for representing faces and their applicability to the task of recognition, and present techniques for identifying faces and detecting eye blinks.

  14. Steady-State Process Modelling

    DEFF Research Database (Denmark)

    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.......This chapter covers the basic principles of steady state modelling and simulation using a number of case studies. Two principal approaches are illustrated that develop the unit operation models from first principles as well as through application of standard flowsheet simulators. The approaches...

  15. Switching Processes in Queueing Models

    CERN Document Server

    Anisimov, Vladimir V

    2008-01-01

    Switching processes, invented by the author in 1977, is the main tool used in the investigation of traffic problems from automotive to telecommunications. The title provides a new approach to low traffic problems based on the analysis of flows of rare events and queuing models. In the case of fast switching, averaging principle and diffusion approximation results are proved and applied to the investigation of transient phenomena for wide classes of overloading queuing networks.  The book is devoted to developing the asymptotic theory for the class of switching queuing models which covers  mode

  16. 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.

  17. Combustion Process Modelling and Control

    Directory of Open Access Journals (Sweden)

    Vladimír Maduda

    2007-10-01

    Full Text Available This paper deals with realization of combustion control system on programmable logic controllers. Control system design is based on analysis of the current state of combustion control systems in technological device of raw material processing area. Control system design is composed of two subsystems. First subsystem is represented by software system for measured data processing and for data processing from simulation of the combustion mathematical model. Outputs are parameters for setting of controller algorithms. Second subsystem consists from programme modules. The programme module is presented by specific control algorithm, for example proportional regulation, programmed proportional regulation, proportional regulation with correction on the oxygen in waste gas, and so on. According to the specific combustion control requirements it is possible built-up concrete control system by programme modules. The programme modules were programmed by Automation studio that is used for development, debugging and testing software for B&R controllers.

  18. Modeling of diffuse molecular gas applied to HD 102065 observations

    CERN Document Server

    Nehme, Cyrine; Boulanger, Francois; Forets, Guillaume Pineau des; Gry, Cecile

    2008-01-01

    Aims. We model a diffuse molecular cloud present along the line of sight to the star HD 102065. We compare our modeling with observations to test our understanding of physical conditions and chemistry in diffuse molecular clouds. Methods. We analyze an extensive set of spectroscopic observations which characterize the diffuse molecular cloud observed toward HD 102065. Absorption observations provide the extinction curve, H2, C I, CO, CH, and CH+ column densities and excitation. These data are complemented by observations of CII, CO and dust emission. Physical conditions are determined using the Meudon PDR model of UV illuminated gas. Results. We find that all observational results, except column densities of CH, CH+ and H2 in its excited (J > 2) levels, are consistent with a cloud model implying a Galactic radiation field (G~0.4 in Draine's unit), a density of 80 cm-3 and a temperature (60-80 K) set by the equilibrium between heating and cooling processes. To account for excited (J >2) H2 levels column densit...

  19. Molecular and Supramolecular Information Processing From Molecular Switches to Unconventional Computing

    CERN Document Server

    Katz, Evgeny

    2012-01-01

    Edited by a renowned and much cited chemist, this book covers the whole span of molecular computers that are based on non-biological systems. The contributions by all the major scientists in the field provide an excellent overview of the latest developments in this rapidly expanding area. A must-have for all researchers working on this very hot topic. Perfectly complements Biomolecular Information Processing, also by Prof. Katz, and available as a two-volume set.

  20. 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

  1. Modelling the Molecular Gas in NGC 6240

    CERN Document Server

    Tunnard, R; Garcia-Burillo, S; Carpio, J Graciá; Fuente, A; Tacconi, L; Neri, R; Usero, A

    2015-01-01

    We present the first observations of H$^{13}$CN$(1-0)$, H$^{13}$CO$^+(1-0)$ and SiO$(2-1)$ in NGC 6240, obtained with the IRAM PdBI. Combining a Markov Chain Monte Carlo (MCMC) code with Large Velocity Gradient (LVG) modelling we derive posterior probability density functions (pdfs) for the dense gas parameters, including mass$-$luminosity conversion factors, finding a large amount of dense molecular gas $(\\sim10^{10}M_\\odot)$ in cold, dense clouds ($T_k\\sim10$ K, $n_{{\\rm H}_2}\\sim10^6$ cm$^{-3}$) with a small volume filling factor $(<0.002)$. Including literature CO data we present simultaneously fitted multi-species, two phase models which spontaneously separate into a hot, diffuse phase ($\\log_{10}\\left(T_k / [{\\rm K}]\\right) = 3.2^{3.3}_{3.1}$, $\\log_{10}\\left(n_{{\\rm H}_2} / [{\\rm cm}^{-3}]\\right)=3.6^{3.8}_{3.5}$) and a cold, dense phase ($\\log_{10}\\left(T_k / [{\\rm K}]\\right) = 0.9^{0.9}_{0.8}$, $\\log_{10}\\left(n_{{\\rm H}_2} / [{\\rm cm}^{-3}]\\right)=6.6^{6.8}_{6.3}$). A restricted three phase model...

  2. 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...... 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...

  3. 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.

  4. 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.

  5. Process for attaching molecular wires and devices to carbon nanotubes and compositions thereof

    Science.gov (United States)

    Tour, James M. (Inventor); Bahr, Jeffrey L. (Inventor); Yang, Jiping (Inventor)

    2008-01-01

    The present invention is directed towards processes for covalently attaching molecular wires and molecular electronic devices to carbon nanotubes and compositions thereof. Such processes utilize diazonium chemistry to bring about this marriage of wire-like nanotubes with molecular wires and molecular electronic devices.

  6. Principles of polymer processing modelling

    Directory of Open Access Journals (Sweden)

    Agassant Jean-François

    2016-01-01

    Full Text Available Polymer processing involves three thermo-mechanical stages: Plastication of solid polymer granules or powder to an homogeneous fluid which is shaped under pressure in moulds or dies and finally cooled and eventually drawn to obtain the final plastic part. Physical properties of polymers (high viscosity, non-linear rheology, low thermal diffusivity as well as the complex shape of most plastic parts make modelling a challenge. Several examples (film blowing extrusion dies, injection moulding, blow moulding are presented and discussed.

  7. 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...

  8. A novel purification process for dodecanedioic acid by molecular distillation

    Institute of Scientific and Technical Information of China (English)

    Jiang Yu; Xigang Yuan; Aiwu Zeng

    2015-01-01

    A novel purification process is involved to obtain the high purity [N 99%(by mass)] dodecanedioic acid (DC12). It involves a re-crystal ization followed by molecular distil ation from the crude product. The objective of this study is to investigate general conditions, feed rate, distil ing temperature and vacuum, necessary for centrifugal distil-lation of DC12. Under the optimum conditions, distilling temperature 180 °C, pressure 30 Pa and feed flow rate 700 ml·h−1, the purity of DC12 in the residence reached 97.55%with a yield of 53.18%by the analysis of gas chromatography. Multiple-pass distillation made a considerable contribution by improving the purity to 99.22%. Additionally, the effect of pretreatment (re-crystallization) on distillation process was revealed through a series of comparative experiments.

  9. Molecular processes of transgenerational acclimation to a warming ocean

    Science.gov (United States)

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

    2015-12-01

    Some animals have the remarkable capacity to acclimate across generations to projected future climate change; 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.

  10. 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.

  11. A Review of Process Modeling Language Paradigms

    Institute of Scientific and Technical Information of China (English)

    MA Qin-hai; GUAN Zhi-min; LI Ying; ZHAO Xi-nan

    2002-01-01

    Process representation or modeling plays an important role in business process engineering.Process modeling languages can be evaluated by the extent to which they provide constructs useful for representing and reasoning about the aspects of a process, and subsequently are chosen for a certain purpose.This paper reviews process modeling language paradigms and points out their advantages and disadvantages.

  12. Integrated Multiscale Modeling of Molecular Computing Devices

    Energy Technology Data Exchange (ETDEWEB)

    Weinan E

    2012-03-29

    The main bottleneck in modeling transport in molecular devices is to develop the correct formulation of the problem and efficient algorithms for analyzing the electronic structure and dynamics using, for example, the time-dependent density functional theory. We have divided this task into several steps. The first step is to developing the right mathematical formulation and numerical algorithms for analyzing the electronic structure using density functional theory. The second step is to study time-dependent density functional theory, particularly the far-field boundary conditions. The third step is to study electronic transport in molecular devices. We are now at the end of the first step. Under DOE support, we have made subtantial progress in developing linear scaling and sub-linear scaling algorithms for electronic structure analysis. Although there has been a huge amount of effort in the past on developing linear scaling algorithms, most of the algorithms developed suffer from the lack of robustness and controllable accuracy. We have made the following progress: (1) We have analyzed thoroughly the localization properties of the wave-functions. We have developed a clear understanding of the physical as well as mathematical origin of the decay properties. One important conclusion is that even for metals, one can choose wavefunctions that decay faster than any algebraic power. (2) We have developed algorithms that make use of these localization properties. Our algorithms are based on non-orthogonal formulations of the density functional theory. Our key contribution is to add a localization step into the algorithm. The addition of this localization step makes the algorithm quite robust and much more accurate. Moreover, we can control the accuracy of these algorithms by changing the numerical parameters. (3) We have considerably improved the Fermi operator expansion (FOE) approach. Through pole expansion, we have developed the optimal scaling FOE algorithm.

  13. Modelling spin Hamiltonian parameters of molecular nanomagnets.

    Science.gov (United States)

    Gupta, Tulika; Rajaraman, Gopalan

    2016-07-12

    Molecular nanomagnets encompass a wide range of coordination complexes possessing several potential applications. A formidable challenge in realizing these potential applications lies in controlling the magnetic properties of these clusters. Microscopic spin Hamiltonian (SH) parameters describe the magnetic properties of these clusters, and viable ways to control these SH parameters are highly desirable. Computational tools play a proactive role in this area, where SH parameters such as isotropic exchange interaction (J), anisotropic exchange interaction (Jx, Jy, Jz), double exchange interaction (B), zero-field splitting parameters (D, E) and g-tensors can be computed reliably using X-ray structures. In this feature article, we have attempted to provide a holistic view of the modelling of these SH parameters of molecular magnets. The determination of J includes various class of molecules, from di- and polynuclear Mn complexes to the {3d-Gd}, {Gd-Gd} and {Gd-2p} class of complexes. The estimation of anisotropic exchange coupling includes the exchange between an isotropic metal ion and an orbitally degenerate 3d/4d/5d metal ion. The double-exchange section contains some illustrative examples of mixed valance systems, and the section on the estimation of zfs parameters covers some mononuclear transition metal complexes possessing very large axial zfs parameters. The section on the computation of g-anisotropy exclusively covers studies on mononuclear Dy(III) and Er(III) single-ion magnets. The examples depicted in this article clearly illustrate that computational tools not only aid in interpreting and rationalizing the observed magnetic properties but possess the potential to predict new generation MNMs.

  14. Integrated Multiscale Modeling of Molecular Computing Devices

    Energy Technology Data Exchange (ETDEWEB)

    Weinan E

    2012-03-29

    The main bottleneck in modeling transport in molecular devices is to develop the correct formulation of the problem and efficient algorithms for analyzing the electronic structure and dynamics using, for example, the time-dependent density functional theory. We have divided this task into several steps. The first step is to developing the right mathematical formulation and numerical algorithms for analyzing the electronic structure using density functional theory. The second step is to study time-dependent density functional theory, particularly the far-field boundary conditions. The third step is to study electronic transport in molecular devices. We are now at the end of the first step. Under DOE support, we have made subtantial progress in developing linear scaling and sub-linear scaling algorithms for electronic structure analysis. Although there has been a huge amount of effort in the past on developing linear scaling algorithms, most of the algorithms developed suffer from the lack of robustness and controllable accuracy. We have made the following progress: (1) We have analyzed thoroughly the localization properties of the wave-functions. We have developed a clear understanding of the physical as well as mathematical origin of the decay properties. One important conclusion is that even for metals, one can choose wavefunctions that decay faster than any algebraic power. (2) We have developed algorithms that make use of these localization properties. Our algorithms are based on non-orthogonal formulations of the density functional theory. Our key contribution is to add a localization step into the algorithm. The addition of this localization step makes the algorithm quite robust and much more accurate. Moreover, we can control the accuracy of these algorithms by changing the numerical parameters. (3) We have considerably improved the Fermi operator expansion (FOE) approach. Through pole expansion, we have developed the optimal scaling FOE algorithm.

  15. 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

  16. 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 represent

  17. Final Report for Integrated Multiscale Modeling of Molecular Computing Devices

    Energy Technology Data Exchange (ETDEWEB)

    Glotzer, Sharon C.

    2013-08-28

    In collaboration with researchers at Vanderbilt University, North Carolina State University, Princeton and Oakridge National Laboratory we developed multiscale modeling and simulation methods capable of modeling the synthesis, assembly, and operation of molecular electronics devices. Our role in this project included the development of coarse-grained molecular and mesoscale models and simulation methods capable of simulating the assembly of millions of organic conducting molecules and other molecular components into nanowires, crossbars, and other organized patterns.

  18. Molecular Tracking, through Processing, of Campylobacter Strains Colonizing Broiler Flocks▿

    Science.gov (United States)

    Elvers, Karen T.; Morris, Victoria K.; Newell, Diane G.; Allen, Vivien M.

    2011-01-01

    Many of the poultry flocks produced in the United Kingdom are colonized with Campylobacter, and the intensive nature of poultry processing usually results in contaminated carcasses. In this study, a previously reported molecular oligonucleotide probe method was used to track a specific flock-colonizing strain(s) on broiler carcasses during processing in two United Kingdom commercial poultry processing plants. Five Campylobacter-positive flocks were sampled at four points along the processing line, postbleed, postpluck, prechill, and postchill, and two Campylobacter-negative flocks processed immediately after positive flocks were sampled prechill. flaA was sequenced from Campylobacter strains isolated from these flocks, and strain-specific probes were synthesized. Skin and cecal samples were plated onto selective agar to give individual colonies, which were transferred onto membranes. These were then hybridized with the strain- and genus-specific probes. For all the 5 positive flocks, there was a significant reduction in campylobacters postbleed compared to postpluck but no subsequent fall on sampling pre- and postchill, and the strain(s) predominating on the carcasses throughout processing came from the flock being processed. This indicates that strains from the abattoir environment were not a significant cause of carcass contamination in flocks with well-established campylobacter colonization. However, negative flocks that were preceded by positive flocks were contaminated by strains that did not generally originate from the predominating strains recovered from the ceca of the previous positive flocks. This suggests that the abattoir environment has a significant role in the contamination of carcasses from negative but not fully colonized flocks. PMID:21705532

  19. Molecular Imaging of Vulnerable Atherosclerotic Plaques in Animal Models

    Directory of Open Access Journals (Sweden)

    Sara Gargiulo

    2016-09-01

    Full Text Available Atherosclerosis is characterized by intimal plaques of the arterial vessels that develop slowly and, in some cases, may undergo spontaneous rupture with subsequent heart attack or stroke. Currently, noninvasive diagnostic tools are inadequate to screen atherosclerotic lesions at high risk of acute complications. Therefore, the attention of the scientific community has been focused on the use of molecular imaging for identifying vulnerable plaques. Genetically engineered murine models such as ApoE−/− and ApoE−/−Fbn1C1039G+/− mice have been shown to be useful for testing new probes targeting biomarkers of relevant molecular processes for the characterization of vulnerable plaques, such as vascular endothelial growth factor receptor (VEGFR-1, VEGFR-2, intercellular adhesion molecule (ICAM-1, P-selectin, and integrins, and for the potential development of translational tools to identify high-risk patients who could benefit from early therapeutic interventions. This review summarizes the main animal models of vulnerable plaques, with an emphasis on genetically altered mice, and the state-of-the-art preclinical molecular imaging strategies.

  20. Molecular Imaging of Vulnerable Atherosclerotic Plaques in Animal Models

    Science.gov (United States)

    Gargiulo, Sara; Gramanzini, Matteo; Mancini, Marcello

    2016-01-01

    Atherosclerosis is characterized by intimal plaques of the arterial vessels that develop slowly and, in some cases, may undergo spontaneous rupture with subsequent heart attack or stroke. Currently, noninvasive diagnostic tools are inadequate to screen atherosclerotic lesions at high risk of acute complications. Therefore, the attention of the scientific community has been focused on the use of molecular imaging for identifying vulnerable plaques. Genetically engineered murine models such as ApoE−/− and ApoE−/−Fbn1C1039G+/− mice have been shown to be useful for testing new probes targeting biomarkers of relevant molecular processes for the characterization of vulnerable plaques, such as vascular endothelial growth factor receptor (VEGFR)-1, VEGFR-2, intercellular adhesion molecule (ICAM)-1, P-selectin, and integrins, and for the potential development of translational tools to identify high-risk patients who could benefit from early therapeutic interventions. This review summarizes the main animal models of vulnerable plaques, with an emphasis on genetically altered mice, and the state-of-the-art preclinical molecular imaging strategies. PMID:27618031

  1. 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 ...

  2. 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.

  3. 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

  4. 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...

  5. Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

    CERN Document Server

    Xu, Ji; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai

    2010-01-01

    Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further spee...

  6. 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.

  7. 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.

  8. 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.

  9. modeling grinding modeling grinding processes as micro processes ...

    African Journals Online (AJOL)

    eobe

    workpiece material dynamics thus allowing for process planning, optimization, and control. In spite of the .... arrangement of the grain vertices at the wheel active surface. ...... on Workpiece Roughness and Process Vibration” J. of the Braz.

  10. SWIFT MODELLER: a Java based GUI for molecular modeling.

    Science.gov (United States)

    Mathur, Abhinav; Shankaracharya; Vidyarthi, Ambarish S

    2011-10-01

    MODELLER is command line argument based software which requires tedious formatting of inputs and writing of Python scripts which most people are not comfortable with. Also the visualization of output becomes cumbersome due to verbose files. This makes the whole software protocol very complex and requires extensive study of MODELLER manuals and tutorials. Here we describe SWIFT MODELLER, a GUI that automates formatting, scripting and data extraction processes and present it in an interactive way making MODELLER much easier to use than before. The screens in SWIFT MODELLER are designed keeping homology modeling in mind and their flow is a depiction of its steps. It eliminates the formatting of inputs, scripting processes and analysis of verbose output files through automation and makes pasting of the target sequence as the only prerequisite. Jmol (3D structure visualization tool) has been integrated into the GUI which opens and demonstrates the protein data bank files created by the MODELLER software. All files required and created by the software are saved in a folder named after the work instance's date and time of execution. SWIFT MODELLER lowers the skill level required for the software through automation of many of the steps in the original software protocol, thus saving an enormous amount of time per instance and making MODELLER very easy to work with.

  11. Managing Analysis Models in the Design Process

    Science.gov (United States)

    Briggs, Clark

    2006-01-01

    Design of large, complex space systems depends on significant model-based support for exploration of the design space. Integrated models predict system performance in mission-relevant terms given design descriptions and multiple physics-based numerical models. Both the design activities and the modeling activities warrant explicit process definitions and active process management to protect the project from excessive risk. Software and systems engineering processes have been formalized and similar formal process activities are under development for design engineering and integrated modeling. JPL is establishing a modeling process to define development and application of such system-level models.

  12. Exactly solvable models for multiatomic molecular Bose-Einstein condensates

    Science.gov (United States)

    Santos, G.

    2011-08-01

    I introduce two families of exactly solvable models for multiatomic hetero-nuclear and homo-nuclear molecular Bose-Einstein condensates through the algebraic Bethe ansatz method. The conserved quantities of the respective models are also shown.

  13. Exactly solvable models for multiatomic molecular Bose-Einstein condensates

    Energy Technology Data Exchange (ETDEWEB)

    Santos, G, E-mail: gfilho@if.ufrgs.br, E-mail: gfilho@cbpf.br [Instituto de Fisica da UFRGS, Av. Bento Goncalves, 9500, Agronomia, Porto Alegre, RS (Brazil)

    2011-08-26

    I introduce two families of exactly solvable models for multiatomic hetero-nuclear and homo-nuclear molecular Bose-Einstein condensates through the algebraic Bethe ansatz method. The conserved quantities of the respective models are also shown. (paper)

  14. Cupola Furnace Computer Process Model

    Energy Technology Data Exchange (ETDEWEB)

    Seymour Katz

    2004-12-31

    The cupola furnace generates more than 50% of the liquid iron used to produce the 9+ million tons of castings annually. The cupola converts iron and steel into cast iron. The main advantages of the cupola furnace are lower energy costs than those of competing furnaces (electric) and the ability to melt less expensive metallic scrap than the competing furnaces. However the chemical and physical processes that take place in the cupola furnace are highly complex making it difficult to operate the furnace in optimal fashion. The results are low energy efficiency and poor recovery of important and expensive alloy elements due to oxidation. Between 1990 and 2004 under the auspices of the Department of Energy, the American Foundry Society and General Motors Corp. a computer simulation of the cupola furnace was developed that accurately describes the complex behavior of the furnace. When provided with the furnace input conditions the model provides accurate values of the output conditions in a matter of seconds. It also provides key diagnostics. Using clues from the diagnostics a trained specialist can infer changes in the operation that will move the system toward higher efficiency. Repeating the process in an iterative fashion leads to near optimum operating conditions with just a few iterations. More advanced uses of the program have been examined. The program is currently being combined with an ''Expert System'' to permit optimization in real time. The program has been combined with ''neural network'' programs to affect very easy scanning of a wide range of furnace operation. Rudimentary efforts were successfully made to operate the furnace using a computer. References to these more advanced systems will be found in the ''Cupola Handbook''. Chapter 27, American Foundry Society, Des Plaines, IL (1999).

  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. 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.

  17. Process Correlation Analysis Model for Process Improvement Identification

    Directory of Open Access Journals (Sweden)

    Su-jin Choi

    2014-01-01

    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.

  18. A Process Model for Establishing Business Process Crowdsourcing

    Directory of Open Access Journals (Sweden)

    Nguyen Hoang Thuan

    2017-06-01

    Full Text Available Crowdsourcing can be an organisational strategy to distribute work to Internet users and harness innovation, information, capacities, and variety of business endeavours. As crowdsourcing is different from other business strategies, organisations are often unsure as to how to best structure different crowdsourcing activities and integrate them with other organisational business processes. To manage this problem, we design a process model guiding how to establish business process crowdsourcing. The model consists of seven components covering the main activities of crowdsourcing processes, which are drawn from a knowledge base incorporating diverse knowledge sources in the domain. The built model is evaluated using case studies, suggesting the adequateness and utility of the model.

  19. A cognitive model of second-year organic chemistry students' conceptualizations of mental molecular rotation

    Science.gov (United States)

    Briggs, Michael W.

    The goal of this research was to answer the question, "What is a plausible explanation (model) of the cognitive structure and processes that facilitate mental molecular rotation?". This work used phenomenographic methodology and techniques of interview and think-aloud protocol. Constructivism was the theoretical framework. At the outset of the research, I designed nine tasks to obtain participant articulations of conceptualizations of mental molecular rotations. Articulations from five second-year organic chemistry students attending a Midwestern research university became the research data. Analysis produced four emerging themes along two axes: visualization representation and modeling cognition. These two axes formed a mental space, which was modeled by structure and processes that facilitated mental molecular rotation. A theoretical cognitive model of mental molecular rotation was based on the work of two researchers: Robbie Case and Richard Lesh. Lesh's "mental model" is composed of cognitive elements and operations, which are distributed over heeded local and global cognitive sub-models whereas Case deals with unheeded central conceptual structures. The models and structures interact to produce new knowledge and facilitate the use of existing knowledge. Two predictions of the theory of mental molecular rotation were elaborated. Students without a set of operations in a central conceptual structure will not be able to mentally rotate molecules. This is true even if a set of components, other than "operation", is constructed. The artifacts of mental molecular rotation can be used to determine the state of construction of the central conceptual structure responsible for mental molecular rotation.

  20. Modeling and Reconstruction of Mixed Functional and Molecular Patterns

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available Functional medical imaging promises powerful tools for the visualization and elucidation of important disease-causing biological processes in living tissue. Recent research aims to dissect the distribution or expression of multiple biomarkers associated with disease progression or response, where the signals often represent a composite of more than one distinct source independent of spatial resolution. Formulating the task as a blind source separation or composite signal factorization problem, we report here a statistically principled method for modeling and reconstruction of mixed functional or molecular patterns. The computational algorithm is based on a latent variable model whose parameters are estimated using clustered component analysis. We demonstrate the principle and performance of the approaches on the breast cancer data sets acquired by dynamic contrast-enhanced magnetic resonance imaging.

  1. CONVERGENCE TO PROCESS ORGANIZATION BY MODEL OF PROCESS MATURITY

    Directory of Open Access Journals (Sweden)

    Blaženka Piuković Babičković

    2015-06-01

    Full Text Available With modern business process orientation binds primarily, process of thinking and process organizational structure. Although the business processes are increasingly a matter of writing and speaking, it is a major problem among the business world, especially in countries in transition, where it has been found that there is a lack of understanding of the concept of business process management. The aim of this paper is to give a specific contribution to overcoming the identified problem, by pointing out the significance of the concept of business process management, as well as the representation of the model for review of process maturity and tools that are recommended for use in process management.

  2. Event-driven process execution model for process virtual machine

    Institute of Scientific and Technical Information of China (English)

    WU Dong-yao; WEI Jun; GAO Chu-shu; DOU Wen-shen

    2012-01-01

    Current orchestration and choreography process engines only serve with dedicate process languages. To solve these problems, an Even~driven Process Execution Model (EPEM) was developed. Formalization and map- ping principles of the model were presented to guarantee the correctness and efficiency for process transformation. As a case study, the EPEM descriptions of Web Services Business Process Execution Language (WS~BPEL) were represented and a Process Virtual Machine (PVM)-OncePVM was implemented in compliance with the EPEM.

  3. Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

    Science.gov (United States)

    Lee, Cheng-Kuang; Pao, Chun-Wei

    2016-08-17

    Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies.

  4. Analog modelling of obduction processes

    Science.gov (United States)

    Agard, P.; Zuo, X.; Funiciello, F.; Bellahsen, N.; Faccenna, C.; Savva, D.

    2012-04-01

    Obduction corresponds to one of plate tectonics oddities, whereby dense, oceanic rocks (ophiolites) are presumably 'thrust' on top of light, continental ones, as for the short-lived, almost synchronous Peri-Arabic obduction (which took place along thousands of km from Turkey to Oman in c. 5-10 Ma). Analog modelling experiments were performed to study the mechanisms of obduction initiation and test various triggering hypotheses (i.e., plate acceleration, slab hitting the 660 km discontinuity, ridge subduction; Agard et al., 2007). The experimental setup comprises (1) an upper mantle, modelled as a low-viscosity transparent Newtonian glucose syrup filling a rigid Plexiglas tank and (2) high-viscosity silicone plates (Rhodrosil Gomme with PDMS iron fillers to reproduce densities of continental or oceanic plates), located at the centre of the tank above the syrup to simulate the subducting and the overriding plates - and avoid friction on the sides of the tank. Convergence is simulated by pushing on a piston at one end of the model with velocities comparable to those of plate tectonics (i.e., in the range 1-10 cm/yr). The reference set-up includes, from one end to the other (~60 cm): (i) the piston, (ii) a continental margin containing a transition zone to the adjacent oceanic plate, (iii) a weakness zone with variable resistance and dip (W), (iv) an oceanic plate - with or without a spreading ridge, (v) a subduction zone (S) dipping away from the piston and (vi) an upper, active continental margin, below which the oceanic plate is being subducted at the start of the experiment (as is known to have been the case in Oman). Several configurations were tested and over thirty different parametric tests were performed. Special emphasis was placed on comparing different types of weakness zone (W) and the extent of mechanical coupling across them, particularly when plates were accelerated. Displacements, together with along-strike and across-strike internal deformation in all

  5. 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.

  6. 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.

  7. 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.

  8. Stochastic model for photoinduced surface relief grating formation through molecular transport in polymer films.

    Energy Technology Data Exchange (ETDEWEB)

    Juan, M.; Plain, J.; Bachelot, R.; Royer, P.; Gray, S. K.; Wiederrecht, G. P.; Univ. de Technologie de Troyes

    2008-09-01

    We use a stochastic model to study photoinduced surface relief grating (SRG) formation due to molecular transport in azobenzene polymer films. The model is shown to reproduce the essential experimental features of SRG formation. In particular, it predicts SRG formation under both p and s polarizations, and the double peaked topographies that can occur at early times of the process. The evolving molecular positions and orientations during exposure are also followed, providing a useful mechanistic picture of SRG dynamics.

  9. 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.

  10. 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

  11. Dust properties inside molecular clouds from coreshine modeling and observations

    CERN Document Server

    Lefèvre, Charlène; Juvela, Mika; Paladini, Roberta; Lallement, Rosine; Marshall, D J; Andersen, Morten; Bacmann, Aurore; Mcgee, Peregrine M; Montier, Ludovic; Noriega-Crespo, Alberto; Pelkonen, V -M; Ristorcelli, Isabelle; Steinacker, Jürgen

    2014-01-01

    Context. Using observations to deduce dust properties, grain size distribution, and physical conditions in molecular clouds is a highly degenerate problem. Aims. The coreshine phenomenon, a scattering process at 3.6 and 4.5 $\\mu$m that dominates absorption, has revealed its ability to explore the densest parts of clouds. We want to use this effect to constrain the dust parameters. The goal is to investigate to what extent grain growth (at constant dust mass) inside molecular clouds is able to explain the coreshine observations. We aim to find dust models that can explain a sample of Spitzer coreshine data. We also look at the consistency with near-infrared data we obtained for a few clouds. Methods. We selected four regions with a very high occurrence of coreshine cases: Taurus-Perseus, Cepheus, Chameleon and L183/L134. We built a grid of dust models and investigated the key parameters to reproduce the general trend of surface bright- nesses and intensity ratios of both coreshine and near-infrared observation...

  12. Aggregation of model asphaltenes: a molecular dynamics study

    Science.gov (United States)

    Costa, J. L. L. F. S.; Simionesie, D.; Zhang, Z. J.; Mulheran, P. A.

    2016-10-01

    Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes.

  13. Fluctuation theorem for the flashing ratchet model of molecular motors

    Science.gov (United States)

    Lacoste, D.; Mallick, K.

    2009-08-01

    Molecular motors convert chemical energy derived from the hydrolysis of adenosine triphosphate (ATP) into mechanical energy. A well-studied model of a molecular motor is the flashing ratchet model. We show that this model exhibits a fluctuation relation known as the Gallavotti-Cohen symmetry. Our study highlights the fact that the symmetry is present only if the chemical and mechanical degrees of freedom are both included in the description.

  14. Modeling of molecular photocells: Application to two-level photovoltaic system with electron-hole interaction.

    Science.gov (United States)

    Nemati Aram, Tahereh; Anghel-Vasilescu, Petrutza; Asgari, Asghar; Ernzerhof, Matthias; Mayou, Didier

    2016-09-28

    We present a novel simple model to describe molecular photocells where the energy conversion process takes place by a single molecular donor-acceptor complex attached to electrodes. By applying quantum scattering theory, an open quantum system method, the coherent molecular photocell is described by a wave function. We analyze photon absorption, energy conversion, and quantum yield of a molecular photocell by considering the effects of electron-hole interaction and non-radiative recombination. We model the exciton creation, dissociation, and subsequent effects on quantum yield in the energy domain. We find that depending on the photocell structure, the electron-hole interaction can normally decrease or abnormally increase the cell efficiency. The proposed model helps to understand the mechanisms of molecular photocells, and it can be used to optimize their yield.

  15. Molecular dynamics modeling of structural battery components

    NARCIS (Netherlands)

    Verners, O.; Van Duin, A.C.T.; Wagemaker, M.; Simone, A.

    2015-01-01

    A crosslinked polymer based solid electrolyte prototype material –poly(propylene glycol) diacrylate– is studied using the reactive molecular dynamics force field ReaxFF. The focus of the study is the evaluation of the effects of equilibration and added plasticizer (ethylene carbonate) or anion compo

  16. Modelling the global tropospheric molecular hydrogen cycle

    NARCIS (Netherlands)

    Pieterse, G.

    2013-01-01

    Would urban air quality and climate improve if we replaced the fossil fuels by molecular hydrogen (H2) as an energy carrier? A quantitative answer to this question requires a thorough understanding of the current role of H2 in the Earth’s atmosphere. On its own, H2 does not impact climate, as for ex

  17. Modelling the global tropospheric molecular hydrogen cycle

    NARCIS (Netherlands)

    Pieterse, G.

    2013-01-01

    Would urban air quality and climate improve if we replaced the fossil fuels by molecular hydrogen (H2) as an energy carrier? A quantitative answer to this question requires a thorough understanding of the current role of H2 in the Earth’s atmosphere. On its own, H2 does not impact climate, as for

  18. A new process sensitivity index to identify important system processes under process model and parametric uncertainty

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Heng [Pacific Northwest National Laboratory, Richland Washington USA; Ye, Ming [Department of Scientific Computing, Florida State University, Tallahassee Florida USA; Walker, Anthony P. [Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge Tennessee USA; Chen, Xingyuan [Pacific Northwest National Laboratory, Richland Washington USA

    2017-04-01

    Hydrological models are always composed of multiple components that represent processes key to intended model applications. When a process can be simulated by multiple conceptual-mathematical models (process models), model uncertainty in representing the process arises. While global sensitivity analysis methods have been widely used for identifying important processes in hydrologic modeling, the existing methods consider only parametric uncertainty but ignore the model uncertainty for process representation. To address this problem, this study develops a new method to probe multimodel process sensitivity by integrating the model averaging methods into the framework of variance-based global sensitivity analysis, given that the model averaging methods quantify both parametric and model uncertainty. A new process sensitivity index is derived as a metric of relative process importance, and the index includes variance in model outputs caused by uncertainty in both process models and model parameters. For demonstration, the new index is used to evaluate the processes of recharge and geology in a synthetic study of groundwater reactive transport modeling. The recharge process is simulated by two models that converting precipitation to recharge, and the geology process is also simulated by two models of different parameterizations of hydraulic conductivity; each process model has its own random parameters. The new process sensitivity index is mathematically general, and can be applied to a wide range of problems in hydrology and beyond.

  19. 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 propertie...

  20. Modeling process flow using diagrams

    NARCIS (Netherlands)

    Kemper, B.; de Mast, J.; Mandjes, M.

    2010-01-01

    In the practice of process improvement, tools such as the flowchart, the value-stream map (VSM), and a variety of ad hoc variants of such diagrams are commonly used. The purpose of this paper is to present a clear, precise, and consistent framework for the use of such flow diagrams in process

  1. Modeling process flow using diagrams

    NARCIS (Netherlands)

    Kemper, B.; de Mast, J.; Mandjes, M.

    2010-01-01

    In the practice of process improvement, tools such as the flowchart, the value-stream map (VSM), and a variety of ad hoc variants of such diagrams are commonly used. The purpose of this paper is to present a clear, precise, and consistent framework for the use of such flow diagrams in process improv

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

    OpenAIRE

    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. From a practical point of view, systems consisting more than two components are more interesting. However, experimental and simulation data on transport diffusion for such systems are scarce. There...

  3. Molecular Modeling and Computational Chemistry at Humboldt State University.

    Science.gov (United States)

    Paselk, Richard A.; Zoellner, Robert W.

    2002-01-01

    Describes a molecular modeling and computational chemistry (MM&CC) facility for undergraduate instruction and research at Humboldt State University. This facility complex allows the introduction of MM&CC throughout the chemistry curriculum with tailored experiments in general, organic, and inorganic courses as well as a new molecular modeling…

  4. Molecular Dynamics Studies of Energy Transfer Processes in Crystal Systems.

    Science.gov (United States)

    1984-11-30

    Computer molecular dynamics studies have been carried out on the problem of attaining a fundamental understanding of shock-induced initiation of...intramolecular energy exchange in shock-loaded systems are presented. Originator-supplied keywords include: Molecular dynamics , Energy transfer, Shock front, Shock wave, Explosives, Shock structure.

  5. Context Based Reasoning in Business Process Models

    OpenAIRE

    Balabko, Pavel; Wegmann, Alain

    2003-01-01

    Modeling approaches often are not adapted to human reasoning: models are ambiguous and imprecise. A same model element may have multiple meanings in different functional roles of a system. Existing modeling approaches do not relate explicitly these functional roles with model elements. A principle that can solve this problem is that model elements should be defined in a context. We believe that the explicit modeling of context is especially useful in Business Process Modeling (BPM) where the ...

  6. Modelling of Batch Process Operations

    DEFF Research Database (Denmark)

    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...

  7. 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.

  8. Steady-State Process Modelling

    DEFF Research Database (Denmark)

    2011-01-01

    This chapter covers the basic principles of steady state modelling and simulation using a number of case studies. Two principal approaches are illustrated that develop the unit operation models from first principles as well as through application of standard flowsheet simulators. The approaches i...

  9. A General Random Walk Model of Molecular Motor

    Institute of Scientific and Technical Information of China (English)

    WANG Xian-Ju; AI Bao-Quan; LIU Guo-Tao; LIU Liang-Gang

    2003-01-01

    A general random walk model framework is presented which can be used to statistically describe the internaldynamics and external mechanical movement of molecular motors along filament track. The motion of molecular motorin a periodic potential and a constant force is considered. We show that the molecular motor's movement becomesslower with the potential barrier increasing, but if the forceis increased, the molecular motor's movement becomesfaster. The relation between the effective rate constant and the potential barrier's height, and that between the effectiverate constant and the value of the force are discussed. Our results are consistent with the experiments and relevanttheoretical consideration, and can be used to explain some physiological phenomena.

  10. Modeling of the continuum and molecular line emission from the Sagittarius B2 molecular cloud

    Energy Technology Data Exchange (ETDEWEB)

    Lis, D.C.; Goldsmith, P.F. (Massachusetts Univ., Amherst (USA))

    1990-06-01

    The continuum and molecular line emission from the Sagittarius B2 molecular cloud are modeled in order to determine the conditions in the core and the envelope of the cloud. The continuum models suggest that the total luminosity of the middle source Sgr B2(M) is an order of magnitude higher than that of the northern source Sgr B2(N). The microturbulent models of the molecular line emission predict the correct spatial intensity distribution of the J = 1 - 0 transitions of C(O-18) and (C-13)O. They have difficulties, however, reproducing the observed intensities of the higher transitions of these molecules. This may indicate that the envelope has a clumpy structure. Sgr B2 differs significantly from typical disk giant molecular clouds in that it has higher mass and luminosity of the continuum sources, much greater H2 column density and mean volume density, and different fractional abundances of many interstellar molecules. 43 refs.

  11. Polarized Molecular Orbital Model Chemistry. II. The PMO Method.

    Science.gov (United States)

    Zhang, Peng; Fiedler, Luke; Leverentz, Hannah R; Truhlar, Donald G; Gao, Jiali

    2011-04-12

    We present a new semiempirical molecular orbital method based on neglect of diatomic differential overlap. This method differs from previous NDDO-based methods in that we include p orbitals on hydrogen atoms to provide a more realistic modeling of polarizability. As in AM1-D and PM3-D, we also include damped dispersion. The formalism is based on the original MNDO one, but in the process of parameterization we make some specific changes to some of the functional forms. The present article is a demonstration of the capability of the new approach, and it presents a successful parametrization for compounds composed only of hydrogen and oxygen atoms, including the important case of water clusters.

  12. Stochastic modeling of cargo transport by teams of molecular motors

    CERN Document Server

    Klein, Sarah; Santen, Ludger

    2014-01-01

    Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.

  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. Modelling [CI] emission from turbulent molecular clouds

    CERN Document Server

    Glover, Simon C O; Micic, Milica; Molina, Faviola

    2014-01-01

    We use detailed numerical simulations of the coupled chemical, thermal and dynamical evolution of the gas in a turbulent molecular cloud to study the usefulness of the [CI] 609 micron and 370 micron fine structure emission lines as tracers of cloud structure. Emission from these lines is observed throughout molecular clouds, and yet the question of what we can learn from them about the physics of the clouds remains largely unexplored. We show that the fact that [CI] emission is widespread within molecular clouds is a simple consequence of the fact that the clouds are dominated by turbulent motions. Turbulence creates large density inhomogeneities, allowing radiation to penetrate deeply into the clouds. As a result, [CI] emitting gas is found throughout the cloud, rather than being concentrated at the edges. We examine how well we can use [CI] emission to trace the structure of the cloud, and show that the integrated intensity of the 609 micron line traces column density accurately over a wide range of visual ...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-10-31

    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.

  17. Modeling Events with Cascades of Poisson Processes

    CERN Document Server

    Simma, Aleksandr

    2012-01-01

    We present a probabilistic model of events in continuous time in which each event triggers a Poisson process of successor events. The ensemble of observed events is thereby modeled as a superposition of Poisson processes. Efficient inference is feasible under this model with an EM algorithm. Moreover, the EM algorithm can be implemented as a distributed algorithm, permitting the model to be applied to very large datasets. We apply these techniques to the modeling of Twitter messages and the revision history of Wikipedia.

  18. Bayesian molecular design with a chemical language model.

    Science.gov (United States)

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

    2017-03-09

    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.

  19. The Computer-Aided Analytic Process Model. Operations Handbook for the Analytic Process Model Demonstration Package

    Science.gov (United States)

    1986-01-01

    Research Note 86-06 THE COMPUTER-AIDED ANALYTIC PROCESS MODEL : OPERATIONS HANDBOOK FOR THE ANALYTIC PROCESS MODEL DE ONSTRATION PACKAGE Ronald G...ic Process Model ; Operations Handbook; Tutorial; Apple; Systems Taxonomy Mod--l; Training System; Bradl1ey infantry Fighting * Vehicle; BIFV...8217. . . . . . . .. . . . . . . . . . . . . . . . * - ~ . - - * m- .. . . . . . . item 20. Abstract -continued companion volume-- "The Analytic Process Model for

  20. DISSYMMETRY MODEL OF MOLECULAR POLARIZABILITY AND OPTICAL ACTIVITY

    Institute of Scientific and Technical Information of China (English)

    周志华; 汤杰

    1991-01-01

    Dissymmetry model of molecular polarizability divided into some layers within a sphere,some rules and sequence according to the magnitude of polarizability replaced by bond refraction for many groups have been suggested.The relationship between the dissymmetry of molecular polarizability arrounding the dissymmetric carbon atom and the direction of optical activity has been discussed .The accuracy is above 95 persent to use our model and rules to determine over 6000 compounds of optical activity.

  1. Structure-based molecular modeling approaches to GPCR oligomerization.

    Science.gov (United States)

    Kaczor, Agnieszka A; Selent, Jana; Poso, Antti

    2013-01-01

    Classical structure-based drug design techniques using G-protein-coupled receptors (GPCRs) as targets focus nearly exclusively on binding at the orthosteric site of a single receptor. Dimerization and oligomerization of GPCRs, proposed almost 30 years ago, have, however, crucial relevance for drug design. Targeting these complexes selectively or designing small molecules that affect receptor-receptor interactions might provide new opportunities for novel drug discovery. In order to study the mechanisms and dynamics that rule GPCRs oligomerization, it is essential to understand the dynamic process of receptor-receptor association and to identify regions that are suitable for selective drug binding, which may be determined with experimental methods such as Förster resonance energy transfer (FRET) or Bioluminescence resonance energy transfer (BRET) and computational sequence- and structure-based approaches. The aim of this chapter is to provide a comprehensive description of the structure-based molecular modeling methods for studying GPCR dimerization, that is, protein-protein docking, molecular dynamics, normal mode analysis, and electrostatics studies.

  2. Stepping and crowding of molecular motors: statistical kinetics from an exclusion process perspective.

    Science.gov (United States)

    Ciandrini, Luca; Romano, M Carmen; Parmeggiani, Andrea

    2014-09-02

    Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These macromolecules, nowadays investigated with advanced experimental techniques to unveil their molecular mechanisms and the properties of their kinetic cycles, are implicated in many biological processes, ranging from biopolymerization (e.g., RNA polymerases and ribosomes) to intracellular transport (motor proteins such as kinesins or dyneins). Although the kinetics of individual motors is well studied on both theoretical and experimental grounds, the repercussions of their stepping cycle on the collective dynamics still remains unclear. Advances in this direction will improve our comprehension of transport process in the natural intracellular medium, where processive motor enzymes might operate in crowded conditions. In this work, we therefore extend contemporary statistical kinetic analysis to study collective transport phenomena of motors in terms of lattice gas models belonging to the exclusion process class. Via numerical simulations, we show how to interpret and use the randomness calculated from single particle trajectories in crowded conditions. Importantly, we also show that time fluctuations and non-Poissonian behavior are intrinsically related to spatial correlations and the emergence of large, but finite, clusters of comoving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions.

  3. Systematic approach for the identification of process reference models

    CSIR Research Space (South Africa)

    Van Der Merwe, A

    2009-02-01

    Full Text Available Process models are used in different application domains to capture knowledge on the process flow. Process reference models (PRM) are used to capture reusable process models, which should simplify the identification process of process models...

  4. Ada COCOMO and the Ada Process Model

    Science.gov (United States)

    1989-01-01

    language, the use of incremental development, and the use of the Ada process model capitalizing on the strengths of Ada to improve the efficiency of software...development. This paper presents the portions of the revised Ada COCOMO dealing with the effects of Ada and the Ada process model . The remainder of...this section of the paper discusses the objectives of Ada COCOMO. Section 2 describes the Ada Process Model and its overall effects on software

  5. 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.

  6. A Review of Kinetic Modeling Methodologies for Complex Processes

    Directory of Open Access Journals (Sweden)

    de Oliveira Luís P.

    2016-05-01

    Full Text Available In this paper, kinetic modeling techniques for complex chemical processes are reviewed. After a brief historical overview of chemical kinetics, an overview is given of the theoretical background of kinetic modeling of elementary steps and of multistep reactions. Classic lumping techniques are introduced and analyzed. Two examples of lumped kinetic models (atmospheric gasoil hydrotreating and residue hydroprocessing developed at IFP Energies nouvelles (IFPEN are presented. The largest part of this review describes advanced kinetic modeling strategies, in which the molecular detail is retained, i.e. the reactions are represented between molecules or even subdivided into elementary steps. To be able to retain this molecular level throughout the kinetic model and the reactor simulations, several hurdles have to be cleared first: (i the feedstock needs to be described in terms of molecules, (ii large reaction networks need to be automatically generated, and (iii a large number of rate equations with their rate parameters need to be derived. For these three obstacles, molecular reconstruction techniques, deterministic or stochastic network generation programs, and single-event micro-kinetics and/or linear free energy relationships have been applied at IFPEN, as illustrated by several examples of kinetic models for industrial refining processes.

  7. 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.

  8. A Process Model for Establishing Business Process Crowdsourcing

    OpenAIRE

    Nguyen Hoang Thuan; Pedro Antunes; David Johnstone

    2017-01-01

    Crowdsourcing can be an organisational strategy to distribute work to Internet users and harness innovation, information, capacities, and variety of business endeavours. As crowdsourcing is different from other business strategies, organisations are often unsure as to how to best structure different crowdsourcing activities and integrate them with other organisational business processes. To manage this problem, we design a process model guiding how to establish business process crowdsourcing....

  9. Total Ship Design Process Modeling

    Science.gov (United States)

    2012-04-30

    Microsoft Project® or Primavera ®, and perform process simulations that can investigate risk, cost, and schedule trade-offs. Prior efforts to capture...planning in the face of disruption, delay, and late‐changing  requirements. ADePT is interfaced with  PrimaVera , the AEC  industry favorite program

  10. Acoustic response of cemented granular sedimentary rocks: molecular dynamics modeling.

    Science.gov (United States)

    García, Xavier; Medina, Ernesto

    2007-06-01

    The effect of cementation processes on the acoustical properties of sands is studied via molecular dynamics simulation methods. We propose numerical methods where the initial uncemented sand is built by simulating the settling process of sediments. Uncemented samples of different porosity are considered by emulating natural mechanical compaction of sediments due to overburden. Cementation is considered through a particle-based model that captures the underlying physics behind the process. In our simulations, we consider samples with different degrees of compaction and cementing materials with distinct elastic properties. The microstructure of cemented sands is taken into account while adding cement at specific locations within the pores, such as grain-to-grain contacts. Results show that the acoustical properties of cemented sands are strongly dependent on the amount of cement, its stiffness relative to the hosting medium, and its location within the pores. Simulation results are in good correspondence with available experimental data and compare favorably with some theoretical predictions for the sound velocity within a range of cement saturation, porosity, and confining pressure.

  11. Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization

    Science.gov (United States)

    Arntsen, Christopher; Chen, Chen; Voth, Gregory A.

    2017-09-01

    We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.

  12. Kinetic model of atomic and molecular emissions in laser-induced breakdown spectroscopy of organic compounds.

    Science.gov (United States)

    Ma, Qianli; Dagdigian, Paul J

    2011-07-01

    A kinetic model previously developed to predict the relative intensities of atomic emission lines in laser-induced breakdown spectroscopy has been extended to include processes related to CN and C(2) molecular emissions. Simulations with this model were performed to predict the relative excited-state populations. The results from the simulations are compared with experimentally determined excited-state populations from 1,064 nm laser irradiation of organic residues on aluminum foil. The model reasonably predicts the relative intensity of the molecular emissions. Significantly, the model reproduces the vastly different temporal profiles of the atomic and molecular emissions. The latter are found to extend to much longer times after the laser pulse, and this appears to be due to the increasing concentration of the molecules versus time. From the simulations, the important processes affecting the CN and C(2) concentrations are identified.

  13. Continuous Molecular Fields Approach Applied to Structure-Activity Modeling

    CERN Document Server

    Baskin, Igor I

    2013-01-01

    The Method of Continuous Molecular Fields is a universal approach to predict various properties of chemical compounds, in which molecules are represented by means of continuous fields (such as electrostatic, steric, electron density functions, etc). The essence of the proposed approach consists in performing statistical analysis of functional molecular data by means of joint application of kernel machine learning methods and special kernels which compare molecules by computing overlap integrals of their molecular fields. This approach is an alternative to traditional methods of building 3D structure-activity and structure-property models based on the use of fixed sets of molecular descriptors. The methodology of the approach is described in this chapter, followed by its application to building regression 3D-QSAR models and conducting virtual screening based on one-class classification models. The main directions of the further development of this approach are outlined at the end of the chapter.

  14. GPstuff: Bayesian Modeling with Gaussian Processes

    NARCIS (Netherlands)

    Vanhatalo, J.; Riihimaki, J.; Hartikainen, J.; Jylänki, P.P.; Tolvanen, V.; Vehtari, A.

    2013-01-01

    The GPstuff toolbox is a versatile collection of Gaussian process models and computational tools required for Bayesian inference. The tools include, among others, various inference methods, sparse approximations and model assessment methods.

  15. Online Rule Generation Software Process Model

    National Research Council Canada - National Science Library

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

    2013-01-01

    .... 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...

  16. Applications of Molecular Modeling in Endocrinology- Review Article

    Directory of Open Access Journals (Sweden)

    Azadeh EBRAHIM-HABIBI

    2015-10-01

    Full Text Available Modeling and simulation techniques are now widely used alongside with their experimental counterparts in order to complement them, or sometimes to bring first insights into the possible outcome of experiments. “Modeling” is a general word that could encompass a wide range of methods that could be applied to a variety of subjects and problems. Here, the use of selected molecular modeling methods has been described in the field of endocrinology, throughout of some concrete examples. Keywords: Molecular modeling, Homology model, Docking, Endocrinology

  17. A comparison between algebraic models of molecular spectroscopy

    CERN Document Server

    Bijker, R; Lemus, R; Arias, J M; Pérez-Bernal, F

    1998-01-01

    We discuss a symmetry-adapted algebraic (or vibron) model for molecular spectroscopy. The model is formulated in terms of tensor operators under the molecular point group. In this way, we have identified interactions that are absent in previous versions of the vibron model, in which the Hamiltonian is expressed in terms of Casimir operators and their products. The inclusion of these new interactions leads to reliable spectroscopic predictions. As an example we study the vibrational excitations of the methane molecule, and compare our results with those obtained in other algebraic models.

  18. Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations

    Energy Technology Data Exchange (ETDEWEB)

    Giorgi, G.L., E-mail: g.giorgi@inrim.it [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy); Roncaglia, M. [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy); Raffa, F.A. [Politecnico di Torino, Dipartimento di Scienza Applicata e Tecnologia, Corso Duca degli Abruzzi 24, I-10129 Torino (Italy); Genovese, M. [INRIM, Strada delle Cacce 91, I-10135 Torino (Italy)

    2015-10-15

    During the long course of evolution, nature has learnt how to exploit quantum effects. In fact, recent experiments reveal the existence of quantum processes whose coherence extends over unexpectedly long time and space ranges. In particular, photosynthetic processes in light-harvesting complexes display a typical oscillatory dynamics ascribed to quantum coherence. Here, we consider the simple model where a dimer made of two chromophores is strongly coupled with a quasi-resonant vibrational mode. We observe the occurrence of wide oscillations of genuine quantum correlations, between electronic excitations and the environment, represented by vibrational bosonic modes. Such a quantum dynamics has been unveiled through the calculation of the negativity of entanglement and the discord, indicators widely used in quantum information for quantifying the resources needed to realize quantum technologies. We also discuss the possibility of approximating additional weakly-coupled off-resonant vibrational modes, simulating the disturbances induced by the rest of the environment, by a single vibrational mode. Within this approximation, one can show that the off-resonant bath behaves like a classical source of noise.

  19. Modeling pellet impact drilling process

    OpenAIRE

    Kovalev, Artem Vladimirovich; Ryabchikov, Sergey Yakovlevich; Isaev, Evgeniy Dmitrievich; Ulyanova, Oksana Sergeevna

    2016-01-01

    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 t...

  20. Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling.

    Science.gov (United States)

    Lupala, Cecylia S; Rasaeifar, Bahareh; Gomez-Gutierrez, Patricia; Perez, Juan J

    2017-08-14

    Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.

  1. 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...

  2. Comparative molecular modelling of biologically active sterols

    Science.gov (United States)

    Baran, Mariusz; Mazerski, Jan

    2015-04-01

    Membrane sterols are targets for a clinically important antifungal agent - amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction of amphotericin B with ergosterol as compared with cholesterol. The compounds studied were chosen on the basis of structural features characteristic for cholesterol and ergosterol and on available experimental data on the ability to form complexes with the antibiotic. Statistical analysis of the data obtained has been performed. The results show similarity of the conformational spaces occupied by all the sterols tested. This suggests that the conformational differences of sterol molecules are not the major feature responsible for the differential sterol - drug affinity.

  3. Interpretive and Formal Models of Discourse Processing.

    Science.gov (United States)

    Bulcock, Jeffrey W.; Beebe, Mona J.

    Distinguishing between interpretive and formal models of discourse processing and between qualitative and quantitative research, this paper argues that formal models are the analogues of interpretive models, and that the two are complementary. It observes that interpretive models of reading are being increasingly derived from qualitative research…

  4. Molecular Model of the Contractile Ring

    CERN Document Server

    Biron, D; Tlusty, Tsvi; Moses, Elisha; 10.1103/PhysRevLett.95.098102

    2010-01-01

    We present a model for the actin contractile ring of adherent animal cells. The model suggests that the actin concentration within the ring and consequently the power that the ring exerts both increase during contraction. We demonstrate the crucial role of actin polymerization and depolymerization throughout cytokinesis, and the dominance of viscous dissipation in the dynamics. The physical origin of two phases in cytokinesis dynamics ("biphasic cytokinesis") follows from a limitation on the actin density. The model is consistent with a wide range of measurements of the midzone of dividing animal cells.

  5. 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

  6. Understanding molecular weight reduction of starch during heating-shearing processes

    NARCIS (Netherlands)

    Einde, van den R.M.; Goot, van der A.J.; Boom, R.M.

    2003-01-01

    Recent understanding of the mechanisms underlying the changes in molecular weight of starch as a function of process parameters during thermomechanical treatment, for example extrusion, holds promise towards more effective optimization of thermomechanical processes according to the desired modificat

  7. Molecular Modeling on the PC (by Matthew F. Schlecht)

    Science.gov (United States)

    Rioux, Reviewed Frank

    2000-06-01

    "Computeraided molecular modeling doesn't exist for its own sake, but to contribute to scientific endeavor, and enable the scientist to work smarter." This is the last sentence of Schlecht's preface and it says something very important about contemporary scientific research in the academic and industrial venues. Owing to the accelerating improvement in computer technology (hardware and software) and its widespread availability, molecular modeling has become a reliable and important tool in chemical research. Consequently, experimentalists have incorporated molecular modeling techniques in their research, and partnerships with computational chemists have become common. This is a wellorganized and thorough monograph that devotes its attention to one type of molecular modeling, molecular mechanics, and one molecular modeling software package, PCMODEL. Schlecht targets two reader-user groups, the novice and the journeyman modeler, and articulates three goals. He wants to provide the novice with an introduction to molecular mechanics, and after that with some practical examples of the use of empirical force field calculations. His third goal is to provide the journeyman modeler with a reference work that will aid "further study and practice". These are potentially conflicting goals, but Schlecht is, in my opinion, successful because of the way his book is organized. A comprehensive treatment such as this one is not meant to be read from cover to cover, because it is both an exposition of basic principles and a user's manual. Therefore, the novice and the experienced modeler will undoubtedly use this book in different ways. For example, a novice modeler might be advised to read the Preface and Chapter 1, which together provide a broad introduction to the historical development and goals of molecular mechanics. From there the novice could go to Chapter 5 and read section 5.1 on the components of the molecular mechanics force field, which is presented in 22 pages with

  8. A Heuristic Molecular Model of Hydrophobic Interactions

    OpenAIRE

    Hummer, G; Garde, S; Garcia, A.E.; Pohorille, A; Pratt, L.R.

    1995-01-01

    Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple heuristic model of hydrophobic effects in terms of density fluctuations is developed. This model accounts quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes; it therefore clarifies the underlying physics...

  9. 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

  10. An Extension to the Weibull Process Model

    Science.gov (United States)

    1981-11-01

    Subt5l . TYPE OF REPORT & PERIOD COVERED AN EXTENSION+TO THE WEIBULL PROCESS MODEL 6. PERFORMING O’G. REPORT NUMBER I. AuTHOR() S. CONTRACT OR GRANT...indicatinq its imrportance to applications. 4 AN EXTENSION TO TE WEIBULL PROCESS MODEL 1. INTRODUCTION Recent papers by Bain and Engelhardt (1980)1 and Crow

  11. Hybrid modelling of anaerobic wastewater treatment processes.

    Science.gov (United States)

    Karama, A; Bernard, O; Genovesi, A; Dochain, D; Benhammou, A; Steyer, J P

    2001-01-01

    This paper presents a hybrid approach for the modelling of an anaerobic digestion process. The hybrid model combines a feed-forward network, describing the bacterial kinetics, and the a priori knowledge based on the mass balances of the process components. We have considered an architecture which incorporates the neural network as a static model of unmeasured process parameters (kinetic growth rate) and an integrator for the dynamic representation of the process using a set of dynamic differential equations. The paper contains a description of the neural network component training procedure. The performance of this approach is illustrated with experimental data.

  12. 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

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

    Science.gov (United States)

    2017-01-01

    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. PMID:28637852

  14. Fermi resonance-algebraic model for molecular vibrational spectra

    Institute of Scientific and Technical Information of China (English)

    侯喜文; 董世海; 谢汨; 马中骐

    1999-01-01

    A Fermi resonance-algebraic model is proposed for molecular vibrations, where a U(2) algebra is used for describing the vibrations of each bond, and Fermi resonances between stretching and bending modes are taken into account. The model for a bent molecule XY2 and a molecule XY3 is successfully applied to fitting the recently observed vibrational spectrum of the water molecule and arsine (AsH3), respectively, and the results are compared with those of other models. Calculations show that algebraic approaches can be used as an effective method to describe molecular vibrations with small standard deviations.

  15. Improving the kinetics from molecular simulations using biased Markov state models

    Science.gov (United States)

    Rudzinski, Joseph F.; Kremer, Kurt; Bereau, Tristan

    Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and experimentally-measured observables. This work presents a robust and systematic framework for reweighting the ensemble of dynamical paths sampled in a molecular simulation in order to ensure consistency with a set of given kinetic observables. The method employs the well-developed Markov state modeling framework in order to efficiently treat simulated dynamical paths. We demonstrate that, for two distinct coarse-grained peptide models, biasing the Markov state model to reproduce a small number of reference kinetic constraints significantly improves the dynamical properties of the model, while simultaneously refining the static equilibrium properties.

  16. VARTM Process Modeling of Aerospace Composite Structures

    Science.gov (United States)

    Song, Xiao-Lan; Grimsley, Brian W.; Hubert, Pascal; Cano, Roberto J.; Loos, Alfred C.

    2003-01-01

    A three-dimensional model was developed to simulate the VARTM composite manufacturing process. The model considers the two important mechanisms that occur during the process: resin flow, and compaction and relaxation of the preform. The model was used to simulate infiltration of a carbon preform with an epoxy resin by the VARTM process. The model predicted flow patterns and preform thickness changes agreed qualitatively with the measured values. However, the predicted total infiltration times were much longer than measured most likely due to the inaccurate preform permeability values used in the simulation.

  17. Declarative business process modelling: principles and modelling languages

    Science.gov (United States)

    Goedertier, Stijn; Vanthienen, Jan; Caron, Filip

    2015-02-01

    The business process literature has proposed a multitude of business process modelling approaches or paradigms, each in response to a different business process type with a unique set of requirements. Two polar paradigms, i.e. the imperative and the declarative paradigm, appear to define the extreme positions on the paradigm spectrum. While imperative approaches focus on explicitly defining how an organisational goal should be reached, the declarative approaches focus on the directives, policies and regulations restricting the potential ways to achieve the organisational goal. In between, a variety of hybrid-paradigms can be distinguished, e.g. the advanced and adaptive case management. This article focuses on the less-exposed declarative approach on process modelling. An outline of the declarative process modelling and the modelling approaches is presented, followed by an overview of the observed declarative process modelling principles and an evaluation of the declarative process modelling approaches.

  18. 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....

  19. Process and Context in Choice Models

    DEFF Research Database (Denmark)

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

    2012-01-01

    We develop a general framework that extends choice models by including an explicit representation of the process and context of decision making. Process refers to the steps involved in decision making. Context refers to factors affecting the process, focusing in this paper on social networks. The...

  20. Will Rule based BPM obliterate Process Models?

    NARCIS (Netherlands)

    Joosten, S.; Joosten, H.J.M.

    2007-01-01

    Business rules can be used directly for controlling business processes, without reference to a business process model. In this paper we propose to use business rules to specify both business processes and the software that supports them. Business rules expressed in smart mathematical notations bring

  1. A Heuristic Molecular Model of Hydrophobic Interactions

    CERN Document Server

    Hummer, G; García, A E; Pohorille, A; Pratt, L R

    1995-01-01

    Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple heuristic model of hydrophobic effects in terms of density fluctuations is developed. This model accounts quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes; it therefore clarifies the underlying physics of hydrophobic effects and permits important applications to conformational equilibria of nonpolar solutes and hydrophobic residues in biopolymers.

  2. Active site modeling in copper azurin molecular dynamics simulations

    NARCIS (Netherlands)

    Rizzuti, B; Swart, M; Sportelli, L; Guzzi, R

    2004-01-01

    Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the po

  3. A dipole interaction model for the molecular second hyperpolarizability

    NARCIS (Netherlands)

    Jensen, L; Sylvester-Hvid, KO; Mikkelsen, KV; Astrand, PO

    2003-01-01

    A dipole interaction model (IM) for calculating the molecular second hyperpolarizability, gamma, of aliphatic and aromatic molecules has been investigated. The model has been parametrized from quantum chemical calculations of gamma at the self-consistent field (SCF) level of theory for 72 molecules.

  4. Reasoning with Atomic-Scale Molecular Dynamic Models

    Science.gov (United States)

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

    The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

  5. 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.

  6. 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.

  7. Applications of Molecular and Materials Modeling

    Science.gov (United States)

    2002-01-01

    nittalabo-e.html Osaka University, Institute for Protein Research Protein modeling Prof. Haruki Nakamura http://www.protein.osaka- u.ac.jp/kessho/members...band structure of YH3. Phys. Rev. B 61, 16491- 16496. Nagashima, U., S. Obara, K. Murakami , T. Yoshii, S. Shirakawa, T. Amisake, K. Kitamura, O. Kitao

  8. 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.

  9. Corn Storage Protein - A Molecular Genetic Model

    Energy Technology Data Exchange (ETDEWEB)

    Messing, Joachim [Rutgers, The State University of New Jersey

    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

  10. Final Report, "Molecular Design of Hydrocarbon Oxidation Catalytic Processes"

    Energy Technology Data Exchange (ETDEWEB)

    Professor Francisco Zaera

    2007-08-09

    The main goal of this project had been to use model systems to correlate selectivities in partial oxidation catalysis with the presence of specific sites on the surface of the catalyst. Extensive work was performed this year on characterizing oxygen-treated nickel surfaces by chemical means. Specifically, the surface chemistry of ammonia coadsorbed with atomic oxygen on Ni(110) single-crystal surfaces was studied by temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). It was determined that at intermediate oxygen coverages direct ammonia adsorption on nickel sites is suppressed, but a new high-temperature reaction regime is generated at 400 K where NHx surface fragments are rehydrogenated concurrently with the production of water and molecular hydrogen. The extensive isotope scrambling and hydrogen transfer seen from nitrogen- to oxygen-containing surface intermediates, and the optimum yields seen for this 400 K state at intermediate oxygen coverages, strongly suggest the direct interaction of the adsorbed ammonia with oxygen atoms at the end of the –Ni–O- rows that form upon reconstruction of the surface. Hydrogen transfer between ammonia and oxygen appears to take place directly via hydrogen bonding, and to be reversible but biased towards water formation. An equilibrium is reached between the produced water and the reacting surface oxygen and hydrogen. The strong influence of the OH surface groups on the thermal chemistry of the adsorbed ammonia was interpreted in terms of the adsorbing geometry of the OH groups on the surface, and of hydrogen bonding between adsorbed OH and NH3 species. In terms of alcohol reactivity, the adsorption of 2-iodoethanol, a precursor for the preparation of 2-hydroxyethyl and oxametallacycle surface species, was found to lead to two configurations involving either just the iodine atom or both iodine and hydroxyl ends of the molecule. A complex chemical behavior starts around 140 K with the

  11. Modeling of percolation process in hemicellulose hydrolysis.

    Science.gov (United States)

    Cahela, D R; Lee, Y Y; Chambers, R P

    1983-01-01

    A mathematical model was developed for a percolation reactor in connection with consecutive first-order reactions. The model was designed to simulated acid-catalyzed cellulose or hemicellulose hydrolysis. The modeling process resulted in an analytically derived reactor equation, including mass-transfer effects, which was found to be useful in process desing and reactor optimization. The modedl was verified by experimental data obtained from hemicellulose hydrolysis.

  12. Hybrid Sludge Modeling in Water Treatment Processes

    OpenAIRE

    Brenda, Marian

    2015-01-01

    Sludge occurs in many waste water and drinking water treatment processes. The numeric modeling of sludge is therefore crucial for developing and optimizing water treatment processes. Numeric single-phase sludge models mainly include settling and viscoplastic behavior. Even though many investigators emphasize the importance of modeling the rheology of sludge for good simulation results, it is difficult to measure, because of settling and the viscoplastic behavior. In this thesis, a new method ...

  13. On the computational modeling of FSW processes

    OpenAIRE

    Agelet de Saracibar Bosch, Carlos; Chiumenti, Michèle; Santiago, Diego de; Cervera Ruiz, Miguel; Dialami, Narges; Lombera, Guillermo

    2010-01-01

    This work deals with the computational modeling and numerical simulation of Friction Stir Welding (FSW) processes. Here a quasi-static, transient, mixed stabilized Eulerian formulation is used. Norton-Hoff and Sheppard-Wright rigid thermoplastic material models have been considered. A product formula algorithm, leading to a staggered solution scheme, has been used. The model has been implemented into the in-house developed FE code COMET. Results obtained in the simulation of FSW process are c...

  14. Molecular Simulations of RNA 2’-O-Transesterification Reaction Models in Solution

    OpenAIRE

    Radak, Brian K.; Harris, Michael E.; York, Darrin M.

    2012-01-01

    We employ quantum mechanical/molecular mechanical umbrella sampling simulations to probe the free energy surfaces of a series of increasingly complex reaction models of RNA 2’-O-transesterification in aqueous solution under alkaline conditions. Such models are valuable for understanding the uncatalyzed processes underlying catalytic cleavage of the phosphodiester backbone of RNA, a reaction of fundamental importance in biology. The chemically reactive atoms are modeled by the AM1/d-PhoT quant...

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

    Energy Technology Data Exchange (ETDEWEB)

    Wyrick, Jonathan; Bartels, Ludwig, E-mail: ludwig.bartels@ucr.edu [Pierce Hall, University of California-Riverside, Riverside, California 92521 (United States); Einstein, T. L. [Department of Physics and Condensed Matter Theory Center, University of Maryland, College Park, Maryland 20742-4111 (United States)

    2015-03-14

    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.

  16. 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.

  17. Molecular motors: how to make models that can be used to convey the concept of molecular ratchets and thermal capture.

    Science.gov (United States)

    DoHarris, Lindsay; Giesler, Amanda; Humber, Brent; Sukumar, Aravin; Janssen, Luke J

    2011-06-01

    A wide variety of cellular processes use molecular motors, including processive motors that move along some form of track (e.g., myosin with actin, kinesin or dynein with tubulin) and polymerases that move along a template (e.g., DNA and RNA polymerases, ribosomes). In trying to understand how these molecular motors actually move, many apply their understanding of how man-made motors work: the latter use some form of energy to exert a force or torque on its load. However, quite a different mechanism has been proposed to possibly account for the movement of molecular motors. Rather than hydrolyzing ATP to push or pull their load, they might use their own thermal vibrational energy as well as that of their load and their environment to move the load, capturing those movements that occur along a desired vector or axis and resisting others; ATP hydrolysis is required to make backward movements impossible. This intriguing thermal capture or Brownian ratchet model is relatively more difficult to convey to students. In this report, we describe several teaching aids that are very easily constructed using widely available household materials to convey the concept of a molecular ratchet.

  18. Extending Model Checking to Object Process Validation

    NARCIS (Netherlands)

    Rein, van H.

    2002-01-01

    Object-oriented techniques allow the gathering and modelling of system requirements in terms of an application area. The expression of data and process models at that level is a great asset in communication with non-technical people in that area, but it does not necessarily lead to consistent models

  19. The canonical equilibrium of constrained molecular models

    CERN Document Server

    Echenique, Pablo; García-Risueño, Pablo

    2011-01-01

    In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. However, as any other element that affects the physical model, the imposition of constraints must be assessed from the point of view of accuracy: both the dynamics and the equilibrium statistical mechanics are model-dependent, and they will be changed if constraints are used. In this review, we investigate the accuracy of constrained models at the level of the equilibrium statistical mechanics distributions produced by the different dynamics. We carefully derive the canonical equilibrium distributions of both the constrained and unconstrained dynamics, comparing the two of them by means of a "stiff" approximation to the latter. We do so both in the case of flexible and hard constraints, i.e., when the value of the constrained coordinates depends on the conformation and when it is a cons...

  20. Preform Characterization in VARTM Process Model Development

    Science.gov (United States)

    Grimsley, Brian W.; Cano, Roberto J.; Hubert, Pascal; Loos, Alfred C.; Kellen, Charles B.; Jensen, Brian J.

    2004-01-01

    Vacuum-Assisted Resin Transfer Molding (VARTM) is a Liquid Composite Molding (LCM) process where both resin injection and fiber compaction are achieved under pressures of 101.3 kPa or less. Originally developed over a decade ago for marine composite fabrication, VARTM is now considered a viable process for the fabrication of aerospace composites (1,2). In order to optimize and further improve the process, a finite element analysis (FEA) process model is being developed to include the coupled phenomenon of resin flow, preform compaction and resin cure. The model input parameters are obtained from resin and fiber-preform characterization tests. In this study, the compaction behavior and the Darcy permeability of a commercially available carbon fabric are characterized. The resulting empirical model equations are input to the 3- Dimensional Infiltration, version 5 (3DINFILv.5) process model to simulate infiltration of a composite panel.

  1. Application of Parallel Processing to the Investigation of Supercritical Droplet Evaporation and Combustion Using Molecular Dynamics

    Science.gov (United States)

    2007-11-02

    Molecular dynamics (MD) implemented on parallel processors was used to model supercritical droplet phenomena occurring in combustion devices. The use...of molecular dynamics allows the modeling of supercritical phenomena without an a priori knowledge of the equation of state or transport properties

  2. 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...

  3. An algebraic approach for simultaneous solution of process and molecular design problems

    Directory of Open Access Journals (Sweden)

    S. Bommareddy

    2010-09-01

    Full Text Available The property integration framework has allowed for simultaneous representation of processes and products from a properties perspective and thereby established a link between molecular and process design problems. The simultaneous approach involves solving two reverse problems. The first reverse problem identifies the property targets corresponding to the desired process performance. The second reverse problem is the reverse of a property prediction problem, which identifies the molecular structures that match the targets identified in the first problem. Group Contribution Methods (GCM are used to form molecular property operators that will be used to track properties. Earlier contributions in this area have worked to include higher order estimation of GCM for solving the molecular design problem. In this work, the accuracy of the property prediction is further enhanced by improving the techniques to enumerate higher order groups. Incorporation of these higher order enumeration techniques increases the efficiency of property prediction and thus the application range of the group contribution methods in molecular design problems. Successful tracking of properties is the key in applying the reverse problem formulation for integrated process and product design problems. An algebraic technique has been developed for solving process and molecular design problems simultaneously. Since both process and molecular property operators target the same optimum process performance, the set of inequality expressions can be solved simultaneously to identify the molecules that meet the desired process performance. Since this approach is based on an algebraic algorithm, any number of properties can be tracked simultaneously.

  4. Systematic improvement of molecular representations for machine learning models

    CERN Document Server

    Huang, Bing

    2016-01-01

    The predictive accuracy of Machine Learning (ML) models of molecular properties depends on the choice of the molecular representation. We introduce a hierarchy of representations based on uniqueness and target similarity criteria. To systematically control target similarity, we rely on interatomic many body expansions including Bonding, Angular, and higher order terms (BA). Addition of higher order contributions systematically increases similarity to the potential energy function as well as predictive accuracy of the resulting ML models. Numerical evidence is presented for the performance of BAML models trained on molecular properties pre-calculated at electron-correlated and density functional theory level of theory for thousands of small organic molecules. Properties studied include enthalpies and free energies of atomization, heatcapacity, zero-point vibrational energies, dipole-moment, polarizability, HOMO/LUMO energies and gap, ionization potential, electron affinity, and electronic excitations. After tr...

  5. 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.

  6. Quasi-classical theory of electronic flux density in electronically adiabatic molecular processes.

    Science.gov (United States)

    Diestler, D J

    2012-11-26

    The standard Born-Oppenheimer (BO) description of electronically adiabatic molecular processes predicts a vanishing electronic flux density (EFD). A previously proposed "coupled-channels" theory permits the extraction of the EFD from the BO wave function for one-electron diatomic systems, but attempts at generalization to many-electron polyatomic systems are frustrated by technical barriers. An alternative "quasi-classical" approach, which eliminates the explicit quantum dynamics of the electrons within a classical framework, yet retains the quantum character of the nuclear motion, appears capable of yielding EFDs for arbitrarily complex systems. Quasi-classical formulas for the EFD in simple systems agree with corresponding coupled-channels formulas. Results of the application of the new quasi-classical formula for the EFD to a model triatomic system indicate the potential of the quasi-classical scheme to elucidate the dynamical role of electrons in electronically adiabatic processes in more complex multiparticle systems.

  7. Statistical mechanics of neocortical interactions: Large-scale EEG influences on molecular processes.

    Science.gov (United States)

    Ingber, Lester

    2016-04-21

    Calculations further support the premise that large-scale synchronous firings of neurons may affect molecular processes. The context is scalp electroencephalography (EEG) during short-term memory (STM) tasks. The mechanism considered is Π=p+qA (SI units) coupling, where p is the momenta of free Ca(2+) waves, q the charge of Ca(2+) in units of the electron charge, and A the magnetic vector potential of current I from neuronal minicolumnar firings considered as wires, giving rise to EEG. Data has processed using multiple graphs to identify sections of data to which spline-Laplacian transformations are applied, to fit the statistical mechanics of neocortical interactions (SMNI) model to EEG data, sensitive to synaptic interactions subject to modification by Ca(2+) waves.

  8. 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.

  9. Breaching the skin barrier--insights from molecular simulation of model membranes.

    Science.gov (United States)

    Notman, Rebecca; Anwar, Jamshed

    2013-02-01

    Breaching the skin's barrier function by design is an important strategy for delivering drugs and vaccines to the body. However, while there are many proposed approaches for reversibly breaching the skin barrier, our understanding of the molecular processes involved is still rudimentary. Molecular simulation offers an unprecedented molecular-level resolution with an ability to reproduce molecular and bulk level properties. We review the basis of the molecular simulation methodology and give applications of relevance to the skin lipid barrier, focusing on permeation of molecules and chemical approaches for breaching the lipid barrier by design. The bulk kinetic model based on Fick's Law describing absorption of a drug through skin has been reconciled with statistical mechanical quantities such as the local excess chemical potential and local diffusion coefficient within the membrane structure. Applications of molecular simulation reviewed include investigations of the structure and dynamics of simple models of skin lipids, calculation of the permeability of molecules in simple model membranes, and mechanisms of action of the penetration enhancers, DMSO, ethanol and oleic acid. The studies reviewed illustrate the power and potential of molecular simulation to yield important physical insights, inform and rationalize experimental studies, and to predict structural changes, and kinetic and thermodynamic quantities. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Two-dimensional model of elastically coupled molecular motors

    Institute of Scientific and Technical Information of China (English)

    Zhang Hong-Wei; Wen Shu-Tang; Chen Gai-Rong; Li Yu-Xiao; Cao Zhong-Xing; Li Wei

    2012-01-01

    A flashing ratchet model of a two-headed molecular motor in a two-dimensional potential is proposed to simulate the hand-over-hand motion of kinesins.Extensive Langevin simulations of the model are performed.We discuss the dependences of motion and efficiency on the model parameters,including the external force and the temperature.A good qualitative agreement with the expected behavior is observed.

  11. 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

  12. 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.

  13. Job Aiding/Training Decision Process Model

    Science.gov (United States)

    1992-09-01

    I[ -, . 1’, oo Ii AL-CR-i1992-0004 AD-A256 947lEE = IIEI ifl ll 1l I JOB AIDING/TRAINING DECISION PROCESS MODEL A R M John P. Zenyuh DTIC S Phillip C...March 1990 - April 1990 4. TITLE AND SUBTITLE S. FUNDING NUMBERS C - F33615-86-C-0545 Job Aiding/Training Decision Process Model PE - 62205F PR - 1121 6...Components to Process Model Decision and Selection Points ........... 32 13. Summary of Subject Recommendations for Aiding Approaches

  14. Fuel Conditioning Facility Electrorefiner Process Model

    Energy Technology Data Exchange (ETDEWEB)

    DeeEarl Vaden

    2005-10-01

    The Fuel Conditioning Facility at the Idaho National Laboratory processes spent nuclear fuel from the Experimental Breeder Reactor II using electro-metallurgical treatment. To process fuel without waiting for periodic sample analyses to assess process conditions, an electrorefiner process model predicts the composition of the electrorefiner inventory and effluent streams. For the chemical equilibrium portion of the model, the two common methods for solving chemical equilibrium problems, stoichiometric and non stoichiometric, were investigated. In conclusion, the stoichiometric method produced equilibrium compositions close to the measured results whereas the non stoichiometric method did not.

  15. MULTI-SCALE GAUSSIAN PROCESSES MODEL

    Institute of Scientific and Technical Information of China (English)

    Zhou Yatong; Zhang Taiyi; Li Xiaohe

    2006-01-01

    A novel model named Multi-scale Gaussian Processes (MGP) is proposed. Motivated by the ideas of multi-scale representations in the wavelet theory, in the new model, a Gaussian process is represented at a scale by a linear basis that is composed of a scale function and its different translations. Finally the distribution of the targets of the given samples can be obtained at different scales. Compared with the standard Gaussian Processes (GP) model, the MGP model can control its complexity conveniently just by adjusting the scale parameter. So it can trade-off the generalization ability and the empirical risk rapidly. Experiments verify the feasibility of the MGP model, and exhibit that its performance is superior to the GP model if appropriate scales are chosen.

  16. Hybrid modelling of a sugar boiling process

    CERN Document Server

    Lauret, Alfred Jean Philippe; Gatina, Jean Claude

    2012-01-01

    The first and maybe the most important step in designing a model-based predictive controller is to develop a model that is as accurate as possible and that is valid under a wide range of operating conditions. The sugar boiling process is a strongly nonlinear and nonstationary process. The main process nonlinearities are represented by the crystal growth rate. This paper addresses the development of the crystal growth rate model according to two approaches. The first approach is classical and consists of determining the parameters of the empirical expressions of the growth rate through the use of a nonlinear programming optimization technique. The second is a novel modeling strategy that combines an artificial neural network (ANN) as an approximator of the growth rate with prior knowledge represented by the mass balance of sucrose crystals. The first results show that the first type of model performs local fitting while the second offers a greater flexibility. The two models were developed with industrial data...

  17. Probabilistic models of language processing and acquisition.

    Science.gov (United States)

    Chater, Nick; Manning, Christopher D

    2006-07-01

    Probabilistic methods are providing new explanatory approaches to fundamental cognitive science questions of how humans structure, process and acquire language. This review examines probabilistic models defined over traditional symbolic structures. Language comprehension and production involve probabilistic inference in such models; and acquisition involves choosing the best model, given innate constraints and linguistic and other input. Probabilistic models can account for the learning and processing of language, while maintaining the sophistication of symbolic models. A recent burgeoning of theoretical developments and online corpus creation has enabled large models to be tested, revealing probabilistic constraints in processing, undermining acquisition arguments based on a perceived poverty of the stimulus, and suggesting fruitful links with probabilistic theories of categorization and ambiguity resolution in perception.

  18. Extracting Realistic Kinetics of Rare Activated Processes from Accelerated Molecular Dynamics Using Kramers' Theory.

    Science.gov (United States)

    Doshi, Urmi; Hamelberg, Donald

    2011-03-08

    The cis-trans isomerization of peptide bonds is very slow, occurring in hundreds of seconds. Kinetic studies of such processes using straightforward molecular dynamics are currently not possible. Here, we use Kramers' rate theory in the high friction regime in combination with accelerated molecular dynamics in explicit solvent to successfully retrieve the normal rate of cis to trans switching in the glycyl-prolyl dipeptide. Our approach bypasses the time-reweighting problem of the hyperdynamics scheme, wherein the addition of the bias potential alters the transition state regions and avoids an accurate estimation of kinetics. By performing accelerated molecular dynamics at a few different levels of acceleration, the rate of isomerization is enhanced as much as 10(10) to 10(11) times. Remarkably, the normal rates obtained by simply extrapolating to zero bias are within an order of experimental estimates. This provides validation from a kinetic standpoint of the ω torsional parameters of the AMBER force field that were recently revised by matching to experimentally measured equilibrium properties. We also provide a comparative analysis of the performance of the widely used water models, i.e., TIP3P and SPC/E, in estimating the kinetics of cis-trans isomerization. Furthermore, we show that the dynamic properties of bulk water can be corrected by adjusting the collision frequency in a Langevin thermostat, which then allows for better reproduction of cis-trans isomerization kinetics and a closer agreement of rates between experiments and simulations.

  19. Examination of Bond Properties through Infrared Spectroscopy and Molecular Modeling in the General Chemistry Laboratory

    Science.gov (United States)

    Csizmar, Clifford M.; Force, Dee Ann; Warner, Don L.

    2012-01-01

    A concerted effort has been made to increase the opportunities for undergraduate students to address scientific problems employing the processes used by practicing chemists. As part of this effort, an infrared (IR) spectroscopy and molecular modeling experiment was developed for the first-year general chemistry laboratory course. In the…

  20. Examination of Bond Properties through Infrared Spectroscopy and Molecular Modeling in the General Chemistry Laboratory

    Science.gov (United States)

    Csizmar, Clifford M.; Force, Dee Ann; Warner, Don L.

    2012-01-01

    A concerted effort has been made to increase the opportunities for undergraduate students to address scientific problems employing the processes used by practicing chemists. As part of this effort, an infrared (IR) spectroscopy and molecular modeling experiment was developed for the first-year general chemistry laboratory course. In the…

  1. 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.

  2. A General Random Walk Model of Molecular Motor

    Institute of Scientific and Technical Information of China (English)

    WANGXian-Ju; AIBao-Quan; LIUGuo-Tao; LIULiang-Gang

    2003-01-01

    A general random walk model framework is presented which can be used to statistically describe the internal dynamics and external mechanical movement of molecular motors along filament track. The motion of molecular motor in a periodic potential and a constant force is considered. We show that the molecular motor's movement becomes slower with the potential barrier increasing, but if the force is increased, the molecular motor''s movement becomes faster. The relation between the effective rate constant and the potential battler's height, and that between the effective rate constant and the value of the force are discussed. Our results are consistent with the experiments and relevant theoretical consideration, and can be used to explain some physiological phenomena.

  3. Markov State Models for Rare Events in Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Marco Sarich

    2013-12-01

    Full Text Available Rare, but important, transition events between long-lived states are a key feature of many molecular systems. In many cases, the computation of rare event statistics by direct molecular dynamics (MD simulations is infeasible, even on the most powerful computers, because of the immensely long simulation timescales needed. Recently, a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs, has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore, we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls.

  4. Mapping variable ring polymer molecular dynamics: A path-integral based method for nonadiabatic processes

    Science.gov (United States)

    Ananth, Nandini

    2013-09-01

    We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral representation of the quantum Boltzmann operator using continuous Cartesian variables for both electronic states and nuclear degrees of freedom. We demonstrate the accuracy of the MV-RPMD approach in calculations of real-time, thermal correlation functions for a range of two-state single-mode model systems with different coupling strengths and asymmetries. Further, we show that the ensemble of classical trajectories employed in these simulations preserves the Boltzmann distribution and provides a direct probe into real-time coupling between electronic state transitions and nuclear dynamics.

  5. Towards a universal competitive intelligence process model

    Directory of Open Access Journals (Sweden)

    Rene Pellissier

    2013-07-01

    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.

  6. 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.

  7. Online Rule Generation Software Process Model

    Directory of Open Access Journals (Sweden)

    Sudeep Marwaha

    2013-07-01

    Full Text Available 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 waterfall model for decision rules generation.

  8. 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…

  9. Active Versus Passive: Receiver Model Transforms for Diffusive Molecular Communication

    CERN Document Server

    Noel, Adam; Makrakis, Dimitrios; Hafid, Abdelhakim

    2016-01-01

    This paper presents an analytical comparison of the active and passive receiver models in diffusive molecular communication. In the active model, molecules are absorbed when they collide with the receiver surface. In the passive model, the receiver is a virtual boundary that does not affect molecule behavior. Two approaches are presented to derive transforms between the active and passive receiver signals. As an example, we unify the two models for an unbounded diffusion-only molecular communication system with a spherical receiver. As time increases in the three-dimensional system, the transform functions have constant scaling factors, such that the receiver models are effectively equivalent. Methods are presented to enable the transformation of stochastic simulations, which are used to verify the transforms and demonstrate that transforming the simulation of a passive receiver can be more efficient and more accurate than the direct simulation of an absorbing receiver.

  10. Molecular Modeling Approach to Cardiovascular Disease Targetting

    Directory of Open Access Journals (Sweden)

    Chandra Sekhar Akula,

    2010-05-01

    Full Text Available Cardiovascular disease, including stroke, is the leading cause of illness and death in the India. A number of studies have shown that inflammation of blood vessels is one of the major factors that increase the incidence of heart diseases, including arteriosclerosis (clogging of the arteries, stroke and myocardial infraction or heart attack. Studies have associated obesity and other components of metabolic syndrome, cardiovascular risk factors, with lowgradeinflammation. Furthermore, some findings suggest that drugs commonly prescribed to the lower cholesterol also reduce this inflammation, suggesting an additional beneficial effect of the stains. The recent development of angiotensin 11 (Ang11 receptor antagonists has enabled to improve significantly the tolerability profile of thisgroup of drugs while maintaining a high clinical efficacy. ACE2 is expressed predominantly in the endothelium and in renal tubular epithelium, and it thus may be an import new cardiovascular target. In the present study we modeled the structure of ACE and designed an inhibitor through using ARGUS lab and the validation of the Drug molecule is done basing on QSAR properties and Cache for this protein through CADD.

  11. Models and Modelling Tools for Chemical Product and Process Design

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    2016-01-01

    The design, development and reliability of a chemical product and the process to manufacture it, need to be consistent with the end-use characteristics of the desired product. One of the common ways to match the desired product-process characteristics is through trial and error based experiments......-based framework is that in the design, development and/or manufacturing of a chemical product-process, the knowledge of the applied phenomena together with the product-process design details can be provided with diverse degrees of abstractions and details. This would allow the experimental resources......, are the needed models for such a framework available? Or, are modelling tools that can help to develop the needed models available? Can such a model-based framework provide the needed model-based work-flows matching the requirements of the specific chemical product-process design problems? What types of models...

  12. MODELLING PURCHASING PROCESSES FROM QUALITY ASPECTS

    Directory of Open Access Journals (Sweden)

    Zora Arsovski

    2008-12-01

    Full Text Available Management has a fundamental task to identify and direct primary and specific processes within purchasing function, applying the up-to-date information infrastructure. ISO 9001:2000 defines a process as a number of interrelated or interactive activities transforming inputs and outputs, and the "process approach" as a systematic identification in management processes employed with the organization and particularly - relationships among the processes. To direct a quality management system using process approach, the organization is to determine the map of its general (basic processes. Primary processes are determined on the grounds of their interrelationship and impact on satisfying customers' needs. To make a proper choice of general business processes, it is necessary to determine the entire business flow, beginning with the customer demand up to the delivery of products or service provided. In the next step the process model is to be converted into data model which is essential for implementation of the information system enabling automation, monitoring, measuring, inspection, analysis and improvement of key purchase processes. In this paper are given methodology and some results of investigation of development of IS for purchasing process from aspects of quality.

  13. Applying CLIPS to control of molecular beam epitaxy processing

    Science.gov (United States)

    Rabeau, Arthur A.; Bensaoula, Abdelhak; Jamison, Keith D.; Horton, Charles; Ignatiev, Alex; Glover, John R.

    1990-01-01

    A key element of U.S. industrial competitiveness in the 1990's will be the exploitation of advanced technologies which involve low-volume, high-profit manufacturing. The demands of such manufacture limit participation to a few major entities in the U.S. and elsewhere, and offset the lower manufacturing costs of other countries which have, for example, captured much of the consumer electronics market. One such technology is thin-film epitaxy, a technology which encompasses several techniques such as Molecular Beam Epitaxy (MBE), Chemical Beam Epitaxy (CBE), and Vapor-Phase Epitaxy (VPE). Molecular Beam Epitaxy (MBE) is a technology for creating a variety of electronic and electro-optical materials. Compared to standard microelectronic production techniques (including gaseous diffusion, ion implantation, and chemical vapor deposition), MBE is much more exact, though much slower. Although newer than the standard technologies, MBE is the technology of choice for fabrication of ultraprecise materials for cutting-edge microelectronic devices and for research into the properties of new materials.

  14. 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.

  15. Mathematical modelling of the calcination process | Olayiwola ...

    African Journals Online (AJOL)

    Mathematical modelling of the calcination process. ... High quality lime is an essential raw material for Electric Arc Furnaces and Basic Oxygen Furnaces ... From the numerical simulation, it is observed that the gas temperature increases as the ...

  16. 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.

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

    Science.gov (United States)

    Tarakanova, Anna; Buehler, Markus J.

    2013-09-01

    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.

  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. A Process Model of Quantum Mechanics

    OpenAIRE

    Sulis, William

    2014-01-01

    A process model of quantum mechanics utilizes a combinatorial game to generate a discrete and finite causal space upon which can be defined a self-consistent quantum mechanics. An emergent space-time M and continuous wave function arise through a non-uniform interpolation process. Standard non-relativistic quantum mechanics emerges under the limit of infinite information (the causal space grows to infinity) and infinitesimal scale (the separation between points goes to zero). The model has th...

  20. A Procedural Model for Process Improvement Projects

    OpenAIRE

    Kreimeyer, Matthias;Daniilidis, Charampos;Lindemann, Udo

    2017-01-01

    Process improvement projects are of a complex nature. It is therefore necessary to use experience and knowledge gained in previous projects when executing a new project. Yet, there are few pragmatic planning aids, and transferring the institutional knowledge from one project to the next is difficult. This paper proposes a procedural model that extends common models for project planning to enable staff on a process improvement project to adequately plan their projects, enabling them to documen...

  1. 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

    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...

  2. Flux Analysis in Process Models via Causality

    CERN Document Server

    Kahramanoğullari, Ozan

    2010-01-01

    We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly recognised model of concurrency, and state transitions of process models, seen as Petri nets. We show that we can this way extract the causal resource dependencies in simulations between individual state transitions as partial orders of events. We propose transformations on the partial orders that provide means for further analysis, and introduce a software tool, which implements these ideas. By means of an example of a published model of the Rho GTP-binding proteins, we argue that this approach can provide the substitute for flux analysis techniques on ordinary differential equation models within the stochastic setting of process algebras.

  3. 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.

  4. Simulation of Dam Break Flow Using Quasi-Molecular Modelling

    Directory of Open Access Journals (Sweden)

    Sitthichai KULSRI

    2007-01-01

    Full Text Available We developed a new method based on quasi-molecular modelling to simulate dam break flow. Each quasi-molecule was a group of particles that interacted in a fashion entirely analogous to classical Newtonian molecular interactions. The tank had a base length of 58.4 cm. A water column with a base length of 14.6 cm and a height of 29.2 cm was initially supported on the right side by a vertical plate drawn up rapidly at time t = 0.0 s. The water fell under the influence of gravity acting vertically downwards. The numerical results were validated by quantitative comparison with a previous study. The predicted height and leading edge of the water column corresponded very well with experimental measurements from a previous study. Therefore, our new method based on quasi-molecular modelling showed its ability to adequately simulate a free surface problem.

  5. Interaction of quercetin with ovalbumin: Spectroscopic and molecular modeling studies

    Energy Technology Data Exchange (ETDEWEB)

    Lu Yan, E-mail: yanlu2001@sohu.co [College of Chemistry and Environmental Science, Henan Normal University, Xinxiang, Henan 453007 (China); Wang Yunlai; Gao Shenghua; Wang Gongke; Yan Changling; Chen Dejun [College of Chemistry and Environmental Science, Henan Normal University, Xinxiang, Henan 453007 (China)

    2009-09-15

    The binding of quercetin (QCT) to ovalbumin (OVA) in aqueous solution was investigated by molecular spectroscopy and modeling at pH 7.4. The fluorescence, synchronous fluorescence and UV-absorption spectroscopies were employed to study the mode and the mechanism for this interaction. QCT binding is characterized by one high affinity binding site with the association constants of the order of 10{sup 5}. The distance between donor (OVA) and acceptor (QCT) was estimated according to Forster's theory of non-radiation energy transfer. Molecular docking showed that the QCT can bind to the active site of OVA. The binding dynamics was expounded by thermodynamic parameters, molecular modeling and accessible surface area calculation, which entails that hydrophobic interactions, hydrogen bonding and electrostatic forces stabilizes the interaction.

  6. 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

  7. Ultrafast molecular processes mapped by femtosecond x-ray diffraction

    Science.gov (United States)

    Elsaesser, Thomas

    2012-02-01

    X-ray diffraction with a femtosecond time resolution allows for mapping photoinduced structural dynamics on the length scale of a chemical bond and in the time domain of atomic and molecular motion. In a pump-probe approach, a femtosecond excitation pulse induces structural changes which are probed by diffracting a femtosecond hard x-ray pulse from the excited sample. The transient angular positions and intensities of diffraction peaks give insight into the momentary atomic or molecular positions and into the distribution of electronic charge density. The simultaneous measurement of changes on different diffraction peaks is essential for determining atom positions and charge density maps with high accuracy. Recent progress in the generation of ultrashort hard x-ray pulses (Cu Kα, wavelength λ=0.154 nm) in laser-driven plasma sources has led to the implementation of the powder diffraction and the rotating crystal method with a time resolution of 100 fs. In this contribution, we report new results from powder diffraction studies of molecular materials. A first series of experiments gives evidence of a so far unknown concerted transfer of electrons and protons in ammonium sulfate [(NH4)2SO4], a centrosymmetric structure. Charge transfer from the sulfate groups results in the sub-100 fs generation of a confined electron channel along the c-axis of the unit cell which is stabilized by transferring protons from the adjacent ammonium groups into the channel. Time-dependent charge density maps display a periodic modulation of the channel's charge density by low-frequency lattice motions with a concerted electron and proton motion between the channel and the initial proton binding site. A second study addresses atomic rearrangements and charge dislocations in the non-centrosymmetric potassium dihydrogen phosphate [KH2PO4, KDP]. Photoexcitation generates coherent low-frequency motions along the LO and TO phonon coordinates, leaving the average atomic positions unchanged

  8. 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...

  9. 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.

  10. 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...

  11. [The model of adaptive primary image processing].

    Science.gov (United States)

    Dudkin, K N; Mironov, S V; Dudkin, A K; Chikhman, V N

    1998-07-01

    A computer model of adaptive segmentation of the 2D visual objects was developed. Primary image descriptions are realised via spatial frequency filters and feature detectors performing as self-organised mechanisms. Simulation of the control processes related to attention, lateral, frequency-selective and cross-orientation inhibition, determines the adaptive image processing.

  12. Laser surface processing and model studies

    CERN Document Server

    Yilbas, Bekir Sami

    2013-01-01

    This book introduces model studies associated with laser surface processing such as conduction limited heating, surface re-melting, Marangoni flow and its effects on the temperature field, re-melting of multi-layered surfaces, laser shock processing, and practical applications. The book provides insight into the physical processes involved with laser surface heating and phase change in laser irradiated region. It is written for engineers and researchers working on laser surface engineering.

  13. Molecular mechanism of interaction between norfloxacin and trypsin studied by molecular spectroscopy and modeling

    Science.gov (United States)

    Lu, Yan; Wang, Gongke; Lu, Xiumin; Lv, Juan; Xu, Meihua; Zhang, Weiwei

    2010-01-01

    The molecular mechanism of the binding of norfloxacin (NRF) to trypsin was investigated by fluorescence, synchronous fluorescence and UV-vis absorbance spectroscopy and molecular modeling at physiological conditions. The quenching mechanism and the binding mode were investigated in terms of the association constants and basic thermodynamic parameters. The results of spectroscopic measurements suggested that NRF have a strong ability to quench the intrinsic fluorescence of trypsin through static quenching procedure. Moreover, fluorescence experiments were also performed at different values of pH to elucidate the effect of pH on the binding. The NRF-trypsin complex was stabilized by hydrophobic forces and hydrogen bonding, via tryptophan residue as indicated from the thermodynamic parameters, which was consistent with the results of molecular docking and accessible surface area calculations.

  14. Molecular dynamics simulations of thermal effects in nanometric cutting process

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Understanding the basic action of how material removing in nanoscale is a critical issue of producing well-formed components.In order to clarify thermal effects on material removal at atomic level,molecular dynamics(MD)simulations of nanometric cutting of mono-crystalline copper are performed with Morse,EAM and Tersoff potential.The effects of cutting speed on temperature distribution are investigated.The simulation results demonstrate that the temperature distribution shows a roughly concentric shape around shear zone and a steep temperature gradient lies in diamond tool,a relative high temperature is located in shear zone and machined surface,but the highest temperature is found in chip.At a high cutting speed mode,the atoms in shear zone with high temperature implies a large stress is built up in a local region.

  15. 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.

  16. United polarizable multipole water model for molecular mechanics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu [Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Wang, Lee-Ping; Pande, Vijay S. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  17. The (mathematical modelling process in biosciences

    Directory of Open Access Journals (Sweden)

    Nestor V. Torres

    2015-12-01

    Full Text Available In this communication we introduce a general framework and discussion on the role of models and the modelling process within the scientific activity in the biosciences realm. The objective is sum up the common procedure during the formalization and analysis of a biological problem under the foundations of Systems Biology, which approach 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 the biology. Then, we present the modelization and analysis process 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 presentation the main features and shortcomings of the process are developed together with a set of rules that could help in the modelling endeavour of any biological system. 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 the modelling are currently posing to the current biology.

  18. Modeling aerosol processes at the local scale

    Energy Technology Data Exchange (ETDEWEB)

    Lazaridis, M.; Isukapalli, S.S.; Georgopoulos, P.G. [Environmental and Occupational Health Sciences Inst., NJ (United States)

    1998-12-31

    This work presents an approach for modeling photochemical gaseous and aerosol phase processes in subgrid plumes from major localized (e.g. point) sources (plume-in-grid modeling), thus improving the ability to quantify the relationship between emission source activity and ambient air quality. This approach employs the Reactive Plume Model (RPM-AERO) which extends the regulatory model RPM-IV by incorporating aerosol processes and heterogeneous chemistry. The physics and chemistry of elemental carbon, organic carbon, sulfate, sodium, chloride and crustal material of aerosols are treated and attributed to the PM size distribution. A modified version of the Carbon Bond IV chemical mechanism is included to model the formation of organic aerosol, and the inorganic multicomponent atmospheric aerosol equilibrium model, SEQUILIB is used for calculating the amounts of inorganic species in particulate matter. Aerosol dynamics modeled include mechanisms of nucleation, condensation and gas/particle partitioning of organic matter. An integrated trajectory-in-grid modeling system, UAM/RPM-AERO, is under continuing development for extracting boundary and initial conditions from the mesoscale photochemical/aerosol model UAM-AERO. The RPM-AERO is applied here to case studies involving emissions from point sources to study sulfate particle formation in plumes. Model calculations show that homogeneous nucleation is an efficient process for new particle formation in plumes, in agreement with previous field studies and theoretical predictions.

  19. Analysis and evaluation of collaborative modeling processes

    NARCIS (Netherlands)

    Ssebuggwawo, D.

    2012-01-01

    Analysis and evaluation of collaborative modeling processes is confronted with many challenges. On the one hand, many systems design and re-engineering projects require collaborative modeling approaches that can enhance their productivity. But, such collaborative efforts, which often consist of the

  20. Model checking Quasi Birth Death processes

    NARCIS (Netherlands)

    Remke, A.K.I.

    2004-01-01

    Quasi-Birth Death processes (QBDs) are a special class of infinite state CTMCs that combines a large degree of modeling expressiveness with efficient solution methods. This work adapts the well-known stochastic logic CSL for use on QBDs as CSL and presents model checking algorithms for so-called lev

  1. 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_18^2+ ...

  2. Promoting Representational Competence with Molecular Models in Organic Chemistry

    Science.gov (United States)

    Stull, Andrew T.; Gainer, Morgan; Padalkar, Shamin; Hegarty, Mary

    2016-01-01

    Mastering the many different diagrammatic representations of molecules used in organic chemistry is challenging for students. This article summarizes recent research showing that manipulating 3-D molecular models can facilitate the understanding and use of these representations. Results indicate that students are more successful in translating…

  3. 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)

  4. Promoting Representational Competence with Molecular Models in Organic Chemistry

    Science.gov (United States)

    Stull, Andrew T.; Gainer, Morgan; Padalkar, Shamin; Hegarty, Mary

    2016-01-01

    Mastering the many different diagrammatic representations of molecules used in organic chemistry is challenging for students. This article summarizes recent research showing that manipulating 3-D molecular models can facilitate the understanding and use of these representations. Results indicate that students are more successful in translating…

  5. Bayesian Network Based XP Process Modelling

    Directory of Open Access Journals (Sweden)

    Mohamed Abouelela

    2010-07-01

    Full Text Available A Bayesian Network based mathematical model has been used for modelling Extreme Programmingsoftware development process. The model is capable of predicting the expected finish time and theexpected defect rate for each XP release. Therefore, it can be used to determine the success/failure of anyXP Project. The model takes into account the effect of three XP practices, namely: Pair Programming,Test Driven Development and Onsite Customer practices. The model’s predictions were validated againsttwo case studies. Results show the precision of our model especially in predicting the project finish time.

  6. Process model patterns for collaborative work

    OpenAIRE

    Lonchamp, Jacques

    1998-01-01

    Colloque avec actes et comité de lecture.; As most real work is collaborative in nature, process model developers have to model collaborative situations. This paper defines generic collaborative patterns, ie, pragmatic and abstract building blocks for modelling recurrent situations. The first part specifies the graphical notation for the solution description. The second part gives some current patterns for the collaborative production of a single document in isolation and for the synchronizat...

  7. Using Perspective to Model Complex Processes

    Energy Technology Data Exchange (ETDEWEB)

    Kelsey, R.L.; Bisset, K.R.

    1999-04-04

    The notion of perspective, when supported in an object-based knowledge representation, can facilitate better abstractions of reality for modeling and simulation. The object modeling of complex physical and chemical processes is made more difficult in part due to the poor abstractions of state and phase changes available in these models. The notion of perspective can be used to create different views to represent the different states of matter in a process. These techniques can lead to a more understandable model. Additionally, the ability to record the progress of a process from start to finish is problematic. It is desirable to have a historic record of the entire process, not just the end result of the process. A historic record should facilitate backtracking and re-start of a process at different points in time. The same representation structures and techniques can be used to create a sequence of process markers to represent a historic record. By using perspective, the sequence of markers can have multiple and varying views tailored for a particular user's context of interest.

  8. Filament winding cylinders. I - Process model

    Science.gov (United States)

    Lee, Soo-Yong; Springer, George S.

    1990-01-01

    A model was developed which describes the filament winding process of composite cylinders. The model relates the significant process variables such as winding speed, fiber tension, and applied temperature to the thermal, chemical and mechanical behavior of the composite cylinder and the mandrel. Based on the model, a user friendly code was written which can be used to calculate (1) the temperature in the cylinder and the mandrel, (2) the degree of cure and viscosity in the cylinder, (3) the fiber tensions and fiber positions, (4) the stresses and strains in the cylinder and in the mandrel, and (5) the void diameters in the cylinder.

  9. Development of models and methods for the molecular simulation of large systems and molecules

    CERN Document Server

    Walter, Jonathan; Horsch, Martin; Vrabec, Jadran; Hasse, Hans

    2010-01-01

    The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new models for carbon dioxide and cyclohexanolare discussed and a new method for the model development is introduced. Force fields and models for the simulation of PNIPAAm hydrogel in pure water and sodium chloride solution are tested and verified and applied to the simulation of nucleation processes.

  10. Modelling of aerosol processes in plumes

    Energy Technology Data Exchange (ETDEWEB)

    Lazaridis, M.; Isukapalli, S.S.; Georgopoulos, P.G. [Norwegian Institute of Air Research, Kjeller (Norway)

    2001-07-01

    A modelling platform for studying photochemical gaseous and aerosol phase processes from localized (e.g., point) sources has been presented. The current approach employs a reactive plume model which extends the regulatory model RPM-IV by incorporating aerosol processes and heterogeneous chemistry. The physics and chemistry of elemental carbon, organic carbon, sulfate, nitrate, ammonium material of aerosols are treated and attributed to the PM size distribution. A modified version of the carbon bond IV chemical mechanism is included to model the formation of organic aerosol. Aerosol dynamics modeled include mechanisms of nucleation, condensation, dry deposition and gas/particle partitioning of organic matter. The model is first applied to a number of case studies involving emissions from point sources and sulfate particle formation in plumes. Model calculations show that homogeneous nucleation is an efficient process for new particle formation in plumes, in agreement with previous field studies and theoretical predictions. In addition, the model is compared with field data from power plant plumes with satisfactory predictions against gaseous species and total sulphate mass measurements. Finally, the plume model is applied to study secondary organic matter formation due to various emission categories such as vehicles and the oil production sector.

  11. 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.

  12. MODELING THE MOLECULAR COMPOSITION IN AN ACTIVE GALACTIC NUCLEUS DISK

    Energy Technology Data Exchange (ETDEWEB)

    Harada, Nanase [Max Planck Institute for Radio Astronomy, D-53121 Bonn (Germany); Thompson, Todd A. [Department of Astronomy, Ohio State University, Columbus, OH 43210 (United States); Herbst, Eric [Departments of Chemistry, Astronomy, and Physics, University of Virginia, Charlottesville, VA 22904 (United States)

    2013-03-10

    We use a high-temperature chemical network to derive the molecular abundances in axisymmetric accretion disk models around active galactic nuclei (AGNs) within 100 pc using simple radial and vertical density and temperature distributions motivated by more detailed physical models. We explore the effects of X-ray irradiation and cosmic-ray ionization on the spatial distribution of the molecular abundances of CO, CN, CS, HCN, HCO{sup +}, HC{sub 3}N, C{sub 2}H, and c-C{sub 3}H{sub 2} using a variety of plausible disk structures. These simple models have molecular regions with an X-ray-dominated region layer, a midplane without the strong influence of X-rays, and a high-temperature region in the inner portion with moderate X-ray flux where families of polyynes (C{sub n}H{sub 2}) and cyanopolyynes can be enhanced. For the high midplane density disks we explore, we find that cosmic rays produced by supernovae do not significantly affect the regions unless the star formation efficiency significantly exceeds that of the Milky Way. We highlight molecular abundance observations and ratios that may distinguish among theoretical models of the density distribution in AGN disks. Finally, we assess the importance of the shock crossing time and the accretion time relative to the formation time for various chemical species. Vertical column densities are tabulated for a number of molecular species at both the characteristic shock crossing time and steady state. Although we do not attempt to fit any particular system or set of observations, we discuss our models and results in the context of the nearby AGN NGC 1068.

  13. Modeling Multivariate Volatility Processes: Theory and Evidence

    Directory of Open Access Journals (Sweden)

    Jelena Z. Minovic

    2009-05-01

    Full Text Available This article presents theoretical and empirical methodology for estimation and modeling of multivariate volatility processes. It surveys the model specifications and the estimation methods. Multivariate GARCH models covered are VEC (initially due to Bollerslev, Engle and Wooldridge, 1988, diagonal VEC (DVEC, BEKK (named after Baba, Engle, Kraft and Kroner, 1995, Constant Conditional Correlation Model (CCC, Bollerslev, 1990, Dynamic Conditional Correlation Model (DCC models of Tse and Tsui, 2002, and Engle, 2002. I illustrate approach by applying it to daily data from the Belgrade stock exchange, I examine two pairs of daily log returns for stocks and index, report the results obtained, and compare them with the restricted version of BEKK, DVEC and CCC representations. The methods for estimation parameters used are maximum log-likehood (in BEKK and DVEC models and twostep approach (in CCC model.

  14. Modeling the VARTM Composite Manufacturing Process

    Science.gov (United States)

    Song, Xiao-Lan; Loos, Alfred C.; Grimsley, Brian W.; Cano, Roberto J.; Hubert, Pascal

    2004-01-01

    A comprehensive simulation model of the Vacuum Assisted Resin Transfer Modeling (VARTM) composite manufacturing process has been developed. For isothermal resin infiltration, the model incorporates submodels which describe cure of the resin and changes in resin viscosity due to cure, resin flow through the reinforcement preform and distribution medium and compaction of the preform during the infiltration. The accuracy of the model was validated by measuring the flow patterns during resin infiltration of flat preforms. The modeling software was used to evaluate the effects of the distribution medium on resin infiltration of a flat preform. Different distribution medium configurations were examined using the model and the results were compared with data collected during resin infiltration of a carbon fabric preform. The results of the simulations show that the approach used to model the distribution medium can significantly effect the predicted resin infiltration times. Resin infiltration into the preform can be accurately predicted only when the distribution medium is modeled correctly.

  15. 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. .

  16. Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.

    Science.gov (United States)

    Chowdhury, Debashish

    2013-06-04

    A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here.

  17. Ancestral process and diffusion model with selection

    CERN Document Server

    Mano, Shuhei

    2008-01-01

    The ancestral selection graph in population genetics introduced by Krone and Neuhauser (1997) is an analogue to the coalescent genealogy. The number of ancestral particles, backward in time, of a sample of genes is an ancestral process, which is a birth and death process with quadratic death and linear birth rate. In this paper an explicit form of the number of ancestral particle is obtained, by using the density of the allele frequency in the corresponding diffusion model obtained by Kimura (1955). It is shown that fixation is convergence of the ancestral process to the stationary measure. The time to fixation of an allele is studied in terms of the ancestral process.

  18. MOLOCH computer code for molecular-dynamics simulation of processes in condensed matter

    Directory of Open Access Journals (Sweden)

    Derbenev I.V.

    2011-01-01

    Full Text Available Theoretical and experimental investigation into properties of condensed matter is one of the mainstreams in RFNC-VNIITF scientific activity. The method of molecular dynamics (MD is an innovative method of theoretical materials science. Modern supercomputers allow the direct simulation of collective effects in multibillion atom sample, making it possible to model physical processes on the atomistic level, including material response to dynamic load, radiation damage, influence of defects and alloying additions upon material mechanical properties, or aging of actinides. During past ten years, the computer code MOLOCH has been developed at RFNC-VNIITF. It is a parallel code suitable for massive parallel computing. Modern programming techniques were used to make the code almost 100% efficient. Practically all instruments required for modelling were implemented in the code: a potential builder for different materials, simulation of physical processes in arbitrary 3D geometry, and calculated data processing. A set of tests was developed to analyse algorithms efficiency. It can be used to compare codes with different MD implementation between each other.

  19. 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.

  20. Mathematical modeling of biomass fuels formation process.

    Science.gov (United States)

    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.

  1. From Business Value Model to Coordination Process Model

    Science.gov (United States)

    Fatemi, Hassan; van Sinderen, Marten; Wieringa, Roel

    The increased complexity of business webs calls for modeling the collaboration of enterprises from different perspectives, in particular the business and process perspectives, and for mutually aligning these perspectives. Business value modeling and coordination process modeling both are necessary for a good e-business design, but these activities have different goals and use different concepts. Nevertheless, the resulting models should be consistent with each other because they refer to the same system from different perspectives. Hence, checking the consistency between these models or producing one based on the other would be of high value. In this paper we discuss the issue of achieving consistency in multi-level e-business design and give guidelines to produce consistent coordination process models from business value models in a stepwise manner.

  2. 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:.

  3. Mathematical model of an optically pumped molecular laser

    CSIR Research Space (South Africa)

    Botha, LR

    2009-07-01

    Full Text Available pumped molecular laser Dr L R Botha, Dr C Bollig, D Esser, C Jacobs, D Preussler SAIP 2009 Durban Page 2 © CSIR 2008 www.csir.co.za Structure of talk • Introduction • Overview of HBr laser • Numerical Model • Comparison... µm laser ring oscillator & pre-amplifier 1.9 µm Optically Pumped Molecular laser @ 4 µm 95:5 HBr Absorption cell Fast detector 2.064 µm ± 1 nm Feedback control box Feedback loop 1 P ie zo m o u nt Fast detector Feedback loop 2 Gas...

  4. Vibrational Distribution of Hydrogen Molecular Ions in High-Energy Ionization Processes

    Institute of Scientific and Technical Information of China (English)

    CHEN Shao-Hao; HE Chun-Long; CHEN Chao; LI Jia-Ming

    2005-01-01

    @@ A theoretical time-dependent wave-packet dynamics method is applied to calculate the distribution of vibrational states of hydrogen molecular ions produced in high-energy ionization processes of hydrogen molecules. The isotope effect is elucidated in agreement with the available experimental measurements. Our proposed method should be readily applied in other atomic and molecular processes considering great advances in electronic computation science and technology.

  5. Multi-level molecular modelling for plasma medicine

    Science.gov (United States)

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

    2016-02-01

    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.

  6. Preliminary results on molecular modeling of asphaltenes using structure elucidation programs in conjunction with molecular simulation programs

    Energy Technology Data Exchange (ETDEWEB)

    Kowalewski, I.; Vandenbroucke, M.; Huc, A.Y.; Taylor, M.J.; Faulon, J.L. [Institut Francais du Petrole, Rueil-Malmaison (France). Division Geologie-Geochimie

    1996-01-01

    Molecular modeling using structure elucidation programs in conjunction with molecular simulation programs has been performed on asphaltene molecules, the heaviest fraction of crude oil, in order to obtain a chemical model allowing the tentative study of their physicochemical properties. Boscan asphaltenes (Venezuela) derived from a marine source rock have been analysed. The different steps of this molecular modeling are described. First, a 3-D chemical representation of Boscan asphaltene is defined from an analytical data set. Second, the results of molecular dynamic simulations indicate that only a few stable conformations are possible due to the high reticulation of the model of the asphaltene unit obtained. 42 refs., 6 figs., 9 tabs.

  7. The impact of accelerator processors for high-throughput molecular modeling and simulation.

    Science.gov (United States)

    Giupponi, G; Harvey, M J; De Fabritiis, G

    2008-12-01

    The recent introduction of cost-effective accelerator processors (APs), such as the IBM Cell processor and Nvidia's graphics processing units (GPUs), represents an important technological innovation which promises to unleash the full potential of atomistic molecular modeling and simulation for the biotechnology industry. Present APs can deliver over an order of magnitude more floating-point operations per second (flops) than standard processors, broadly equivalent to a decade of Moore's law growth, and significantly reduce the cost of current atom-based molecular simulations. In conjunction with distributed and grid-computing solutions, accelerated molecular simulations may finally be used to extend current in silico protocols by the use of accurate thermodynamic calculations instead of approximate methods and simulate hundreds of protein-ligand complexes with full molecular specificity, a crucial requirement of in silico drug discovery workflows.

  8. 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.

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... 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....

  10. 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.......A process model (PM) represents the graphical depiction of a business process, for instance, the entire process from online ordering a book until the parcel is delivered to the customer. Knowledge about relevant factors for creating PMs of high quality is lacking. The present study investigated...... 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...

  11. Molecular basis of processing wheat gluten toward biobased materials.

    Science.gov (United States)

    Lagrain, Bert; Goderis, Bart; Brijs, Kristof; Delcour, Jan A

    2010-03-08

    The unique properties of the wheat grain reside primarily in the gluten-forming storage proteins of its endosperm. Wheat gluten's structural and functional properties have led to an expanding diversity of applications in food products. However, its viscoelastic properties and low water solubility also are very interesting features for nonfood applications. Moreover, gluten is annually renewable and perfectly biodegradable. In the processing and setting of gluten containing products, temperature plays a very important role. In this review, the structure and reactivity of gluten are discussed and the importance of sulfhydryl (SH) and disulfide (SS) groups is demonstrated. Wheat gluten aggregation upon thermosetting proceeds through direct covalent cross-linking in and between its protein groups, glutenin and gliadin. Predominant reactions include SH oxidation and SH/SS interchange reactions leading to the formation of SS cross-links. Additionally, thermal treatment of gluten can result in the formation of other than SS covalent bonds. We here review two main technological approaches to make gluten-based materials: wet processes resulting in thin films and dry processes, such as extrusion or compression molding, exploiting the thermoplastic properties of proteins under low moisture conditions and potentially resulting in very useful materials. Gluten bioplastics can also be reinforced with natural fibers, resulting in biocomposites. Although a lot of progress has been made the past decade, the current gluten materials are still outperformed by their synthetic polymer counterparts.

  12. Causally nonseparable processes admitting a causal model

    Science.gov (United States)

    Feix, Adrien; Araújo, Mateus; Brukner, Časlav

    2016-08-01

    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.

  13. 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...

  14. Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

    DEFF Research Database (Denmark)

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

    2016-01-01

    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......)-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...... 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...

  15. 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.

  16. Stochastic differential equation model to Prendiville processes

    Science.gov (United States)

    Granita, Bahar, Arifah

    2015-10-01

    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.

  17. Interferences in Photodetachment of a Negative Molecular Ion Model

    Institute of Scientific and Technical Information of China (English)

    A. Afaq; DU Meng-Li

    2008-01-01

    By employing a two-center model, the total and differential cross sections in the photodetachment of "a negative molecular ion" are studied theoretically and obtained for the case of light polarization parallel to the molecular axis. We find that in contrast to the smooth behavior of the total cross section for perpendicular polarized light, the cross section for parallel polarized light shows an interesting oscillatory structure. The oscillations in the total cross section may provide a method to determine the distance between the two centers. We explain the oscillation in the total cross section as an interference effect using closed-orbit theory. We also calculated the detached-electron flux distributions on a screen placed at a large distance from the negative molecular ion. The distributions display multiple-ring-like interference patterns. Such interference patterns are similar to those in the photodetachment microscopy experiments.

  18. 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.

  19. 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.

  20. Recognition processes at a functionalized lipid surface observed with molecular resolution

    DEFF Research Database (Denmark)

    Vaknin, D.; Als-Nielsen, J.; Piepenstock, M.;

    1991-01-01

    chosen as a model system to investigate the structural characteristics of a recognition process on a molecular length scale. Changes in the neutron reflection from the surfaces of NaCl aqueous (H2O or D2O) protein solutions (10(-8) M SA) were used to monitor the interaction of the protein...... with a monolayer of a biotinylated lipid in situ. Refinement of the reflectivity data and independent fluorescence microscopic observation of the interface using FITC-labeled SA showed that the protein forms macroscopically homogeneous (and presumably crystalline) domains covering a large portion of the surface...... with each protein molecule. Quantitative binding was found to occur at biotin surface concentrations as low as 1 molecule/1,250 angstrom 2 (compared with approximately 1 molecule/40 angstrom 2 for dense packing). This study demonstrates the application of a promising new tool for the systematic...

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

    OpenAIRE

    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...

  2. Modeling heterogeneous chemical processes on aerosol surface

    Institute of Scientific and Technical Information of China (English)

    Junjun Deng; Tijian Wang; Li Liu; Fei Jiang

    2010-01-01

    To explore the possible impact of heterogeneous chemical processes on atmospheric trace components,a coupled box model including gas-phase chemical processes,aerosol thermodynamic equilibrium processes,and heterogeneous chemical processes on the surface of dust,black carbon(BC)and sea salt is set up to simulate the effects of heterogeneous chemistry on the aerosol surface,and analyze the primary factors affecting the heterogeneous processes.Results indicate that heterogeneous chemical processes on the aerosol surface in the atmosphere will affect the concentrations of trace gases such as H2O2,HO2,O3,NO2,NO3,HNO3 and SO2,and aerosols such as SO42-,NO3-and NH4+.Sensitivity tests suggest that the magnitude of the impact of heterogeneous processes strongly depends on aerosol concentration and the surface uptake coefficients used in the box model.However,the impact of temperature on heterogeneous chemical processes is considerably less.The"renoxification"of HNO3 will affect the components of the troposphere such as nitrogen oxide and ozone.

  3. Multiscale simulation of molecular processes in cellular environments

    Science.gov (United States)

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

    2016-11-01

    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'.

  4. 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'.

  5. Incorporating evolutionary processes into population viability models.

    Science.gov (United States)

    Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

    2015-06-01

    We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence.

  6. Comparison of two turbulent models in simulating evaporating liquid film in a wiped molecular distillator

    Institute of Scientific and Technical Information of China (English)

    XIANG Aishuang; XU Songlin

    2005-01-01

    Velocity field of evaporating liquid film in a wiped molecular distillator was simulated with a computational fluid dynamics (CFD) software, and two turbulent models treating near-wall flow were compared. Differences between wiped and other molecular distillations were introduced to explain why turbulent model should be used in this simulation. Three assumptions were made in order to simplify simulating processes. In rotating coordinate system, fixed other settings, the above two turbulent models were used, and the volume of fluid (VOF) multiphase model was also applied to tracking the liquid-gas surface. Both of the simulating results are basically identical with real situation and were compared in several aspects. It was concluded that both of the turbulent models are suitable in this simulation.

  7. 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...

  8. 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.

  9. A process algebra model of QED

    Science.gov (United States)

    Sulis, William

    2016-03-01

    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.

  10. Coupling lattice Boltzmann and molecular dynamics models for dense fluids

    Science.gov (United States)

    Dupuis, A.; Kotsalis, E. M.; Koumoutsakos, P.

    2007-04-01

    We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of two- and three-dimensional flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.

  11. Molecular Code Division Multiple Access: Gaussian Mixture Modeling

    Science.gov (United States)

    Zamiri-Jafarian, Yeganeh

    Communications between nano-devices is an emerging research field in nanotechnology. Molecular Communication (MC), which is a bio-inspired paradigm, is a promising technique for communication in nano-network. In MC, molecules are administered to exchange information among nano-devices. Due to the nature of molecular signals, traditional communication methods can't be directly applied to the MC framework. The objective of this thesis is to present novel diffusion-based MC methods when multi nano-devices communicate with each other in the same environment. A new channel model and detection technique, along with a molecular-based access method, are proposed in here for communication between asynchronous users. In this work, the received molecular signal is modeled as a Gaussian mixture distribution when the MC system undergoes Brownian noise and inter-symbol interference (ISI). This novel approach demonstrates a suitable modeling for diffusion-based MC system. Using the proposed Gaussian mixture model, a simple receiver is designed by minimizing the error probability. To determine an optimum detection threshold, an iterative algorithm is derived which minimizes a linear approximation of the error probability function. Also, a memory-based receiver is proposed to improve the performance of the MC system by considering previously detected symbols in obtaining the threshold value. Numerical evaluations reveal that theoretical analysis of the bit error rate (BER) performance based on the Gaussian mixture model match simulation results very closely. Furthermore, in this thesis, molecular code division multiple access (MCDMA) is proposed to overcome the inter-user interference (IUI) caused by asynchronous users communicating in a shared propagation environment. Based on the selected molecular codes, a chip detection scheme with an adaptable threshold value is developed for the MCDMA system when the proposed Gaussian mixture model is considered. Results indicate that the

  12. Model-Free Adaptive Heating Process Control

    OpenAIRE

    Ivana LUKÁČOVÁ; Piteľ, Ján

    2009-01-01

    The aim of this paper is to analyze the dynamic behaviour of a Model-Free Adaptive (MFA) heating process control. The MFA controller is designed as three layer neural network with proportional element. The method of backward propagation of errors was used for neural network training. Visualization and training of the artificial neural network was executed by Netlab in Matlab environment. Simulation of the MFA heating process control with outdoor temperature compensation has proved better resu...

  13. Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control.

    Science.gov (United States)

    Lebuhn, Michael; Weiß, Stefan; Munk, Bernhard; Guebitz, Georg M

    2015-01-01

    Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

  14. Identifying the molecular basis of host-parasite coevolution: merging models and mechanisms.

    Science.gov (United States)

    Dybdahl, Mark F; Jenkins, Christina E; Nuismer, Scott L

    2014-07-01

    Mathematical models of the coevolutionary process have uncovered consequences of host-parasite interactions that go well beyond the traditional realm of the Red Queen, potentially explaining several important evolutionary transitions. However, these models also demonstrate that the specific consequences of coevolution are sensitive to the structure of the infection matrix, which is embedded in models to describe the likelihood of infection in encounters between specific host and parasite genotypes. Traditional cross-infection approaches to estimating infection matrices might be unreliable because evolutionary dynamics and experimental sampling lead to missing genotypes. Consequently, our goal is to identify the likely structure of infection matrices by synthesizing molecular mechanisms of host immune defense and parasite counterdefense with coevolutionary models. This synthesis reveals that the molecular mechanisms of immune reactions, although complex and diverse, conform to two basic models commonly used within coevolutionary theory: matching infection and targeted recognition. Our synthesis also overturns conventional wisdom, revealing that the general models are not taxonomically restricted but are applicable to plants, invertebrates, and vertebrates. Finally, our synthesis identifies several important areas for future research that should improve the explanatory power of coevolutionary models. The most important among these include empirical studies to identify the molecular hotspots of genotypic specificity and theoretical studies examining the consequences of matrices that more accurately represent multistep infection processes and quantitative defenses.

  15. VUV diagnostic of electron impact processes in low temperature molecular hydrogen plasma

    CERN Document Server

    Komppula, J

    2015-01-01

    Novel methods for diagnostics of molecular hydrogen plasma processes, such as ionization, production of high vibrational levels, dissociation of molecules via excitation to singlet and triplet states and production of metastable states, are presented for molecular hydrogen plasmas in corona equilibrium. The methods are based on comparison of rate coefficients of plasma processes and optical emission spectroscopy of lowest singlet and triplet transitions, i.e. Lyman-band ($B^1\\Sigma^+_u \\rightarrow X^1\\Sigma^+_g$) and molecular continuum ($a^3\\Sigma^+_g \\rightarrow b^3\\Sigma^+_u$), of the hydrogen molecule in VUV wavelength range. Comparison of rate coefficients of spin-allowed and/or spin-forbidden excitations reduces the uncertainty caused by the non-equilibrium distributions of electron energy and molecular vibrational level, which are typically known poorly in plasma sources. The described methods are applied to estimate the rates of various plasma processes in a filament arc discharge.

  16. HYDROLOGICAL PROCESSES MODELLING USING ADVANCED HYDROINFORMATIC TOOLS

    Directory of Open Access Journals (Sweden)

    BEILICCI ERIKA

    2014-03-01

    Full Text Available The water has an essential role in the functioning of ecosystems by integrating the complex physical, chemical, and biological processes that sustain life. Water is a key factor in determining the productivity of ecosystems, biodiversity and species composition. Water is also essential for humanity: water supply systems for population, agriculture, fisheries, industries, and hydroelectric power depend on water supplies. The modelling of hydrological processes is an important activity for water resources management, especially now, when the climate change is one of the major challenges of our century, with strong influence on hydrological processes dynamics. Climate change and needs for more knowledge in water resources require the use of advanced hydroinformatic tools in hydrological processes modelling. The rationale and purpose of advanced hydroinformatic tools is to develop a new relationship between the stakeholders and the users and suppliers of the systems: to offer the basis (systems which supply useable results, the validity of which cannot be put in reasonable doubt by any of the stakeholders involved. For a successful modelling of hydrological processes also need specialists well trained and able to use advanced hydro-informatics tools. Results of modelling can be a useful tool for decision makers to taking efficient measures in social, economical and ecological domain regarding water resources, for an integrated water resources management.

  17. SWOT Analysis of Software Development Process Models

    Directory of Open Access Journals (Sweden)

    Ashish B. Sasankar

    2011-09-01

    Full Text Available Software worth billions and trillions of dollars have gone waste in the past due to lack of proper techniques used for developing software resulting into software crisis. Historically , the processes of software development has played an important role in the software engineering. A number of life cycle models have been developed in last three decades. This paper is an attempt to Analyze the software process model using SWOT method. The objective is to identify Strength ,Weakness ,Opportunities and Threats of Waterfall, Spiral, Prototype etc.

  18. Temperature Modelling of the Biomass Pretreatment Process

    DEFF Research Database (Denmark)

    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...... distribution. Therefore, an accurate temperature model is critical for observing the biomass pretreatment. More than that, the biomass is also pushed with a constant horizontal speed along the reactor in order to ensure a continuous throughput. The goal of this paper is to derive a temperature model...

  19. Fundamentals of Numerical Modelling of Casting Processes

    DEFF Research Database (Denmark)

    Pryds, Nini; Thorborg, Jesper; Lipinski, Marek;

    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...

  20. Integrated Multiscale Modeling of Molecular Computing Devices. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Schulze, Tim [Univ. of Tennessee, Knoxville, TN (United States)

    2012-11-01

    The general theme of this research has been to expand the capabilities of a simulation technique, Kinetic Monte Carlo (KMC) and apply it to study self-assembled nano-structures on epitaxial thin films. KMC simulates thin film growth and evolution by replacing the detailed dynamics of the system's evolution, which might otherwise be studied using molecular dynamics, with an appropriate stochastic process.

  1. Integrated Multiscale Modeling of Molecular Computing Devices. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Schulze, Tim [Univ. of Tennessee, Knoxville, TN (United States)

    2012-11-01

    The general theme of this research has been to expand the capabilities of a simulation technique, Kinetic Monte Carlo (KMC) and apply it to study self-assembled nano-structures on epitaxial thin films. KMC simulates thin film growth and evolution by replacing the detailed dynamics of the system's evolution, which might otherwise be studied using molecular dynamics, with an appropriate stochastic process.

  2. A Mathematical Model of Cigarette Smoldering Process

    Directory of Open Access Journals (Sweden)

    Chen P

    2014-12-01

    Full Text Available A mathematical model for a smoldering cigarette has been proposed. In the analysis of the cigarette combustion and pyrolysis processes, a receding burning front is defined, which has a constant temperature (~450 °C and divides the cigarette into two zones, the burning zone and the pyrolysis zone. The char combustion processes in the burning zone and the pyrolysis of virgin tobacco and evaporation of water in the pyrolysis zone are included in the model. The hot gases flow from the burning zone, are assumed to go out as sidestream smoke during smoldering. The internal heat transport is characterized by effective thermal conductivities in each zone. Thermal conduction of cigarette paper and convective and radiative heat transfer at the outer surface were also considered. The governing partial differential equations were solved using an integral method. Model predictions of smoldering speed as well as temperature and density profiles in the pyrolysis zone for different kinds of cigarettes were found to agree with the experimental data. The model also predicts the coal length and the maximum coal temperatures during smoldering conditions. The model provides a relatively fast and efficient way to simulate the cigarette burning processes. It offers a practical tool for exploring important parameters for cigarette smoldering processes, such as tobacco components, properties of cigarette paper, and heat generation in the burning zone and its dependence on the mass burn rate.

  3. Processing and Modeling of Porous Copper Using Sintering Dissolution Process

    Science.gov (United States)

    Salih, Mustafa Abualgasim Abdalhakam

    The growth of porous metal has produced materials with improved properties as compared to non-metals and solid metals. Porous metal can be classified as either open cell or closed cell. Open cell allows a fluid media to pass through it. Closed cell is made up of adjacent sealed pores with shared cell walls. Metal foams offer higher strength to weight ratios, increased impact energy absorption, and a greater tolerance to high temperatures and adverse environmental conditions when compared to bulk materials. Copper and its alloys are examples of these, well known for high strength and good mechanical, thermal and electrical properties. In the present study, the porous Cu was made by a powder metallurgy process, using three different space holders, sodium chloride, sodium carbonate and potassium carbonate. Several different samples have been produced, using different ratios of volume fraction. The densities of the porous metals have been measured and compared to the theoretical density calculated using an equation developed for these foams. The porous structure was determined with the removal of spacer materials through sintering process. The sintering process of each spacer material depends on the melting point of the spacer material. Processing, characterization, and mechanical properties were completed. These tests include density measurements, compression tests, computed tomography (CT) and scanning electron microscopy (SEM). The captured morphological images are utilized to generate the object-oriented finite element (OOF) analysis for the porous copper. Porous copper was formed with porosities in the range of 40-66% with density ranges from 3 to 5.2 g/cm3. A study of two different methods to measure porosity was completed. OOF (Object Oriented Finite Elements) is a desktop software application for studying the relationship between the microstructure of a material and its overall mechanical, dielectric, or thermal properties using finite element models based on

  4. 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.

  5. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    Energy Technology Data Exchange (ETDEWEB)

    Splettstoesser, Thomas [University of Heidelberg; Holmes, Kenneth [Max Planck Institute, Heidelberg, Germany; Noe, Frank [DFG Research Center Matheon, FU Berlin, Germany; Smith, Jeremy C [ORNL

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  6. On the coalescence-dispersion modeling of turbulent molecular mixing

    Science.gov (United States)

    Givi, Peyman; Kosaly, George

    1987-01-01

    The general coalescence-dispersion (C/D) closure provides phenomenological modeling of turbulent molecular mixing. The models of Curl and Dopazo and O'Brien appear as two limiting C/D models that bracket the range of results one can obtain by various models. This finding is used to investigate the sensitivtiy of the results to the choice of the model. Inert scalar mixing is found to be less model-sensitive than mixing accompanied by chemical reaction. Infinitely fast chemistry approximation is used to relate the C/D approach to Toor's earlier results. Pure mixing and infinite rate chemistry calculations are compared to study further a recent result of Hsieh and O'Brien who found that higher concentration moments are not sensitive to chemistry.

  7. Insights into the molecular interactions between aminopeptidase and amyloid beta peptide using molecular modeling techniques.

    Science.gov (United States)

    Dhanavade, Maruti J; Sonawane, Kailas D

    2014-08-01

    Amyloid beta (Aβ) peptides play a central role in the pathogenesis of Alzheimer's disease. The accumulation of Aβ peptides in AD brain was caused due to overproduction or insufficient clearance and defects in the proteolytic degradation of Aβ peptides. Hence, Aβ peptide degradation could be a promising therapeutic approach in AD treatment. Recent experimental report suggests that aminopeptidase from Streptomyces griseus KK565 (SGAK) can degrade Aβ peptides but the interactive residues are yet to be known in detail at the atomic level. Hence, we developed the three-dimensional model of aminopeptidase (SGAK) using SWISS-MODEL, Geno3D and MODELLER. Model built by MODELLER was used for further studies. Molecular docking was performed between aminopeptidase (SGAK) with wild-type and mutated Aβ peptides. The docked complex of aminopeptidase (SGAK) and wild-type Aβ peptide (1IYT.pdb) shows more stability than the other complexes. Molecular docking and MD simulation results revealed that the residues His93, Asp105, Glu139, Glu140, Asp168 and His255 are involved in the hydrogen bonding with Aβ peptide and zinc ions. The interactions between carboxyl oxygen atoms of Glu139 of aminopeptidase (SGAK) with water molecule suggest that the Glu139 may be involved in the nucleophilic attack on Ala2-Glu3 peptide bond of Aβ peptide. Hence, amino acid Glu139 of aminopeptidase (SGAK) might play an important role to degrade Aβ peptides, a causative agent of Alzheimer's disease.

  8. Internet User Behaviour Model Discovery Process

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available The Academy of Economic Studies has more than 45000 students and about 5000 computers with Internet access which are connected to AES network. Students can access internet on these computers through a proxy server which stores information about the way the Internet is accessed. In this paper, we describe the process of discovering internet user behavior models by analyzing proxy server raw data and we emphasize the importance of such models for the e-learning environment.

  9. Internet User Behaviour Model Discovery Process

    OpenAIRE

    Dragos Marcel VESPAN

    2007-01-01

    The Academy of Economic Studies has more than 45000 students and about 5000 computers with Internet access which are connected to AES network. Students can access internet on these computers through a proxy server which stores information about the way the Internet is accessed. In this paper, we describe the process of discovering internet user behavior models by analyzing proxy server raw data and we emphasize the importance of such models for the e-learning environment.

  10. The Automation of Nowcast Model Assessment Processes

    Science.gov (United States)

    2016-09-01

    S) Leelinda P Dawson, John W Raby, and Jeffrey A Smith 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION...model runs .............................13 Fig. 6 An example PSA log file, ps_auto_log, using DDA, one case- study date, 3 domains, 3 model runs, and...case study date could be set for each run. This process was time-consuming when multiple configurations were required by the user. Also, each run

  11. 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...

  12. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    Science.gov (United States)

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.

  13. Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.

    Science.gov (United States)

    Soteras, Ignacio; Curutchet, Carles; Bidon-Chanal, Axel; Dehez, François; Ángyán, János G; Orozco, Modesto; Chipot, Christophe; Luque, F Javier

    2007-11-01

    The main thrust of this investigation is the development of models of distributed atomic polarizabilities for the treatment of induction effects in molecular mechanics simulations. The models are obtained within the framework of the induced dipole theory by fitting the induction energies computed via a fast but accurate MP2/Sadlej-adjusted perturbational approach in a grid of points surrounding the molecule. Particular care is paid in the examination of the atomic quantities obtained from models of implicitly and explicitly interacting polarizabilities. Appropriateness and accuracy of the distributed models are assessed by comparing the molecular polarizabilities recovered from the models and those obtained experimentally and from MP2/Sadlej calculations. The behavior of the models is further explored by computing the polarization energy for aromatic compounds in the context of cation-π interactions and for selected neutral compounds in a TIP3P aqueous environment. The present results suggest that the computational strategy described here constitutes a very effective tool for the development of distributed models of atomic polarizabilities and can be used in the generation of new polarizable force fields.

  14. Improving the process of process modelling by the use of domain process patterns

    Science.gov (United States)

    Koschmider, Agnes; Reijers, Hajo A.

    2015-01-01

    The use of business process models has become prevalent in a wide area of enterprise applications. But while their popularity is expanding, concerns are growing with respect to their proper creation and maintenance. An obvious way to boost the efficiency of creating high-quality business process models would be to reuse relevant parts of existing models. At this point, however, limited support exists to guide process modellers towards the usage of appropriate model content. In this paper, a set of content-oriented patterns is presented, which is extracted from a large set of process models from the order management and manufacturing production domains. The patterns are derived using a newly proposed set of algorithms, which are being discussed in this paper. The authors demonstrate how such Domain Process Patterns, in combination with information on their historic usage, can support process modellers in generating new models. To support the wider dissemination and development of Domain Process Patterns within and beyond the studied domains, an accompanying website has been set up.

  15. Modeling stroke rehabilitation processes using the Unified Modeling Language (UML).

    Science.gov (United States)

    Ferrante, Simona; Bonacina, Stefano; Pinciroli, Francesco

    2013-10-01

    In organising and providing rehabilitation procedures for stroke patients, the usual need for many refinements makes it inappropriate to attempt rigid standardisation, but greater detail is required concerning workflow. The aim of this study was to build a model of the post-stroke rehabilitation process. The model, implemented in the Unified Modeling Language, was grounded on international guidelines and refined following the clinical pathway adopted at local level by a specialized rehabilitation centre. The model describes the organisation of the rehabilitation delivery and it facilitates the monitoring of recovery during the process. Indeed, a system software was developed and tested to support clinicians in the digital administration of clinical scales. The model flexibility assures easy updating after process evolution. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Assessing High School Chemistry Students' Modeling Sub-Skills in a Computerized Molecular Modeling Learning Environment

    Science.gov (United States)

    Dori, Yehudit Judy; Kaberman, Zvia

    2012-01-01

    Much knowledge in chemistry exists at a molecular level, inaccessible to direct perception. Chemistry instruction should therefore include multiple visual representations, such as molecular models and symbols. This study describes the implementation and assessment of a learning unit designed for 12th grade chemistry honors students. The organic…

  17. Buckling induced delamination of graphene composites through hybrid molecular modeling

    Science.gov (United States)

    Cranford, Steven W.

    2013-01-01

    The efficiency of graphene-based composites relies on mechanical stability and cooperativity, whereby separation of layers (i.e., delamination) can severely hinder performance. Here we study buckling induced delamination of mono- and bilayer graphene-based composites, utilizing a hybrid full atomistic and coarse-grained molecular dynamics approach. The coarse-grain model allows exploration of an idealized model material to facilitate parametric variation beyond any particular molecular structure. Through theoretical and simulation analyses, we show a critical delamination condition, where ΔD∝kL4, where ΔD is the change in bending stiffness (eV), k the stiffness of adhesion (eV/Å4), and L the length of the adhered section (Å).

  18. The Role of Molecular Modeling in TiO₂ Photocatalysis.

    Science.gov (United States)

    Cinar, Zekiye

    2017-03-30

    Molecular Modeling methods play a very important role in TiO₂ photocatalysis. Recent advances in TiO₂ photocatalysis have produced a number of interesting surface phenomena, reaction products, and various novel visible light active photocatalysts with improved properties. Quantum mechanical calculations appear promising as a means of describing the mechanisms and the product distributions of the photocatalytic degradation reactions of organic pollutants in both gas and aqueous phases. Since quantum mechanical methods utilize the principles of particle physics, their use may be extended to the design of new photocatalysts. This review introduces molecular modeling methods briefly and emphasizes the use of these methods in TiO₂ photocatalysis. The methods used for obtaining information about the degradabilities of the pollutant molecules, predicting reaction mechanisms, and evaluating the roles of the dopants and surface modifiers are explained.

  19. A model-data based systems approach to process intensification

    DEFF Research Database (Denmark)

    Gani, Rafiqul

    In recent years process intensification (PI) has attracted much interest as a potential means of process improvement to meet the demands, such as, for sustainable production. A variety of intensified equipment are being developed that potentially creates options to meet these demands...... for focused validation of only the promising candidates in the second-stage. This approach, however, would be limited to intensification based on “known” unit operations, unless the PI process synthesis/design is considered at a lower level of aggregation, namely the phenomena level. That is, the model....... Here, established procedures for computer aided molecular design is adopted since combination of phenomena to form unit operations with desired objectives is, in principle, similar to combining atoms to form molecules with desired properties. The concept of the phenomena-based synthesis/design method...

  20. 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.

  1. Counting Processes for Retail Default Modeling

    DEFF Research Database (Denmark)

    Kiefer, Nicholas Maximilian; Larson, C. Erik

    in a discrete state space. In a simple case, the states could be default/non-default; in other models relevant for credit modeling the states could be credit scores or payment status (30 dpd, 60 dpd, etc.). Here we focus on the use of stochastic counting processes for mortgage default modeling, using data...... on high LTV mortgages. Borrowers seeking to finance more than 80% of a house's value with a mortgage usually either purchase mortgage insurance, allowing a first mortgage greater than 80% from many lenders, or use second mortgages. Are there differences in performance between loans financed...

  2. Integrated Process Model on Intercultural Competence

    Directory of Open Access Journals (Sweden)

    Diana Bebenova - Nikolova

    2016-08-01

    Full Text Available The paper proposes an integrated model on intercultural competence, which attempts to present intercultural communication and competence from the term point of the dialectical approach, described by Martin and Nakayama (2010. The suggested concept deploys from previously developed and accepted models, both structure-oriented and process-oriented. At the same time it replies to the principles of the “Theory of Models” as outlined by Balboni and Caon (2014. In the near future, the model will be applied to assess intercultural competence of cross-border project teams, working under the CBC program between Romania – Bulgaria 2007-2014.

  3. 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.

  4. Modeling molecular hydrogen emission in M dwarf exoplanetary systems

    Science.gov (United States)

    Evonosky, William; France, Kevin; Kruczek, Nick E.; Youngblood, Allison; Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars (MUSCLES)

    2017-01-01

    Exoplanets orbiting low-mass stars are prime candidates for atmospheric characterization due to their astronomical abundance and short orbital periods. These planets orbit stars that are often more active than main sequence solar-type stars. They are exposed to differing levels of ultraviolet radiation which can cause traditional “biosignature” gases to be generated abiotically, potentially causing false-positive identifications of life. We modeled the recently discovered molecular hydrogen emission in the ultraviolet spectra (1350 - 1650 Å) as arising from the stellar surface, excited by radiation generated in the upper chromosphere. The model was compared with observed hydrogen emission from the “Measurements of the Ultraviolet Spectral Characteristics of Low-mass Exoplanet host Stars” (MUSCLES) survey by conducting a grid search and implementing a chi-squared minimization routine. We considered only progressions from the [1, 4] and [1, 7] first excited electronic levels. Our modeling procedure varied the atomic hydrogen column density (in the chromosphere) as well as the photospheric molecular hydrogen column density and temperature. The model required as an input a reconstructed intrinsic Lyman α profile which served as the pumping radiation for the molecular hydrogen. We found that an atomic hydrogen column density of log10N(H I) = 14.13 ± 0.16 cm-2 represents a breaking point above which there is not enough Lyman α flux available to excite a significant molecular hydrogen population into the [1, 7] state. We also present H2 temperatures which may suggest that star spots on low mass stars persist longer, and encompass more area than star spots on solar-type stars.

  5. Phase Computations and Phase Models for Discrete Molecular Oscillators.

    OpenAIRE

    Demir, Alper; Şuvak, Önder

    2012-01-01

    RESEARCH Open Access Phase computations and phase models for discrete molecular oscillators Onder Suvak* and Alper Demir Abstract Background: Biochemical oscillators perform crucial functions in cells, e.g., they set up circadian clocks. The dynamical behavior of oscillators is best described and analyzed in terms of the scalar quantity, phase. A rigorous and useful definition for phase is based on the so-called isochrons of oscillators. Phase computation techniques for ...

  6. Kinetic modelling of molecular hydrogen transport in microporous carbon materials.

    Science.gov (United States)

    Hankel, Marlies; Zhang, Hong; Nguyen, Thanh X; Bhatia, Suresh K; Gray, Stephen K; Smith, Sean C

    2011-05-07

    The proposal of kinetic molecular sieving of hydrogen isotopes is explored by employing statistical rate theory methods to describe the kinetics of molecular hydrogen transport in model microporous carbon structures. A Lennard-Jones atom-atom interaction potential is utilized for the description of the interactions between H(2)/D(2) and the carbon framework, while the requisite partition functions describing the thermal flux of molecules through the transition state are calculated quantum mechanically in view of the low temperatures involved in the proposed kinetic molecular sieving application. Predicted kinetic isotope effects for initial passage from the gas phase into the first pore mouth are consistent with expectations from previous modeling studies, namely, that at sufficiently low temperatures and for sufficiently narrow pore mouths D(2) transport is dramatically favored over H(2). However, in contrast to expectations from previous modeling, the absence of any potential barrier along the minimum energy pathway from the gas phase into the first pore mouth yields a negative temperature dependence in the predicted absolute rate coefficients-implying a negative activation energy. In pursuit of the effective activation barrier, we find that the minimum potential in the cavity is significantly higher than in the pore mouth for nanotube-shaped models, throwing into question the common assumption that passage through the pore mouths should be the rate-determining step. Our results suggest a new mechanism that, depending on the size and shape of the cavity, the thermal activation barrier may lie in the cavity rather than at the pore mouth. As a consequence, design strategies for achieving quantum-mediated kinetic molecular sieving of H(2)/D(2) in a microporous membrane will need, at the very least, to take careful account of cavity shape and size in addition to pore-mouth size in order to ensure that the selective step, namely passage through the pore mouth, is also

  7. 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.

  8. 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.

  9. 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…

  10. 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,…

  11. 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…

  12. Modeling of Reaction Processes Controlled by Diffusion

    CERN Document Server

    Revelli, J

    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 differe...

  13. Kinetics and modeling of anaerobic digestion process

    DEFF Research Database (Denmark)

    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...

  14. Dynamic Process of Money Transfer Models

    CERN Document Server

    Wang, Y; Wang, Yougui; Ding, Ning

    2005-01-01

    We have studied numerically the statistical mechanics of the dynamic phenomena, including money circulation and economic mobility, in some transfer models. The models on which our investigations were performed are the basic model proposed by A. Dragulescu and V. Yakovenko [1], the model with uniform saving rate developed by A. Chakraborti and B.K. Chakrabarti [2], and its extended model with diverse saving rate [3]. The velocity of circulation is found to be inversely related with the average holding time of money. In order to check the nature of money transferring process in these models, we demonstrated the probability distributions of holding time. In the model with uniform saving rate, the distribution obeys exponential law, which indicates money transfer here is a kind of Poisson process. But when the saving rate is set diversely, the holding time distribution follows a power law. The velocity can also be deduced from a typical individual's optimal choice. In this way, an approach for building the micro-...

  15. Iron and steel industry process model

    Energy Technology Data Exchange (ETDEWEB)

    Sparrow, F.T.

    1978-07-01

    The model depicts expected energy-consumption characteristics of the iron and steel industry and ancillary industries for the next 25 years by means of a process model of the major steps in steelmaking from ore mining and scrap recycling to the final finishing of carbon, alloy, and stainless steel into steel products such as structural steel, slabs, plates, tubes, and bars. Two plant types are modelled: fully integrated mills and minimills. User-determined inputs into the model are: (a) projected energy materials prices for the horizon; (b) projected costs of capacity expansion and replacement; (c) energy conserving options - both operating modes and investments; (d) internal rate of return required on projects; and (e) growth in finished steel demand. Nominal input choices in the model are: DOE baseline projections for oil, gas, distillates, residuals, and electricity for energy, and 1975 actual prices for materials; actual 1975 costs; adding new technologies; 15% after taxes; and 1975 actual demand with 1.5% growth/year. Output of the model includes: energy use by type, by process, and by time period, both in total and intensity (Btu/ton); energy-conservation options chosen; and utilization rates for existing capacity, and the capacity expansion decisions of the model.

  16. 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

  17. Modeling Low-temperature Geochemical Processes

    Science.gov (United States)

    Nordstrom, D. K.

    2003-12-01

    Geochemical modeling has become a popular and useful tool for a wide number of applications from research on the fundamental processes of water-rock interactions to regulatory requirements and decisions regarding permits for industrial and hazardous wastes. In low-temperature environments, generally thought of as those in the temperature range of 0-100 °C and close to atmospheric pressure (1 atm=1.01325 bar=101,325 Pa), complex hydrobiogeochemical reactions participate in an array of interconnected processes that affect us, and that, in turn, we affect. Understanding these complex processes often requires tools that are sufficiently sophisticated to portray multicomponent, multiphase chemical reactions yet transparent enough to reveal the main driving forces. Geochemical models are such tools. The major processes that they are required to model include mineral dissolution and precipitation; aqueous inorganic speciation and complexation; solute adsorption and desorption; ion exchange; oxidation-reduction; or redox; transformations; gas uptake or production; organic matter speciation and complexation; evaporation; dilution; water mixing; reaction during fluid flow; reaction involving biotic interactions; and photoreaction. These processes occur in rain, snow, fog, dry atmosphere, soils, bedrock weathering, streams, rivers, lakes, groundwaters, estuaries, brines, and diagenetic environments. Geochemical modeling attempts to understand the redistribution of elements and compounds, through anthropogenic and natural means, for a large range of scale from nanometer to global. "Aqueous geochemistry" and "environmental geochemistry" are often used interchangeably with "low-temperature geochemistry" to emphasize hydrologic or environmental objectives.Recognition of the strategy or philosophy behind the use of geochemical modeling is not often discussed or explicitly described. Plummer (1984, 1992) and Parkhurst and Plummer (1993) compare and contrast two approaches for

  18. Managing risks in business model innovation processes

    DEFF Research Database (Denmark)

    Taran, Yariv; Boer, Harry; Lindgren, Peter

    2010-01-01

    ) innovation is a risky enterprise, many companies are still choosing not to apply any risk management in the BM innovation process. The objective of this paper is to develop a better understanding of how risks are handled in the practice of BM innovation. An analysis of the BM innovation experiences of two......Companies today, in some industries more than others, invest more capital and resources just to stay competitive, develop more diverse solutions, and increasingly start thinking more radically when considering their business models. However, despite the understanding that business model (BM...... industrial companies shows that both companies are experiencing high levels of uncertainty and complexity during their innovation processes and are, consequently, struggling to find new processes for handling the risks involved. Based on the two companies’ experiences, various testable propositions are put...

  19. Virtual-Wall Model for Molecular Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    Lijuan Qian

    2016-12-01

    Full Text Available A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules. This force is first calculated and then stored in the memory. A fluid molecule appearing in the wall force field is subjected to the force from the wall molecules. The force can then be determined by the position of the molecule relative to the wall. This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. The time reduction is significant for small fluid density and channel height. The virtual-wall model is applied to Poiseuille and Couette flows, and to a flow in a channel with a rough surface. Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. The appropriate bin size and cut-off radius in the virtual-wall model are also discussed.

  20. Modeling The Molecular Composition in an AGN Disk

    CERN Document Server

    Harada, Nanase; Herbst, Eric

    2013-01-01

    We use a high-temperature chemical network to derive the molecular abundances in axisymmetric accretion disk models around active galactic nuclei (AGNs) within 100 pc using simple radial and vertical density and temperature distributions motivated by more detailed physical models. We explore the effects of X-ray irradiation and cosmic ray ionization on the spatial distribution of the molecular abundances of CO, CN, CS, HCN, HCO+, HC3N, C2H, and c-C3H2 using a variety of plausible disk structures. These simple models have molecular regions with a layer of X-ray dominated regions, a midplane without the strong influence of X-rays, and a high-temperature region in the inner portion with moderate X-ray flux where families of polyynes (C$_{\\rm n}$H$_{2}$) and cyanopolyynes can be enhanced. For the high midplane density disks we explore, we find that cosmic rays produced by supernovae do not significantly affect the regions unless the star formation efficiency significantly exceeds that of the Milky Way. We highlig...